Select Publications

Visit our Google Scholar for an updated list.

Lineage-specific chromatin binding of FOXA1 is regulated by LSD1-mediated Demethylation
Gao S, Chen S, Han D, Zhou F, Barrett D, Luong MP, Han W, Avery AM, Petricca J, Yuan M, Asara JM, Macoska JA, Balk SP#, He H#, Cai C#
Nature Genetics. In press. IF=27.13

Structural basis of human helicase DDX21 in RNA binding, unwinding, and antiviral signal activation
Chen Z, Hu X, Xie F, Li Z, Kuang S, Zhan B, Gao W, Chen X, Gao S, Li Y, Wang Y, Qian F, Ding C, Gan J, Ji C, Zhou Z, Huang J, He H, Li J
Advanced Science. 2020. PMID: 32714761. IF=15.8

The DNA methylation landscape of advanced prostate cancer
Zhao S, Chen W, Li H, Foye A, Zhang M, Sjostrom M, Aggarwal R, Playdle D, Liao A, Alumkal J, Das R, Chou J, Hua J, Barnard T, Bailey A, Chow E, Perry M, Dang H, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Chang SL, Houlahan K, Shiah YJ, Beer T, Thomas G, Chi K, Gleave M, Zoubeidi A, Reiter R, Witte O, Kim MY, Fong L, Spratt D, Morgan T, Bose R, Huang F, Li H, Shenoy T, Goodarzi H, Asangani I, Sandhu S, Lang J, Mahajan N, Lara P Evans C, Febbo P, Batzoglou S, Knudsen K, He H, Huang J, Zwart W, Costello J, Luo J, Tomlins S, Wyatt A, Dehm S, Ashworth A, Gilbert L, Boutros P, Farh K, Maher C, Small E, Quigley D, Chinnaiyan A, Rettig M, Chesner L, Feng F
Nature Genetics. 2020. PMID: 32661466. IF=27.13

Hypercholesterolemia risk-associated GPR146 is an orphan G-protein coupled receptor that regulates blood cholesterol levels in humans and mice
Han F, Liu X, Chen C, Liu Y, Du M, Zhou Y, Liu Y, Song B, and He H, Yan Wang
Cell Research. 2020. PMID: 32203133. IF=15.39

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer
Zhou S, Hawley JR, Soares F, Grillo G, Teng M, Madani Tonekaboni SA, Hua JT, Kron KJ, Mazrooei P, Ahmed M, Arlidge C, Yun HY, Livingstone J, Huang V, Yamaguchi TN, Espiritu SMG, Zhu Y, Severson TM, Murison A, Cameron S, Zwart W, van der Kwast T, Pugh TJ, Fraser M, Boutros PC, Bristow RG, He H, Lupien M
Nature Communications. 2020. PMID: 31974375. IF=12.35

Early-life programming of mesenteric lymph node stromal cell identity by the lymphotoxin pathway regulates adult mucosal immunity
Li C, Lam E, Perez-Shibayama C, Ward LA, Zhang J, Lee D, Nguyen A, Ahmed M, Brownlie E, Korneev KV, Rojas O, Sun T, Navarre W, He H, Liao S, Martin A, Ludewig B, Gommerman JL
Science Immunology. 2019. PMID: 31862865. IF=10.55

Gastrointestinal transcription factors drive lineage-specific developmental programs in organ specification and cancer
Francis R, Guo H, Yung T, Dirks PB, He H#, Kim TH#
Science Advances. 2019. PMID: 31844668. IF=12.8

Cistrome-partitioning reveals convergence of somatic mutations and risk-variants on master transcription regulators in primary prostate tumors
Mazrooei P, Kron K, Zhu Y, Zhou S, Grillo G, Mehdi T, Ahmed M, Severson TM, Guilhamon P, Armstrong NS, Huang V, Yamaguchi TN, Fraser M, van der Kwast T, Boutros PC, He H, Bergman A, Bristow RG, Zwart W, Lupien M
Cancer Cell. 2019. PMID: 31735626. IF=22.84

N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis
Kuppers D, Arora S, Lim Y, Lim A, Carter L, Corrin P, Plaisier C, Basom R, Delrow J, Wang S, He H, Torok-Storb B, Dr. Hsieh A, Paddison PJ
Nature Communications. 2019. PMID: 31601799. IF=12.35

Landscape of noncoding RNA in prostate cancer
Hua J, Chen S, He H
Trends in Genetics. 2019. PMID: 31623872. IF=6.98

ZBTB7A mediates the transcriptional repression activity of androgen receptor in prostate cancer
Han D, Chen S, Han W, Gao S, Owiredu J, Patalano S, Macoska J, Balk S, He H#, Cai C#
Cancer Research. 2019. PMID: 31444154. IF=9.13

Forkhead domain mutations in FOXA1 drive prostate cancer progression
Gao S, Chen S, Han D, Barrett D, Han W, Ahmed M, Patalano S, Macoska J, He H#, Cai C#
Cell Research. 2019. PMID: 31324883. IF=15.39

Genome-wide germline correlates of the epigenetic landscape of prostate cancer
Houlahan K, Shiah YJ, Gusev A, Yuan J, Ahmed M, Shettv A, Ramanand SG, Yao CQ, Bell C, C’Connor E, Huang V, Fraser M, Heisler LE, Livingstone J, Yamaguchi TN, Rouette A, Foucal A, Espiritu S, Sinha A, Sam M, Timms L, Johns J, Wong A, Murison A, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Lupien M, Fradet Y, Tetu B, McPherson JD, Pasaniuc B, Kislinger T, Chua TLK, Pomerantz M, van der Kwast T, Freedman ML, Mani RS, He H, Bristow RG#, Boutros PC#
Nature Medicine. 2019. PMID: 31591588. IF=32.62

Serum exosomal miRNA as non-invasive biomarkers to predict aggressive prostate cancer after radical prostatectomy
Hoey C, Ahmed M, Ghiam A, Fotouhighiam A, Vesprini D, Huang X, Commisso K, Commisso A, Loblaw DA, He H#, Liu S#
Journal of Translational Medicine. 2019. IF=3.8

DNA-dependent protein kinase drives prostate cancer progression through transcriptional regulation of the Wnt signaling pathway
Kothari V, Goodwin JF, Zhao SG, Drake JM, Yin Y, Chang SL, Evans JR, Wilder-Romans K, Gabbara K, Dylgjeri E, Chou J, Sun G, Tomlins SA, Mehra R, Hege K, Filvaroff EH, Schaeffer EM, Karnes RJ, Quigley DA, Rathkopf D, He H, Speers C, Spratt DE, Gilbert LA, Ashworth A, Chinnaiyan AM, Raj GV, Knudsen KE, Feng FY
Clin Cancer Res. 2019. PMID: 31266829. IF=10.20

Estrogen receptor signaling is reprogrammed during breast tumorigenesis
Chi D, Singhal H, Li L, Xiao T, Liu W, Pun M, Jeselsohn R, He H, Lim E, Vadhi R, Rao P, Long H, Garber J, Brown M
PNAS. 2019. PMID: 31110002. IF=9.42

Widespread and functional RNA circularization in localized prostate cancer
Chen S, Huang V, Xu Xin, Julie L, Soares F*, Jeon J, Zeng Y, Hua J, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua M, Heisler L, Foucal A, Fox N, Fraser M, Bhandari V, Shiah Y, Guan J, Orian M, Picar V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Tetu B, Liu S, Feng F, Wu X, Y Shao, Komor M, Sahinalp C, Collins C, Hoogstrate Y, Jong M, Fijneman R, Fei T, Jenster G, van der Kwat T, Bristow RG, Boutros P#, He H#
Cell. 2019. PMID: 30735634. IF=30.41

ONECUT2 is a driver of neuroendocrine prostate cancer
Guo H, Ci X, Ahmed M, Hua J, Soares F, Lin D, Puca L, Vosoughi A, Xue H, Li E, Su P, Chen S, Tran N, Liang Y, Zhang Y, Xu X, Xu J, Sheahan A, Ba-Alawi W, Zhang S, Mahamud O, Vellanki RN, Gleave M, Bristow RG, Haibe-Kains B, Poirier J, Rudin C, Tsao MS, Wouters BG, Fazli L, Feng F, Ellis L, Kwast T, Berlin A, Koritzinsky M, Boutros PC, Zoubeidi A, Beltran H, Wang YZ#, He H#
Nature Communications. 2019. PMID: 30655535. IF=12.35

TMPRSS2-ERG activates NO-cGMP signaling in prostate cancer cells
Zhou F, Gao S, Han D, Han W, Chen S, Patalano S, Macoska JA, He H, Cai C
Oncogene. 2019. PMID: 30718921. IF=8.56

Refined MeRIP-seq protocol for epitranscriptome analysis with low input materials
Wang S, Zeng Y, Soares F, Ahmed M, Guo H, Moran M, Tsao M, He H
PLOS Biology. 2018. PMID: 30212448. IF=9.80

Risk SNPs mediated promoter-enhancer switching drives prostate cancer through lncRNA PCAT19
Hua J, Ahmed M, Guo H, Zhang Y, Chen S, Soares F, Lu J, Zhou S, Wang M, Li H, Larson N, McDonnell S, Patel P, Liang Y, Yao CQ, Kwast T, Lupien M, Feng F, Zoubeidi A, Tsao M, Thibodeau SN, Boutros P, He H
Cell. 2018. PMID: 30033362. IF=30.41

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer
Quigley D, Dang H, Zhao S, Lloyd P, Aggarwal R, Alumkal J, Foye A, Kothari V, Perry M, Bailey A, Playdle D, Barnard T, Zhang L, Zhang J, Youngren J, Cieslik M, Parolia A, Beer T, Thomas G, Chi K, Gleave M, Lack N, Zoubeidi A, Reiter R, Rettig M, Witte O, Ryan C, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodazi H, Gilbert L, Lara P, Evans C, Goldstein T, Stuart J, Tomlins S, Spratt D, Cheetham K, Cheng D, Farh K, Gehring J, Hakenberg J, Liao A, Febbo P, Shon J, Batzoglou S, Knudsen K, He H, Huang J, Wyatt A, Dehm S, Ashworth A, Chinnaiyan A, Maher C, Small E, Feng F
Cell. 2018. PMID: 30033370. IF=30.41

LSD1 Ablation in Tumor Cells Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade
Sheng W, LaFleur M, Nguyen T, Chen S, Chakravarthy A, Conway J, Li Y, Chen H, Yang H, Hsu P, Allen E, Freeman G, De Carvalho D, He H, Sharpe A, Shi Y
Cell. 2018. PMID: 29937226. IF=30.41

A heterochromatin gene signature unveils HP1α mediating neuroendocrine prostate cancer development and aggressiveness
Ci X, Hao J, Dong X, Choi S, Xue H, Wu R, Qu S, Gout PW, Fang Zhang F, Haegert AM, Fazli L, Crea F, Ong C, Zoubeidi A, He H, Gleave M, Collins C, Lin D, Wang YZ
Cancer Research. 2018. PMID: 29487201. IF =9.28

Reactivation of Androgen Receptor-Regulated Lipid Biosynthesis Drives the Progression of Castration-Resistant Prostate Cancer
Han W, Gao S, Barrett D, Han D, Macoska J, Ahemd M, He H#, Cai C#
Oncogene. 2017. PMID: 29059155. IF=8.56

LSD1 Mediated Epigenetic Reprogramming Drives CENPE Expression and Prostate Cancer Progression
Liang Y, Ahmed M, Guo H, Soares F, Hua J, Gao S, Lu C, Poon C, Langstein J, Ekram M, Li B, Davicioni E, Takhar M, Erho N, Karnes R, Chadwick D, Kwast T, Boutors P, Arrowsmith C, Feng FY, Joshua A, Cai C, He H#
Cancer Research. 2017. PMID: 28916652. IF=9.28

Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing
Fei T, Chen Y, Xiao T, Li W, Cato L, Zhang P, Cotter MB, Bowden M, Rosina LT, Zhao SG, Wu Q, Feng Y, Loda M, He H, Liu X, Brown M
PNAS. 2017. PMID: 28611215. IF=9.42

Transcriptional Landscape of the Breast Cancer Cell Cycle
Liu Y, Chen S, Wang S, Soares F, Fischer M, Meng F, Du Z, Lin C, Meyer C, Decaprio JA, Brown M#, Liu X#, He H#
PNAS. 2017. PMID: 28289232. IF=9.42

Variant Set Enrichment: A Fast Method to Identify Disease-Associated Functional Genomic Regions
Ahmed M, Sallari R, Guo H, Moore J, He H#, Lupien M#
BioData Mining. 2017. PMID: 28239419. IF=1.64

Noncoding RNA for personalized prostate cancer treatment: utilize the “dark matters” of the genome?
Hua J, Lu J, Isaev K, Ahmed M, Guo H, Soares F, He H#
Personalized Medicine. 2017. IF=1.00

K48-linked ubiquitination of KLF4 by the E3 ligase Mule controls T cell proliferation through cell cycle regulation
Hao ZY, Sheng Y, Li WY, Duncan GS, Sylvester J, Lin GHY, Snow BE, Brenner D, You-Ten A, Su YW, Haight J, Inoue S, Wakeham A, Elford A, Hamilton S, Liang Y, Zuniga-Pflucker JC, He H, Ohashi PS, Mak TW
Nature Communications. 2017. PMID: 28084302. IF=11.33

Genomic hallmarks of localized, non-indolent prostate cancer
Fraser M, Sabelnykov V.Y, Yamaguchi T.N, Heisler L.E, Livingstone J, Huang W,… He H, Fradet Y, Tetu B, Kwast T, McPherson J.D, Bristow R.G, Boutros P.C.
Nature. 2016. PMID: 28068672. IF=38.14

Androgen Receptor Tumor Suppressor Function Mediated by Recruitment of Retinoblastoma Protein
Gao Y, Gao S, He H, Liu X, Chen S, Ma F, Liu X.S, Brown M, Balk S, Chen S, Cai C
Cell Reports. 2016. PMID: 27760327. IF=7.87

Modulation of long noncoding RNAs underlying genetic predispositions to prostate cancer
Guo H, Ahmed M, Zhang F, Yao CQ, Liang Y, Hua J, Soares F, Sun Y, Langstein J, Li Y, Poon C, Bailey S, Desai K, Fei T, Li Q, Sendorek DH, Fraser M, Prensner JR, Pugh TJ, Pomerantz M, Bristow RG, Lupien M, Feng FY, Boutros PC, Freedman ML, Walsh MJ, He H#.
Nature Genetics. 2016. PMID: 27526323. IF=31.62

Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles
Wang S, Zang C, Xiao T, Fan J, Mei S, Qian Q, Wu Q, Xu K, He H, Brown M, Meyer CA, Liu X.S
Genome Research. 2016. PMID: 27466232. IF=11.35

High-dimensional genomic data bias correction and data integration using MANCIE
Zang C, Wang T, Deng K, Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He H, Brown M, Liu J, Xie Y, Liu X
Nature communications. 2016. PMID: 27072482. IF=11.33

SOX9 drives WNT pathway activation in Prostate Cancer
Ma F, Ye H, He H, Gerrin SJ, Chen S, Tanenbaum BA, Cai C, Sowalsky A, He L, Wang H, Balk SP, Yuan X
J Clin Invest. 2016. PMID: 27043282. IF=12.58

Response and resistance to BET bromodomain inhibitors in triple negative breast cancer
Shu S, Lin CY, He H, Doherty E, Brown J, Mohammed H, D’Santos C, Mckeown M, Ott C, Qi J, Ni M, Rao PK, Duarte M, Chiang C, Anders L, Young RA, Carroll JS, Long H, Brown M, Liu XS, Meyer CA, Bradner JE, Polyak K
Nature. 2016. PMID: 26735014. IF=38.14

Integrative Analysis Revealed the collaboration between EZH2 and E2F1 in transcriptional regulation of cancer-related genes
Xu H, Xu K, He H, Zang C, Chen C, Chen Y, Qin Q, Wang S, Wang C, Hu S, Li F, Long H, Brown M, Liu X.S
Molecular Cancer Research. 2015. PMID: 26659825. IF=4.50

PLZF, a Tumor Suppressor Genetically Lost in Metastatic Castration-Resistant Prostate Cancer, Is a Mediator of Resistance to Androgen Deprivation Therapy
Hsieh CL, Botta G, Gao S, Li T, Van Allen EM, Treacy DJ, Cai C, He H, Sweeney CJ, Brown M, Balk SP, Nelson PS, Garraway LA, Kantoff PW
Cancer Res. 2015. PMID: 25808865. IF=9.28

Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity
Cai C#, He H#, Chen S, Yu Z, Gao Y, Chen S, Schüle R, Liu X.S, Brown M and Balk S.P
Cell Reports. 2014. PMID: 25482560. IF=7.21

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
He H, Meyer CA, Hu SS, Chen MW, Zang CZ, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M
Nature Methods. 2014. PMID: 24317252. IF=25.95