{"id":27,"date":"2020-07-29T14:31:00","date_gmt":"2020-07-29T14:31:00","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/polaklab\/?page_id=27"},"modified":"2021-06-28T17:47:21","modified_gmt":"2021-06-28T17:47:21","slug":"publications","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/polaklab\/publications\/","title":{"rendered":"Lab Publications"},"content":{"rendered":"<h2 style=\"text-align: justify\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-69\" src=\"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-content\/uploads\/sites\/359\/2020\/07\/PP.jpg\" alt=\"\" width=\"993\" height=\"629\" srcset=\"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-content\/uploads\/sites\/359\/2020\/07\/PP.jpg 993w, https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-content\/uploads\/sites\/359\/2020\/07\/PP-300x190.jpg 300w, https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-content\/uploads\/sites\/359\/2020\/07\/PP-768x486.jpg 768w\" sizes=\"auto, (max-width: 993px) 100vw, 993px\" \/><\/h2>\n<h2><strong> Preprint<\/strong><\/h2>\n<ul>\n<li><span style=\"font-weight: 400\">Kubler K, Karlic R, ,\u2026 , Foulkes WD<strong>*<\/strong>, <strong>Polak P*, <\/strong>Getz G<strong>*<\/strong>.\u00a0<\/span><span style=\"font-weight: 400\"><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/517565v1\">Tumor mutational landscape is a record of the pre-malignant state<\/a>. <\/span><b>bioRxiv<\/b><\/li>\n<\/ul>\n<h2>Peer-reviewed publications<\/h2>\n<p><span style=\"font-weight: 400\">\u00a02021<\/span><\/p>\n<ul>\n<li style=\"font-weight: 400;text-align: justify\"><b>Ahuno ST<\/b><span style=\"font-weight: 400\">, <\/span><span style=\"font-weight: 400\">Doebley A-L, Ahearn TU, Yarney J, Titiloye N, Hamel N, Adjei E, Joe-Nat Clegg- Lamptey J-N, Edusei L, Awuah B, Song X, Vanderpuye V, Abubakar M, Duggan M, Stover D, Nyarko K, Bartlett JMS, Aitpillah F, Ansong D,\u00a0 Gardner KL, Boateng FA, Bowcock AM, Caldas C, Foulkes WD, Beatrice WS,\u00a0 Wiafe-Addai, Garcia-Closas M, Kwarteng A<\/span><span style=\"font-weight: 400\">, Ha G*, Figueroa JD*, <\/span><strong>Polak P*<\/strong><span style=\"font-weight: 400\">.<\/span><a href=\"https:\/\/www.medrxiv.org\/content\/10.1101\/2020.10.25.20217133v1\"> <span style=\"font-weight: 400\">Circulating tumor DNA is readily detectable among Ghanaian breast cancer patients supporting non-invasive cancer genomic studies in Africa<\/span><\/a><span style=\"font-weight: 400\">. medRxiv, 2020. <\/span><span style=\"font-weight: 400\"><span style=\"font-weight: 400\">npj Precision Oncology (in press)<\/span><\/span>&nbsp;<\/li>\n<li style=\"font-weight: 400;text-align: justify\"><span style=\"font-weight: 400\">Foulkes WD , <\/span><strong>Polak P<\/strong><b>. <\/b><span style=\"color: #3366ff\">Li-Fraumeni Syndrome in the Cancer Genomics EraJNCI<\/span>: Journal of the National Cancer Institute (in press)<\/li>\n<li style=\"text-align: justify\"><span style=\"font-weight: 400\">Matis\u00a0 TS, Zayed N , Labraki B,\u00a0 de la Durantaye M,\u00a0 Matis\u00a0 TA , Valenzuela\u00a0 JC, Hamel\u00a0 N , Atayan A, Rivera BP, Tabach Y, Tonin PN, , Orthwein A, Mes-Masson A-M, El-Haffaf ZE , Foulkes WD , and <\/span><strong>Polak P.<\/strong> <span style=\"font-weight: 400;color: #3366ff\">Current gene panels account for nearly all homologous recombination repair-associated multiple-case breast cancer families <\/span><span style=\"font-weight: 400\"><span style=\"font-weight: 400\">(in press)<\/span><\/span>&nbsp;<\/li>\n<li style=\"text-align: justify\"><span style=\"font-weight: 400\">Singh H, Ha K, Hornick JL, Madha S, Cejas P, Jajoo K, Singh P, <\/span><strong>Polak P<\/strong><span style=\"font-weight: 400\"><strong>,<\/strong> Lee H, Shivdasani RA. <\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34090884\/\"><span style=\"font-weight: 400\">Hybrid stomach-intestinal chromatin states underlie human Barrett&#8217;s metaplasia.<\/span><\/a><span style=\"font-weight: 400\"><span style=\"font-weight: 400\"> Gastroenterology. 2021 Jun 3:S0016-5085(21)03084-5. doi: 10.1053\/j.gastro.2021.05.057. Online ahead of print. PMID: 34090884<\/span><\/span>&nbsp;<\/li>\n<li style=\"text-align: justify\"><span style=\"font-weight: 400\">Sigel K, Zhou M, Park YA, Mutetwa T, Nadkarni G, Yeh C, <\/span><strong>Polak P<\/strong><span style=\"font-weight: 400\"><strong>,<\/strong> Sigel C, Conroy T, Juzyna B, Ychou M, Fojo T, Wisnivesky JP, Bates SE. <\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33714591\/\"><span style=\"font-weight: 400\">Gemcitabine plus nab-paclitaxel versus FOLFIRINOX for unresected pancreatic cancer: Comparative effectiveness and evaluation of tumor growth in veterans.<\/span><\/a> <span style=\"font-weight: 400\">Semin Oncol. 2021 Feb 23:S0093-7754(21)00006-3. doi: 10.1053\/j.seminoncol.2021.02.001. Online ahead of print. PMID: 33714591<\/span><\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2020<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li><strong><span style=\"font-weight: 400\">Wang Y, Park JYP, Pacis A, Denroche RE, Jang GH, Zhang A, Cuggia A, Domecq C,\u00a0 \u00a0 Monlong J, Raitses-Gurevich M, Grant RC, Borgida A, Holter S, Stossel C, Bu S, Masoomian M, Lungu IM, Bartlett JMS, Wilson JM, Gao ZH, Riazalhosseini Y, Asselah J, Bouganim N, Cabrera T, Boucher LM, Valenti D, Biagi J, Greenwood CMT, <\/span>Polak P<span style=\"font-weight: 400\">, Foulkes WD, Golan T, O&#8217;Kane GM, Fischer SE, Knox JJ, Gallinger S, Zogopoulos G.<\/span><span style=\"font-weight: 400\"> A<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32816949\/\"> Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous Recombination-deficient Pancreatic Cancer<\/a>.<\/span><b>\u00a0Clin Cancer Res<\/b><span style=\"font-weight: 400\">. 2020 Oct 15;26(20):5462-5476 PMID: 32816949<\/span><\/strong>.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><strong>Mutetwa T,<\/strong>\u00a0Foulkes WD, <strong>Polak P<\/strong><b>.<\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32846071\/\"><span style=\"font-weight: 400\">Olaparib for Metastatic Castration-Resistant Prostate Cancer<\/span><\/a><span style=\"font-weight: 400\">. <\/span>The New England Journal of Medicine 2020. PMID: 383(9)890.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400;text-align: left\"><strong>Hughley R<\/strong>, Karlic R, Himanshu J, Turnbull C, Foulkes WD, <strong>Polak P<\/strong><b>.\u00a0<\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32668122\/\">Etiologic Index &#8211; A Case-Only Measure of <i>BRCA1\/2<\/i>-Associated Cancer Risk.\u00a0<\/a> The New England Journal of Medicine. 2020. PMID: 32668122.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400\"><span style=\"font-weight: 400\">Foulkes WD,<\/span> <strong>Polak P.<\/strong>\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32668120\/\">Bilateral Tumors &#8211; Inherited or Acquired? <\/a>The New England Journal of Medicine. 2020\u00a0Jul 16;383(3):280-282.PMID: 32668120.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><span style=\"font-weight: 400\">Sanford JA,<\/span> <strong>Nogiec CD<\/strong><b>,\u00a0<span style=\"font-weight: 400\">Lindholm ME, Adkins JN, Amar D, Dasari S, Drugan JK, Fern\u00e1ndez FM, Radom-Aizik S, Schenk S, Snyder MP, Tracy RP, Vanderboom P, Trappe S, Walsh MJ; Molecular Transducers of Physical Activity Consortium.<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32589957\/\"><span style=\"font-weight: 400\">Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise.<\/span><\/a>\u00a0<span style=\"font-weight: 400\">Cell. 2020 Jun 25;181(7):1464-1474. doi: 10.1016\/j.cell.2020.06.004.\u00a0<\/span><span style=\"font-weight: 400\"><span style=\"font-weight: 400\">PMID: 32589957 Review.<\/span><\/span><\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400\"><span style=\"font-weight: 400\">Koga Y, Song H, Chalmers ZR, Newberg J, Kim E, Carrot-Zhang J, Piou D,<\/span> <strong>Polak P<\/strong><span style=\"font-weight: 400\">, Abdulkadir SA, Ziv E, Meyerson M, Frampton GM, Campbell JD, Huang FW.\u00a0<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32651179\/\">Genomic Profiling of<\/a>\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32651179\/\">Prostate Cancers from Men with African and European Ancestry.\u00a0<\/a>Clin Cancer Res. 2020 Jul 10. doi: 10.1158\/1078-0432.CCR-19-4112. Online ahead of print. PMID: 32651179<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400\"><span style=\"font-weight: 400\">Sigel K, Swartz T, Golden E, Paranjpe I, Somani S, Richter F, De Freitas JK, Miotto R, Zhao S,<\/span> <strong>Polak P<\/strong><span style=\"font-weight: 400\"><strong>, Mutetwa T<\/strong>, Factor S, Mehandru S, Mullen M, Cossarini F, Bottinger E, Fayad Z, Merad <\/span><span style=\"font-weight: 400\">M, Gnjatic S, Aberg J, Charney A, Nadkarni G, Glicksberg BS.\u00a0<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32594164\/\">Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City.\u00a0<\/a>Clin Infect Dis. 2020 Jun 28:ciaa880. doi: 10.1093\/cid\/ciaa880. Online ahead of print. PMID: 32594164<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400;text-align: justify\"><span style=\"font-weight: 400\">Ha K, Fujita M, Karli\u0107 R, Yang S, Xue R, Zhang C, Bai F, Zhang N, Hoshida Y,<\/span><strong>Polak P<\/strong><b>,<\/b><span style=\"font-weight: 400\"> Nakagawa H, Kim HG, Lee H. \u00a0 (2020)\u00a0<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32083210\/\">Somatic mutation landscape reveals differential variability of cell-of-origin for primary liver cancer.<\/a>\u00a0 \u00a0<b>Heliyon<\/b>;6(2):e03350<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400\"><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32025007\/\"><span style=\"font-weight: 400\">Pan-cancer analysis of whole genomes<\/span><\/a><span style=\"font-weight: 400\">. (2020)\u00a0<\/span>ICGC\/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.\u00a0\u00a0<b>Nature.<\/b>578(7793):82-93.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Jiao W*, Atwal G*,\u00a0<\/span><\/b><strong>Polak P<\/strong><b>*,<span style=\"font-weight: 400\"> Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD; PCAWG Consortium. (2020).\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32024849\/\">A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns<\/a>.\u00a0<b>Nature Communication.<\/b> 2020 Feb 5;11(1):728.<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2019<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Yizhak K, Aguet F, Kim J, Hess JM, K\u00fcbler K, Grimsby J, Frazer R, Zhang H, Haradhvala NJ, Rosebrock D, Livitz D, Li X, Arich-Landkof E, Shoresh N, Stewart C, Segr\u00e8 AV, Branton PA, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Ardlie KG, Getz G. (2019)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/31171663\/\">RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues.\u00a0<\/a><b>Science<\/b>. 7;364(6444).<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Castellsagu\u00e9 E, Li R, Aligue R, Gonz\u00e1lez S, Sanz J, Martin E, Velasco \u00c0, Capell\u00e1 G, Stewart CJR, Vidal A, Majewski J, Rivera B, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Matias-Guiu X, Brunet J, Foulkes WD. (2019)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/30362666\/\">Novel POLE pathogenic germline variants in a family with multiple primary tumors results in distinct mutational signatures.\u00a0\u00a0<\/a><b>Human Mutation. <\/b>40(1):36-41. doi: 10.1002\/humu.23676.<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2018<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">30) Miao D, Margolis CA, Vokes NI, Liu D, Taylor-Weiner A, Wankowicz SM, Adeegbe D, Keliher D, Schilling B, Tracy A, Manos M, Chau NG, Hanna GJ, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Rodig SJ, Signoretti S, Sholl LM, Engelman JA, Getz G, J\u00e4nne PA, Haddad RI, Choueiri TK, Barbie DA, Haq R, Awad MM, Schadendorf D, Hodi FS, Bellmunt J, Wong KK, Hammerman P, Van Allen EM. (2018)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/30150660\/\">Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors.\u00a0<\/a><b>Nature Genetics.<\/b> 1271-1281. doi: 10.1038\/s41588-018-0200-2.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Gopal RK, K\u00fcbler K, Calvo SE, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Livitz D, Rosebrock D, Sadow PM, Campbell B, Donovan SE, Amin S, Gigliotti BJ, Grabarek Z, Hess JM, Stewart C, Braunstein LZ, Arndt PF, Mordecai S, Shih AR, Chaves F, Zhan T, Lubitz CC, Kim J, Iafrate AJ, Wirth L, Parangi S, Leshchiner I, Daniels GH, Mootha VK, Dias-Santagata D, Getz G, McFadden DG. (2018)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/30107175\/\">Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in H\u00fcrthle Cell Carcinoma.\u00a0<\/a><b>Cancer Cell.;<\/b>34(2):242-255.e5. doi: 10.1016\/j.ccell.2018.06.013.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D; PCF\/SU2C International Prostate Cancer Dream Team, Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M. (2018)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29909985\/\">Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing.\u00a0<\/a><b>\u00a0Cell.<\/b>;174(2):433-447.e19. doi: 10.1016\/j.cell.2018.05.036. Epub 2018 Jun 18.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Rivera B, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Foulkes WD. (2018)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29394477\/\">Monogenic Diseases of DNA Repair.\u00a0<\/a><b>New England Journal Medicine.<\/b> 378(5):491<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><span style=\"font-weight: 400\">\u00a0<\/span><b><span style=\"font-weight: 400\">Wardell CP, Fujita M, Yamada T, Simbolo M, Fassan M, Karlic R, <\/span><\/b><strong>Polak P<\/strong><b>,<span style=\"font-weight: 400\"> Kim J, Hatanaka\u00a0<\/span><\/b>Y, Maejima K, Lawlor RT, Nakanishi Y, Mitsuhashi T, Fujimoto A, Furuta M, Ruzzenente A, Conci S, Oosawa A, Sasaki-Oku A, Nakano K, Tanaka H, Yamamoto Y, Michiaki K, Kawakami Y, Aikata H, Ueno M, Hayami S, Gotoh K, Ariizumi SI, Yamamoto M, Yamaue H, Chayama K, Miyano S, Getz G, Scarpa A, Hirano S, Nakamura T, Nakagawa H.(2018) <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29360550\/\">Genomic Characterization of Biliary Tract Cancers Identifies Driver Genes and Predisposing Mutations.\u00a0<\/a><b>Journal of Hepatology<\/b> pii: S0168-8278(18)30021-7<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2017<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400\"><span style=\"font-weight: 400\">Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G,\u00a0<\/span>Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, Stewart C, Rosenberg M, Francis JM, Zhang CZ, Cohen O, Oh C, Ding H, <strong>Polak P<\/strong><b>, <\/b>Lloyd M, Mahmud S, Helvie K, Merrill MS, Santiago RA, O&#8217;Connor EP, Jeong SH, Leeson R, Barry RM, Kramkowski JF, Zhang Z, Polacek L, Lohr JG, Schleicher M, Lipscomb E, Saltzman A, Oliver NM, Marini L, Waks AG, Harshman LC, Tolaney SM, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Johannessen CM, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Love JC, Meyerson M. (2017)\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29109393\/\">Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.\u00a0<\/a><b>Nature Communication <\/b>8(1):1324<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Maruvka YE, Mouw KW, Karlic R, Parasuraman P, Kamburov A, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Haradhvala NJ,\u00a0<\/span><\/b>Hess JM, Rheinbay E, Brody Y, Koren A, Braunstein LZ, D&#8217;Andrea A, Lawrence MS, Bass A, Bernards A, Michor F, Getz G. (2017) <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28892075\/\">Analysis of somatic microsatellite indels identifies driver events in human tumors.\u00a0<\/a><b>Nature Biotechnology <\/b>35(10):951-959<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><strong>Polak P<\/strong><b>*,<span style=\"font-weight: 400\"> Kim J*, Braunstein LZ*, Tao G., Karlic R., Rosebrock D., Livitz D., K\u00fcbler K., Mouw KW.,\u00a0<\/span><\/b>Haradhvala NJ., Kamburov A, Maruvka YE., Leshchiner I., Lander ES., Golub TR.,\u00a0Zick A., \u00a0Lawrence MS., Haber DA, Laird PW, Shen H., <a href=\"http:\/\/www.nature.com\/articles\/ncomms8014\">Ellisen<\/a> LW., D\u2019Andrea A., Chanock SJ., Foulkes WD and Getz G \u00a0(2017)\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28825726\/\">A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer.\u00a0\u00a0<\/a><b>Nature Genetics<\/b> 49(10):1476-1486\u00a0*Equal contribution<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Cancer Genome Atlas Research Network (<\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28052061\/\">Integrated genomic characterization of oesophageal carcinoma.\u00a0<\/a><b>Nature <\/b>2017 12;541(7636):169-175.<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2016<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Kim J.*, Mouw KW. *, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">.*, Braunstein LZ., Kamburov A., Kwiatkowski D., Rosenberg JE., Van\u00a0<\/span><\/b>Allen EM., D\u2019Andrea A., Getz G., (2016) <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27111033\/\">Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors.\u00a0\u00a0<\/a>\u00a0<b>Nature Genetics<\/b> 48, 600\u2013606\u00a0\u00a0*Equal contribution<\/li>\n<li><b><span style=\"font-weight: 400\">Haradhvala, N.*, <\/span><\/b><strong>Polak P<\/strong><b>.*,<span style=\"font-weight: 400\"> Koren A., Stojanov P., Covington K., Shinbrot E., Hess J., Rheinbay, E., Kim\u00a0<\/span><\/b>J., Maruvka, Y., Braunstein LZ., Wheeler D., Lawrence M., Getz G. (2016) <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/26806129\/\">Mutational strand asymmetries in cancer genomes reveal Mechanisms of DNA Damage and repair.\u00a0<\/a><b>Cell <\/b>164(3):538-49\u00a0\u00a0*Equal contribution<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2015<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Kazanov MD, Roberts SA, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR. (2015)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/26527001\/\">APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions.\u00a0<\/a><b>Cell Reports<\/b>. 10;13(6):1103-1109.<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Kasar S., Jaegil K., Improgo R., Tiao G., <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Lawrence MS., Kiezun A., Fernandes S., Bahl S.,\u00a0<\/span><\/b>Sougnez C., Gabriel S., Lander ES., Haesook K., Getz G., Brown JR (2015) Whole-genome sequencing reveals two Activation-Induced Cytidine Deaminase signatures during Indolent Chronic Lymphocytic Leukemia evolution.\u00a0\u00a0<b>Nature Communications<\/b> 6: 8866<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Kamburov A., Lawrence MS., <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Leshchiner I., Lage K, Golub TR., Lander ES, Getz G. (2015)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/26392535\/\">Comprehensive assessment of cancer missense mutation clustering in protein structures.\u00a0<\/a><b>Proc Natl Acad Sci U S A.<\/b> 112(40): E5486-95<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Francioli LC. *, <\/span><\/b><strong>Polak P.<\/strong><b>*,<span style=\"font-weight: 400\"> Koren A.*, Menelaou A., Chun S., Renkens I., Genome of the Netherlands Consortium, van Duijn CN., Swertz M., Wijmenga C., van Ommen G., Slagboom PE., Boomsma DI., Ye K., Guryev G., Arndt PF., Kloosterman, WP., de Bakker PIW., Sunyaev, SR. (2015)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25985141\/\">Genome-wide patterns and properties of de novo mutations in humans.\u00a0\u00a0<\/a><b>Nature Genetics<\/b> 47(7):822-826.\u00a0*Equal contribution<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><strong>Polak, P<\/strong><b>,<span style=\"font-weight: 400\"> * Karlic, R*., Koren, A., Thurman, B., Sandstrom, Lawrence, M. S., R., Reynolds, A., Rynes,\u00a0<\/span><\/b>E., Vlahovicek, K., Stamatoyannopoulos, J., Sunyaev, S.\u00a0(2015) <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25693567\/\">Cell-of-origin chromatin organization shapes the mutational landscape of cancer.\u00a0\u00a0<\/a><b>Nature <\/b>518(7539):360-364.\u00a0*Equal contribution<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400\"><span style=\"font-weight: 400\">Roadmap Epigenomics Consortium (2015)\u00a0<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25693563\/\">Integrative analysis of 111 reference human epigenomes.\u00a0<\/a><b>Nature<\/b> 518(7539):317-330.<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2014<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Koren A., <\/span><a href=\"blank\"><span style=\"font-weight: 400\">Handsaker<\/span><\/a><span style=\"font-weight: 400\"> RE., <\/span><a href=\"blank\"><span style=\"font-weight: 400\">Kamitaki<\/span><\/a><span style=\"font-weight: 400\"> N., Karlic R., <\/span><a href=\"blank\"><span style=\"font-weight: 400\">Ghosh<\/span><\/a><span style=\"font-weight: 400\"> S., <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Eggan K., McCarrol S.A. (2014)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25416942\/\">Genetic Variation in Human DNA Replication Timing\u00a0<\/a><b>Cell<\/b> 159 (5) 1015-1026<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Francioli, LC., Genome of the Netherlands Project Consortium (<\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">.), De-Bakker, P. I. W. (2014)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/24974849\/\">Whole-genome sequence variation, population structure and demographic history of the Netherlands <\/a>\u00a0 \u00a0<b>Nature Genetics <\/b>46, 818-825<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li><strong>Polak, P<\/strong><b><span style=\"font-weight: 400\">*, Lawrence, MS.*, Haugen, E., Stoletzki Nm, Stojanov, P., Thurman, RE.,\u00a0<\/span><\/b>Garraway, LA., Mirkin S., Getz, G., Stamatoyannopoulos JA., Sunyaev, SR. (2014) <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/24336318\/\">Reduced local mutation density in regulatory DNA of cancer genomes linked to DNA repair\u00a0<\/a><b>Nature Biotechnology <\/b>32, 71-75\u00a0\u00a0*Equal contribution<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2013<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Lawrence, MS.*, Stojanov P*., <\/span><\/b><strong>Polak P<\/strong><b>.*<span style=\"font-weight: 400\">, Kryukov GV., Cibulskis K., Sivachenko A., Carter SL., Stewart\u00a0<\/span><\/b>C., Mermel CH., Roberts SA., Kiezun A., Hammerman PS., McKenna A., Drier Y., Zou, L., Ramos, A.H., Pugh TJ., Stransky N., Helman E., Kim J., Sougnez C., Ambrogio L., Nickerson E., Shefler E., Cort\u00e9s ML., Auclair D., Saksena G., Voet D., Noble M., DiCara D, Lin P., Lichtenstein L., Heiman DI., Fennell T., Imielinski M., Hernandez B., Hodis E., Baca S., Dulak AM., Lohr J., Landau DA., Wu C., Melendez-Zajgla J., Hidalgo-Miranda A., Koren, A., McCarroll SA., Mora J., Lee, RS., Crompton B, Onofrio R., Parkin M., Winckler W., Ardlie K., Gabriel SB., Roberts CW., Biegel JA., Stegmaier K., Bass, AJ., Garraway LA., Meyerson,M., Golub, TR., Gordenin,DA., Sunyaev SR., Lander ES., Getz G. (2013)\u00a0 <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/23770567\/\">Mutational heterogeneity in cancer and the search for new cancer-associated genes.\u00a0\u00a0<\/a><b>Nature <\/b>499 (7457):214-218.*Equal contribution4<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2012<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li><b><span style=\"font-weight: 400\">Koren A, <\/span><\/b><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">, Nemesh J, Michaelson JJ, Sebat J , Sunyaev SR, McCarroll SA. (2012)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/23176822\/\">Differential relationship of DNA replication timing to different forms of human mutation and variation.\u00a0<\/a><b>American Journal of Human Genetics<\/b> 91(6):1033-40<\/li>\n<\/ul>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400\"><span style=\"font-weight: 400\">Neale BM., Kou Y., Liu L., Ma\u2019ayan A, Samocha KE., Sabo A., Lin CF., Stevens C., Wang LS., Makarov\u00a0<\/span>V., <strong>Polak P<\/strong><b>.<\/b> et al. (2012)\u00a0\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/22495311\/\">Patterns and rates of exonic de novo mutations in autism spectrum disorders\u00a0<\/a><b>Nature <\/b>485 (7397) 242-245.<\/li>\n<\/ul>\n<h3 style=\"text-align: justify\"><strong>2011-2006<\/strong><\/h3>\n<ul style=\"text-align: justify\">\n<li style=\"font-weight: 400\"><span style=\"font-weight: 400\">Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Un X, Turanov AA, Yang\u00a0<\/span>P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, <strong>Polak P<\/strong> et al. (2011)\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/21993625\/\">Genome sequencing reveals insights into physiology and longevity of the naked mole rat.\u00a0\u00a0<\/a><b>Nature<\/b> 479 (7372) 223-7<\/li>\n<li style=\"font-weight: 400\"><strong>Polak P<\/strong><b>,<span style=\"font-weight: 400\"> R. Querfurth R., Arndt PF. (2010)<\/span><\/b>\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/20565875\/\">The evolution of transcription-associated biases of mutations across vertebrates.\u00a0\u00a0<\/a><b>BMC Evolutionary Biology<\/b> 10<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify\"><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">. and Arndt PF. (2009)\u00a0\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/20333189\/\">Long Range bi-directional strand asymmetries originate at CpG islands in the human genome\u00a0<\/a><b>Genome Biology and Evolution <\/b>2009, 189<\/li>\n<li style=\"text-align: justify\"><strong>Polak P<\/strong><b>. <span style=\"font-weight: 400\">and Arndt PF. (2008)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/18463301\/\">Transcription induces strand-specific mutations at the 5&#8242; end of human genes,\u00a0<\/a><b>Genome Research<\/b> 18, 1216-1223.<\/li>\n<li style=\"text-align: justify\"><strong>Polak P<\/strong><b><span style=\"font-weight: 400\">. and Wolansky, G. (2007) n<\/span><\/b><a href=\"https:\/\/www.esaim-cocv.org\/articles\/cocv\/abs\/2007\/03\/cocv0521\/cocv0521.html\">The Lazy Travelling Salesman Problem,\u00a0<\/a><b>Control, Optimization and Calculus of Variations<\/b> 13, (3) 538-552<\/li>\n<li style=\"text-align: justify\"><strong>Polak P.<\/strong><b> <span style=\"font-weight: 400\">and E. Domany E., (2006)\u00a0<\/span><\/b><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1513395\/\">Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes.\u00a0\u00a0<\/a><b>BMC Genomics <\/b>7 p. 133<\/li>\n<li style=\"text-align: justify\"><b><span style=\"font-weight: 400\">Geva-Zatorsky N., Rosenfeld N., Itzkovitz S., Milo R., Sigal A., Dekel E., Yarnitzky T., Liron Y., <\/span><\/b><strong>Polak \u00a0P<\/strong><b>.,<span style=\"font-weight: 400\"> Lahav G. and Alon,U. (2006)\u00a0<\/span><\/b><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/16773083\/\">Oscillations and variability in the p53 system<\/a>,\u00a0\u00a0Molecular Systems Biology 2<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Preprint Kubler K, Karlic R, ,\u2026 , Foulkes WD*, Polak P*, Getz G*.\u00a0Tumor mutational landscape is a record of the pre-malignant state. bioRxiv Peer-reviewed publications \u00a02021 Ahuno ST, Doebley A-L, Ahearn TU, Yarney J, Titiloye N, Hamel N, Adjei E, Joe-Nat Clegg- Lamptey J-N, Edusei L, Awuah B, Song X, Vanderpuye V, Abubakar M, Duggan [&hellip;]<\/p>\n","protected":false},"author":146,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-27","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-json\/wp\/v2\/pages\/27","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-json\/wp\/v2\/users\/146"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-json\/wp\/v2\/comments?post=27"}],"version-history":[{"count":26,"href":"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-json\/wp\/v2\/pages\/27\/revisions"}],"predecessor-version":[{"id":289,"href":"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-json\/wp\/v2\/pages\/27\/revisions\/289"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/polaklab\/wp-json\/wp\/v2\/media?parent=27"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}