HUANG LAB | COMPUTATIONAL OMICS




PUBLICATIONS

Lab Members | Mentored Members with External Affiliations | *Co-first Authors | #Co-corresponding Authors

2019

A Genotype Concordance Assessment between Consumer Genetic Testing Services.
Batra P, Huang KL.
Submitted. [GitHub]

Ancestry-Specific Predisposing Germline Variants in Cancer.
Oak N, Gümüş ZH, Ding L, Plon SE, TCGA Analysis Network, Huang KL.
In review. [GitHub]

AeQTL: eQTL analysis using region-based aggregation of rare variants.
Dong G, Wendl MC, Zhang B, Ding L, Huang KL.
In revision. [GitHub]

Systematic discovery of spatially interacting phosphorylation sites and mutations in cancer.
Huang KL, Scott AD, Weerasinghe A, Liu R, Zhou DC, Wang LB, Sengupta S, Lai CW, Wu Y, Ruggles K, Payne SH, Raphael B, Fenyö D, Chen K, Mills G, Ding L.
In revision. [GitHub]

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.

2018

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][GDC (controlled-access germline data)]

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. [Correspondence][Gene Google Trend Data]

2017

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]

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]

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.

2016

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.

2015

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.