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New and related publications are presented on the Open Box Science platform for scientists around the world to freely hear and discuss!

ISMMS Lab Members | Volunteer/Collaboration Team Members | *Co-first Authors | #Co-corresponding Authors | “Consortium authorship



Genomic and molecular features distinguish young adult cancer from later-onset cancer
Lee W, Wang Z, Saffern M, Jun T, Huang KL
Cell Reports 2021. [GitHub]

Pan-cancer Proteogenomic Investigations Identify Post-Transcriptional Kinase Targets
Elmas A, Tharakan S, Jaladanki S, Galsky M, Liu T, Huang KL
Communications Biology 2021. [GitHub]

Genomic Determinants of Homologous Recombination Deficiency across Human Cancers
Qing T, X Wang, Jun T, Ding L, Pusztai L#, Huang KL#.
Cancers 2021.

Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes
Wang Z, Fan X, Shen Y, Pagadala MS, Signer R, Cygan KJ, Fairbrother WG, Carter H, Chung WK#, Huang KL#.
Genome Medicine 2021. [GitHub]

Analytical protocol to identify local ancestry-associated molecular features in cancer
Carrot-Zhang J, Han S, Zhou W, Damrauer JS, Kemal A; Cancer Genome Atlas Analysis Network”, Cherniack AD, Beroukhim R.
STAR Protoc. 2021.

Prediction of individual COVID-19 diagnosis using baseline demographics and lab data
Zhang J, Jun T, Frank J, Nirenberg S, Kovatch P, Huang KL.
Scientific Reports 2021. [GitHub]

Analysis of sex-specific risk factors and clinical outcomes in COVID-19
Jun T, Nirenberg S, Weinberger T, Sharma N, Pujadas E, Cordon-Cardo C, Kovatch P, Huang KL.
Communications Medicine 2021.

The Functional Hallmarks of Cancer Predisposition Genes
Capellini A*, Williams M*, Onel K#, Huang KL#.
Cancer Manag Res. 2021.

Genetic dependency of Alzheimer’s disease-associated genes across cells and tissue types
Jaladanki SK*, Elmas A*, Malave GS, Huang KL.
Scientific Reports 2021.

Phenome-wide and expression quantitative trait locus associations of COVID-19 genetic risk loci
Moon C, Schilder BM, Raj T, Huang KL.
iScience 2021.

Diverse Immune Response of DNA Damage Repair-Deficient Tumors
Qing T, Jun T, Lindblad KE, Lujambio A, Marczyk M, Pusztai L#, Huang KL#.
Cell Reports Medicine 2021. [GitHub]

Systematic discovery of spatially interacting phosphorylation sites and mutations in cancer
Huang KL#, Scott AD, Zhou DC, Wang LB, Weerasinghe A, Elmas A, Liu R, Sengupta S, Wu Y, Wendl MC, Wyczalkowski MA, Baral J, Sengupta S, Lai CW, Ruggles K, Payne SH, Raphael B, Fenyö D, Chen K, Mills G, Ding L#.
Nature Communications 2021. [GitHub for software][GitHub for analysis scripts]

AeQTL: eQTL analysis using region-based aggregation of rare variants
Dong G, Wendl M, Zhang B, Ding L, Huang KL.
Pac Symp Biocomput. 2021. [GitHub]


Shared Immunogenic Poly-Epitope Frameshift Mutations in Microsatellite Unstable Tumors
Roudko V, Bozkus CC, Orfanelli T, McClain CB, Carr C, O’Donnell T, Chakraborty L, Samstein R, Huang KL, Blank SV, Greenbaum B, Bhardwaj N.
Cell 2020.

Risk prediction of late-onset Alzheimer’s disease implies an oligogenic architecture
Zhang Q, Sidorenko J, Couvy-Duchesne B, Marioni RE, Wright MJ, Goate AM, Marcora E, Huang KL, Porter T, Laws SM; Australian Imaging Biomarkers and Lifestyle (AIBL) Study, Sachdev PS, Mather KA, Armstrong NJ, Thalamuthu A, Brodaty H, Yengo L, Yang J, Wray NR, McRae AF, Visscher PM.
Nature Communications 2020.

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium”.
Nature Communications 2020.

Sex differences in oncogenic mutational processes.
Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, Boutros PC; PCAWG Consortium”.
Nature Communications 2020.

Cooperation between distinct cancer driver genes underlies inter-tumor heterogeneity in hepatocellular carcinoma
Molina-Sánchez P, Ruiz de Galarreta M, Yao MA, Lindblad KE, Bresnahan E, Bitterman E, Martin TC, Rubenstein T, Nie K, Golas J, Choudhary S, Bárcena-Varela M, Elmas A, Miguela V, Ding Y, Kan Z, Grinspan LT, Huang KL, Parsons RE, Shields DJ, Rollins RA, Lujambio A.
Gastroenterology 2020.

Ancestry-Specific Predisposing Germline Variants in Cancer
Oak N, Cherniack AD, Mashl RJ; TCGA Analysis Network, Hirsch FR, Ding L, Beroukhim R, Gümüş ZH, Plon SE, Huang KL.
Genome Medicine 2020. [bioRxiv][GitHub]

Genotype Concordance and Polygenic Risk Score Estimation across Consumer Genetic Testing Data
Batra P, Huang KL.
Annals of Human Genetics 2020. [bioRxiv][GitHub]

Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer 
Carrot-Zhang J*, Chambwe N*, Damrauer JS*, Knijnenburg TA*, Robertson AG*, Yau C*, Zhou W*, Berger AC*, Huang KL*, Newberg JY*, Mashl RJ, Romanel A, Sayaman RW, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E, Cancer Genome Atlas Analysis Network, Cherniack AD, Beroukhim R.
Cancer Cell 2020.

Ten Simple Rules for landing on the right job after your PhD or postdoc
Huang KL.
PLoS Computational Biology 2020. [YouTube]

Pan-cancer analysis of whole genomes
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium”.
Nature 2020.


Regulated phosphosignaling associated with breast cancer subtypes and druggability
Huang KL#, Wu Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies S, Ellis MJ, Fenyö D, Chen F, Townsend RR, Carr SA, Ding L#.
Molecular and Cellular Proteomics 2019. [GitHub]

Mannose Phosphate Isomerase and Mannose Regulate Hepatic Stellate Cell Activation and Fibrosis in Zebrafish and Humans
DeRossi C, Bambino K, Morrison J, Sakarin I, Villacorta-Martin C, Zhang C, Ellis JL, Fiel MI, Ybanez M, Lee YA, Huang KL, Yin C, Sakaguchi TF, Friedman SL, Villanueva A, Chu J.
Hepatology 2019.

Functional analysis of BARD1 missense variants in homology-directed repair and damage sensitivity
Adamovich AI, Banerjee T, Wingo M, Duncan K, Ning J, Martins Rodrigues F, Huang KL, Lee C, Chen F, Ding L, Parvin JD.
PLoS Genetics 2019.


Framework for microRNA variant annotation and prioritization using human population and disease datasets
Oak N, Ghosh R, Huang KL, Wheeler DA, Ding L, Plon SE.
Human Mutation. 2018 Oct 10. [GitHub]

CharGer: Clinical Characterization of Germline Variants
Scott AD#, Huang KL, Weerasinghe A, Mashl RJ, Gao Q, Martins Rodrigues F, Wyczalkowski M, Ding L#.
Bioinformatics. 2018 Aug 9. [GitHub]

Integrative omics analyses broaden treatment targets in human cancer
Sengupta S*, Sun SQ*, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Fenyö D, Townsend RR, Dipersio JF, Chen F, Ding L.
Genome Medicine. 2018 Jul 27;10(1):60.

Pathogenic Germline Variants in 10,389 Adult Cancers
Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F#, Ding L#.
Cell. 2018 Apr 5;173(2):355-370.e14. [GitHub] [Controlled-access variant-call data available: GDC] [Presentation: YouTube]

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
Ding L#, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA#, Getz G#; Cancer Genome Atlas Research Network.
Cell. 2018 Apr 5;173(2):305-320.e10.

Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types
Cao Y, Zhou W, Li L, Wang J, Gao Z, Jiang Y, Jiang X, Shan A, Bailey MH, Huang KL, Sun SQ, McLellan MD, Niu B, Wang W, Ding L, Ning G.
Cell Research. 2018 May;28(5):601-604.

Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyö D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX.
Cancer Research. 2018 May 15;78(10):2732-2746.

Most popular public searches on gene names
Huang KL.
Nature. 2018 Jan 25;553(7689):405. [Gene Google Trend Data]


Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner
Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyö D, Held JM.
Science Signalling. 2017 Aug 8;10(491).

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer’s disease
Huang KL*, Marcora E*, Pimenova AA, Di Narzo AF, Kapoor M, Jin SC, Harari O, Bertelsen S, Fairfax BP, Czajkowski J, Chouraki V, Grenier-Boley B, Bellenguez C, Deming Y, McKenzie A, Raj T, Renton AE, Budde J, Smith A, Fitzpatrick A, Bis JC, DeStefano A, Adams HHH, Ikram MA, van der Lee S, Del-Aguila JL, Fernandez MV, Ibañez L; International Genomics of Alzheimer’s Project; Alzheimer’s Disease Neuroimaging Initiative, Sims R, Escott-Price V, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Lambert JC, van Duijn C, Launer L, Seshadri S, Williams J, Amouyel P, Schellenberg GD, Zhang B, Borecki I, Kauwe JSK, Cruchaga C, Hao K, Goate AM.
Nature Neuroscience. 2017 Aug;20(8):1052-1061. [GitHub][YouTube]

GenomeVIP: a cloud platform for genomic variant discovery and interpretation
Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael BJ, Wendl MC, Ding L.
Genome Research. 2017 Aug;27(8):1450-1459. [GitHub]

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts
Huang KL*, Li S*, Mertins P*, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Townsend RR, Chen X, Carr SA#, Ellis MJ#, Ding L#.
Nature Communications. 2017 Mar 28;8:14864. [GitHub][Shared multi-omic data for the PDX cohort][YouTube]

Genome-wide association study identifies four novel loci associated with Alzheimer’s endophenotypes and disease modifiers
Deming Y, Li Z, Kapoor M, Harari O, Del-Aguila JL, Black K, Carrell D, Cai Y, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Huang KL, Bertelsen S, Fagan AM, Holtzman DM, Morris JC, Kim S, Saykin AJ, De Jager PL, Albert M, Moghekar A, O’Brien R, Riemenschneider M, Petersen RC, Blennow K, Zetterberg H, Minthon L, Van Deerlin VM, Lee VM, Shaw LM, Trojanowski JQ, Schellenberg G, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Peskind ER, Li G, Di Narzo AF; Alzheimer’s Disease Neuroimaging Initiative (ADNI); Alzheimer Disease Genetic Consortium (ADGC), Kauwe JS, Goate AM, Cruchaga C.
Acta Neuropathol. 2017 May;133(5):839-856.


Chitinase-3-like 1 protein (CHI3L1) locus influences cerebrospinal fluid levels of YKL-40
Deming Y, Black K, Carrell D, Cai Y, Del-Aguila JL, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Bertelsen S, Huang KL, Sutphen CL, Tarawneh R, Fagan AM, Holtzman DM, Morris JC, Goate AM, Dougherty JD, Cruchaga C.
BMC Neurology. 2016 Nov 10;16(1):217.

Proteogenomics connects somatic mutations to signalling in breast cancer
Mertins P*, Mani DR*, Ruggles KV*, Gillette MA*, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ#, Carr SA#; NCI CPTAC.
Nature. 2016 Jun 2;534(7605):55-62.

Systematic discovery of complex insertions and deletions in human cancers
Ye K, Wang J, Jayasinghe R, Lameijer EW, McMichael JF, Ning J, McLellan MD, Xie M, Cao S, Yellapantula V, Huang KL, Scott A, Foltz S, Niu B, Johnson KJ, Moed M, Slagboom PE, Chen F, Wendl MC, Ding L.
Nature Medicine. 2016 Jan;22(1):97-104.

Pan-cancer methylation and expression profiling of adenocarcinomas revealed epigenetic silencing in the WNT signaling pathway
Li J*, Huang KL*, Zhang T, Li H, Zhao J, Wang H.
Neoplasma. 2016.


Patterns and functional implications of rare germline variants across 12 cancer types
Lu C*, Xie M*, Wendl MC*, Wang J*, McLellan MD*, Leiserson MD*, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, Dipersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L.
Nature Communications. 2015 Dec 22;6:10086.