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CATS Publications

An acknowledgement of support from the Icahn School of Medicine at Mount Sinai should appear in a publication of any material, whether copyrighted or not, based on or developed with Mount Sinai-supported computing resources. A stipulation of the National Institutes of Health (NIH) S10 award includes an accurate acknowledgement statement in publications that utilized NIH-funded resources. Click here for accurate acknowledgement statements for CATS nodes.

2023-2024
2022-2023
2021-2022

Year 2 (06/2023- 06/2024): 169

1. Gleason A, Richter F, Beller N, Arivazhagan N, Feng R, Holmes E, Glicksberg BS, Morton SU, La Vega-Talbott M, Fields M. Accurate prediction of neurologic changes in critically ill infants using pose AI. medRxiv. 2024:2024.04. 17.24305953.
2. Ma Y, Bendl J, Hartley BJ, Fullard JF, Abdelaal R, Ho S-M, Kosoy R, Gochman P, Rapoport J, Hoffman GE. Activity-Dependent Transcriptional Program in NGN2+ Neurons Enriched for Genetic Risk for Brain-Related Disorders. Biological Psychiatry. 2024;95(2):187-98.
3. Shelton BA, Sawinski D, Peter I, Maclennan PA, Pelletier NF, Nadkarni G, Julian B, Saag M, Fatima H, Crane H, Lee W, Moore RD, Christopoulos K, Jacobson JM, Eron JJ, Kumar V, Locke JE. African American/Black race, apolipoprotein L1 , and serum creatinine among persons with HIV. Aids. 2023;37(15):2349-57. Epub 20230830. doi: 10.1097/qad.0000000000003708. PubMed PMID: 37650767; PMCID: PMC10843645.
4. Midya V, Nagdeo K, Lane J, Torres-Olascoaga L, Martínez G, Horton M, Gennings C, Téllez-Rojo M, Wright R, Arora M. Akkermansia muciniphila modifies the association between metal exposure during pregnancy and depressive symptoms in late childhood2024.
5. Roussos P, Kosoy R, Fullard J, Bendl J, Kleopoulos S, Shao Z, Argyriou S, Mathur D, Vicari J, Ma Y, Humphrey J, Brophy E, Raj T, Katsel P, Voloudakis G, Lee D, Bennett D, Haroutunian V, Hoffman G. Alzheimer’s disease transcriptional landscape in ex-vivo human microglia. Res Sq. 2024. Epub 20240126. doi: 10.21203/rs.3.rs-3851590/v1. PubMed PMID: 38343831; PMCID: PMC10854306.
6. Lercher A, Cheong JG, Jiang C, Hoffmann HH, Ashbrook AW, Yin YS, Quirk C, DeGrace EJ, Chiriboga L, Rosenberg BR, Josefowicz SZ, Rice CM. Antiviral innate immune memory in alveolar macrophages following SARS-CoV-2 infection. bioRxiv. 2023. Epub 20231127. doi: 10.1101/2023.11.24.568354. PubMed PMID: 38076887; PMCID: PMC10705235.
7. Elias P, Jain S, Poterucha T, Randazzo M, Lopez Jimenez F, Khera R, Perez M, Ouyang D, Pirruccello J, Salerno M, Einstein A, Avram R, Tison G, Nadkarni G, Natarajan V, Pierson E, Beecy A, Kumaraiah D, Haggerty C, Avari Silva JN, Maddox TM. Artificial Intelligence for Cardiovascular Care – Part 1: Advances: JACC Review Topic of the Week. J Am Coll Cardiol. 2024. Epub 20240326. doi: 10.1016/j.jacc.2024.03.400. PubMed PMID: 38593946.
8. Jain S, Elias P, Poterucha T, Randazzo M, Lopez Jimenez F, Khera R, Perez M, Ouyang D, Pirruccello J, Salerno M, Einstein A, Avram R, Tison G, Nadkarni G, Natarajan V, Pierson E, Beecy A, Kumaraiah D, Haggerty C, Avari Silva JN, Maddox TM. Artificial Intelligence in Cardiovascular Care – Part 2: Applications: JACC Review Topic of the Week. J Am Coll Cardiol. 2024. Epub 20240326. doi: 10.1016/j.jacc.2024.03.401. PubMed PMID: 38593945.
9. Oikonomou EK, Holste G, Coppi A, McNamara RL, Nadkarni GN, Baloescu C, Krumholz HM, Wang Z, Khera R. Artificial intelligence-guided detection of under-recognized cardiomyopathies on point-of-care cardiac ultrasound. medRxiv. 2024. Epub 20240315. doi: 10.1101/2024.03.10.24304044. PubMed PMID: 38559021; PMCID: PMC10980112.
10. Freudenberg-Hua Y, Li W, Lee UJ, Ma Y, Koppel J, Goate A. Association between pre-dementia psychiatric diagnoses and all-cause dementia is independent from polygenic dementia risks in the UK Biobank. EBioMedicine. 2024;101:104978. Epub 20240205. doi: 10.1016/j.ebiom.2024.104978. PubMed PMID: 38320878; PMCID: PMC10944156.
11. Abbott EE, Buckler DG, Hsu JY, Abella BS, Richardson LD, Carr BG, Zebrowski AM. Association of Racial Residential Segregation With Long-Term Outcomes and Readmissions After Out-of-Hospital Cardiac Arrest Among Medicare Beneficiaries. J Am Heart Assoc. 2023;12(19):e030138. Epub 20230926. doi: 10.1161/jaha.123.030138. PubMed PMID: 37750559; PMCID: PMC10727234.
12. Wong WJ, Emdin C, Bick AG, Zekavat SM, Niroula A, Pirruccello JP, Dichtel L, Griffin G, Uddin MM, Gibson CJ, Kovalcik V, Lin AE, McConkey ME, Vromman A, Sellar RS, Kim PG, Agrawal M, Weinstock J, Long MT, Yu B, Banerjee R, Nicholls RC, Dennis A, Kelly M, Loh PR, McCarroll S, Boerwinkle E, Vasan RS, Jaiswal S, Johnson AD, Chung RT, Corey K, Levy D, Ballantyne C, Ebert BL, Natarajan P. Author Correction: Clonal haematopoiesis and risk of chronic liver disease. Nature. 2023;619(7970):E47. doi: 10.1038/s41586-023-06375-z. PubMed PMID: 37400552.
13. Graham SE, Clarke SL, Wu KH, Kanoni S, Zajac GJM, Ramdas S, Surakka I, Ntalla I, Vedantam S, Winkler TW, Locke AE, Marouli E, Hwang MY, Han S, Narita A, Choudhury A, Bentley AR, Ekoru K, Verma A, Trivedi B, Martin HC, Hunt KA, Hui Q, Klarin D, Zhu X, Thorleifsson G, Helgadottir A, Gudbjartsson DF, Holm H, Olafsson I, Akiyama M, Sakaue S, Terao C, Kanai M, Zhou W, Brumpton BM, Rasheed H, Ruotsalainen SE, Havulinna AS, Veturi Y, Feng Q, Rosenthal EA, Lingren T, Pacheco JA, Pendergrass SA, Haessler J, Giulianini F, Bradford Y, Miller JE, Campbell A, Lin K, Millwood IY, Hindy G, Rasheed A, Faul JD, Zhao W, Weir DR, Turman C, Huang H, Graff M, Mahajan A, Brown MR, Zhang W, Yu K, Schmidt EM, Pandit A, Gustafsson S, Yin X, Luan J, Zhao JH, Matsuda F, Jang HM, Yoon K, Medina-Gomez C, Pitsillides A, Hottenga JJ, Willemsen G, Wood AR, Ji Y, Gao Z, Haworth S, Mitchell RE, Chai JF, Aadahl M, Yao J, Manichaikul A, Warren HR, Ramirez J, Bork-Jensen J, Kårhus LL, Goel A, Sabater-Lleal M, Noordam R, Sidore C, Fiorillo E, McDaid AF, Marques-Vidal P, Wielscher M, Trompet S, Sattar N, Møllehave LT, Thuesen BH, Munz M, Zeng L, Huang J, Yang B, Poveda A, Kurbasic A, Lamina C, Forer L, Scholz M, Galesloot TE, Bradfield JP, Daw EW, Zmuda JM, Mitchell JS, Fuchsberger C, Christensen H, Brody JA, Feitosa MF, Wojczynski MK, Preuss M, Mangino M, Christofidou P, Verweij N, Benjamins JW, Engmann J, Kember RL, Slieker RC, Lo KS, Zilhao NR, Le P, Kleber ME, Delgado GE, Huo S, Ikeda DD, Iha H, Yang J, Liu J, Leonard HL, Marten J, Schmidt B, Arendt M, Smyth LJ, Cañadas-Garre M, Wang C, Nakatochi M, Wong A, Hutri-Kähönen N, Sim X, Xia R, Huerta-Chagoya A, Fernandez-Lopez JC, Lyssenko V, Ahmed M, Jackson AU, Yousri NA, Irvin MR, Oldmeadow C, Kim HN, Ryu S, Timmers P, Arbeeva L, Dorajoo R, Lange LA, Chai X, Prasad G, Lorés-Motta L, Pauper M, Long J, Li X, Theusch E, Takeuchi F, Spracklen CN, Loukola A, Bollepalli S, Warner SC, Wang YX, Wei WB, Nutile T, Ruggiero D, Sung YJ, Hung YJ, Chen S, Liu F, Yang J, Kentistou KA, Gorski M, Brumat M, Meidtner K, Bielak LF, Smith JA, Hebbar P, Farmaki AE, Hofer E, Lin M, Xue C, Zhang J, Concas MP, Vaccargiu S, van der Most PJ, Pitkänen N, Cade BE, Lee J, van der Laan SW, Chitrala KN, Weiss S, Zimmermann ME, Lee JY, Choi HS, Nethander M, Freitag-Wolf S, Southam L, Rayner NW, Wang CA, Lin SY, Wang JS, Couture C, Lyytikäinen LP, Nikus K, Cuellar-Partida G, Vestergaard H, Hildalgo B, Giannakopoulou O, Cai Q, Obura MO, van Setten J, Li X, Schwander K, Terzikhan N, Shin JH, Jackson RD, Reiner AP, Martin LW, Chen Z, Li L, Highland HM, Young KL, Kawaguchi T, Thiery J, Bis JC, Nadkarni GN, Launer LJ, Li H, Nalls MA, Raitakari OT, Ichihara S, Wild SH, Nelson CP, Campbell H, Jäger S, Nabika T, Al-Mulla F, Niinikoski H, Braund PS, Kolcic I, Kovacs P, Giardoglou T, Katsuya T, Bhatti KF, de Kleijn D, de Borst GJ, Kim EK, Adams HHH, Ikram MA, Zhu X, Asselbergs FW, Kraaijeveld AO, Beulens JWJ, Shu XO, Rallidis LS, Pedersen O, Hansen T, Mitchell P, Hewitt AW, Kähönen M, Pérusse L, Bouchard C, Tönjes A, Chen YI, Pennell CE, Mori TA, Lieb W, Franke A, Ohlsson C, Mellström D, Cho YS, Lee H, Yuan JM, Koh WP, Rhee SY, Woo JT, Heid IM, Stark KJ, Völzke H, Homuth G, Evans MK, Zonderman AB, Polasek O, Pasterkamp G, Hoefer IE, Redline S, Pahkala K, Oldehinkel AJ, Snieder H, Biino G, Schmidt R, Schmidt H, Chen YE, Bandinelli S, Dedoussis G, Thanaraj TA, Kardia SLR, Kato N, Schulze MB, Girotto G, Jung B, Böger CA, Joshi PK, Bennett DA, De Jager PL, Lu X, Mamakou V, Brown M, Caulfield MJ, Munroe PB, Guo X, Ciullo M, Jonas JB, Samani NJ, Kaprio J, Pajukanta P, Adair LS, Bechayda SA, de Silva HJ, Wickremasinghe AR, Krauss RM, Wu JY, Zheng W, den Hollander AI, Bharadwaj D, Correa A, Wilson JG, Lind L, Heng CK, Nelson AE, Golightly YM, Wilson JF, Penninx B, Kim HL, Attia J, Scott RJ, Rao DC, Arnett DK, Hunt SC, Walker M, Koistinen HA, Chandak GR, Yajnik CS, Mercader JM, Tusié-Luna T, Aguilar-Salinas CA, Villalpando CG, Orozco L, Fornage M, Tai ES, van Dam RM, Lehtimäki T, Chaturvedi N, Yokota M, Liu J, Reilly DF, McKnight AJ, Kee F, Jöckel KH, McCarthy MI, Palmer CNA, Vitart V, Hayward C, Simonsick E, van Duijn CM, Lu F, Qu J, Hishigaki H, Lin X, März W, Parra EJ, Cruz M, Gudnason V, Tardif JC, Lettre G, t Hart LM, Elders PJM, Damrauer SM, Kumari M, Kivimaki M, van der Harst P, Spector TD, Loos RJF, Province MA, Psaty BM, Brandslund I, Pramstaller PP, Christensen K, Ripatti S, Widén E, Hakonarson H, Grant SFA, Kiemeney L, de Graaf J, Loeffler M, Kronenberg F, Gu D, Erdmann J, Schunkert H, Franks PW, Linneberg A, Jukema JW, Khera AV, Männikkö M, Jarvelin MR, Kutalik Z, Cucca F, Mook-Kanamori DO, van Dijk KW, Watkins H, Strachan DP, Grarup N, Sever P, Poulter N, Rotter JI, Dantoft TM, Karpe F, Neville MJ, Timpson NJ, Cheng CY, Wong TY, Khor CC, Sabanayagam C, Peters A, Gieger C, Hattersley AT, Pedersen NL, Magnusson PKE, Boomsma DI, de Geus EJC, Cupples LA, van Meurs JBJ, Ghanbari M, Gordon-Larsen P, Huang W, Kim YJ, Tabara Y, Wareham NJ, Langenberg C, Zeggini E, Kuusisto J, Laakso M, Ingelsson E, Abecasis G, Chambers JC, Kooner JS, de Vries PS, Morrison AC, North KE, Daviglus M, Kraft P, Martin NG, Whitfield JB, Abbas S, Saleheen D, Walters RG, Holmes MV, Black C, Smith BH, Justice AE, Baras A, Buring JE, Ridker PM, Chasman DI, Kooperberg C, Wei WQ, Jarvik GP, Namjou B, Hayes MG, Ritchie MD, Jousilahti P, Salomaa V, Hveem K, Åsvold BO, Kubo M, Kamatani Y, Okada Y, Murakami Y, Thorsteinsdottir U, Stefansson K, Ho YL, Lynch JA, Rader DJ, Tsao PS, Chang KM, Cho K, O’Donnell CJ, Gaziano JM, Wilson P, Rotimi CN, Hazelhurst S, Ramsay M, Trembath RC, van Heel DA, Tamiya G, Yamamoto M, Kim BJ, Mohlke KL, Frayling TM, Hirschhorn JN, Kathiresan S, Boehnke M, Natarajan P, Peloso GM, Brown CD, Morris AP, Assimes TL, Deloukas P, Sun YV, Willer CJ. Author Correction: The power of genetic diversity in genome-wide association studies of lipids. Nature. 2023;618(7965):E19-e20. doi: 10.1038/s41586-023-06194-2. PubMed PMID: 37237109; PMCID: PMC10355188.
14. Khunte A, Sangha V, Oikonomou EK, Dhingra LS, Aminorroaya A, Coppi A, Shankar SV, Mortazavi BJ, Bhatt DL, Krumholz HM, Nadkarni GN, Vaid A, Khera R. Automated Diagnostic Reports from Images of Electrocardiograms at the Point-of-Care. medRxiv. 2024. Epub 20240218. doi: 10.1101/2024.02.17.24302976. PubMed PMID: 38405776; PMCID: PMC10889032.
15. Nargesi AA, Adejumo P, Dhingra L, Rosand B, Hengartner A, Coppi A, Benigeri S, Sen S, Ahmad T, Nadkarni GN, Lin Z, Ahmad FS, Krumholz HM, Khera R. Automated Identification of Heart Failure with Reduced Ejection Fraction using Deep Learning-based Natural Language Processing. medRxiv. 2023. Epub 20230911. doi: 10.1101/2023.09.10.23295315. PubMed PMID: 37745445; PMCID: PMC10516088.
16. Romero-Molina C, Neuner SM, Ryszawiec M, Pébay A, Dominantly Inherited Alzheimer N, Marcora E, Goate A. Autosomal Dominant Alzheimer’s Disease Mutations in Human Microglia Are Not Sufficient to Trigger Amyloid Pathology in WT Mice but Might Affect Pathology in 5XFAD Mice. Int J Mol Sci. 2024;25(5). Epub 20240222. doi: 10.3390/ijms25052565. PubMed PMID: 38473822; PMCID: PMC10932392.
17. Podleśny-Drabiniok A, Novikova G, Liu Y, Dunst J, Temizer R, Giannarelli C, Marro S, Kreslavsky T, Marcora E, Goate AM. BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer’s disease and other disorders of lipid-rich tissues. Nat Commun. 2024;15(1):2058. Epub 20240306. doi: 10.1038/s41467-024-46315-7. PubMed PMID: 38448474; PMCID: PMC10917780.
18. Yeh SY, Estill M, Lardner CK, Browne CJ, Minier-Toribio A, Futamura R, Beach K, McManus CA, Xu SJ, Zhang S, Heller EA, Shen L, Nestler EJ. Cell Type-Specific Whole-Genome Landscape of ΔFOSB Binding in the Nucleus Accumbens After Chronic Cocaine Exposure. Biol Psychiatry. 2023;94(5):367-77. Epub 20230102. doi: 10.1016/j.biopsych.2022.12.021. PubMed PMID: 36906500; PMCID: PMC10314970.
19. Aleman A, van Kesteren M, Zajdman AK, Srivastava K, Cognigni C, Mischka J, Chen LY, Upadhyaya B, Serebryakova K, Nardulli JR, Lyttle N, Kappes K, Jackson H, Gleason CR, Oostenink A, Cai GY, Van Oekelen O, van Bakel H, Sordillo EM, Cordon-Cardo C, Merad M, Jagannath S, Wajnberg A, Simon V, Parekh S. Cellular mechanisms associated with sub-optimal immune responses to SARS-CoV-2 bivalent booster vaccination in patients with Multiple Myeloma. EBioMedicine. 2023;98:104886. Epub 20231122. doi: 10.1016/j.ebiom.2023.104886. PubMed PMID: 37995467; PMCID: PMC10708991.
20. Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Stout L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, De Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Winfree S, Jefferson N, Türkmen A, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S, Jain S, Rauchman M, Eadon MT. The chromatin landscape of healthy and injured cell types in the human kidney. Nat Commun. 2024;15(1):433. Epub 20240110. doi: 10.1038/s41467-023-44467-6. PubMed PMID: 38199997; PMCID: PMC10781985.
21. Halawani D, Wang Y, Ramakrishnan A, Estill M, He X, Shen L, Friedel RH, Zou H. Circadian clock regulator Bmal1 gates axon regeneration via Tet3 epigenetics in mouse sensory neurons. Nat Commun. 2023;14(1):5165. Epub 20230824. doi: 10.1038/s41467-023-40816-7. PubMed PMID: 37620297; PMCID: PMC10449865.
22. Lee AM, Xu Y, Hooper SR, Abraham AG, Hu J, Xiao R, Matheson MB, Brunson C, Rhee EP, Coresh J, Vasan RS, Schrauben S, Kimmel PL, Warady BA, Furth SL, Hartung EA, Denburg MR. Circulating Metabolomic Associations with Neurocognitive Outcomes in Pediatric CKD. Clin J Am Soc Nephrol. 2023;19(1):13-25. Epub 20231023. doi: 10.2215/cjn.0000000000000318. PubMed PMID: 37871960; PMCID: PMC10843217.
23. Cathomas F, Lin H-Y, Chan KL, Li L, Parise LF, Alvarez J, Durand-de Cuttoli R, Aubry AV, Muhareb S, Desland F, Shimo Y, Ramakrishnan A, Estill M, Ferrer-Pérez C, Parise EM, Wilk CM, Kaster MP, Wang J, Sowa A, Janssen WG, Costi S, Rahman A, Fernandez N, Campbell M, Swirski FK, Nestler EJ, Shen L, Merad M, Murrough JW, Russo SJ. Circulating myeloid-derived MMP8 in stress susceptibility and depression. Nature. 2024;626(8001):1108-15. doi: 10.1038/s41586-023-07015-2.
24. Su CY, Zhou S, Gonzalez-Kozlova E, Butler-Laporte G, Brunet-Ratnasingham E, Nakanishi T, Jeon W, Morrison DR, Laurent L, Afilalo J, Afilalo M, Henry D, Chen Y, Carrasco-Zanini J, Farjoun Y, Pietzner M, Kimchi N, Afrasiabi Z, Rezk N, Bouab M, Petitjean L, Guzman C, Xue X, Tselios C, Vulesevic B, Adeleye O, Abdullah T, Almamlouk N, Moussa Y, DeLuca C, Duggan N, Schurr E, Brassard N, Durand M, Del Valle DM, Thompson R, Cedillo MA, Schadt E, Nie K, Simons NW, Mouskas K, Zaki N, Patel M, Xie H, Harris J, Marvin R, Cheng E, Tuballes K, Argueta K, Scott I, Greenwood CMT, Paterson C, Hinterberg MA, Langenberg C, Forgetta V, Pineau J, Mooser V, Marron T, Beckmann ND, Kim-Schulze S, Charney AW, Gnjatic S, Kaufmann DE, Merad M, Richards JB. Circulating proteins to predict COVID-19 severity. Sci Rep. 2023;13(1):6236. Epub 20230417. doi: 10.1038/s41598-023-31850-y. PubMed PMID: 37069249; PMCID: PMC10107586.
25. Cheung KL, Zhao L, Sharma R, Ghosh AA, Appiah M, Sun Y, Jaganathan A, Hu Y, LeJeune A, Xu F, Han X, Wang X, Zhang F, Ren C, Walsh MJ, Xiong H, Tsankov A, Zhou MM. Class IIa HDAC4 and HDAC7 cooperatively regulate gene transcription in Th17 cell differentiation. Proc Natl Acad Sci U S A. 2024;121(18):e2312111121. Epub 20240424. doi: 10.1073/pnas.2312111121. PubMed PMID: 38657041; PMCID: PMC11067014.
26. Nadkarni GN, Sakhuja A. Clinical Informatics in Critical Care Medicine. Yale J Biol Med. 2023;96(3):397-405. Epub 20230929. doi: 10.59249/wttu3055. PubMed PMID: 37780994; PMCID: PMC10524812.
27. Mushtaq A, Alburquerque B, Chung M, Fabre S, Sullivan MJ, Nowak M, Sordillo EM, Polanco J, van Bakel H, Gitman MR. Clinical, microbiological and genomic characterization of Gram-negative bacteria with dual carbapenemases as identified by rapid molecular testing. JAC-Antimicrobial Resistance. 2024;6(1):dlad137.
28. Eoli A, Ibing S, Schurmann C, Nadkarni GN, Heyne HO, Böttinger E. A clustering approach to improve our understanding of the genetic and phenotypic complexity of chronic kidney disease. Sci Rep. 2024;14(1):9642. Epub 20240426. doi: 10.1038/s41598-024-59747-4. PubMed PMID: 38671065; PMCID: PMC11053134.
29. Seah C, Signer R, Deans M, Bader H, Rusielewicz T, Hicks EM, Young H, Cote A, Townsley K, Xu C, Hunter CJ, McCarthy B, Goldberg J, Dobariya S, Holtzherimer PE, Young KA, Noggle SA, Krystal JH, Paull D, Girgenti MJ, Yehuda R, Brennand KJ, Huckins LM. Common genetic variation impacts stress response in the brain. bioRxiv. 2023. Epub 20231228. doi: 10.1101/2023.12.27.573459. PubMed PMID: 38234801; PMCID: PMC10793429.
30. Lee DSM, Cardone KM, Zhang DY, Abramowitz S, DePaolo JS, Aragam KG, Biddinger K, Conery M, Dilitikas O, Hoffman-Andrews L, Judy RL, Khan A, Kulo I, Puckelwartz MJ, Reza N, Satterfield BA, Singhal P, Arany ZP, Cappola TP, Carruth E, Day SM, Do R, Haggarty CM, Joseph J, McNally E, Nadkarni G, Owens AT, Rader DJ, Ritchie MD, Sun Y, Voight BF, Levin MG, Damrauer SM. Common- and rare-variant genetic architecture of heart failure across the allele frequency spectrum. medRxiv. 2023. Epub 20231002. doi: 10.1101/2023.07.16.23292724. PubMed PMID: 37503172; PMCID: PMC10371173.
31. Prescott RA, Pankow AP, de Vries M, Crosse K, Patel RS, Alu M, Loomis C, Torres V, Koralov S, Ivanova E, Dittmann M, Rosenberg BR. A comparative study of in vitro air-liquid interface culture models of the human airway epithelium evaluating cellular heterogeneity and gene expression at single cell resolution. bioRxiv. 2023. Epub 20230228. doi: 10.1101/2023.02.27.530299. PubMed PMID: 36909601; PMCID: PMC10002689.
32. Brin D, Sorin V, Vaid A, Soroush A, Glicksberg BS, Charney AW, Nadkarni G, Klang E. Comparing ChatGPT and GPT-4 performance in USMLE soft skill assessments. Sci Rep. 2023;13(1):16492. Epub 20231001. doi: 10.1038/s41598-023-43436-9. PubMed PMID: 37779171; PMCID: PMC10543445.
33. Takkavatakarn K, Dai Y, Hsun Wen H, Kauffman J, Charney A, Coca SG, Nadkarni GN, Chan L. Comparison of predicting cardiovascular disease hospitalization using individual, ZIP code-derived, and machine learning model-predicted educational attainment in New York City. PLoS One. 2024;19(2):e0297919. Epub 20240208. doi: 10.1371/journal.pone.0297919. PubMed PMID: 38329973; PMCID: PMC10852236.
34. Eisfeld AJ, Anderson LN, Fan S, Walters KB, Halfmann PJ, Westhoff Smith D, Thackray LB, Tan Q, Sims AC, Menachery VD, Schäfer A, Sheahan TP, Cockrell AS, Stratton KG, Webb-Robertson BM, Kyle JE, Burnum-Johnson KE, Kim YM, Nicora CD, Peralta Z, N’Jai A U, Sahr F, van Bakel H, Diamond MS, Baric RS, Metz TO, Smith RD, Kawaoka Y, Waters KM. A compendium of multi-omics data illuminating host responses to lethal human virus infections. Sci Data. 2024;11(1):328. Epub 20240402. doi: 10.1038/s41597-024-03124-3. PubMed PMID: 38565538; PMCID: PMC10987564.
35. Guan L, Babujee L, Browning VL, Presler R, Pattinson D, Nguyen HLK, Hoang VMP, Le MQ, van Bakel H, Neumann G, Kawaoka Y. Continued Circulation of Highly Pathogenic H5 Influenza Viruses in Vietnamese Live Bird Markets in 2018-2021. Viruses. 2023;15(7). Epub 20230721. doi: 10.3390/v15071596. PubMed PMID: 37515281; PMCID: PMC10384249.
36. Dong P, Voloudakis G, Fullard JF, Hoffman GE, Roussos P. Convergence of the dysregulated regulome in schizophrenia with polygenic risk and evolutionarily constrained enhancers. Mol Psychiatry. 2023. Epub 20231225. doi: 10.1038/s41380-023-02370-y. PubMed PMID: 38145985.
37. Mews P, Cunningham AM, Scarpa J, Ramakrishnan A, Hicks EM, Bolnick S, Garamszegi S, Shen L, Mash DC, Nestler EJ. Convergent abnormalities in striatal gene networks in human cocaine use disorder and mouse cocaine administration models. Sci Adv. 2023;9(6):eadd8946. Epub 20230210. doi: 10.1126/sciadv.add8946. PubMed PMID: 36763659; PMCID: PMC9916993.
38. Lucarelli N, Ginley B, Zee J, Mimar S, Paul AS, Jain S, Han SS, Rodrigues L, Ozrazgat-Baslanti T, Wong ML, Nadkarni G, Clapp WL, Jen KY, Sarder P. Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. Kidney360. 2023;4(12):1726-37. Epub 20231114. doi: 10.34067/kid.0000000000000299. PubMed PMID: 37966063; PMCID: PMC10758512.
39. Salas-Estrada L, Provasi D, Qiu X, Kaniskan H, Huang XP, DiBerto JF, Lamim Ribeiro JM, Jin J, Roth BL, Filizola M. De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework. J Chem Inf Model. 2023;63(16):5056-65. Epub 20230809. doi: 10.1021/acs.jcim.3c00651. PubMed PMID: 37555591; PMCID: PMC10466374.
40. Richter F, Rutherford KD, Cooke AJ, Meshkati M, Eddy-Abrams V, Greene D, Kosowsky J, Park Y, Aggarwal S, Burke RJ. A deep intronic PKHD1 variant identified by SpliceAI in a deceased neonate with autosomal recessive polycystic kidney disease. American Journal of Kidney Diseases. 2024.
41. Klang E, Sourosh A, Nadkarni GN, Sharif K, Lahat A. Deep Learning and Gastric Cancer: Systematic Review of AI-Assisted Endoscopy. Diagnostics (Basel). 2023;13(24). Epub 20231206. doi: 10.3390/diagnostics13243613. PubMed PMID: 38132197; PMCID: PMC10742887.
42. Vaid A, Takkavatakarn K, Divers J, Charytan DM, Chan L, Nadkarni GN. Deep Learning on Electrocardiograms for Prediction of In-hospital Intradialytic Hypotension in Patients with ESKD. Kidney360. 2023;4(9):e1293-e6. Epub 20230707. doi: 10.34067/kid.0000000000000208. PubMed PMID: 37418626; PMCID: PMC10547223.
43. Paranjpe I, Wang X, Anandakrishnan N, Haydak JC, Van Vleck T, DeFronzo S, Li Z, Mendoza A, Liu R, Fu J, Forrest I, Zhou W, Lee K, O’Hagan R, Dellepiane S, Menon KM, Gulamali F, Kamat S, Gusella GL, Charney AW, Hofer I, Cho JH, Do R, Glicksberg BS, He JC, Nadkarni GN, Azeloglu EU. Deep learning on electronic medical records identifies distinct subphenotypes of diabetic kidney disease driven by genetic variations in the Rho pathway. medRxiv. 2023. Epub 20230907. doi: 10.1101/2023.09.06.23295120. PubMed PMID: 37732187; PMCID: PMC10508814.
44. Chandrashekar PB, Alatkar S, Wang J, Hoffman GE, He C, Jin T, Khullar S, Bendl J, Fullard JF, Roussos P, Wang D. DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype-phenotype prediction. Genome Med. 2023;15(1):88. Epub 20231031. doi: 10.1186/s13073-023-01248-6. PubMed PMID: 37904203; PMCID: PMC10617196.
45. Ramakrishnan A, Wangensteen G, Kim S, Nestler EJ, Shen L. DeepRegFinder: deep learning-based regulatory elements finder. Bioinform Adv. 2024;4(1):vbae007. Epub 20240114. doi: 10.1093/bioadv/vbae007. PubMed PMID: 38343388; PMCID: PMC10858349.
46. Als TD, Kurki MI, Grove J, Voloudakis G, Therrien K, Tasanko E, Nielsen TT, Naamanka J, Veerapen K, Levey DF, Bendl J, Bybjerg-Grauholm J, Zeng B, Demontis D, Rosengren A, Athanasiadis G, Bækved-Hansen M, Qvist P, Bragi Walters G, Thorgeirsson T, Stefánsson H, Musliner KL, Rajagopal VM, Farajzadeh L, Thirstrup J, Vilhjálmsson BJ, McGrath JJ, Mattheisen M, Meier S, Agerbo E, Stefánsson K, Nordentoft M, Werge T, Hougaard DM, Mortensen PB, Stein MB, Gelernter J, Hovatta I, Roussos P, Daly MJ, Mors O, Palotie A, Børglum AD. Depression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses. Nat Med. 2023;29(7):1832-44. Epub 20230718. doi: 10.1038/s41591-023-02352-1. PubMed PMID: 37464041; PMCID: PMC10839245.
47. Nadkarni GN, Stapleton S, Takale D, Edwards K, Moran K, Mosoyan G, Hansen MK, Donovan MJ, Heerspink HJL, Fleming F, Coca SG. Derivation and independent validation of kidneyintelX.dkd: A prognostic test for the assessment of diabetic kidney disease progression. Diabetes Obes Metab. 2023;25(12):3779-87. Epub 20230918. doi: 10.1111/dom.15273. PubMed PMID: 37722962.
48. Gulamali F, Jayaraman P, Sawant AS, Desman J, Fox B, Chang A, Soong BY, Arivazaghan N, Reynolds AS, Duong SQ. Derivation, External Validation and Clinical Implications of a deep learning approach for intracranial pressure estimation using non-cranial waveform measurements. medRxiv. 2024:2024.01. 30.24301974.
49. Schilling J, Shokouhi S, Montgomery A, Nadkarni GN, Charney AW, Shanker A, Singh R, Jhaveri K, Singh KS, Khadke P, Jain P. Development of a decentralized cohort for studying post-acute sequelae of COVID-19 in India in the Data4life Study. Commun Med (Lond). 2023;3(1):117. Epub 20230825. doi: 10.1038/s43856-023-00349-y. PubMed PMID: 37626117; PMCID: PMC10457339.
50. Thaweethai T, Jolley SE, Karlson EW, Levitan EB, Levy B, McComsey GA, McCorkell L, Nadkarni GN, Parthasarathy S, Singh U, Walker TA, Selvaggi CA, Shinnick DJ, Schulte CCM, Atchley-Challenner R, Alba GA, Alicic R, Altman N, Anglin K, Argueta U, Ashktorab H, Baslet G, Bassett IV, Bateman L, Bedi B, Bhattacharyya S, Bind MA, Blomkalns AL, Bonilla H, Bush PA, Castro M, Chan J, Charney AW, Chen P, Chibnik LB, Chu HY, Clifton RG, Costantine MM, Cribbs SK, Davila Nieves SI, Deeks SG, Duven A, Emery IF, Erdmann N, Erlandson KM, Ernst KC, Farah-Abraham R, Farner CE, Feuerriegel EM, Fleurimont J, Fonseca V, Franko N, Gainer V, Gander JC, Gardner EM, Geng LN, Gibson KS, Go M, Goldman JD, Grebe H, Greenway FL, Habli M, Hafner J, Han JE, Hanson KA, Heath J, Hernandez C, Hess R, Hodder SL, Hoffman MK, Hoover SE, Huang B, Hughes BL, Jagannathan P, John J, Jordan MR, Katz SD, Kaufman ES, Kelly JD, Kelly SW, Kemp MM, Kirwan JP, Klein JD, Knox KS, Krishnan JA, Kumar A, Laiyemo AO, Lambert AA, Lanca M, Lee-Iannotti JK, Logarbo BP, Longo MT, Luciano CA, Lutrick K, Maley JH, Marathe JG, Marconi V, Marshall GD, Martin CF, Matusov Y, Mehari A, Mendez-Figueroa H, Mermelstein R, Metz TD, Morse R, Mosier J, Mouchati C, Mullington J, Murphy SN, Neuman RB, Nikolich JZ, Ofotokun I, Ojemakinde E, Palatnik A, Palomares K, Parimon T, Parry S, Patterson JE, Patterson TF, Patzer RE, Peluso MJ, Pemu P, Pettker CM, Plunkett BA, Pogreba-Brown K, Poppas A, Quigley JG, Reddy U, Reece R, Reeder H, Reeves WB, Reiman EM, Rischard F, Rosand J, Rouse DJ, Ruff A, Saade G, Sandoval GJ, Schlater SM, Shepherd F, Sherif ZA, Simhan H, Singer NG, Skupski DW, Sowles A, Sparks JA, Sukhera FI, Taylor BS, Teunis L, Thomas RJ, Thorp JM, Thuluvath P, Ticotsky A, Tita AT, Tuttle KR, Urdaneta AE, Valdivieso D, VanWagoner TM, Vasey A, Verduzco-Gutierrez M, Wallace ZS, Ward HD, Warren DE, Weiner SJ, Welch S, Whiteheart SW, Wiley Z, Wisnivesky JP, Yee LM, Zisis S, Horwitz LI, Foulkes AS. Development of a Definition of Postacute Sequelae of SARS-CoV-2 Infection. Jama. 2023;329(22):1934-46. doi: 10.1001/jama.2023.8823. PubMed PMID: 37278994; PMCID: PMC10214179.
51. Hirten RP, Danieletto M, Landell K, Zweig M, Golden E, Orlov G, Rodrigues J, Alleva E, Ensari I, Bottinger E, Nadkarni GN, Fuchs TJ, Fayad ZA. Development of the ehive Digital Health App: Protocol for a Centralized Research Platform. JMIR Res Protoc. 2023;12:e49204. Epub 20231116. doi: 10.2196/49204. PubMed PMID: 37971801; PMCID: PMC10690532.
52. Kashani KB, Awdishu L, Bagshaw SM, Barreto EF, Claure-Del Granado R, Evans BJ, Forni LG, Ghosh E, Goldstein SL, Kane-Gill SL, Koola J, Koyner JL, Liu M, Murugan R, Nadkarni GN, Neyra JA, Ninan J, Ostermann M, Pannu N, Rashidi P, Ronco C, Rosner MH, Selby NM, Shickel B, Singh K, Soranno DE, Sutherland SM, Bihorac A, Mehta RL. Digital health and acute kidney injury: consensus report of the 27th Acute Disease Quality Initiative workgroup. Nat Rev Nephrol. 2023;19(12):807-18. Epub 20230814. doi: 10.1038/s41581-023-00744-7. PubMed PMID: 37580570.
53. Kittrell HD, DiMenna FJ, Arad AD, Oh W, Hofer I, Walker RW, Loos RJF, Albu JB, Nadkarni GN. Discrepancy between predicted and measured exercise intensity for eliciting the maximal rate of lipid oxidation. Nutr Metab Cardiovasc Dis. 2023;33(11):2189-98. Epub 20230715. doi: 10.1016/j.numecd.2023.07.014. PubMed PMID: 37567789.
54. Verma A, Huffman JE, Rodriguez A, Conery M, Liu M, Ho YL, Kim Y, Heise DA, Guare L, Panickan VA, Garcon H, Linares F, Costa L, Goethert I, Tipton R, Honerlaw J, Davies L, Whitbourne S, Cohen J, Posner DC, Sangar R, Murray M, Wang X, Dochtermann DR, Devineni P, Shi Y, Nandi TN, Assimes TL, Brunette CA, Carroll RJ, Clifford R, Duvall S, Gelernter J, Hung A, Iyengar SK, Joseph J, Kember R, Kranzler H, Levey D, Luoh SW, Merritt VC, Overstreet C, Deak JD, Grant SFA, Polimanti R, Roussos P, Sun YV, Venkatesh S, Voloudakis G, Justice A, Begoli E, Ramoni R, Tourassi G, Pyarajan S, Tsao PS, O’Donnell CJ, Muralidhar S, Moser J, Casas JP, Bick AG, Zhou W, Cai T, Voight BF, Cho K, Gaziano MJ, Madduri RK, Damrauer SM, Liao KP. Diversity and Scale: Genetic Architecture of 2,068 Traits in the VA Million Veteran Program. medRxiv. 2023. Epub 20230629. doi: 10.1101/2023.06.28.23291975. PubMed PMID: 37425708; PMCID: PMC10327290.
55. Godino A, Salery M, Minier-Toribio AM, Patel V, Fullard JF, Parise EM, Martinez-Rivera FJ, Morel C, Roussos P, Blitzer RD, Nestler EJ. Dopaminoceptive D1 and D2 neurons in ventral hippocampus arbitrate approach and avoidance in anxiety. bioRxiv. 2023. Epub 20230728. doi: 10.1101/2023.07.25.550554. PubMed PMID: 37546856; PMCID: PMC10402022.
56. Neff RA, Bosch-Gutierrez A, Sun Y, Katsyv I, Song WM, Wang M, Walsh MJ, Zhang B. Dysfunction of ubiquitin protein ligase MYCBP2 leads to cell resilience in human breast cancers. NAR Cancer. 2023;5(3):zcad036. Epub 20230710. doi: 10.1093/narcan/zcad036. PubMed PMID: 37435531; PMCID: PMC10331931.
57. Provasi D, Filizola M. Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques. J Phys Chem B. 2023;127(50):10691-9. Epub 20231211. doi: 10.1021/acs.jpcb.3c05306. PubMed PMID: 38084046.
58. Recto K, Kachroo P, Huan T, Van Den Berg D, Lee GY, Bui H, Lee DH, Gereige J, Yao C, Hwang SJ, Joehanes R, Weiss ST, O’Connor GT, Levy D, DeMeo DL. Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma. EBioMedicine. 2023;95:104758. Epub 20230818. doi: 10.1016/j.ebiom.2023.104758. PubMed PMID: 37598461; PMCID: PMC10462855.
59. Grams ME, Coresh J, Matsushita K, Ballew SH, Sang Y, Surapaneni A, Alencar de Pinho N, Anderson A, Appel LJ, Ärnlöv J, Azizi F, Bansal N, Bell S, Bilo HJG, Brunskill NJ, Carrero JJ, Chadban S, Chalmers J, Chen J, Ciemins E, Cirillo M, Ebert N, Evans M, Ferreiro A, Fu EL, Fukagawa M, Green JA, Gutierrez OM, Herrington WG, Hwang SJ, Inker LA, Iseki K, Jafar T, Jassal SK, Jha V, Kadota A, Katz R, Köttgen A, Konta T, Kronenberg F, Lee BJ, Lees J, Levin A, Looker HC, Major R, Melzer Cohen C, Mieno M, Miyazaki M, Moranne O, Muraki I, Naimark D, Nitsch D, Oh W, Pena M, Purnell TS, Sabanayagam C, Satoh M, Sawhney S, Schaeffner E, Schöttker B, Shen JI, Shlipak MG, Sinha S, Stengel B, Sumida K, Tonelli M, Valdivielso JM, van Zuilen AD, Visseren FLJ, Wang AY, Wen CP, Wheeler DC, Yatsuya H, Yamagata K, Yang JW, Young A, Zhang H, Zhang L, Levey AS, Gansevoort RT. Estimated Glomerular Filtration Rate, Albuminuria, and Adverse Outcomes: An Individual-Participant Data Meta-Analysis. Jama. 2023;330(13):1266-77. doi: 10.1001/jama.2023.17002. PubMed PMID: 37787795; PMCID: PMC10548311.
60. Klang E, Sourosh A, Nadkarni GN, Sharif K, Lahat A. Evaluating the role of ChatGPT in gastroenterology: a comprehensive systematic review of applications, benefits, and limitations. Therap Adv Gastroenterol. 2023;16:17562848231218618. Epub 20231225. doi: 10.1177/17562848231218618. PubMed PMID: 38149123; PMCID: PMC10750546.
61. Menez S, Coca SG, Moledina DG, Wen Y, Chan L, Thiessen-Philbrook H, Obeid W, Garibaldi BT, Azeloglu EU, Ugwuowo U, Sperati CJ, Arend LJ, Rosenberg AZ, Kaushal M, Jain S, Wilson FP, Parikh CR. Evaluation of Plasma Biomarkers to Predict Major Adverse Kidney Events in Hospitalized Patients With COVID-19. Am J Kidney Dis. 2023;82(3):322-32.e1. Epub 20230530. doi: 10.1053/j.ajkd.2023.03.010. PubMed PMID: 37263570; PMCID: PMC10229201.
62. Patra BG, Lepow LA, Kumar PKRJ, Vekaria V, Sharma MM, Adekkanattu P, Fennessy B, Hynes G, Landi I, Sanchez-Ruiz JA. Extracting Social Support and Social Isolation Information from Clinical Psychiatry Notes: Comparing a Rule-based NLP System and a Large Language Model. arXiv preprint arXiv:240317199. 2024.
63. Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N. Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nat Commun. 2024;15(1):216. Epub 20240103. doi: 10.1038/s41467-023-44090-5. PubMed PMID: 38172101; PMCID: PMC10764789.
64. Liu CZ, Prasad A, Jadhav B, Liu Y, Gu M, Sharp AJ, Gelb BD. Feeder-free generation and characterization of endocardial and cardiac valve cells from human pluripotent stem cells. iScience. 2024;27(1):108599. Epub 20231130. doi: 10.1016/j.isci.2023.108599. PubMed PMID: 38170020; PMCID: PMC10758960.
65. Vaid A, Jiang J, Sawant A, Lerakis S, Argulian E, Ahuja Y, Lampert J, Charney A, Greenspan H, Narula J, Glicksberg B, Nadkarni GN. A foundational vision transformer improves diagnostic performance for electrocardiograms. NPJ Digit Med. 2023;6(1):108. Epub 20230606. doi: 10.1038/s41746-023-00840-9. PubMed PMID: 37280346; PMCID: PMC10242218.
66. Wang D, Scalici A, Wang Y, Lin H, Pitsillides A, Heard-Costa N, Cruchaga C, Ziegemeier E, Bis JC, Fornage M, Boerwinkle E, De Jager PL, Wijsman E, Dupuis J, Renton AE, Seshadri S, Goate AM, DeStefano AL, Peloso GM. Frequency of Variants in Mendelian Alzheimer’s Disease Genes within the Alzheimer’s Disease Sequencing Project (ADSP). medRxiv. 2024. Epub 20240329. doi: 10.1101/2023.10.24.23297227. PubMed PMID: 37961373; PMCID: PMC10635182.
67. Galsky MD, Daneshmand S, Izadmehr S, Gonzalez-Kozlova E, Chan KG, Lewis S, Achkar BE, Dorff TB, Cetnar JP, Neil BO, D’Souza A, Mamtani R, Kyriakopoulos C, Jun T, Gogerly-Moragoda M, Brody R, Xie H, Nie K, Kelly G, Horowitz A, Kinoshita Y, Ellis E, Nose Y, Ioannou G, Cabal R, Del Valle DM, Haines GK, Wang L, Mouw KW, Samstein RM, Mehrazin R, Bhardwaj N, Yu M, Zhao Q, Kim-Schulze S, Sebra R, Zhu J, Gnjatic S, Sfakianos J, Pal SK. Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial. Nat Med. 2023;29(11):2825-34. Epub 20231002. doi: 10.1038/s41591-023-02568-1. PubMed PMID: 37783966; PMCID: PMC10667093.
68. Cochran JN, Acosta-Uribe J, Esposito BT, Madrigal L, Aguillón D, Giraldo MM, Taylor JW, Bradley J, Fulton-Howard B, Andrews SJ, Acosta-Baena N, Alzate D, Garcia GP, Piedrahita F, Lopez HE, Anderson AG, Rodriguez-Nunez I, Roberts K, Dominantly Inherited Alzheimer N, Absher D, Myers RM, Beecham GW, Reitz C, Rizzardi LF, Fernandez MV, Goate AM, Cruchaga C, Renton AE, Lopera F, Kosik KS. Genetic associations with age at dementia onset in the PSEN1 E280A Colombian kindred. Alzheimers Dement. 2023;19(9):3835-47. Epub 20230323. doi: 10.1002/alz.13021. PubMed PMID: 36951251; PMCID: PMC10514237.
69. Farrell K, Humphrey J, Chang T, Zhao Y, Leung YY, Kuksa PP, Patil V, Lee W-P, Kuzma AB, Valladares O, Cantwell LB, Wang H, Ravi A, Sanctis CD, Han N, Christie TD, Whitney K, Krassner MM, Walsh H, Kim S, Dangoor D, Iida MA, Casella A, Walker RH, Nirenberg MJ, Renton AE, Babrowicz B, Coppola G, Raj T, Höglinger GU, Golbe LI, Morris HR, Hardy J, Revesz T, Warner TT, Jaunmuktane Z, Mok KY, Rademakers R, Dickson DW, Ross OA, Wang L-S, Goate A, Schellenberg G, Geschwind DH, group Pgs, Crary JF, Naj A. Genetic, transcriptomic, histological, and biochemical analysis of progressive supranuclear palsy implicates glial activation and novel risk genes. bioRxiv. 2023:2023.11.09.565552. doi: 10.1101/2023.11.09.565552.
70. Forrest IS, Duffy Á, Park JK, Vy HMT, Pasquale LR, Nadkarni GN, Cho JH, Do R. Genome-first evaluation with exome sequence and clinical data uncovers underdiagnosed genetic disorders in a large healthcare system. Cell Rep Med. 2024:101518. Epub 20240414. doi: 10.1016/j.xcrm.2024.101518. PubMed PMID: 38642551.
71. Burstein D, Griffen TC, Therrien K, Bendl J, Venkatesh S, Dong P, Modabbernia A, Zeng B, Mathur D, Hoffman G, Sysko R, Hildebrandt T, Voloudakis G, Roussos P. Genome-wide analysis of a model-derived binge eating disorder phenotype identifies risk loci and implicates iron metabolism. Nat Genet. 2023;55(9):1462-70. Epub 20230807. doi: 10.1038/s41588-023-01464-1. PubMed PMID: 37550530; PMCID: PMC10947608.
72. Li JH, Brenner LN, Kaur V, Figueroa K, Schroeder P, Huerta-Chagoya A, Udler MS, Leong A, Mercader JM, Florez JC. Genome-wide association analysis identifies ancestry-specific genetic variation associated with acute response to metformin and glipizide in SUGAR-MGH. Diabetologia. 2023;66(7):1260-72. Epub 20230526. doi: 10.1007/s00125-023-05922-7. PubMed PMID: 37233759; PMCID: PMC10790310.
73. Klarin D, Devineni P, Sendamarai AK, Angueira AR, Graham SE, Shen YH, Levin MG, Pirruccello JP, Surakka I, Karnam PR, Roychowdhury T, Li Y, Wang M, Aragam KG, Paruchuri K, Zuber V, Shakt GE, Tsao NL, Judy RL, Vy HMT, Verma SS, Rader DJ, Do R, Bavaria JE, Nadkarni GN, Ritchie MD, Burgess S, Guo DC, Ellinor PT, LeMaire SA, Milewicz DM, Willer CJ, Natarajan P, Tsao PS, Pyarajan S, Damrauer SM. Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program. Nat Genet. 2023;55(7):1106-15. Epub 20230612. doi: 10.1038/s41588-023-01420-z. PubMed PMID: 37308786; PMCID: PMC10335930.
74. Pérez-Lara G, Olivares-Yañez C, van Bakel H, Larrondo LF, Canessa P. Genome-Wide Characterization of Light-Regulated Gene Expression in Botrytis cinerea Reveals Underlying Complex Photobiology. Int J Mol Sci. 2023;24(10). Epub 20230513. doi: 10.3390/ijms24108705. PubMed PMID: 37240051; PMCID: PMC10218500.
75. Vy HMT, Coca SG, Sawant A, Sakhuja A, Gutierrez OM, Cooper R, Loos RJF, Horowitz CR, Do R, Nadkarni GN. Genome-Wide Polygenic Risk Score for CKD in Individuals with APOL1 High-Risk Genotypes. Clin J Am Soc Nephrol. 2024;19(3):374-6. Epub 20231114. doi: 10.2215/cjn.0000000000000379. PubMed PMID: 37962879; PMCID: PMC10937008.
76. Hughes O, Bentley AR, Breeze CE, Aguet F, Xu X, Nadkarni G, Sun Q, Lin BM, Gilliland T, Meyer MC, Du J, Raffield LM, Kramer H, Morton RW, Gouveia MH, Atkinson EG, Valladares-Salgado A, Wacher-Rodarte N, Dueker ND, Guo X, Hai Y, Adeyemo A, Best LG, Cai J, Chen G, Chong M, Doumatey A, Eales J, Goodarzi MO, Ipp E, Irvin MR, Jiang M, Jones AC, Kooperberg C, Krieger JE, Lange EM, Lanktree MB, Lash JP, Lotufo PA, Loos RJF, Ha My VT, Peralta-Romero J, Qi L, Raffel LJ, Rich SS, Rodriquez EJ, Tarazona-Santos E, Taylor KD, Umans JG, Wen J, Young BA, Yu Z, Zhang Y, Ida Chen YD, Rundek T, Rotter JI, Cruz M, Fornage M, Lima-Costa MF, Pereira AC, Paré G, Natarajan P, Cole SA, Carson AP, Lange LA, Li Y, Perez-Stable EJ, Do R, Charchar FJ, Tomaszewski M, Mychaleckyj JC, Rotimi C, Morris AP, Franceschini N. Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas. Cell Genom. 2024;4(1):100468. Epub 20231222. doi: 10.1016/j.xgen.2023.100468. PubMed PMID: 38190104; PMCID: PMC10794846.
77. Cohen O, Sánchez-de-la-Torre M, Al-Taie Z, Khan S, Kundel V, Kovacic JC, Gracia-Lavedan E, de Batlle J, Nadkarni G, Barbé F, Suárez-Fariñas M, Shah NA. Heterogeneous Effects of CPAP in Non-Sleepy OSA on CVD Outcomes: Post-hoc Machine Learning Analysis of the ISAACC Trial (ECSACT Study). Ann Am Thorac Soc. 2024. Epub 20240215. doi: 10.1513/AnnalsATS.202309-799OC. PubMed PMID: 38358332.
78. Guan L, Zhong G, Fan S, Plisch EM, Presler R, Gu C, Babujee L, Pattinson D, Le Khanh Nguyen H, Hoang VMP, Le MQ, van Bakel H, Neumann G, Kawaoka Y. Highly Pathogenic H5 Influenza Viruses Isolated between 2016 and 2017 in Vietnamese Live Bird Markets. Viruses. 2023;15(5). Epub 20230429. doi: 10.3390/v15051093. PubMed PMID: 37243179; PMCID: PMC10223276.
79. Liu N, Konuma T, Sharma R, Wang D, Zhao N, Cao L, Ju Y, Liu D, Wang S, Bosch A, Sun Y, Zhang S, Ji D, Nagatoishi S, Suzuki N, Kikuchi M, Wakamori M, Zhao C, Ren C, Zhou TJ, Xu Y, Meslamani J, Fu S, Umehara T, Tsumoto K, Akashi S, Zeng L, Roeder RG, Walsh MJ, Zhang Q, Zhou MM. Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin. Mol Cell. 2023;83(13):2206-21.e11. Epub 20230612. doi: 10.1016/j.molcel.2023.05.022. PubMed PMID: 37311463.
80. Phan HV, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns CB, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR. Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology. Sci Transl Med. 2024;16(743):eadj5154. Epub 20240417. doi: 10.1126/scitranslmed.adj5154. PubMed PMID: 38630846.
81. Marallano VJ, Ughetta ME, Tejero R, Nanda S, Ramalingam R, Stalbow L, Sattiraju A, Huang Y, Ramakrishnan A, Shen L, Wojcinski A, Kesari S, Zou H, Tsankov AM, Friedel RH. Hypoxia drives shared and distinct transcriptomic changes in two invasive glioma stem cell lines. Sci Rep. 2024;14(1):7246. Epub 20240327. doi: 10.1038/s41598-024-56102-5. PubMed PMID: 38538643; PMCID: PMC10973515.
82. Aranda CJ, Gonzalez-Kozlova E, Saunders SP, Fernandes-Braga W, Ota M, Narayanan S, He JS, Del Duca E, Swaroop B, Gnjatic S, Shattner G, Reibman J, Soter NA, Guttman-Yassky E, Curotto de Lafaille MA. IgG memory B cells expressing IL4R and FCER2 are associated with atopic diseases. Allergy. 2023;78(3):752-66. Epub 20221219. doi: 10.1111/all.15601. PubMed PMID: 36445014; PMCID: PMC9991991.
83. Haslund-Gourley BS, Woloszczuk K, Hou J, Connors J, Cusimano G, Bell M, Taramangalam B, Fourati S, Mege N, Bernui M, Altman MC, Krammer F, van Bakel H, Maecker HT, Rouphael N, Diray-Arce J, Wigdahl B, Kutzler MA, Cairns CB, Haddad EK, Comunale MA. IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. Nat Commun. 2024;15(1):404. Epub 20240109. doi: 10.1038/s41467-023-44211-0. PubMed PMID: 38195739; PMCID: PMC10776791.
84. LaMarche NM, Hegde S, Park MD, Maier BB, Troncoso L, Le Berichel J, Hamon P, Belabed M, Mattiuz R, Hennequin C, Chin T, Reid AM, Reyes-Torres I, Nemeth E, Zhang R, Olson OC, Doroshow DB, Rohs NC, Gomez JE, Veluswamy R, Hall N, Venturini N, Ginhoux F, Liu Z, Buckup M, Figueiredo I, Roudko V, Miyake K, Karasuyama H, Gonzalez-Kozlova E, Gnjatic S, Passegué E, Kim-Schulze S, Brown BD, Hirsch FR, Kim BS, Marron TU, Merad M. An IL-4 signalling axis in bone marrow drives pro-tumorigenic myelopoiesis. Nature. 2024;625(7993):166-74. Epub 20231206. doi: 10.1038/s41586-023-06797-9. PubMed PMID: 38057662.
85. Coffey DG, Maura F, Gonzalez-Kozlova E, Diaz-Mejia JJ, Luo P, Zhang Y, Xu Y, Warren EH, Dawson T, Lee B, Xie H, Smith E, Ciardiello A, Cho HJ, Rahman A, Kim-Schulze S, Diamond B, Lesokhin A, Kazandjian D, Pugh TJ, Green DJ, Gnjatic S, Landgren O. Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma. Nat Commun. 2023;14(1):5335. Epub 20230902. doi: 10.1038/s41467-023-40966-8. PubMed PMID: 37660077; PMCID: PMC10475030.
86. Escalera A, Laporte M, Turner S, Karakus U, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Khalil Z, van Bakel H, Smith D, García-Sastre A, Aydillo T. The impact of S2 mutations on Omicron SARS-CoV-2 cell surface expression and fusogenicity. Emerg Microbes Infect. 2024;13(1):2297553. Epub 20240213. doi: 10.1080/22221751.2023.2297553. PubMed PMID: 38112266; PMCID: PMC10866063.
87. Vaid A, Sawant A, Suarez-Farinas M, Lee J, Kaul S, Kovatch P, Freeman R, Jiang J, Jayaraman P, Fayad Z, Argulian E, Lerakis S, Charney AW, Wang F, Levin M, Glicksberg B, Narula J, Hofer I, Singh K, Nadkarni GN. Implications of the Use of Artificial Intelligence Predictive Models in Health Care Settings : A Simulation Study. Ann Intern Med. 2023;176(10):1358-69. Epub 20231010. doi: 10.7326/m23-0949. PubMed PMID: 37812781.
88. Bertucci T, Bowles KR, Lotz S, Qi L, Stevens K, Goderie SK, Borden S, Oja LM, Lane K, Lotz R, Lotz H, Chowdhury R, Joy S, Arduini BL, Butler DC, Miller M, Baron H, Sandhof CA, Silva MC, Haggarty SJ, Karch CM, Geschwind DH, Goate AM, Temple S. Improved Protocol for Reproducible Human Cortical Organoids Reveals Early Alterations in Metabolism with MAPT Mutations. bioRxiv. 2023. Epub 20230711. doi: 10.1101/2023.07.11.548571. PubMed PMID: 37503195; PMCID: PMC10369860.
89. Ufongene C, Van Hyfte G, Agarwal P, Blank LJ, Goldstein J, Mathew B, Lin JY, Navis A, McCarthy L, Gururangan K, Peschansky V, Kwon CS, Cohen A, Chan AHW, Dhamoon M, Deng P, Gutzwiller EM, Hao Q, He C, Heredia Nunez WD, Klenofsky B, Lemus HN, Marcuse L, Roberts M, Schorr EM, Singh A, Tantillo G, Young J, Balchandani P, Festa J, Naasan G, Charney A, Nadkarni G, Jetté N. In-hospital outcomes in patients with and without epilepsy diagnosed with COVID-19-A cohort study. Epilepsia. 2023;64(10):2725-37. Epub 20230728. doi: 10.1111/epi.17715. PubMed PMID: 37452760.
90. Anandakrishnan N, Yi Z, Sun Z, Liu T, Haydak J, Eddy S, Jayaraman P, DeFronzo S, Saha A, Sun Q, Yang D, Mendoza A, Mosoyan G, Wen HH, Schaub JA, Fu J, Kehrer T, Menon R, Otto EA, Godfrey B, Suarez-Farinas M, Leffters S, Twumasi A, Meliambro K, Charney AW, García-Sastre A, Campbell KN, Gusella GL, He JC, Miorin L, Nadkarni GN, Wisnivesky J, Li H, Kretzler M, Coca SG, Chan L, Zhang W, Azeloglu EU. Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury. medRxiv. 2024. Epub 20240319. doi: 10.1101/2024.03.18.24304401. PubMed PMID: 38562892; PMCID: PMC10984064.
91. Lampert J, Power D, Havaldar S, Govindarajulu U, Kawamura I, Maan A, Miller MA, Menon K, Koruth J, Whang W, Bagiella E, Bayes-Genis A, Musikantow D, Turagam M, Bayes de Luna A, Halperin J, Dukkipati SR, Vaid A, Nadkarni G, Glicksberg B, Fuster V, Reddy VY. Interatrial Block Association With Adverse Cardiovascular Outcomes in Patients Without a History of Atrial Fibrillation. JACC Clin Electrophysiol. 2023;9(8 Pt 3):1804-15. Epub 20230621. doi: 10.1016/j.jacep.2023.04.006. PubMed PMID: 37354170.
92. Vasquez-Rios G, Oh W, Lee S, Bhatraju P, Mansour SG, Moledina DG, Gulamali FF, Siew ED, Garg AX, Sarder P, Chinchilli VM, Kaufman JS, Hsu CY, Liu KD, Kimmel PL, Go AS, Wurfel MM, Himmelfarb J, Parikh CR, Coca SG, Nadkarni GN. Joint Modeling of Clinical and Biomarker Data in Acute Kidney Injury Defines Unique Subphenotypes with Differing Outcomes. Clin J Am Soc Nephrol. 2023;18(6):716-26. Epub 20230328. doi: 10.2215/cjn.0000000000000156. PubMed PMID: 36975209; PMCID: PMC10278836.
93. Abbott EE, Oh W, Dai Y, Feuer C, Chan L, Carr BG, Nadkarni GN. Joint Modeling of Social Determinants and Clinical Factors to Define Subphenotypes in Out-of-Hospital Cardiac Arrest Survival: Cluster Analysis. JMIR Aging. 2023;6:e51844. Epub 20231206. doi: 10.2196/51844. PubMed PMID: 38059569; PMCID: PMC10721134.
94. Artsi Y, Sorin V, Konen E, Glicksberg BS, Nadkarni G, Klang E. Large language models for generating medical examinations: systematic review. BMC Med Educ. 2024;24(1):354. Epub 20240329. doi: 10.1186/s12909-024-05239-y. PubMed PMID: 38553693; PMCID: PMC10981304.
95. Shahab O, El Kurdi B, Shaukat A, Nadkarni G, Soroush A. Large language models: a primer and gastroenterology applications. Therap Adv Gastroenterol. 2024;17:17562848241227031. Epub 20240222. doi: 10.1177/17562848241227031. PubMed PMID: 38390029; PMCID: PMC10883116.
96. Moscati A, Faucon AB, Arnaiz-Yépez C, Lönn SL, Sundquist J, Sundquist K, Belbin GM, Nadkarni G, Cho JH, Loos RJF, Davis LK, Kendler KS. Life is pain: Fibromyalgia as a nexus of multiple liability distributions. Am J Med Genet B Neuropsychiatr Genet. 2023;192(7-8):171-82. Epub 20230619. doi: 10.1002/ajmg.b.32949. PubMed PMID: 37334860.
97. Rahman S, Dong P, Apontes P, Fernando MB, Kosoy R, Townsley KG, Girdhar K, Bendl J, Shao Z, Misir R, Tsankova N, Kleopoulos SP, Brennand KJ, Fullard JF, Roussos P. Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome. Nucleic Acids Res. 2023;51(20):11142-61. doi: 10.1093/nar/gkad798. PubMed PMID: 37811875; PMCID: PMC10639075.
98. Vaid A, Duong SQ, Lampert J, Kovatch P, Freeman R, Argulian E, Croft L, Lerakis S, Goldman M, Khera R, Nadkarni GN. Local large language models for privacy-preserving accelerated review of historic echocardiogram reports. J Am Med Inform Assoc. 2024. Epub 20240430. doi: 10.1093/jamia/ocae085. PubMed PMID: 38687616.
99. Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Efthymiou AG, Navarro E, Muller BZ, Snijders GJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing. medRxiv. 2023. Epub 20231201. doi: 10.1101/2023.12.01.23299073. PubMed PMID: 38076956; PMCID: PMC10705658.
100. Takkavatakarn K, Oh W, Chan L, Hofer I, Shawwa K, Kraft M, Shah N, Kohli-Seth R, Nadkarni GN, Sakhuja A. Machine learning derived serum creatinine trajectories in acute kidney injury in critically ill patients with sepsis. Crit Care. 2024;28(1):156. Epub 20240510. doi: 10.1186/s13054-024-04935-x. PubMed PMID: 38730421; PMCID: PMC11084026.
101. Chen R, Petrazzini BO, Nadkarni G, Rocheleau G, Bansal M, Do R. Machine Learning Enables Single-Score Assessment of MASLD Presence and Severity. medRxiv. 2023. Epub 20231025. doi: 10.1101/2023.10.24.23297423. PubMed PMID: 37961657; PMCID: PMC10635186.
102. Forrest IS, Petrazzini BO, Duffy Á, Park JK, O’Neal AJ, Jordan DM, Rocheleau G, Nadkarni GN, Cho JH, Blazer AD, Do R. A machine learning model identifies patients in need of autoimmune disease testing using electronic health records. Nat Commun. 2023;14(1):2385. Epub 20230425. doi: 10.1038/s41467-023-37996-7. PubMed PMID: 37169741; PMCID: PMC10130143.
103. Takkavatakarn K, Oh W, Cheng E, Nadkarni GN, Chan L. Machine learning models to predict end-stage kidney disease in chronic kidney disease stage 4. BMC Nephrol. 2023;24(1):376. Epub 20231219. doi: 10.1186/s12882-023-03424-7. PubMed PMID: 38114923; PMCID: PMC10731874.
104. Cohen J, Duong SQ, Arivazhagan N, Barris DM, Bebiya S, Castaldo R, Gayanilo M, Hopkins K, Kailas M, Kong G, Ma X, Marshall M, Paul EA, Tan M, Yau JL, Nadkarni GN, Ezon D. Machine Learning Quantification of Pulmonary Regurgitation Fraction from Echocardiography. Pediatr Cardiol. 2024. Epub 20240510. doi: 10.1007/s00246-024-03511-y. PubMed PMID: 38730015.
105. Wilks SH, Mühlemann B, Shen X, Türeli S, LeGresley EB, Netzl A, Caniza MA, Chacaltana-Huarcaya JN, Corman VM, Daniell X, Datto MB, Dawood FS, Denny TN, Drosten C, Fouchier RAM, Garcia PJ, Halfmann PJ, Jassem A, Jeworowski LM, Jones TC, Kawaoka Y, Krammer F, McDanal C, Pajon R, Simon V, Stockwell MS, Tang H, van Bakel H, Veguilla V, Webby R, Montefiori DC, Smith DJ. Mapping SARS-CoV-2 antigenic relationships and serological responses. Science. 2023;382(6666):eadj0070. Epub 20231006. doi: 10.1126/science.adj0070. PubMed PMID: 37797027.
106. Mills AG, Dupper AC, Chacko KI, Alburquerque B, Nadkarni D, Berbel Caban A, Fox L, Gitman MR, Obla A, van Bakel H, Altman DR. Methicillin-resistant Staphylococcus aureus bacteremia with elevated vancomycin minimum inhibitory concentrations. Antimicrob Steward Healthc Epidemiol. 2023;3(1):e87. Epub 20230502. doi: 10.1017/ash.2023.163. PubMed PMID: 37179762; PMCID: PMC10173282.
107. Amar D, Gay NR, Jimenez-Morales D, Beltran PMJ, Ramaker ME, Raja AN, Zhao B, Sun Y, Marwaha S, Gaul D, Hershman SG, Xia A, Lanza I, Fernandez FM, Montgomery SB, Hevener AL, Ashley EA, Walsh MJ, Sparks LM, Burant CF, Rector RS, Thyfault J, Wheeler MT, Goodpaster BH, Coen PM, Schenk S, Bodine SC, Lindholm ME. The mitochondrial multi-omic response to exercise training across tissues. bioRxiv. 2023. Epub 20230113. doi: 10.1101/2023.01.13.523698. PubMed PMID: 36711881; PMCID: PMC9882193.
108. Chen DC, Scherzer R, Ix JH, Kramer HJ, Crews DC, Nadkarni G, Gutierrez O, Bullen AL, Ilori T, Garimella PS, Shlipak MG, Estrella MM. Modification of Association of Cystatin C With Kidney and Cardiovascular Outcomes by Obesity. Am J Kidney Dis. 2024;83(4):489-96.e1. Epub 20231020. doi: 10.1053/j.ajkd.2023.08.021. PubMed PMID: 37866793; PMCID: PMC10960714.
109. Nair VD, Pincas H, Smith GR, Zaslavsky E, Ge Y, Amper MAS, Vasoya M, Chikina M, Sun Y, Raja AN, Mao W, Gay NR, Esser KA, Smith KS, Zhao B, Wiel L, Singh A, Lindholm ME, Amar D, Montgomery S, Snyder MP, Walsh MJ, Sealfon SC. Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures. Cell Genom. 2024:100421. Epub 20240429. doi: 10.1016/j.xgen.2023.100421. PubMed PMID: 38697122.
110. Dunn AD, Robinson SA, Nwokafor C, Estill M, Ferrante J, Shen L, Lemchi CO, Creus-Muncunill J, Ramirez A, Mengaziol J, Brynildsen JK, Leggas M, Horn J, Ehrlich ME, Blendy JA. Molecular and long-term behavioral consequences of neonatal opioid exposure and withdrawal in mice. Front Behav Neurosci. 2023;17:1202099. Epub 20230621. doi: 10.3389/fnbeh.2023.1202099. PubMed PMID: 37424750; PMCID: PMC10324024.
111. Zilberg G, Parpounas AK, Warren AL, Yang S, Wacker D. Molecular basis of human trace amine-associated receptor 1 activation. Nature Communications. 2024;15(1):108.
112. Cohn H, Bloom N, Cai GY, Clark JJ, Tarke A, Bermúdez-González MC, Altman DR, Lugo LA, Lobo FP, Marquez S, Chen JQ, Ren W, Qin L, Yates JL, Hunt DT, Lee WT, Crotty S, Krammer F, Grifoni A, Sette A, Simon V, Coelho CH. Mpox vaccine and infection-driven human immune signatures: an immunological analysis of an observational study. Lancet Infect Dis. 2023;23(11):1302-12. Epub 20230717. doi: 10.1016/s1473-3099(23)00352-3. PubMed PMID: 37475115; PMCID: PMC10826035.
113. Coleman C, Wang M, Wang E, Micallef C, Shao Z, Vicari JM, Li Y, Yu K, Cai D, Peng J, Haroutunian V, Fullard JF, Bendl J, Zhang B, Roussos P. Multi-omic atlas of the parahippocampal gyrus in Alzheimer’s disease. Sci Data. 2023;10(1):602. Epub 20230908. doi: 10.1038/s41597-023-02507-2. PubMed PMID: 37684260; PMCID: PMC10491684.
114. Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell Rep Med. 2023;4(6):101079. Epub 20230523. doi: 10.1016/j.xcrm.2023.101079. PubMed PMID: 37327781; PMCID: PMC10203880.
115. Zhu K, Bendl J, Rahman S, Vicari JM, Coleman C, Clarence T, Latouche O, Tsankova NM, Li A, Brennand KJ, Lee D, Yuan GC, Fullard JF, Roussos P. Multi-omic profiling of the developing human cerebral cortex at the single-cell level. Sci Adv. 2023;9(41):eadg3754. Epub 20231012. doi: 10.1126/sciadv.adg3754. PubMed PMID: 37824614; PMCID: PMC10569714.
116. Oikonomou EK, Holste G, Yuan N, Coppi A, McNamara RL, Haynes NA, Vora AN, Velazquez EJ, Li F, Menon V, Kapadia SR, Gill TM, Nadkarni GN, Krumholz HM, Wang Z, Ouyang D, Khera R. A Multimodal Video-Based AI Biomarker for Aortic Stenosis Development and Progression. JAMA Cardiol. 2024. Epub 20240406. doi: 10.1001/jamacardio.2024.0595. PubMed PMID: 38581644; PMCID: PMC10999005.
117. Redlener M, Buckler DG, Sondheim SE, Yeturu SK, Loo GT, Munjal KG, Jarvis J, Crowe RP. A National Assessment of EMS Performance at the Response and Agency Level. Prehosp Emerg Care. 2024:1-8. Epub 20240212. doi: 10.1080/10903127.2023.2283886. PubMed PMID: 38347669.
118. Butelman ER, Goldstein RZ, Nwaneshiudu CA, Girdhar K, Roussos P, Russo SJ, Alia-Klein N. Neuroimmune Mechanisms of Opioid Use Disorder and Recovery: Translatability to Human Studies, and Future Research Directions. Neuroscience. 2023;528:102-16. Epub 20230809. doi: 10.1016/j.neuroscience.2023.07.031. PubMed PMID: 37562536; PMCID: PMC10720374.
119. Girdhar K, Bendl J, Baumgartner A, Therrien K, Venkatesh S, Mathur D, Dong P, Rahman S, Kleopoulos SP, Misir R, Reach SM, Auluck PK, Marenco S, Lewis DA, Haroutunian V, Funk C, Voloudakis G, Hoffman GE, Fullard JF, Roussos P. The neuronal chromatin landscape in adult schizophrenia brains is linked to early fetal development. Res Sq. 2023. Epub 20231002. doi: 10.21203/rs.3.rs-3393581/v1. PubMed PMID: 37886514; PMCID: PMC10602154.
120. Gururangan K, Peschansky VJ, Van Hyfte G, Agarwal P, Blank LJ, Mathew B, Goldstein J, Kwon CS, McCarthy L, Cohen A, Chan AHW, Deng P, Dhamoon M, Gutzwiller E, Hao Q, He C, Klenofsky B, Lemus HN, Marcuse L, Navis A, Heredia Nunez WD, Luckey MN, Schorr EM, Singh A, Tantillo GB, Ufongene C, Young JJ, Balchandani P, Festa JR, Naasan G, Charney AW, Nadkarni GN, Jetté N. Neuropsychiatric complications of coronavirus disease 2019: Mount Sinai Health System cohort study. J Neurol. 2024. Epub 20240424. doi: 10.1007/s00415-024-12370-9. PubMed PMID: 38656620.
121. Telpoukhovskaia MA, Murdy TJ, Marola OJ, Charland K, MacLean M, Luquez T, Lish AM, Neuner S, Dunn A, Onos KD, Wiley J, Archer D, Huentelman MJ, Arnold M, Menon V, Goate A, Van Eldik LJ, Territo PR, Howell GR, Carter GW, O’Connell KMS, Kaczorowski CC. New directions for Alzheimer’s disease research from the Jackson Laboratory Center for Alzheimer’s and Dementia Research 2022 workshop. Alzheimers Dement (N Y). 2024;10(1):e12458. Epub 20240310. doi: 10.1002/trc2.12458. PubMed PMID: 38469553; PMCID: PMC10925728.
122. Thangaraj PM, Shankar SV, Huang S, Nadkarni G, Mortazavi B, Oikonomou EK, Khera R. A Novel Digital Twin Strategy to Examine the Implications of Randomized Control Trials for Real-World Populations. medRxiv. 2024. Epub 20240326. doi: 10.1101/2024.03.25.24304868. PubMed PMID: 38585929; PMCID: PMC10996766.
123. Lampert J, Vaid A, Whang W, Koruth J, Miller MA, Langan MN, Musikantow D, Turagam M, Maan A, Kawamura I, Dukkipati S, Nadkarni GN, Reddy VY. A Novel ECG-Based Deep Learning Algorithm to Predict Cardiomyopathy in Patients With Premature Ventricular Complexes. JACC Clin Electrophysiol. 2023;9(8 Pt 2):1437-51. Epub 20230719. doi: 10.1016/j.jacep.2023.05.025. PubMed PMID: 37480862.
124. Oh W, Jayaraman P, Tandon P, Chaddha US, Kovatch P, Charney AW, Glicksberg BS, Nadkarni GN. A novel method leveraging time series data to improve subphenotyping and application in critically ill patients with COVID-19. Artif Intell Med. 2024;148:102750. Epub 20231220. doi: 10.1016/j.artmed.2023.102750. PubMed PMID: 38325922; PMCID: PMC10864255.
125. Torre D, Fstkchyan YS, Ho JSY, Cheon Y, Patel RS, Degrace EJ, Mzoughi S, Schwarz M, Mohammed K, Seo JS, Romero-Bueno R, Demircioglu D, Hasson D, Tang W, Mahajani SU, Campisi L, Zheng S, Song WS, Wang YC, Shah H, Francoeur N, Soto J, Salfati Z, Weirauch MT, Warburton P, Beaumont K, Smith ML, Mulder L, Villalta SA, Kessenbrock K, Jang C, Lee D, De Rubeis S, Cobos I, Tam O, Hammell MG, Seldin M, Shi Y, Basu U, Sebastiano V, Byun M, Sebra R, Rosenberg BR, Benner C, Guccione E, Marazzi I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Mol Cell. 2023;83(23):4255-71.e9. Epub 20231122. doi: 10.1016/j.molcel.2023.10.036. PubMed PMID: 37995687; PMCID: PMC10842741.
126. Ufongene C, Van Hyfte G, Agarwal P, Goldstein J, Mathew B, Navis A, McCarthy L, Kwon CS, Gururangan K, Balchandani P, Marcuse L, Naasan G, Singh A, Young J, Charney A, Nadkarni G, Jette N, Blank LJ. Older adults with epilepsy and COVID-19: Outcomes in a multi-hospital health system. Seizure. 2024;114:33-9. Epub 20231126. doi: 10.1016/j.seizure.2023.11.018. PubMed PMID: 38039805; PMCID: PMC10841585.
127. Pryce KD, Serafini RA, Ramakrishnan A, Nicolais A, Giosan IM, Polizu C, Torres-Berrío A, Vuppala S, Kronman H, Ruiz A, Gaspari S, Peña CJ, Sakloth F, Mitsi V, van Duzer J, Mazitschek R, Jarpe M, Shen L, Nestler EJ, Zachariou V. Oxycodone withdrawal induces HDAC1/HDAC2-dependent transcriptional maladaptations in the reward pathway in a mouse model of peripheral nerve injury. Nature Neuroscience. 2023;26(7):1229-44. doi: 10.1038/s41593-023-01350-3.
128. Mayourian J, La Cava WG, Vaid A, Nadkarni GN, Ghelani SJ, Mannix R, Geva T, Dionne A, Alexander ME, Duong SQ, Triedman JK. Pediatric ECG-Based Deep Learning to Predict Left Ventricular Dysfunction and Remodeling. Circulation. 2024;149(12):917-31. Epub 20240205. doi: 10.1161/circulationaha.123.067750. PubMed PMID: 38314583; PMCID: PMC10948312.
129. van Gerwen M, Colicino E, Guan H, Dolios G, Nadkarni GN, Vermeulen RCH, Wolff MS, Arora M, Genden EM, Petrick LM. Per- and polyfluoroalkyl substances (PFAS) exposure and thyroid cancer risk. EBioMedicine. 2023;97:104831. Epub 20231024. doi: 10.1016/j.ebiom.2023.104831. PubMed PMID: 37884429; PMCID: PMC10667111.
130. Jayaraman P, Rajagopal M, Paranjpe I, Liharska L, Suarez-Farinas M, Thompson R, Del Valle DM, Beckmann N, Oh W, Gulamali FF, Kauffman J, Gonzalez-Kozlova E, Dellepiane S, Vasquez-Rios G, Vaid A, Jiang J, Chen A, Sakhuja A, Chen S, Kenigsberg E, He JC, Coca SG, Chan L, Schadt E, Merad M, Kim-Schulze S, Gnjatic S, Tsalik E, Langley R, Charney AW, Nadkarni GN. Peripheral Transcriptomics in Acute and Long-Term Kidney Dysfunction in SARS-CoV2 Infection. medRxiv. 2023. Epub 20231027. doi: 10.1101/2023.10.25.23297469. PubMed PMID: 37961671; PMCID: PMC10635190.
131. Jadhav B, Garg P, van Vugt J, Ibanez K, Gagliardi D, Lee W, Shadrina M, Mokveld T, Dolzhenko E, Martin-Trujillo A, Gies SL, Rocca C, Barbosa M, Jain M, Lahiri N, Lachlan K, Houlden H, Paten B, Veldink J, Tucci A, Sharp AJ. A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability. medRxiv. 2023. Epub 20231212. doi: 10.1101/2023.05.03.23289461. PubMed PMID: 37205357; PMCID: PMC10187445.
132. Manigbas C, Jadhav B, Garg P, Shadrina M, Lee W, Martin-Trujillo A, Sharp A. A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank. medRxiv. 2024:2024.01. 22.24301630.
133. Yashaswini CN, Qin T, Bhattacharya D, Amor C, Lowe S, Lujambio A, Wang S, Friedman SL. Phenotypes and ontogeny of senescent hepatic stellate cells in metabolic dysfunction-associated steatotic liver disease. Journal of Hepatology. 2024.
134. Honigberg MC, Truong B, Khan RR, Xiao B, Bhatta L, Vy HMT, Guerrero RF, Schuermans A, Selvaraj MS, Patel AP, Koyama S, Cho SMJ, Vellarikkal SK, Trinder M, Urbut SM, Gray KJ, Brumpton BM, Patil S, Zöllner S, Antopia MC, Saxena R, Nadkarni GN, Do R, Yan Q, Pe’er I, Verma SS, Gupta RM, Haas DM, Martin HC, van Heel DA, Laisk T, Natarajan P. Polygenic prediction of preeclampsia and gestational hypertension. Nat Med. 2023;29(6):1540-9. Epub 20230529. doi: 10.1038/s41591-023-02374-9. PubMed PMID: 37248299; PMCID: PMC10330886.
135. Ibañez K, Jadhav B, Facchini S, Garg P, Zanovello M, Martin-Trujillo A, Gies SJ, Deforie VG, Gagliardi D, Hensman D, Moutsianas L, Shoai M, Caulfield MJ, Cortese A, Escott-Price V, Hardy J, Houlden H, Sharp AJ, Tucci A. POPULATION FREQUENCY OF REPEAT EXPANSIONS INDICATES INCREASED DISEASE PREVALENCE ESTIMATES ACROSS DIFFERENT POPULATIONS. medRxiv. 2023. Epub 20230706. doi: 10.1101/2023.07.03.23292162. PubMed PMID: 37461547; PMCID: PMC10350132.
136. El-Achkar TM, Eadon MT, Kretzler M, Himmelfarb J. Precision Medicine in Nephrology: An Integrative Framework of Multidimensional Data in the Kidney Precision Medicine Project. Am J Kidney Dis. 2024;83(3):402-10. Epub 20231013. doi: 10.1053/j.ajkd.2023.08.015. PubMed PMID: 37839688; PMCID: PMC10922684.
137. Midya V, Nagdeo K, Lane JM, Torres-Olascoaga LA, Torres-Calapiz M, Gennings C, Horton MK, Téllez-Rojo MM, Wright RO, Arora M. Prenatal metal exposures and childhood gut microbial signatures are associated with depression score in late childhood. Science of The Total Environment. 2024;916:170361.
138. Ulrich RJ, Podkowik M, Tierce R, Irnov I, Putzel G, Samhadaneh N, Lacey KA, Boff D, Morales SM, Makita S. Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus. bioRxiv. 2024:2024.04. 17.589803.
139. Clark J, Hoxie I, Adelsberg D, Sapse I, Andreata-Santos R, Yong J, Amanat F, Tcheou J, Raskin A, Singh G. Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination. bioRxiv. 2024:2024.02. 28.582613.
140. Nair VD, Pincas H, Amper MAS, Ge Y, Vasoya M, Raja AN, Walsh MJ, Sealfon SC. Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing. STAR Protoc. 2024;5(2):103007. Epub 20240430. doi: 10.1016/j.xpro.2024.103007. PubMed PMID: 38691461; PMCID: PMC11070626.
141. Wang Q, Antone J, Alsop E, Reiman R, Funk C, Bendl J, Dudley JT, Liang WS, Karr TL, Roussos P, Bennett DA, De Jager PL, Serrano GE, Beach TG, Keuren-Jensen KV, Mastroeni D, Reiman EM, Readhead BP. A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer’s disease. bioRxiv. 2023. Epub 20231024. doi: 10.1101/2023.10.20.563319. PubMed PMID: 37961404; PMCID: PMC10634692.
142. Choi J, Ehrlich ME, Roussos P, Wang P, Yuan GC, Song X. QuadST: A Powerful and Robust Approach for Identifying Cell-Cell Interaction-Changed Genes on Spatially Resolved Transcriptomics. bioRxiv. 2023. Epub 20231207. doi: 10.1101/2023.12.04.570019. PubMed PMID: 38106025; PMCID: PMC10723309.
143. Duong SQ, Vaid A, My VTH, Butler LR, Lampert J, Pass RH, Charney AW, Narula J, Khera R, Sakhuja A, Greenspan H, Gelb BD, Do R, Nadkarni GN. Quantitative Prediction of Right Ventricular Size and Function From the ECG. J Am Heart Assoc. 2024;13(1):e031671. Epub 20231229. doi: 10.1161/jaha.123.031671. PubMed PMID: 38156471; PMCID: PMC10863807.
144. Tokita J, Lam D, Vega A, Wang S, Amoruso L, Muller T, Naik N, Rathi S, Martin S, Zabetian A, Liu C, Sinfield C, McNicholas T, Fleming F, Coca SG, Nadkarni GN, Tun R, Kattan M, Donovan MJ, Rahim AK. A Real-World Precision Medicine Program Including the KidneyIntelX Test Effectively Changes Management Decisions and Outcomes for Patients With Early-Stage Diabetic Kidney Disease. J Prim Care Community Health. 2024;15:21501319231223437. doi: 10.1177/21501319231223437. PubMed PMID: 38185870; PMCID: PMC10773280.
145. Griggs E, Trageser K, Naughton S, Yang EJ, Mathew B, Van Hyfte G, Hellmers L, Jette N, Estill M, Shen L, Fischer T, Pasinetti GM. Recapitulation of pathophysiological features of AD in SARS-CoV-2-infected subjects. Elife. 2023;12. Epub 20230707. doi: 10.7554/eLife.86333. PubMed PMID: 37417740; PMCID: PMC10361716.
146. Hirten RP, Danieletto M, Landell K, Zweig M, Golden E, Pyzik R, Kaur S, Chang H, Helmus D, Sands BE, Charney D, Nadkarni G, Bagiella E, Keefer L, Fayad ZA. Remote Short Sessions of Heart Rate Variability Biofeedback Monitored With Wearable Technology: Open-Label Prospective Feasibility Study. JMIR Ment Health. 2024;11:e55552. Epub 20240425. doi: 10.2196/55552. PubMed PMID: 38663011; PMCID: PMC11082734.
147. Horwitz LI, Thaweethai T, Brosnahan SB, Cicek MS, Fitzgerald ML, Goldman JD, Hess R, Hodder SL, Jacoby VL, Jordan MR, Krishnan JA, Laiyemo AO, Metz TD, Nichols L, Patzer RE, Sekar A, Singer NG, Stiles LE, Taylor BS, Ahmed S, Algren HA, Anglin K, Aponte-Soto L, Ashktorab H, Bassett IV, Bedi B, Bhadelia N, Bime C, Bind MC, Black LJ, Blomkalns AL, Brim H, Castro M, Chan J, Charney AW, Chen BK, Chen LQ, Chen P, Chestek D, Chibnik LB, Chow DC, Chu HY, Clifton RG, Collins S, Costantine MM, Cribbs SK, Deeks SG, Dickinson JD, Donohue SE, Durstenfeld MS, Emery IF, Erlandson KM, Facelli JC, Farah-Abraham R, Finn AV, Fischer MS, Flaherman VJ, Fleurimont J, Fonseca V, Gallagher EJ, Gander JC, Gennaro ML, Gibson KS, Go M, Goodman SN, Granger JP, Greenway FL, Hafner JW, Han JE, Harkins MS, Hauser KSP, Heath JR, Hernandez CR, Ho O, Hoffman MK, Hoover SE, Horowitz CR, Hsu H, Hsue PY, Hughes BL, Jagannathan P, James JA, John J, Jolley S, Judd SE, Juskowich JJ, Kanjilal DG, Karlson EW, Katz SD, Kelly JD, Kelly SW, Kim AY, Kirwan JP, Knox KS, Kumar A, Lamendola-Essel MF, Lanca M, Lee-Lannotti JK, Lefebvre RC, Levy BD, Lin JY, Logarbo BP, Jr., Logue JK, Longo MT, Luciano CA, Lutrick K, Malakooti SK, Mallett G, Maranga G, Marathe JG, Marconi VC, Marshall GD, Martin CF, Martin JN, May HT, McComsey GA, McDonald D, Mendez-Figueroa H, Miele L, Mittleman MA, Mohandas S, Mouchati C, Mullington JM, Nadkarni GN, Nahin ER, Neuman RB, Newman LT, Nguyen A, Nikolich JZ, Ofotokun I, Ogbogu PU, Palatnik A, Palomares KTS, Parimon T, Parry S, Parthasarathy S, Patterson TF, Pearman A, Peluso MJ, Pemu P, Pettker CM, Plunkett BA, Pogreba-Brown K, Poppas A, Porterfield JZ, Quigley JG, Quinn DK, Raissy H, Rebello CJ, Reddy UM, Reece R, Reeder HT, Rischard FP, Rosas JM, Rosen CJ, Rouphael NG, Rouse DJ, Ruff AM, Saint Jean C, Sandoval GJ, Santana JL, Schlater SM, Sciurba FC, Selvaggi C, Seshadri S, Sesso HD, Shah DP, Shemesh E, Sherif ZA, Shinnick DJ, Simhan HN, Singh U, Sowles A, Subbian V, Sun J, Suthar MS, Teunis LJ, Thorp JM, Jr., Ticotsky A, Tita ATN, Tragus R, Tuttle KR, Urdaneta AE, Utz PJ, VanWagoner TM, Vasey A, Vernon SD, Vidal C, Walker T, Ward HD, Warren DE, Weeks RM, Weiner SJ, Weyer JC, Wheeler JL, Whiteheart SW, Wiley Z, Williams NJ, Wisnivesky JP, Wood JC, Yee LM, Young NM, Zisis SN, Foulkes AS. Researching COVID to Enhance Recovery (RECOVER) adult study protocol: Rationale, objectives, and design. PLoS One. 2023;18(6):e0286297. Epub 20230623. doi: 10.1371/journal.pone.0286297. PubMed PMID: 37352211; PMCID: PMC10289397.
148. Mitsi V, Ruiz A, Polizu C, Farzinpour Z, Ramakrishnan A, Serafini RA, Parise EM, Floodstrand M, Sial OK, Gaspari S, Tang CY, Nestler EJ, Schmidt EF, Shen L, Zachariou V. RGS4 Actions in Mouse Prefrontal Cortex Modulate Behavioral and Transcriptomic Responses to Chronic Stress and Ketamine. Mol Pharmacol. 2024;105(4):272-85. Epub 20240314. doi: 10.1124/molpharm.123.000753. PubMed PMID: 38351270; PMCID: PMC10949159.
149. Srivastava K, Carreño JM, Gleason C, Monahan B, Singh G, Abbad A, Tcheou J, Raskin A, Kleiner G, van Bakel H, Sordillo EM, Krammer F, Simon V. SARS-CoV-2-infection- and vaccine-induced antibody responses are long lasting with an initial waning phase followed by a stabilization phase. Immunity. 2024;57(3):587-99.e4. Epub 20240222. doi: 10.1016/j.immuni.2024.01.017. PubMed PMID: 38395697; PMCID: PMC11066813.
150. Maury EA, Sherman MA, Genovese G, Gilgenast TG, Kamath T, Burris SJ, Rajarajan P, Flaherty E, Akbarian S, Chess A, McCarroll SA, Loh PR, Phillips-Cremins JE, Brennand KJ, Macosko EZ, Walters JTR, O’Donovan M, Sullivan P, Sebat J, Lee EA, Walsh CA. Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions. Cell Genom. 2023;3(8):100356. Epub 20230706. doi: 10.1016/j.xgen.2023.100356. PubMed PMID: 37601975; PMCID: PMC10435376.
151. Sakai-Tagawa Y, Yamayoshi S, Halfmann PJ, Wilson N, Bobholz M, Vuyk WC, Wei W, Ries H, O’Connor DH, Friedrich TC, Sordillo EM, van Bakel H, Simon V, Kawaoka Y. Sensitivity of rapid antigen tests for Omicron subvariants of SARS-CoV-2. J Med Virol. 2023;95(5):e28788. doi: 10.1002/jmv.28788. PubMed PMID: 37212288.
152. Gonzalez-Reiche AS, Alshammary H, Schaefer S, Patel G, Polanco J, Carreño JM, Amoako AA, Rooker A, Cognigni C, Floda D, van de Guchte A, Khalil Z, Farrugia K, Assad N, Zhang J, Alburquerque B, Sominsky LA, Gleason C, Srivastava K, Sebra R, Ramirez JD, Banu R, Shrestha P, Krammer F, Paniz-Mondolfi A, Sordillo EM, Simon V, van Bakel H. Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants. Nat Commun. 2023;14(1):3235. Epub 20230603. doi: 10.1038/s41467-023-38867-x. PubMed PMID: 37270625; PMCID: PMC10239218.
153. Chan JC, Alenina N, Cunningham AM, Ramakrishnan A, Shen L, Bader M, Maze I. Serotonin transporter-dependent histone serotonylation in placenta contributes to the neurodevelopmental transcriptome. bioRxiv. 2023. Epub 20231114. doi: 10.1101/2023.11.14.567020. PubMed PMID: 38014301; PMCID: PMC10680709.
154. Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. bioRxiv. 2024. Epub 20240330. doi: 10.1101/2024.03.18.585576. PubMed PMID: 38562822; PMCID: PMC10983939.
155. Pruvost M, Patzig J, Yattah C, Selcen I, Hernandez M, Park HJ, Moyon S, Liu S, Morioka MS, Shopland L, Al-Dalahmah O, Bendl J, Fullard JF, Roussos P, Goldman J, He Y, Dupree JL, Casaccia P. The stability of the myelinating oligodendrocyte transcriptome is regulated by the nuclear lamina. Cell Rep. 2023;42(8):112848. Epub 20230728. doi: 10.1016/j.celrep.2023.112848. PubMed PMID: 37515770; PMCID: PMC10600948.
156. Felt K, Stauffer M, Salas-Estrada L, Guzzo PR, Xie D, Huang J, Filizola M, Chakrapani S. Structural basis for partial agonism in 5-HT(3A) receptors. Nat Struct Mol Biol. 2024;31(4):598-609. Epub 20240104. doi: 10.1038/s41594-023-01140-2. PubMed PMID: 38177669.
157. Zilberg G, Parpounas AK, Warren AL, Fiorillo B, Provasi D, Filizola M, Wacker D. Structural insights into the unexpected agonism of tetracyclic antidepressants at serotonin receptors 5-HT(1e)R and 5-HT(1F)R. Sci Adv. 2024;10(16):eadk4855. Epub 20240417. doi: 10.1126/sciadv.adk4855. PubMed PMID: 38630816; PMCID: PMC11023502.
158. Amar D, Gay NR, Jean-Beltran PM, Bae D, Dasari S, Dennis C, Evans CR, Gaul DA, Ilkayeva O, Ivanova AA, Kachman MT, Keshishian H, Lanza IR, Lira AC, Muehlbauer MJ, Nair VD, Piehowski PD, Rooney JL, Smith KS, Stowe CL, Zhao B, Clark NM, Jimenez-Morales D, Lindholm ME, Many GM, Sanford JA, Smith GR, Vetr NG, Zhang T, Almagro Armenteros JJ, Avila-Pacheco J, Bararpour N, Ge Y, Hou Z, Marwaha S, Presby DM, Natarajan Raja A, Savage EM, Steep A, Sun Y, Wu S, Zhen J, Bodine SC, Esser KA, Goodyear LJ, Schenk S, Montgomery SB, Fernández FM, Sealfon SC, Snyder MP, Adkins JN, Ashley E, Burant CF, Carr SA, Clish CB, Cutter G, Gerszten RE, Kraus WE, Li JZ, Miller ME, Nair KS, Newgard C, Ortlund EA, Qian W-J, Tracy R, Walsh MJ, Wheeler MT, Dalton KP, Hastie T, Hershman SG, Samdarshi M, Teng C, Tibshirani R, Cornell E, Gagne N, May S, Bouverat B, Leeuwenburgh C, Lu C-j, Pahor M, Hsu F-C, Rushing S, Walkup MP, Nicklas B, Rejeski WJ, Williams JP, Xia A, Albertson BG, Barton ER, Booth FW, Caputo T, Cicha M, De Sousa LGO, Farrar R, Hevener AL, Hirshman MF, Jackson BE, Ke BG, Kramer KS, Lessard SJ, Makarewicz NS, Marshall AG, Nigro P, Powers S, Ramachandran K, Rector RS, Richards CZT, Thyfault J, Yan Z, Zang C, Amper MAS, Balci AT, Chavez C, Chikina M, Chiu R, Gritsenko MA, Guevara K, Hansen JR, Hennig KM, Hung C-J, Hutchinson-Bunch C, Jin CA, Liu X, Maner-Smith KM, Mani DR, Marjanovic N, Monroe ME, Moore RJ, Moore SG, Mundorff CC, Nachun D, Nestor MD, Nudelman G, Pearce C, Petyuk VA, Pincas H, Ramos I, Raskind A, Rirak S, Robbins JM, Rubenstein AB, Ruf-Zamojski F, Sagendorf TJ, Seenarine N, Soni T, Uppal K, Vangeti S, Vasoya M, Vornholt A, Yu X, Zaslavsky E, Zebarjadi N, Bamman M, Bergman BC, Bessesen DH, Buford TW, Chambers TL, Coen PM, Cooper D, Haddad F, Gadde K, Goodpaster BH, Harris M, Huffman KM, Jankowski CM, Johannsen NM, Kohrt WM, Lester B, Melanson EL, Moreau KL, Musi N, Newton RL, Radom-Aizik S, Ramaker ME, Rankinen T, Rasmussen BB, Ravussin E, Schauer IE, Schwartz RS, Sparks LM, Thalacker-Mercer A, Trappe S, Trappe TA, Volpi E, MoTr PAC SG, Primary a, Lead A, Lead Data G, Analysts, Animal Study L, Manuscript Writing Group L, Manuscript Writing G, Senior L, Co-corresponding A, MoTr PACSG, Bioinformatics C, Biospecimens R, Administrative Coordinating C, Data Management A, Quality Control C, Exercise Intervention C, Nih, Preclinical Animal Study S, Chemical Analysis S, Clinical S. Temporal dynamics of the multi-omic response to endurance exercise training. Nature. 2024;629(8010):174-83. doi: 10.1038/s41586-023-06877-w.
159. Serafini RA, Estill M, Pekarskaya EA, Sakloth F, Shen L, Javitch JA, Zachariou V. Tianeptine promotes lasting antiallodynic effects in a mouse model of neuropathic pain. Neuropsychopharmacology. 2023;48(11):1680-9. Epub 20230720. doi: 10.1038/s41386-023-01645-w. PubMed PMID: 37474762; PMCID: PMC10517169.
160. Kwak SH, Hernandez-Cancela RB, DiCorpo DA, Condon DE, Merino J, Wu P, Brody JA, Yao J, Guo X, Ahmadizar F, Meyer M, Sincan M, Mercader JM, Lee S, Haessler J, Vy HMT, Lin Z, Armstrong ND, Gu S, Tsao NL, Lange LA, Wang N, Wiggins KL, Trompet S, Liu S, Loos RJF, Judy R, Schroeder PH, Hasbani NR, Bos MM, Morrison AC, Jackson RD, Reiner AP, Manson JE, Chaudhary NS, Carmichael LK, Chen YI, Taylor KD, Ghanbari M, van Meurs J, Pitsillides AN, Psaty BM, Noordam R, Do R, Park KS, Jukema JW, Kavousi M, Correa A, Rich SS, Damrauer SM, Hajek C, Cho NH, Irvin MR, Pankow JS, Nadkarni GN, Sladek R, Goodarzi MO, Florez JC, Chasman DI, Heckbert SR, Kooperberg C, Dupuis J, Malhotra R, de Vries PS, Liu CT, Rotter JI, Meigs JB. Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People With Type 2 Diabetes. Diabetes Care. 2024. Epub 20240423. doi: 10.2337/dc23-2274. PubMed PMID: 38652672.
161. Green A, Rachoin JS, Schorr C, Dellinger P, Casey JD, Park I, Gupta S, Baron RM, Shaefi S, Hunter K, Leaf DE. Timing of invasive mechanical ventilation and death in critically ill adults with COVID-19: A multicenter cohort study. PLoS One. 2023;18(6):e0285748. Epub 20230628. doi: 10.1371/journal.pone.0285748. PubMed PMID: 37379286; PMCID: PMC10306211.
162. Pillai TK, Johnson KE, Song T, Gregianini TS, Tatiana GB, Wang G, Medina RA, Van Bakel H, García-Sastre A, Nelson MI, Ghedin E, Veiga ABG. Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil. Virus Evol. 2023;9(1):vead027. Epub 20230425. doi: 10.1093/ve/vead027. PubMed PMID: 37207002; PMCID: PMC10191192.
163. Godino A, Salery M, Durand-de Cuttoli R, Estill MS, Holt LM, Futamura R, Browne CJ, Mews P, Hamilton PJ, Neve RL, Shen L, Russo SJ, Nestler EJ. Transcriptional control of nucleus accumbens neuronal excitability by retinoid X receptor alpha tunes sensitivity to drug rewards. Neuron. 2023;111(9):1453-67.e7. Epub 20230307. doi: 10.1016/j.neuron.2023.02.013. PubMed PMID: 36889314; PMCID: PMC10164098.
164. Salery M, Godino A, Xu YQ, Fullard JF, Durand-de Cuttoli R, LaBanca AR, Holt LM, Russo SJ, Roussos P, Nestler EJ. Transcriptional correlates of cocaine-associated learning in striatal ARC ensembles. bioRxiv. 2023. Epub 20231214. doi: 10.1101/2023.12.13.571585. PubMed PMID: 38168167; PMCID: PMC10760161.
165. Browne CJ, Futamura R, Minier-Toribio A, Hicks EM, Ramakrishnan A, Martínez-Rivera FJ, Estill M, Godino A, Parise EM, Torres-Berrío A, Cunningham AM, Hamilton PJ, Walker DM, Huckins LM, Hurd YL, Shen L, Nestler EJ. Transcriptional signatures of heroin intake and relapse throughout the brain reward circuitry in male mice. Sci Adv. 2023;9(23):eadg8558. Epub 20230609. doi: 10.1126/sciadv.adg8558. PubMed PMID: 37294757; PMCID: PMC10256172.
166. Cohen P, DeGrace EJ, Danziger O, Patel RS, Barrall EA, Bobrowski T, Kehrer T, Cupic A, Miorin L, García-Sastre A, Rosenberg BR. Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single-cell RNA sequencing. Microbiol Spectr. 2023;11(5):e0077623. Epub 20230907. doi: 10.1128/spectrum.00776-23. PubMed PMID: 37676044; PMCID: PMC10580996.
167. Prytkova I, Liu Y, Fernando M, Gameiro-Ros I, Popova D, Kamarajan C, Xuei X, Chorlian DB, Edenberg HJ, Tischfield JA, Porjesz B, Pang ZP, Hart RP, Goate A, Slesinger PA. Upregulated GIRK2 Counteracts Ethanol-Induced Changes in Excitability and Respiration in Human Neurons. J Neurosci. 2024;44(16). Epub 20240417. doi: 10.1523/jneurosci.0918-23.2024. PubMed PMID: 38350999; PMCID: PMC11026340.
168. Turner S, Alisoltani A, Bratt D, Cohen-Lavi L, Dearlove BL, Drosten C, Fischer WM, Fouchier RAM, Gonzalez-Reiche AS, Jaroszewski L, Khalil Z, LeGresley E, Johnson M, Jones TC, Mühlemann B, O’Connor D, Sedova M, Shukla M, Theiler J, Wallace ZS, Yoon H, Zhang Y, van Bakel H, Degrace MM, Ghedin E, Godzik A, Hertz T, Korber B, Lemieux J, Niewiadomska AM, Post DJ, Rolland M, Scheuermann R, Smith DJ. US National Institutes of Health Prioritization of SARS-CoV-2 Variants. Emerg Infect Dis. 2023;29(5). Epub 20230413. doi: 10.3201/eid2905.221646. PubMed PMID: 37054986; PMCID: PMC10124642.
169. Sorin V, Glicksberg BS, Artsi Y, Barash Y, Konen E, Nadkarni GN, Klang E. Utilizing large language models in breast cancer management: systematic review. J Cancer Res Clin Oncol. 2024;150(3):140. Epub 20240319. doi: 10.1007/s00432-024-05678-6. PubMed PMID: 38504034; PMCID: PMC10950983.

Year 1 (06/2022- 06/2023): 122 

1. Sen, U., Coleman, C., and Sen, T. Stearoyl coenzyme A desaturase-1: multitasker in cancer, metabolism, and ferroptosis. Trends in Cancer.
2. A first update on mapping the human genetic architecture of COVID-19. (2022). Nature 608, E1-e10. PMC9352569.
3. Abbott, E.E., Buckler, D.G., Hsu, J.Y., Jacoby, S.F., Abella, B.S., Richardson, L.D., Carr, B.G., and Zebrowski, A.M. (2022). Survival After Out-of-Hospital Cardiac Arrest: The Role of Racial Residential Segregation. J Urban Health 99, 998-1011. PMC9727016.
4. Aydillo, T., Gonzalez-Reiche, A.S., Stadlbauer, D., Amper, M.A., Nair, V.D., Mariottini, C., Sealfon, S.C., van Bakel, H., Palese, P., Krammer, F., and García-Sastre, A. (2022). Transcriptome signatures preceding the induction of anti-stalk antibodies elicited after universal influenza vaccination. NPJ Vaccines 7, 160. PMC9741632.
5. Bendl, J., Hauberg, M.E., Girdhar, K., Im, E., Vicari, J.M., Rahman, S., Fernando, M.B., Townsley, K.G., Dong, P., Misir, R., et al. (2022). The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease. Nat Neurosci 25, 1366-1378. PMC9581463.
6. Bigdeli, T.B., Voloudakis, G., Barr, P.B., Gorman, B.R., Genovese, G., Peterson, R.E., Burstein, D.E., Velicu, V.I., Li, Y., Gupta, R., et al. (2022). Penetrance and Pleiotropy of Polygenic Risk Scores for Schizophrenia, Bipolar Disorder, and Depression Among Adults in the US Veterans Affairs Health Care System. JAMA Psychiatry 79, 1092-1101. PMC9475441.
7. Butler-Laporte, G., Gonzalez-Kozlova, E., Su, C.Y., Zhou, S., Nakanishi, T., Brunet-Ratnasingham, E., Morrison, D., Laurent, L., Afilalo, J., Afilalo, M., et al. (2022). The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals. Clin Proteomics 19, 34. PMC9516500.
8. Chaudhary, N.S., Armstrong, N.D., Hidalgo, B.A., Gutiérrez, O.M., Hellwege, J.N., Limdi, N.A., Reynolds, R.J., Judd, S.E., Nadkarni, G.N., Lange, L., et al. (2022). SMOC2 gene interacts with APOL1 in the development of end-stage kidney disease: A genome-wide association study. Front Med (Lausanne) 9, 971297. PMC9554233.
9. Chauhan, K., Wen, H.H., Gupta, N., Nadkarni, G., Coca, S., and Chan, L. (2022). Higher Symptom Frequency and Severity After the Long Interdialytic Interval in Patients on Maintenance Intermittent Hemodialysis. Kidney Int Rep 7, 2630-2638. PMC9727533.
10. Datta, S., Morassi Sasso, A., Kiwit, N., Bose, S., Nadkarni, G., Miotto, R., and Böttinger, E.P. (2022). Predicting hypertension onset from longitudinal electronic health records with deep learning. JAMIA Open 5, ooac097. PMC9696747.
11. Dong, P., Hoffman, G.E., Apontes, P., Bendl, J., Rahman, S., Fernando, M.B., Zeng, B., Vicari, J.M., Zhang, W., Girdhar, K., et al. (2022). Population-level variation in enhancer expression identifies disease mechanisms in the human brain. Nat Genet 54, 1493-1503. PMC9547946.
12. Duty, J.A., Kraus, T., Zhou, H., Zhang, Y., Shaabani, N., Yildiz, S., Du, N., Singh, A., Miorin, L., Li, D., et al. (2022). Discovery and intranasal administration of a SARS-CoV-2 broadly acting neutralizing antibody with activity against multiple Omicron subvariants. Med 3, 705-721.e711. PMC9359501.
13. Eadon, M.T., Cavanaugh, K.L., Orlando, L.A., Christian, D., Chakraborty, H., Steen-Burrell, K.A., Merrill, P., Seo, J., Hauser, D., Singh, R., et al. (2022). Design and rationale of GUARDD-US: A pragmatic, randomized trial of genetic testing for APOL1 and pharmacogenomic predictors of antihypertensive efficacy in patients with hypertension. Contemp Clin Trials 119, 106813. PMC9928488.
14. Forrest, I.S., Chan, L., Chaudhary, K., Saha, A., Wen, H.H., Cepin, C.L., Marquez-Luna, C., Rocheleau, G., Cho, J., Narula, J., et al. (2022). Genome-first recall of healthy individuals by polygenic risk score reveals differences in coronary artery calcium. Am Heart J 250, 29-33.
15. Fulton, S.L., Wenderski, W., Lepack, A.E., Eagle, A.L., Fanutza, T., Bastle, R.M., Ramakrishnan, A., Hays, E.C., Neal, A., Bendl, J., et al. (2022). Rescue of deficits by Brwd1 copy number restoration in the Ts65Dn mouse model of Down syndrome. Nat Commun 13, 6384. PMC9606253.
16. Gorski, M., Rasheed, H., Teumer, A., Thomas, L.F., Graham, S.E., Sveinbjornsson, G., Winkler, T.W., Günther, F., Stark, K.J., Chai, J.F., et al. (2022). Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies. Kidney Int 102, 624-639. PMC10034922.
17. Grams, M.E., Brunskill, N.J., Ballew, S.H., Sang, Y., Coresh, J., Matsushita, K., Surapaneni, A., Bell, S., Carrero, J.J., Chodick, G., et al. (2022). Development and Validation of Prediction Models of Adverse Kidney Outcomes in the Population With and Without Diabetes. Diabetes Care 45, 2055-2063. PMC9472501.
18. Gulamali, F.F., Sawant, A.S., Kovatch, P., Glicksberg, B., Charney, A., Nadkarni, G.N., and Oermann, E. (2022). Autoencoders for sample size estimation for fully connected neural network classifiers. NPJ Digit Med 5, 180. PMC9747810.
19. Gulamali, F.F., Sawant, A.S., and Nadkarni, G.N. (2022). Machine learning for risk stratification in kidney disease. Curr Opin Nephrol Hypertens 31, 548-552. PMC9529795.
20. Hernandez, M.M., Banu, R., Shrestha, P., Gonzalez-Reiche, A.S., van de Guchte, A., Farrugia, K., Sebra, R., Gitman, M.R., Nowak, M.D., Cordon-Cardo, C., et al. (2022). A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants. Microbiol Spectr 10, e0173622. PMC9604185.
21. Hirten, R.P., Tomalin, L., Danieletto, M., Golden, E., Zweig, M., Kaur, S., Helmus, D., Biello, A., Pyzik, R., Bottinger, E.P., et al. (2022). Evaluation of a machine learning approach utilizing wearable data for prediction of SARS-CoV-2 infection in healthcare workers. JAMIA Open 5, ooac041. PMC9129173.
22. Honarvar, H., Agarwal, C., Somani, S., Vaid, A., Lampert, J., Wanyan, T., Reddy, V.Y., Nadkarni, G.N., Miotto, R., Zitnik, M., et al. (2022). Enhancing convolutional neural network predictions of electrocardiograms with left ventricular dysfunction using a novel sub-waveform representation. Cardiovasc Digit Health J 3, 220-231. PMC9596304.
23. Hsuan, C., Zebrowski, A., Lin, M.P., Buckler, D.G., and Carr, B.G. (2022). Emergency departments in the United States treating high proportions of patients with ambulatory care sensitive conditions: a retrospective cross-sectional analysis. BMC Health Services Research 22, 854.
24. Jiang, J., Chan, L., and Nadkarni, G.N. (2022). The promise of artificial intelligence for kidney pathophysiology. Curr Opin Nephrol Hypertens 31, 380-386.
25. Katanski, C.D., Alshammary, H., Watkins, C.P., Huang, S., Gonzales-Reiche, A., Sordillo, E.M., van Bakel, H., Lolans, K., Simon, V., and Pan, T. (2022). tRNA abundance, modification and fragmentation in nasopharyngeal swabs as biomarkers for COVID-19 severity. Front Cell Dev Biol 10, 999351. PMC9664364.
26. Katsel, P., Fam, P., Tan, W., Khan, S., Gama-Sosa, M., De Gasperi, R., Roussos, P., Robinson, A., Cooper, I., Schnaider-Beeri, M., and Haroutunian, V. (2022). Engagement of vascular early response genes typifies mild cognitive impairment. Alzheimers Dement 18, 1357-1369.
27. Kelly, T.N., Sun, X., He, K.Y., Brown, M.R., Taliun, S.A.G., Hellwege, J.N., Irvin, M.R., Mi, X., Brody, J.A., Franceschini, N., et al. (2022). Insights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension. Hypertension 79, 1656-1667. PMC9593435.
28. Khan, A., Turchin, M.C., Patki, A., Srinivasasainagendra, V., Shang, N., Nadukuru, R., Jones, A.C., Malolepsza, E., Dikilitas, O., Kullo, I.J., et al. (2022). Genome-wide polygenic score to predict chronic kidney disease across ancestries. Nat Med 28, 1412-1420. PMC9329233.
29. Kong, R., Patel, A.S., Sato, T., Jiang, F., Yoo, S., Bao, L., Sinha, A., Tian, Y., Fridrikh, M., Liu, S., et al. (2022). Transcriptional Circuitry of NKX2-1 and SOX1 Defines an Unrecognized Lineage Subtype of Small-Cell Lung Cancer. Am J Respir Crit Care Med 206, 1480-1494. PMC9757094.
30. Konigorski, S., Wernicke, S., Slosarek, T., Zenner, A.M., Strelow, N., Ruether, D.F., Henschel, F., Manaswini, M., Pottbäcker, F., Edelman, J.A., et al. (2022). StudyU: A Platform for Designing and Conducting Innovative Digital N-of-1 Trials. J Med Internet Res 24, e35884. PMC9297132.
31. Kosoy, R., Fullard, J.F., Zeng, B., Bendl, J., Dong, P., Rahman, S., Kleopoulos, S.P., Shao, Z., Girdhar, K., Humphrey, J., et al. (2022). Genetics of the human microglia regulome refines Alzheimer’s disease risk loci. Nat Genet 54, 1145-1154. PMC9388367.
32. Kousathanas, A., Pairo-Castineira, E., Rawlik, K., Stuckey, A., Odhams, C.A., Walker, S., Russell, C.D., Malinauskas, T., Wu, Y., Millar, J., et al. (2022). Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 607, 97-103. PMC9259496.
33. Levin, M.G., Tsao, N.L., Singhal, P., Liu, C., Vy, H.M.T., Paranjpe, I., Backman, J.D., Bellomo, T.R., Bone, W.P., Biddinger, K.J., et al. (2022). Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure. Nat Commun 13, 6914. PMC9663424.
34. Li, Z., Li, X., Zhou, H., Gaynor, S.M., Selvaraj, M.S., Arapoglou, T., Quick, C., Liu, Y., Chen, H., Sun, R., et al. (2022). A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nat Methods 19, 1599-1611. PMC10008172.
35. Liu, D., Zinski, A., Mishra, A., Noh, H., Park, G.H., Qin, Y., Olorife, O., Park, J.M., Abani, C.P., Park, J.S., et al. (2022). Impact of schizophrenia GWAS loci converge onto distinct pathways in cortical interneurons vs glutamatergic neurons during development. Mol Psychiatry 27, 4218-4233.
36. Liu, H., Doke, T., Guo, D., Sheng, X., Ma, Z., Park, J., Vy, H.M.T., Nadkarni, G.N., Abedini, A., Miao, Z., et al. (2022). Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. Nat Genet 54, 950-962.
37. Lizewski, R.A., Sealfon, R.S.G., Park, S.W., Smith, G.R., Porter, C.K., Gonzalez-Reiche, A.S., Ge, Y., Miller, C.M., Goforth, C.W., Pincas, H., et al. (2022). SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures. Epidemiology 33, 797-807. PMC9531985.
38. Maier, H.E., Balmaseda, A., Saborio, S., Ojeda, S., Barilla, C., Sanchez, N., Lopez, R., Plazaola, M., Cerpas, C., van Bakel, H., et al. (2022). Protection Associated with Previous SARS-CoV-2 Infection in Nicaragua. N Engl J Med 387, 568-570. PMC9342422.
39. Mattheisen, M., Grove, J., Als, T.D., Martin, J., Voloudakis, G., Meier, S., Demontis, D., Bendl, J., Walters, R., Carey, C.E., et al. (2022). Identification of shared and differentiating genetic architecture for autism spectrum disorder, attention-deficit hyperactivity disorder and case subgroups. Nat Genet 54, 1470-1478.
40. Nadkarni, G.N., and Kotanko, P. (2022). The Future of Artificial Intelligence and Machine Learning in Kidney Health and Disease. Adv Chronic Kidney Dis 29, 425-426.
41. Nadkarni, G.N., Takale, D., Neal, B., Mahaffey, K.W., Yavin, Y., Hansen, M.K., Fleming, F., Heerspink, H.J.L., and Coca, S.G. (2022). A Post Hoc Analysis of KidneyIntelX and Cardiorenal Outcomes in Diabetic Kidney Disease. Kidney360 3, 1599-1602. PMC9528375.
42. Neyra, J.A., Lambert, J., Ortiz-Soriano, V., Cleland, D., Colquitt, J., Adams, P., Bissell, B.D., Chan, L., Nadkarni, G.N., Tolwani, A., and Goldstein, S.L. (2022). Assessment of prescribed vs. achieved fluid balance during continuous renal replacement therapy and mortality outcome. PLoS One 17, e0272913. PMC9409548.
43. Olivero, N.B., Gonzalez-Reiche, A.S., Re, V.E., Castro, G.M., Pisano, M.B., Sicilia, P., Barbas, M.G., Khan, Z., van de Guchte, A., Dutta, J., et al. (2022). Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina. BMC Genomics 23, 510. PMC9282626.
44. Ozonoff, A., Schaenman, J., Jayavelu, N.D., Milliren, C.E., Calfee, C.S., Cairns, C.B., Kraft, M., Baden, L.R., Shaw, A.C., Krammer, F., et al. (2022). Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine 83, 104208. PMC9359694.
45. Pai, B., Tome-Garcia, J., Cheng, W.S., Nudelman, G., Beaumont, K.G., Ghatan, S., Panov, F., Caballero, E., Sarpong, K., Marcuse, L., et al. (2022). High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy. Acta Neuropathol Commun 10, 149. PMC9590125.
46. Petrazzini, B.O., Vaid, A., Park, J.K., Marquez-Luna, C., Vy, H.M., Saha, A., Chaudhary, K., Cho, J., Chan, L., Argulian, E., et al. (2022). Short-term prediction of coronary artery disease using serum metabolomic patterns. Am Heart J Plus 24. PMC9924019.
47. Ramos, S.I., Mussa, Z.M., Falk, E.N., Pai, B., Giotti, B., Allette, K., Cai, P., Dekio, F., Sebra, R., Beaumont, K.G., et al. (2022). An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics. Nat Commun 13, 7671. PMC9744747.
48. Richardson, T.E., Walker, J.M., Abdullah, K.G., McBrayer, S.K., Viapiano, M.S., Mussa, Z.M., Tsankova, N.M., Snuderl, M., and Hatanpaa, K.J. (2022). Chromosomal instability in adult-type diffuse gliomas. Acta Neuropathol Commun 10, 115. PMC9386991.
49. Rowland, B., Venkatesh, S., Tardaguila, M., Wen, J., Rosen, J.D., Tapia, A.L., Sun, Q., Graff, M., Vuckovic, D., Lettre, G., et al. (2022). Transcriptome-wide association study in UK Biobank Europeans identifies associations with blood cell traits. Hum Mol Genet 31, 2333-2347. PMC9307312.
50. Saha, A., Ericksen, P., Liriano Cepin, C., Nadkarni, G.N., and Chan, L. (2022). Unplanned 30-Day Readmission Rates for Autosomal Dominant Polycystic Kidney Disease: Insight from the Nationwide Readmissions Database. Blood Purif, 1-9.
51. Sapa, H., Gutiérrez, O.M., Shlipak, M.G., Katz, R., Ix, J.H., Sarnak, M.J., Cushman, M., Rhee, E.P., Kimmel, P.L., Vasan, R.S., et al. (2022). Association of Uremic Solutes With Cardiovascular Death in Diabetic Kidney Disease. Am J Kidney Dis 80, 502-512.e501. PMC9554797.
52. Sauerwald, N., Zhang, Z., Ramos, I., Nair, V.D., Soares-Schanoski, A., Ge, Y., Mao, W., Alshammary, H., Gonzalez-Reiche, A.S., van de Guchte, A., et al. (2022). Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection. Cell Syst 13, 924-931.e924. PMC9623453.
53. Selvaraj, M.S., Li, X., Li, Z., Pampana, A., Zhang, D.Y., Park, J., Aslibekyan, S., Bis, J.C., Brody, J.A., Cade, B.E., et al. (2022). Whole genome sequence analysis of blood lipid levels in >66,000 individuals. Nat Commun 13, 5995. PMC9553944.
54. Sen, S., Spasic, A., Sinha, A., Wang, J., Bush, M., Li, J., Nešić, D., Zhou, Y., Angiulli, G., Morgan, P., et al. (2022). Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3. Journal of Chemical Information and Modeling 62, 5607-5621.
55. Shelton, B.A., Sawinski, D., MacLennan, P.A., Lee, W., Wyatt, C., Nadkarni, G., Fatima, H., Mehta, S., Crane, H.M., Porrett, P., et al. (2022). Associations between female birth sex and risk of chronic kidney disease development among people with HIV in the USA: A longitudinal, multicentre, cohort study. EClinicalMedicine 53, 101653. PMC9489495.
56. Stadlbauer, D., McMahon, M., Turner, H.L., Zhu, X., Wan, H., Carreño, J.M., O’Dell, G., Strohmeier, S., Khalil, Z., Luksza, M., et al. (2022). Antibodies targeting the neuraminidase active site inhibit influenza H3N2 viruses with an S245N glycosylation site. Nature communications 13, 7864.
57. Sun, D., Singh, D.K., Carcamo, S., Filipescu, D., Khalil, B., Huang, X., Miles, B.A., Westra, W., Sproll, K.C., Hasson, D., et al. (2022). MacroH2A impedes metastatic growth by enforcing a discrete dormancy program in disseminated cancer cells. Sci Adv 8, eabo0876.
58. Sunderraj, A., Cho, C., Cai, X., Gupta, S., Mehta, R., Isakova, T., Leaf, D.E., and Srivastava, A. (2022). Modulation of the Association Between Age and Death by Risk Factor Burden in Critically Ill Patients With COVID-19. Crit Care Explor 4, e0755. PMC9426819.
59. Tahir, U.A., Katz, D.H., Avila-Pachecho, J., Bick, A.G., Pampana, A., Robbins, J.M., Yu, Z., Chen, Z.Z., Benson, M.D., Cruz, D.E., et al. (2022). Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals. Nat Commun 13, 4923. PMC9395431.
60. Takashita, E., Yamayoshi, S., Simon, V., van Bakel, H., Sordillo, E.M., Pekosz, A., Fukushi, S., Suzuki, T., Maeda, K., Halfmann, P., et al. (2022). Efficacy of Antibodies and Antiviral Drugs against Omicron BA.2.12.1, BA.4, and BA.5 Subvariants. N Engl J Med 387, 468-470. PMC9342381.
61. Tan, J., Chromikova, V., O’Dell, G., Sordillo, E.M., Simon, V., van Bakel, H., Krammer, F., and McMahon, M. (2022). Murine Broadly Reactive Antineuraminidase Monoclonal Antibodies Protect Mice from Recent Influenza B Virus Isolates and Partially Inhibit Virus Transmission in the Guinea Pig Model. mSphere 7, e0092721. PMC9599422.
62. Thibord, F., Klarin, D., Brody, J.A., Chen, M.H., Levin, M.G., Chasman, D.I., Goode, E.L., Hveem, K., Teder-Laving, M., Martinez-Perez, A., et al. (2022). Cross-Ancestry Investigation of Venous Thromboembolism Genomic Predictors. Circulation 146, 1225-1242. PMC10152894.
63. Tokita, J., Vega, A., Sinfield, C., Naik, N., Rathi, S., Martin, S., Wang, S., Amoruso, L., Zabetian, A., Coca, S.G., et al. (2022). Real World Evidence and Clinical Utility of KidneyIntelX on Patients With Early-Stage Diabetic Kidney Disease: Interim Results on Decision Impact and Outcomes. J Prim Care Community Health 13, 21501319221138196. PMC9677284.
64. Vaid, A., Jiang, J.J., Sawant, A., Singh, K., Kovatch, P., Charney, A.W., Charytan, D.M., Divers, J., Glicksberg, B.S., Chan, L., and Nadkarni, G.N. (2022). Automated Determination of Left Ventricular Function Using Electrocardiogram Data in Patients on Maintenance Hemodialysis. Clin J Am Soc Nephrol 17, 1017-1025. PMC9269621.
65. Vasbinder, A., Meloche, C., Azam, T.U., Anderson, E., Catalan, T., Shadid, H., Berlin, H., Pan, M., O’Hayer, P., Padalia, K., et al. (2022). Relationship Between Preexisting Cardiovascular Disease and Death and Cardiovascular Outcomes in Critically Ill Patients With COVID-19. Circ Cardiovasc Qual Outcomes 15, e008942. PMC9575399.
66. Voloudakis, G., Vicari, J.M., Venkatesh, S., Hoffman, G.E., Dobrindt, K., Zhang, W., Beckmann, N.D., Higgins, C.A., Argyriou, S., Jiang, S., et al. (2022). A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility. NPJ Genom Med 7, 52. PMC9441828.
67. Vy, H.M.T., Lin, B.M., Gulamali, F.F., Kooperberg, C., Graff, M., Wong, J., Campbell, K.N., Matise, T.C., Coresh, J., Thomas, F., et al. (2022). Genome-Wide Epistatic Interaction between DEF1B and APOL1 High-Risk Genotypes for Chronic Kidney Disease. Clin J Am Soc Nephrol 17, 1522-1525. PMC9528279.
68. Wang, P., Karakose, E., Argmann, C., Wang, H., Balev, M., Brody, R.I., Rivas, H.G., Liu, X., Wood, O., Liu, H., et al. (2022). Disrupting the DREAM complex enables proliferation of adult human pancreatic β cells. J Clin Invest 132. PMC9337832.
69. Winkler, T.W., Rasheed, H., Teumer, A., Gorski, M., Rowan, B.X., Stanzick, K.J., Thomas, L.F., Tin, A., Hoppmann, A., Chu, A.Y., et al. (2022). Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals. Commun Biol 5, 580. PMC9192715.
70. Zhou, R.W., Xu, J., Martin, T.C., Zachem, A.L., He, J., Ozturk, S., Demircioglu, D., Bansal, A., Trotta, A.P., Giotti, B., et al. (2022). A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Nat Commun 13, 6041. PMC9576746.
71. Ahn, D., Provasi, D., Duc, N.M., Xu, J., Salas-Estrada, L., Spasic, A., Yun, M.W., Kang, J., Gim, D., Lee, J., et al. (2023). Gαs slow conformational transition upon GTP binding and a novel Gαs regulator. iScience 26, 106603.
72. Anderson, E.E., Dyzenhaus, S., Ilmain, J.K., Sullivan, M.J., van Bakel, H., and Torres, V.J. (2023). SarS Is a Repressor of Staphylococcus aureus Bicomponent Pore-Forming Leukocidins. Infect Immun 91, e0053222. PMC10112191.
73. Aslam, S., Rajendran, M., Kriti, D., Kurland, A., Johnson, J., van Bakel, H., Krammer, F., García-Sastre, A., and Ayllon, J. (2023). Generation of a high yield vaccine backbone for influenza B virus in embryonated chicken eggs. npj Vaccines 8, 12.
74. Burstein, D., Hoffman, G., Mathur, D., Venkatesh, S., Therrien, K., Fanous, A.H., Bigdeli, T.B., Harvey, P.D., Roussos, P., and Voloudakis, G. (2023). Detecting and Adjusting for Hidden Biases due to Phenotype Misclassification in Genome-Wide Association Studies. medRxiv. PMC9882426.
75. Crouse, A., Nadkarni, G., and Might, M. (2023). A Primer in Precision Nephrology: Optimizing Outcomes in Kidney Health and Disease through Data-Driven Medicine. Kidney360 4, e544-e554.
76. Dellepiane, S., Paranjpe, I., Rajagopal, M., Kamat, S., O’Hagan, R., Gulamali, F., Rein, J.L., Charney, A.W., Do, R., Coca, S., et al. (2023). Cannabis Use and CKD: Epidemiological Associations and Mendelian Randomization. Kidney Med 5, 100582. PMC9879977.
77. Demontis, D., Walters, G.B., Athanasiadis, G., Walters, R., Therrien, K., Nielsen, T.T., Farajzadeh, L., Voloudakis, G., Bendl, J., Zeng, B., et al. (2023). Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains. Nat Genet 55, 198-208.
78. Duong, S.Q., Vaid, A., Vy, H.M.T., Butler, L.R., Lampert, J., Pass, R.H., Charney, A.W., Narula, J., Khera, R., Greenspan, H., et al. (2023). Quantitative prediction of right ventricular and size and function from the electrocardiogram. medRxiv. PMC10168487.
79. Dyzenhaus, S., Sullivan, M.J., Alburquerque, B., Boff, D., van de Guchte, A., Chung, M., Fulmer, Y., Copin, R., Ilmain, J.K., O’Keefe, A., et al. (2023). MRSA lineage USA300 isolated from bloodstream infections exhibit altered virulence regulation. Cell Host Microbe 31, 228-242.e228. PMC9911362.
80. Esai Selvan, M., Onel, K., Gnjatic, S., Klein, R.J., and Gümüş, Z.H. (2023). Germline rare deleterious variant load alters cancer risk, age of onset and tumor characteristics. NPJ Precis Oncol 7, 13. PMC9883433.
81. Forrest, I.S., Petrazzini, B.O., Duffy, Á., Park, J.K., Marquez-Luna, C., Jordan, D.M., Rocheleau, G., Cho, J.H., Rosenson, R.S., Narula, J., et al. (2023). Machine learning-based marker for coronary artery disease: derivation and validation in two longitudinal cohorts. Lancet 401, 215-225. PMC10069625.
82. Grams, M.E., Brunskill, N.J., Ballew, S.H., Sang, Y., Coresh, J., Matsushita, K., Surapaneni, A., Bell, S., Carrero, J.J., Chodick, G., et al. (2023). The Kidney Failure Risk Equation: Evaluation of Novel Input Variables including eGFR Estimated Using the CKD-EPI 2021 Equation in 59 Cohorts. J Am Soc Nephrol 34, 482-494.
83. Gulamali, F.F., and Nadkarni, G.N. (2023). Federated Learning in Risk Prediction: A Primer and Application to COVID-19-Associated Acute Kidney Injury. Nephron 147, 52-56. PMC9839890.
84. Hansen, C.S., McQuillin, A., Claire, D.S., Mill, J., Hannon, E., Sharp, A.J., and Janecka, M. (2023). Assessing the burden of rare DNA methylation deviations in schizophrenia. bioRxiv, 2023.2001.2009.523073.
85. Hirten, R.P., Suprun, M., Danieletto, M., Zweig, M., Golden, E., Pyzik, R., Kaur, S., Helmus, D., Biello, A., Landell, K., et al. (2023). A machine learning approach to determine resilience utilizing wearable device data: analysis of an observational cohort. JAMIA Open 6, ooad029. PMC10152991.
86. Hoffman, G.E., Lee, D., Bendl, J., Fnu, P., Hong, A., Casey, C., Alvia, M., Shao, Z., Argyriou, S., Therrien, K., et al. (2023). Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet. bioRxiv. PMC10055252.
87. Jadhav, B., Garg, P., Vugt, J.J.F.A.v., Garikano, K.I., Gagliardi, D., Lee, W., Martin-Trujillo, A., Gies, S.L., Barbosa, M., Jain, M., et al. (2023). A GCC repeat expansion in <em>AFF3</em> is a significant cause of intellectual disability. medRxiv, 2023.2005.2003.23289461.
88. Jain, N., Richter, F., Adzhubei, I., Sharp, A.J., and Gelb, B.D. (2023). Small open reading frames: a comparative genetics approach to validation. BMC Genomics 24, 226.
89. Jiang, J., Chan, L., Kauffman, J., Narula, J., Charney, A.W., Oh, W., and Nadkarni, G. (2023). Impact of Vaccination on Major Adverse Cardiovascular Events in Patients With COVID-19 Infection. J Am Coll Cardiol 81, 928-930. PMC9939951.
90. Kotanko, P., and Nadkarni, G.N. (2023). Advances in Chronic Kidney Disease Lead Editorial Outlining the Future of Artificial Intelligence/Machine Learning in Nephrology. Adv Kidney Dis Health 30, 2-3.
91. Kotini, A.G., Carcamo, S., Cruz-Rodriguez, N., Olszewska, M., Wang, T., Demircioglu, D., Chang, C.J., Bernard, E., Chao, M.P., Majeti, R., et al. (2023). Patient-Derived iPSCs Faithfully Represent the Genetic Diversity and Cellular Architecture of Human Acute Myeloid Leukemia. Blood Cancer Discov, Of1-of18.
92. Li, X., Quick, C., Zhou, H., Gaynor, S.M., Liu, Y., Chen, H., Selvaraj, M.S., Sun, R., Dey, R., Arnett, D.K., et al. (2023). Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. Nat Genet 55, 154-164. PMC10084891.
93. Liharska, L.E., Park, Y.J., Ziafat, K., Wilkins, L., Silk, H., Linares, L.M., Thompson, R.C., Vornholt, E., Sullivan, B., Cohen, V., et al. (2023). A study of gene expression in the living human brain. medRxiv. PMC10168405.
94. Linder, J.E., Allworth, A., Bland, S.T., Caraballo, P.J., Chisholm, R.L., Clayton, E.W., Crosslin, D.R., Dikilitas, O., DiVietro, A., Esplin, E.D., et al. (2023). Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med 25, 100006. PMC10085845.
95. Mark, P.B., Carrero, J.J., Matsushita, K., Sang, Y., Ballew, S.H., Grams, M.E., Coresh, J., Surapaneni, A., Brunskill, N.J., Chalmers, J., et al. (2023). Major cardiovascular events and subsequent risk of kidney failure with replacement therapy: a CKD Prognosis Consortium study. Eur Heart J 44, 1157-1166.
96. Martin-Trujillo, A., Garg, P., Patel, N., Jadhav, B., and Sharp, A.J. (2023). Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation. Genome Res 33, 184-196. PMC10069470.
97. Matsushita, K., Kaptoge, S., Hageman, S.H.J., Sang, Y., Ballew, S.H., Grams, M.E., Surapaneni, A., Sun, L., Arnlov, J., Bozic, M., et al. (2023). Including measures of chronic kidney disease to improve cardiovascular risk prediction by SCORE2 and SCORE2-OP. Eur J Prev Cardiol 30, 8-16. PMC9839538.
98. Mohammed Ismail, W., Mazzone, A., Ghiraldini, F.G., Kaur, J., Bains, M., Munankarmy, A., Bagwell, M.S., Safgren, S.L., Moore-Weiss, J., Buciuc, M., et al. (2023). MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming. Commun Biol 6, 215. PMC9950461.
99. Nadkarni, G., Paranjpe, I., Jayaraman, P., Su, C.Y., Zhou, S., Chen, S., Valle, D.D., Thompson, R., Kenigsberg, E., Zhao, S., et al. (2023). Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection. Res Sq. PMC10055503.
100. Nadkarni, G.N. (2023). Introduction to Artificial Intelligence and Machine Learning in Nephrology. Clin J Am Soc Nephrol 18, 392-393.
101. Oh, W., and Nadkarni, G.N. (2023). Federated Learning in Health care Using Structured Medical Data. Adv Kidney Dis Health 30, 4-16.
102. Pacheco, J.A., Rasmussen, L.V., Wiley, K., Jr., Person, T.N., Cronkite, D.J., Sohn, S., Murphy, S., Gundelach, J.H., Gainer, V., Castro, V.M., et al. (2023). Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network. Sci Rep 13, 1971. PMC9898520.
103. Paniz-Mondolfi, A., Guerra, S., Muñoz, M., Luna, N., Hernandez, M.M., Patino, L.H., Reidy, J., Banu, R., Shrestha, P., Liggayu, B., et al. (2023). Evaluation and validation of an RT-PCR assay for specific detection of monkeypox virus (MPXV). J Med Virol 95, e28247.
104. Park, J.K., Petrazzini, B.O., Saha, A., Vaid, A., Vy, H.M.T., Márquez-Luna, C., Chan, L., Nadkarni, G.N., and Do, R. (2023). Machine Learning Identifies Plasma Metabolites Associated With Heart Failure in Underrepresented Populations With the TTR V122I Variant. J Am Heart Assoc 12, e027736.
105. Patiño, L.H., Guerra, S., Muñoz, M., Luna, N., Farrugia, K., van de Guchte, A., Khalil, Z., Gonzalez-Reiche, A.S., Hernandez, M.M., Banu, R., et al. (2023). Phylogenetic landscape of Monkeypox Virus (MPV) during the early outbreak in New York City, 2022. Emerg Microbes Infect 12, e2192830. PMC10114986.
106. Plancarte, M., Kovalenko, G., Baldassano, J., Ramírez, A.L., Carrillo, S., Duignan, P.J., Goodfellow, I., Bortz, E., Dutta, J., van Bakel, H., and Coffey, L.L. (2023). Human influenza A virus H1N1 in marine mammals in California, 2019. PLoS One 18, e0283049. PMC10062622.
107. Puryear, W., Sawatzki, K., Hill, N., Foss, A., Stone, J.J., Doughty, L., Walk, D., Gilbert, K., Murray, M., Cox, E., et al. (2023). Highly Pathogenic Avian Influenza A(H5N1) Virus Outbreak in New England Seals, United States. Emerg Infect Dis 29, 786-791. PMC10045683.
108. Rajagopal, V.M., Ganna, A., Coleman, J.R.I., Allegrini, A., Voloudakis, G., Grove, J., Als, T.D., Horsdal, H.T., Petersen, L., Appadurai, V., et al. (2023). Genome-wide association study of school grades identifies genetic overlap between language ability, psychopathology and creativity. Sci Rep 13, 429. PMC9829693.
109. Shibahara, D., Akanuma, N., Kobayashi, I.S., Heo, E., Ando, M., Fujii, M., Jiang, F., Prin, P.N., Pan, G., Wong, K.K., et al. (2023). TIP60 is required for tumorigenesis in non-small cell lung cancer. Cancer Sci.
110. Song, X., Ji, J., Rothstein, J.H., Alexeeff, S.E., Sakoda, L.C., Sistig, A., Achacoso, N., Jorgenson, E., Whittemore, A.S., Klein, R.J., et al. (2023). MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer. Nature communications 14, 377.
111. St John, A., Perault, A.I., Giacometti, S.I., Sommerfield, A.G., DuMont, A.L., Lacey, K.A., Zheng, X., Sproch, J., Petzold, C., Dancel-Manning, K., et al. (2023). Capsular Polysaccharide Is Essential for the Virulence of the Antimicrobial-Resistant Pathogen Enterobacter hormaechei. mBio 14, e0259022. PMC10127600.
112. Stone, G.W., Farkouh, M.E., Lala, A., Tinuoye, E., Dressler, O., Moreno, P.R., Palacios, I.F., Goodman, S.G., Esper, R.B., Abizaid, A., et al. (2023). Randomized Trial of Anticoagulation Strategies for Noncritically Ill Patients Hospitalized With COVID-19. J Am Coll Cardiol 81, 1747-1762. PMC9987252.
113. Storey, C.M., Altai, M., Bicak, M., Veach, D.R., Lückerath, K., Adrian, G., McDevitt, M.R., Kalidindi, T., Park, J.E., Herrmann, K., et al. (2023). Quantitative In Vivo Imaging of the Androgen Receptor Axis Reveals Degree of Prostate Cancer Radiotherapy Response. Mol Cancer Res 21, 307-315.
114. Thompson, R.C., Simons, N.W., Wilkins, L., Cheng, E., Del Valle, D.M., Hoffman, G.E., Cervia, C., Fennessy, B., Mouskas, K., Francoeur, N.J., et al. (2023). Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae. Nat Med 29, 236-246. PMC9873574.
115. Thrane, K., Winge, M.C.G., Wang, H., Chen, L., Guo, M.G., Andersson, A., Abalo, X.M., Yang, X., Kim, D.S., Longo, S.K., et al. (2023). Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells. J Invest Dermatol.
116. Vaid, A., Argulian, E., Lerakis, S., Beaulieu-Jones, B.K., Krittanawong, C., Klang, E., Lampert, J., Reddy, V.Y., Narula, J., Nadkarni, G.N., and Glicksberg, B.S. (2023). Multi-center retrospective cohort study applying deep learning to electrocardiograms to identify left heart valvular dysfunction. Commun Med (Lond) 3, 24. PMC9929085.
117. Vasquez-Rios, G., Oh, W., Lee, S., Bhatraju, P., Mansour, S.G., Moledina, D.G., Gulamali, F.F., Siew, E.D., Garg, A.X., Sarder, P., et al. (2023). Joint Modeling of Clinical and Biomarker Data in Acute Kidney Injury Defines Unique Subphenotypes with Differing Outcomes: The ASSESS-AKI Study. Clin J Am Soc Nephrol.
118. Wang, E., Wang, M., Guo, L., Fullard, J.F., Micallef, C., Bendl, J., Song, W.M., Ming, C., Huang, Y., Li, Y., et al. (2023). Genome-wide methylomic regulation of multiscale gene networks in Alzheimer’s disease. Alzheimers Dement.
119. Weinstock, J.S., Gopakumar, J., Burugula, B.B., Uddin, M.M., Jahn, N., Belk, J.A., Bouzid, H., Daniel, B., Miao, Z., Ly, N., et al. (2023). Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. Nature 616, 755-763.
120. Wong, W.J., Emdin, C., Bick, A.G., Zekavat, S.M., Niroula, A., Pirruccello, J.P., Dichtel, L., Griffin, G., Uddin, M.M., Gibson, C.J., et al. (2023). Clonal haematopoiesis and risk of chronic liver disease. Nature 616, 747-754.
121. Wu, Y., Gettler, K., Kars, M.E., Giri, M., Li, D., Bayrak, C.S., Zhang, P., Jain, A., Maffucci, P., Sabic, K., et al. (2023). Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients. Nat Commun 14, 2256. PMC10119186.
122. Zeng, B., Bendl, J., Deng, C., Lee, D., Misir, R., Reach, S.M., Kleopoulos, S.P., Auluck, P., Marenco, S., Lewis, D.A., et al. (2023). Genetic regulation of cell-type specific chromatin accessibility shapes the etiology of brain diseases. bioRxiv. PMC10120699.

Deployment (06/2021 – 06/2022): 49

1. Zheutlin AB, Vieira L, Shewcraft RA, Li S, Wang Z, et al. 2022. Improving postpartum hemorrhage risk prediction using longitudinal electronic medical records. Journal of the American Medical Informatics Association : JAMIA 29:296-305
2. Zhang L, Chun Y, Ho H-e, Arditi Z, Lo T, et al. 2022. Multiscale study of the oral and gut environments in children with high- and low-threshold peanut allergy. Journal of Allergy and Clinical Immunology
3. Xu P, Wang M, Song W-M, Wang Q, Yuan G-C, et al. 2022. The landscape of human tissue and cell type specific expression and co-regulation of senescence genes. Molecular neurodegeneration 17:5-
4. Wang M, Song W-m, Ming C, Wang Q, Zhou X, et al. 2022. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and application. Molecular Neurodegeneration 17:17
5. Wang C, Lashua LP, Carter CE, Johnson SK, Wang M, et al. 2022. Sex disparities in influenza: A multiscale network analysis. iScience 25:104192
6. van der Heide V, Jangra S, Cohen P, Rathnasinghe R, Aslam S, et al. 2022. Limited extent and consequences of pancreatic SARS-CoV-2 infection. Cell Rep 38:110508-
7. Tantillo GB, Jetté N, Gururangan K, Agarwal P, Marcuse L, et al. 2022. Electroencephalography at the height of a pandemic: EEG findings in patients with COVID-19. Clin Neurophysiol 137:102-12
8. Tan J, O’Dell G, Hernandez MM, Sordillo EM, Kahn Z, et al. 2022. Human Anti-neuraminidase Antibodies Reduce Airborne Transmission of Clinical Influenza Virus Isolates in the Guinea Pig Model. J Virol 96:e01421-21
9. Song X, Ru M, Steinsnyder Z, Tkachuk K, Kopp RP, et al. 2022. SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death. Cancer Epidemiology, Biomarkers & Prevention:OF1-OF7
10. Song X, Ji J, Rothstein JH, Alexeeff SE, Sakoda LC, et al. 2022. MiXcan: a Framework for Cell-Type-Specific Transcriptome-Wide Association Studies with an Application to Breast Cancer. bioRxiv:2022.03.15.484509
11. Schoenfeld DA, Zhou R, Zairis S, Su W, Steinbach N, et al. 2022. Loss of PBRM1 Alters Promoter Histone Modifications and Activates ALDH1A1 to Drive Renal Cell Carcinoma. Molecular Cancer Research:OF1-OF15
12. Richter F, Strasser AS, Suarez-Farinas M, Zhao S, Nadkarni GN, et al. 2022. Neonatal outcomes during the COVID-19 pandemic in New York City. Pediatr Res 91:477-9
13. Ricardo AC, Chen J, Toth-Manikowski SM, Meza N, Joo M, et al. 2022. Hispanic ethnicity and mortality among critically ill patients with COVID-19. PLoS One 17:e0268022-e
14. Reategui Schwarz E, van de Guchte A, Dupper AC, Caban AB, Nadkarni D, et al. 2022. Everybody nose: molecular and clinical characteristics of nasal colonization during active methicillin-resistant Staphylococcus aureus bloodstream infection. BMC Infect Dis 22:400-
15. Ramírez JD, Castañeda S, Ballesteros N, Muñoz M, Hernández M, et al. 2022. Hotspots for SARS-CoV-2 Omicron variant spread: Lessons from New York City. J Med Virol 94:2911-4
16. Petrazzini BO, Chaudhary K, Márquez-Luna C, Forrest IS, Rocheleau G, et al. 2022. Coronary Risk Estimation Based on Clinical Data in Electronic Health Records. J Am Coll Cardiol 79:1155-66
17. Patel R, Li Z, Zimmerman BS, Fink MY, Wells JD, et al. 2022. Impact of body mass index on the efficacy of aromatase inhibitors in patients with metastatic breast cancer. Breast Cancer Research and Treatment 192:313-9
18. Olsen SN, Godfrey L, Healy JP, Choi YA, Kai Y, et al. 2022. MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape. Molecular Cell 82:1140-55.e11
19. Mukherjee S, Bandlamudi C, Hellmann MD, Kemel Y, Drill E, et al. 2022. Germline Pathogenic Variants Impact Clinicopathology of Advanced Lung Cancer. Cancer Epidemiology, Biomarkers & Prevention:OF1-OF10
20. Menez S, Moledina DG, Thiessen-Philbrook H, Wilson FP, Obeid W, et al. 2022. Prognostic Significance of Urinary Biomarkers in Patients Hospitalized With COVID-19. Am J Kidney Dis 79:257-67.e1
21. McKenzie AT, Marx G, Koenigsberg D, Sawyer M, Iida MA, et al. 2022. Interpretable deep learning of myelin histopathology in age-related cognitive impairment. bioRxiv:2022.06.06.495016
22. Mack PC, Gomez JE, Rodilla AM, Carreño JM, Hsu C-Y, et al. 2022. Longitudinal COVID-19-vaccination-induced antibody responses and Omicron neutralization in patients with lung cancer. Cancer Cell:S1535-6108(22)00174-X
23. Machlovi SI, Neuner SM, Hemmer BM, Khan R, Liu Y, et al. 2022. APOE4 confers transcriptomic and functional alterations to primary mouse microglia. Neurobiology of Disease 164:105615
24. Loftus TJ, Shickel B, Ozrazgat-Baslanti T, Ren Y, Glicksberg BS, et al. 2022. Artificial intelligence-enabled decision support in nephrology. Nature Reviews Nephrology
25. Li S, Jun T, Tyler J, Schadt E, Kao Y-H, et al. 2022. Inpatient Administration of Alpha-1-Adrenergic Receptor Blocking Agents Reduces Mortality in Male COVID-19 Patients. Frontiers in medicine 9:849222-
26. Kulkarni KR, Schafer M, Berner LA, Fiore VG, Heflin M, et al. 2022. An interpretable and predictive connectivity-based neural signature for chronic cannabis use. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
27. Kong Y, Cao L, Deikus G, Fan Y, Mead EA, et al. 2022. Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science 375:515-22
28. Klein RJ, Vertosick E, Sjoberg D, Ulmert D, Rönn A-C, et al. 2022. Prostate cancer polygenic risk score and prediction of lethal prostate cancer. NPJ Precis Oncol 6:25-
29. Kirkpatrick Roubidoux E, Sano K, McMahon M, Carreño JM, Capuano C, et al. 2022. Novel Epitopes of the Influenza Virus N1 Neuraminidase Targeted by Human Monoclonal Antibodies. J Virol 96:e0033222-e
30. Hernandez MM, Banu R, Gonzalez-Reiche AS, van de Guchte A, Khan Z, et al. 2022. Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach. J Med Virol 94:1606-16
31. Halfmann PJ, Iida S, Iwatsuki-Horimoto K, Maemura T, Kiso M, et al. 2022. SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters. Nature 603:687-92
32. Garg P, Jadhav B, Lee W, Rodriguez OL, Martin-Trujillo A, Sharp AJ. 2022. A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits. The American Journal of Human Genetics 109:1065-76
33. Gao X, Wang Y, Ribeiro CF, Manokaran C, Chang H, et al. 2022. Blocking PI3K p110β Attenuates Development of PTEN-Deficient Castration-Resistant Prostate Cancer. Molecular Cancer Research 20:673-85
34. Forrest IS, Nadkarni GN, Do R. 2022. Penetrance of Deleterious Clinical Variants—Reply. JAMA 327:1927-
35. Forrest IS, Chaudhary K, Vy HMT, Petrazzini BO, Bafna S, et al. 2022. Population-Based Penetrance of Deleterious Clinical Variants. JAMA 327:350-9
36. Fiore VG, Gu X. 2022. Similar network compositions, but distinct neural dynamics underlying belief updating in environments with and without explicit outcomes. NeuroImage 247:118821
37. Farrell K, Kim S, Han N, Iida MA, Gonzalez EM, et al. 2022. Genome-wide association study and functional validation implicates JADE1 in tauopathy. Acta Neuropathologica 143:33-53
38. Farkouh ME, Stone GW, Lala A, Bagiella E, Moreno PR, et al. 2022. Anticoagulation in Patients With COVID-19: JACC Review Topic of the Week. J Am Coll Cardiol 79:917-28
39. Esposito D, Pant I, Shen Y, Qiao RF, Yang X, et al. 2022. ROCK1 mechano-signaling dependency of human malignancies driven by TEAD/YAP activation. Nature Communications 13:703
40. Escalera A, Gonzalez-Reiche AS, Aslam S, Mena I, Laporte M, et al. 2022. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host Microbe 30:373-87.e7
41. Di’Narzo AF, Houten SM, Kosoy R, Huang R, Vaz FM, et al. 2022. Integrative Analysis of the Inflammatory Bowel Disease Serum Metabolome Improves Our Understanding of Genetic Etiology and Points to Novel Putative Therapeutic Targets. Gastroenterology 162:828-43.e11
42. Del Rossi N, Chen JG, Yuan G-C, Dries R. 2022. Analyzing Spatial Transcriptomics Data Using Giotto. Current Protocols 2:e405
43. DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, et al. 2022. Defining the risk of SARS-CoV-2 variants on immune protection. Nature 605:640-52
44. Danziger O, Patel RS, DeGrace EJ, Rosen MR, Rosenberg BR. 2022. Inducible CRISPR activation screen for interferon-stimulated genes identifies OAS1 as a SARS-CoV-2 restriction factor. PLoS Pathog 18:e1010464-e
45. Chen T-Y, Gonzalez-Kozlova E, Soleymani T, La Salvia S, Kyprianou N, et al. 2022. Extracellular vesicles carry distinct proteo-transcriptomic signatures that are different from their cancer cell of origin. iScience 25:104414
46. Carreño JM, Alshammary H, Tcheou J, Singh G, Raskin AJ, et al. 2022. Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron. Nature 602:682-8
47. Carcamo S, Nguyen CB, Grossi E, Filipescu D, Alpsoy A, et al. 2022. Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. Cell Rep 39
48. Birnbaum R, Mahjani B, Loos RJF, Sharp AJ. 2022. Clinical Characterization of Copy Number Variants Associated With Neurodevelopmental Disorders in a Large-scale Multiancestry Biobank. JAMA Psychiatry 79:250-9
49. Badrinath S, Dellacherie MO, Li A, Zheng S, Zhang X, et al. 2022. A vaccine targeting resistant tumours by dual T cell plus NK cell attack. Nature