Publications

* first author, # corresponding author

2024

  1. Mohammed Ismail W, Fernandez J, Binder M, Lasho TL, Kim M, Geyer S, Mazzone A, Finke CM, Mangaonkar AA, Lee JH, Wang L , Kim KH, Simon VA, Rakhshan Rohakthar F, Munankarmy A, Byeon SK, Schwager SM, Harington JJ, Snyder MR, Robertson KD, Pandey A, Wieben ED, Chia N, Gaspar-Maia A, Patnaik MM. Single cell multiomics reveal divergent effects of DNMT3A and TET2 mutant clonal hematopoiesis in inflammatory response. Blood Adv. 2024 Dec 4. doi: 10.1182/bloodadvances.2024014467.

  2. Gomez PT, Carver CM, Rodriguez SL, Wang L, Zhang X, Schafer MJ. Aging and senescent fates of oligodendrocyte precursor cells in the mouse brain. NPJ Aging. 2024 Oct 22;10(1):47. doi: 10.1038/s41514-024-00176-y.

  3. Li Q, Zhang Y, Luo S, Zhang Z, Oberg L. A, Kozono E. D, Lu H, Sarkaria N. J, Ma L#, and Wang L #. Identify Non-mutational p53 Functional Deficiency in Human Cancers. Genomics Proteomics Bioinformatics. 2024 Sep 26. doi: 10.1093/gpbjnl/qzae064.

  4. Hlady RA, Zhao X, El Khoury LY, Wagner RT, Luna A, Pham K, Pyrosopoulos NT, Jain D, Wang L, Liu C, Robertson KD. Epigenetic heterogeneity hotspots in human liver disease progression. Hepatology. 2024 Jul 19;. doi: 10.1097/HEP.0000000000001023

  5. Chiang CC, Schwedt TJ, Dumkrieger G, Wang L, Chao CJ, Ouellette HA, Banerjee I, Chen YC, Jones BM, Burke KM, Wang H, Murray AM, Montenegro MM, Stern JI, Whealy M, Kissoon N, Cutrer FM. Advancing toward precision migraine treatment: Predicting responses to preventive medications with machine learning models based on patient and migraine features. Headache. 2024 Aug 23. doi: 10.1111/head.14806.

2023

  1. Santasusagna S, Zhu S, Jawalagatti V, Carceles-Cordon M, Ertel A, Garcia-Longarte S, Song WM, Fujiwara N, Li P, Mendizabal I, Petrylak DP, Kelly WK, Reddy EP, Wang L, Schiewer MJ, Lujambio A, Karnes J, Knudsen KE, Cordon-Cardo C, Dong H, Huang H, Carracedo A, Hoshida Y, Rodriguez-Bravo V, Domingo-Domenech J. Master transcription factor reprograming unleashes selective translation promoting castration resistance and immune evasion in lethal prostate cancer. Cancer Discov. 2023 Sep 7;. doi: 10.1158/2159-8290.CD-23-0306.

  2. Wang L#. Reference-guided search for open reading frames. Nature Computational Science. doi: 10.1038/s43588-023-00497-0

  3. Ma T, Guo L, Yan H, and Wang L#. Cobind: quantitative analysis of the genomic overlaps. Bioinformatics Advances, 2023 Aug 7;3(1):vbad104. doi: 10.1093/bioadv/vbad104

  4. Ding D, Blee AM, Zhang J, Pan Y, Becker NA, Maher LJ III, Jimenez R, Wang L#, Huang H. Gain-of-function mutant p53 together with ERG proto-oncogene drive prostate cancer by beta-catenin activation and pyrimidine synthesis. Nat Commun 14, 4671 (2023). https://doi.org/10.1038/s41467-023-40352-4

  5. Zhang J, Wei J, Sun R, Sheng H, Yin K, Pan Y, Jimenez R, Chen S, Cui XL, Zou Z, Yue Z, Emch MJ, Hawse JR, Wang L, He HH, Xia S, Han B, He C, Huang H. A lncRNA from the FTO locus acts as a suppressor of the m(6)A writer complex and p53 tumor suppression signaling. Mol Cell. 2023 Jul 12:S1097-2765(23)00471-9. doi: 10.1016/j.molcel.2023.06.024.

  6. Sun R, Yan B, Li H, Ding D, Wang L, Pang J, Ye D, Huang H. Androgen receptor variants confer castration resistance in prostate cancer by counteracting antiandrogen-induced ferroptosis. Cancer Res. 2023 Aug 1:CAN-23-0285. doi: 10.1158/0008-5472.CAN-23-0285.

  7. Wang T, Wagner R, Hlady R, Pan X, Zhao X, Kim S, Wang L, Lee J, Luo H, Castle EP, Ho T, Robertson K. SETD2 loss in renal epithelial cells drives epithelial to mesenchymal transition in a TGF-β independent manner. Mol Oncol. 2023 Jul 7. doi: 10.1002/1878-0261.13487

  8. Sperger J, Helzer K, Stahlfeld K, Jiang D, Singh A, Kaufmann K, Niles D, Heninger E, Rydzewski N, Wang L, Wang L, Yang R, Ren Y, Engle J, Huang P, Kyriakopoulos, C, Slovin S, Soule H, Zhao S, Kohli M, Tagawa S, Cai W, Dehm S, and Lang J. Expression and therapeutic targeting of Trop-2 in treatment resistant prostate cancer. Clin Cancer Res. 2023 Mar 20:CCR-22-1305. doi: 10.1158/1078-0432.CCR-22-1305.

  9. El Khoury LY, Pan X, Hlady RA, Wagner RT, Shaikh S, Wang L, Humphreys MR, Castle EP, Stanton ML, Ho TH, Robertson KD. Extensive intratumor regional epigenetic heterogeneity in clear cell renal cell carcinoma targets kidney enhancers and is associated with poor outcome. Clin Epigenetics. 2023 Apr 29;15(1):71. doi: 10.1186/s13148-023-01471-3.

2022

  1. Li Q, Zhang Y, Zhang Z, Oberg L. A, Kozono E. D, Lu H, Sarkaria N. J, Ma L, and Wang L#. Identify non-mutational p53 loss of function in human cancers. (Submitted)

  2. Ding D, Zheng R, Tian Y, Jimenez R, Hou X, Weroha S, Wang L, Lei S, Huang H. Retinoblastoma protein as an intrinsic BRD4 inhibitor modulates small molecule BET inhibitor sensitivity in cancer. Nat Commun. 2022 Oct 23;13(1):6311. doi: 10.1038/s41467-022-34024-y.

  3. Larson NB, Oberg AL, Adjei AA, Wang L. A clinician’s guide to bioinformatics for next-generation sequencing. J Thorac Oncol. 2022 Nov 12;S1556-0864(22)01908-6. doi: 10.1016/j.jtho.2022.11.006

  4. Yanchus C, Drucker KL, Kollmeyer TM, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo SB, Ali A, Decker PA, Kosel ML, Panda A, Al-Zahrani KN, Jiang L, Browning JWL, Lowden C, Geuenich M, Hernandez JJ, Gosio JT, Ahmed M, Loganathan SK, Berman J, Trcka D, Michealraj KA, Fortin J, Carson B, Hollingsworth EW, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He HH, Murphy DJ, Wang L, Abyzov A, Dennis JW, Maass PG, Campbell K, Wilson MD, Lachance DH, Wrensch M, Wiencke J, Mak T, Pennacchio LA, Dickel DE, Visel A, Wrana J, Taylor MD, Zadeh G, Dirks P, Eckel-Passow JE, Attisano L, Pombo A, Ida CM, Kvon EZ, Jenkins RB, Schramek D. A non-coding single nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science. 2022 Oct 6;. doi: 10.1126/science.abj2890

  5. Sun R, Wei T, Ding D, Zhang J, Chen S, He H. H, Wang L, Huang H. CYCLIN K downregulation induces androgen receptor gene intronic polyadenylation and castration resistance in prostate cancer. Proc Natl Acad Sci U S A. 2022 Sep 27;119(39):e2205509119. doi: 10.1073/pnas.2205509119.

2021

  1. Ma J, Shi Q, Cui G, Sheng H, Botuyan MV, Zhou Y, Yan Y, He Y, Wang L, Wang Y, Mer G, Ye D, Wang C, Huang H. SPOP mutation induces replication over-firing by impairing Geminin ubiquitination and triggers replication catastrophe upon ATR inhibition. Nat Commun. 2021 Oct 1;12(1):5779. doi: 10.1038/s41467-021-26049-6.

  2. Zhang J, Gao K, Xie H, Wang D, Zhang P, Wei T, Yan Y, Pan Y, Ye W, Chen H, Shi Q, Li Y, Zhao SM, Hou X, Weroha SJ, Wang Y, Zhang J, Karnes RJ, He HH, Wang L, Wang C, Huang H. SPOP mutation induces DNA methylation via stabilizing GLP/G9a8. Nat Commun. 2021 Sep 29;12(1):5716. DOI: 10.1038/s41467-021-25951-3.

  3. Lavoie RR, Gargollo PC, Ahmed ME, Kim Y, Baer E, Phelps DA, Charlesworth CM, Madden BJ, Wang L, Houghton PJ, Cheville J, Dong H, Granberg CF, Lucien F. Surfaceome Profiling of Rhabdomyosarcoma Reveals B7-H3 as a Mediator of Immune Evasion. Cancers. 2021; 13(18):4528. doi: https://doi.org/10.3390/cancers13184528.

  4. Wu D, Wang L, Huang H. Protocol to apply spike-in ChIP-seq to capture massive histone acetylation in human cells. STAR Protocols 2021 Jul 17; doi: 10.1016/j.xpro.2021.100681.

  5. Wei T, Lu J, Ma T, Huang H, Kocher JP, Wang L#. Re-evaluate fusion genes in prostate cancer. Cancer Informatics 2021 Jun 21; doi: 10.1177/11769351211027592.

  6. Huang Z, Tang B, Yang Y, Yang Z, Shi L, Bai Y, Yan B, Karnes RJ, Zhang J, Jimenez R, Wang L, Wei Q, Yang J, Xu W, Jia Z, Huang H. MAP3K7-IKK inflammatory signaling modulates AR protein degradation and prostate cancer progression. Cancer Res. 2021 Jun 22:canres.4194.2020. doi: 10.1158/0008-5472.CAN-20-4194.

  7. Wang D, Ma J, Botuyan MV, Cui G, Yan Y, Ding D, Zhou Y, Krueger EW, Pei J, Wu X, Wang L , Pei H, McNiven MA, Ye D, Mer G, Huang H. ATM-phosphorylated SPOP contributes to 53BP1 exclusion from chromatin during DNA replication. Sci Adv. 2021 Jun; 7 (25) Epub 2021 June 18. doi: 10.1126/sciadv.abd9208

  8. He Y, Wang L, Wei T, Xiao YT, Sheng H, Su H, Hollern DP, Zhang X, Ma J, Wen S, Xie H, Yan Y, Pan Y, Hou X, Tang X, Suman VJ, Carter JM, Weinshilboum R, Wang L, Kalari KR, Weroha SJ, Bryce AH, Boughey JC, Dong H, Perou CM, Ye D, Goetz MP, Ren S, Huang H. FOXA1 overexpression suppresses interferon signaling and immune response in cancer. J Clin Invest. 2021 Jun 8 Epub 2021 June 08. doi: 10.1172/JCI147025

  9. Zhou Y, Jin X, Ma J, Ding D, Huang Z, Sheng H, Yan Y, Pan Y, Wei T, Wang L, Wu H, Huang H. HDAC5 loss impairs RB repression of pro-oncogenic genes and confers CDK4/6 inhibitor resistance in cancer. Cancer Res. 2021 Jan 8;. doi: 10.1158/0008-5472.CAN-20-2828.

  10. El Khoury LY, Fu S, Hlady RA, Wagner RT, Wang L, Eckel-Passow JE, Castle EP, Stanton ML, Thompson RH, Parker AS, Ho TH, Robertson KD. Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer. Clin Epigenetics 2021 Jan 18; 13(1):12. doi: 10.1186/s13148-020-00998-z.

  11. Wu D, Yan Y, Wei T, Ye Z, Xiao Y, Pan Y, Orme J, Wang D, Wang L#, Ren S#, Huang H#. An acetyl-histone vulnerability in PI3K/AKT inhibition-resistant cancers is targetable by both BET and HDAC inhibitors. Cell Rep. 2021 Feb 16;34(7):108744. doi: 10.1016/j.celrep.2021.108744.

  12. Tang B, Sun R, Wang D, Sheng H, Wei T, Wang L, Zhang J, Ho TH, Yang L, Wei Q, Huang H. ZMYND8 preferentially binds phosphorylated EZH2 to promote a PRC2-dependent to -independent function switch in hypoxia-inducible factor–activated cancer. Proc Natl Acad Sci USA February 23, 2021 118 (8) e2019052118; doi: 10.1073/pnas.2019052118.

  13. He Y, Wei T, Ye Z, Orme JJ, Lin D, Sheng H, Fazli L, Jeffrey Karnes R, Jimenez R, Wang L, Wang L, Gleave ME, Wang Y, Shi L, Huang H. A noncanonical AR addiction drives enzalutamide resistance in prostate cancer. Nat Commun. 2021 Mar 9; 12 (1):1521 Epub 2021 Mar 09. doi: 10.1038/s41467-021-21860-7.

  14. X Xu, B Wang, Z Jiang, Q Chen, K Mao, X Shi, C Yan, J Hu, Y Zha, C Ma, Zhang J, Guo R, Wang L, Zhao S, Liu H, Zhang Q, Zhang Y. Novel risk factors for craniofacial microsomia and assessment of their utility in clinic diagnosis. Hum Mol Genet. 2021 Feb 22;ddab055. doi:10.1093/hmg/ddab055.

  15. Cutrer FM, Moyer A, Atkinson E, Wang L, Tian S, Wu Y, Garza I, Robertson C, Huebert C, Moore B, Klein CJ. Genetic variants related to successful migraine prophylaxis with verapamil. Molecular Genetics & Genomic Medicine 2021 Apr 7. doi:https://doi.org/10.1002/mgg3.1680.

2020

  1. Du M, Tian Y, Tan W, Wang L, Wang L, Kilari D, Huang CC, Wang L, Kohli M. Plasma cell-free DNA-based predictors of response to abiraterone acetate/prednisone and prognostic factors in metastatic castration-resistant prostate cancer. Prostate Cancer Prostatic Dis. 2020 Mar 18. doi: 10.1038/s41391-020-0224-4.

  2. Liu L, Wang G, Wang L, Yu C, Li M, Song S, Hao L, Ma L, Zhang Z. Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling. Biol Direct. 2020 Jun 15; 15 (1):10 Epub 2020 June 15. doi: 10.1186/s13062-020-00264-5.

  3. Li Y, Wang L#. RNA Coding Potential Prediction Using Alignment-Free Logistic Regression Model. Methods Mol Biol (book chapter). 2020 Dec 17. doi: 10.1007/978-1-0716-1158-6_3.

2019

  1. Wei T, Nie J, Larson NB, Ye Z, Eckel Passow JE, Robertson KD, Kocher JA, Wang L#. CpGtools: A Python Package for DNA Methylation Analysis. Bioinformatics. 2019 Dec 6 Epub 2019 Dec 06. doi: 10.1093/bioinformatics/btz916.

  2. Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi AA, Bajic VB, Ma L, Zhang Z. Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics. 2019 Sep 1; 35 (17):2949-2956. doi: 10.1093/bioinformatics/btz008.

  3. Wang L*, Marek GW 3rd*, Hlady RA*, Wagner RT, Zhao X, Clark VC, Fan AX, Liu C, Brantly M, Robertson KD. Alpha-1 Antitrypsin Deficiency Liver Disease, Mutational Homogeneity Modulated by Epigenetic Heterogeneity With Links to Obesity. Hepatology. 2019 Jul; 70 (1):51-66 Epub 2019 Mar 20. doi: 10.1002/hep.30526.

  4. Zhao Y, Ding L, Wang D, Ye Z, He Y, Ma L, Zhu R, Pan Y, Wu Q, Pang K, Hou X, Weroha SJ, Han C, Coleman R, Coleman I, Karnes RJ, Zhang J, Nelson PS, Wang L, Huang H. EZH2 cooperates with gain-of-function p53 mutants to promote cancer growth and metastasis. EMBO J. 2019 Mar 1; 38 (5) Epub 2019 Feb 05. doi: 10.15252/embj.201899599.

  5. Jimenez RE, Atwell TD, Sicotte H, Eckloff B, Wang L, Barman P, Sinnwell JP, Eiken PW, McMenomy BP, Tan W, Wang L, Carlson RE, Kohli M. A Prospective Correlation of Tissue Histopathology With Nucleic Acid Yield in Metastatic Castration-Resistant Prostate Cancer Biopsy Specimens. Mayo Clin Proc Innov Qual Outcomes. 2019 Mar; 3 (1):14-22 Epub 2019 Feb 26. doi: 10.1016/j.mayocpiqo.2018.12.005.

  6. Jin X, Ding D, Yan Y, Li H, Wang B, Ma L, Ye Z, Ma T, Wu Q, Rodrigues DN, Kohli M, Jimenez R, Wang L, Goodrich DW, de Bono J, Dong H, Wu H, Zhu R, Huang H. Phosphorylated RB Promotes Cancer Immunity by Inhibiting NF-kappaB Activation and PD-L1 Expression. Mol Cell. 2019 Jan 3; 73 (1):22-35.e6 Epub 2018 Dec 06. Doi: 10.1016/j.molcel.2018.10.034.

  7. Ma T, Ye Z, Wang L#. Genome Wide Approaches to Identify Protein-DNA Interactions. Curr Med Chem. 2019; 26 (42):7641-7654. doi: 10.2174/0929867325666180530115711.

2018

  1. Blee AM, He Y, Yang Y, Ye Z, Yan Y, Pan Y, Ma T, Dugdale J, Kuehn E, Kohli M, Jimenez R, Chen Y, Xu W, Wang L#, Huang H. TMPRSS2-ERG Controls Luminal Epithelial Lineage and Antiandrogen Sensitivity in PTEN and TP53-Mutated Prostate Cancer. Clin Cancer Res. 2018 Sep 15;24(18):4551-4565. doi: 10.1158/1078-0432.CCR-18-0653.

  2. Kohli M, Li J, Du M, Hillman DW, Dehm SM, Tan W, Carlson R, Campion MB, Wang L, Wang L, Zhang H, Zhang P, Kilari D, Huang CC, Wang L. Prognostic association of plasma cell-free DNA-based androgen receptor amplification and circulating tumor cells in pre-chemotherapy metastatic castration-resistant prostate cancer patients. Prostate Cancer Prostatic Dis. 2018 Sep;21(3):411-418. doi: 10.1038/s41391-018-0043-z.

  3. Xu Y, Lee JH, Li Z, Wang L, Ordog T, Bailey RC. A droplet microfluidic platform for efficient enzymatic chromatin digestion enables robust determination of nucleosome positioning. Lab Chip. 2018 Aug 21;18(17):2583-2592. doi: 10.1039/c8lc00599k.

  4. Jin X, Yan Y, Wang D, Ding D, Ma T, Ye Z, Jimenez R, Wang L, Wu H, Huang H. DUB3 Promotes BET Inhibitor Resistance and Cancer Progression by Deubiquitinating BRD4. Mol Cell. 2018 Aug 16;71(4):592-605.e4. doi: 10.1016/j.molcel.2018.06.036.

  5. Gao P, Xia JH, Sipeky C, Dong XM, Zhang Q, Yang Y, Zhang P, Cruz SP, Zhang K, Zhu J, Lee HM, Suleman S, Giannareas N, Liu S, Tammela TLJ, Auvinen A, Wang X, Huang Q, Wang L, Manninen A, Vaarala MH, Wang L, Schleutker J, Wei GH, PRACTICAL Consortium. Biology and Clinical Implications of the 19q13 Aggressive Prostate Cancer Susceptibility Locus. Cell. 2018 Jul 26;174(3):576-589.e18. doi: 10.1016/j.cell.2018.06.003.

  6. Ye Z, Dong H, Li Y, Ma T, Huang H, Leong HS, Eckel-Passow J, Kocher JA, Liang H, Wang L#. Prevalent Homozygous Deletions of Type I Interferon and Defensin Genes in Human Cancers Associate with Immunotherapy Resistance. Clin Cancer Res. 2018 Jul 15;24(14):3299-3308. doi: 10.1158/1078-0432.CCR-17-3008.

  7. Qin S, Liu D, Kohli M, Wang L, Vedell PT, Hillman DW, Niu N, Yu J, Weinshilboum RM, Wang L. TSPYL Family Regulates CYP17A1 and CYP3A4 Expression: Potential Mechanism Contributing to Abiraterone Response in Metastatic Castration-Resistant Prostate Cancer. Clin Pharmacol Ther. 2018 Jul;104(1):201-210. doi: 10.1002/cpt.907.

  8. Yan Y, An J, Yang Y, Wu D, Bai Y, Cao W, Ma L, Chen J, Yu Z, He Y, Jin X, Pan Y, Ma T, Wang S, Hou X, Weroha SJ, Karnes RJ, Zhang J, Westendorf JJ, Wang L, Chen Y, Xu W, Zhu R, Wang D, Huang H. Dual inhibition of AKT-mTOR and AR signaling by targeting HDAC3 in PTEN- or SPOP-mutated prostate cancer. EMBO Mol Med. 2018 Apr;10(4):e8478. doi: 10.15252/emmm.201708478.

  9. Ren S*, Wei GH*, Liu D*, Wang L*, Hou Y, Zhu S, Peng L, Zhang Q, Cheng Y, Su H, Zhou X, Zhang J, Li F, Zheng H, Zhao Z, Yin C, He Z, Gao X, Zhau HE, Chu CY, Wu JB, Collins C, Volik SV, Bell R, Huang J, Wu K, Xu D, Ye D, Yu Y, Zhu L, Qiao M, Lee HM, Yang Y, Zhu Y, Shi X, Chen R, Wang Y, Xu W, Cheng Y, Xu C, Gao X, Zhou T, Yang B, Hou J, Liu L, Zhang Z, Zhu Y, Qin C, Shao P, Pang J, Chung LWK, Xu J, Wu CL, Zhong W, Xu X, Li Y, Zhang X, Wang J, Yang H, Wang J, Huang H, Sun Y. Whole-genome and Transcriptome Sequencing of Prostate Cancer Identify New Genetic Alterations Driving Disease Progression. Eur Urol. 2018 Mar;73(3):322-339. doi: 10.1016/j.eururo.2017.08.027.

  10. He Y, Lu J, Ye Z, Hao S, Wang L, Kohli M, Tindall DJ, Li B, Zhu R, Wang L#, Huang H. Androgen receptor splice variants bind to constitutively open chromatin and promote abiraterone-resistant growth of prostate cancer. Nucleic Acids Res. 2018 Feb 28;46(4):1895-1911. doi: 10.1093/nar/gkx1306.

  11. Wang L*, Dehm SM, Hillman DW, Sicotte H, Tan W, Gormley M, Bhargava V, Jimenez R, Xie F, Yin P, Qin S, Quevedo F, Costello BA, Pitot HC, Ho T, Ho T, Bryce AH, Ye Z, Li Y, Eiken P, Vedell PT, Barman P, McMenomy BP, Atwell TD, Carlson RE, Ellingson M, Eckloff BW, Qin R, Ou F, Hart SN, Huang H, Jen J, Wieben ED, Kalari KR, Weinshilboum RM, Wang L, Kohli M. A prospective genome-wide study of prostate cancer metastases reveals association of wnt pathway activation and increased cell cycle proliferation with primary resistance to abiraterone acetate-prednisone. Ann Oncol. 2018 Feb 1;29(2):352-360. doi: 10.1093/annonc/mdx689.

  12. He Y, Zhao Y, Wang L, Bohrer LR, Wang L, Pan Y, Wang L, Huang H. LSD1 promotes S-phase entry and tumorigenesis via chromatin co-occupation with E2F1 and selective H3K9 demethylation. Oncogene. 2018 Jan 25;37(4):534-543. doi: 10.1038/onc.2017.353.

2017

  1. Zhang X, Saarinen AM, Hitosugi T, Wang Z, Wang L, Ho TH, Liu J. Inhibition of intracellular lipolysis promotes human cancer cell adaptation to hypoxia. Elife. 2017 Dec 19;6:e31132. doi: 10.7554/eLife.31132.

  2. Zhang P, Wang D, Zhao Y, Ren S, Gao K, Ye Z, Wang S, Pan CW, Zhu Y, Yan Y, Yang Y, Wu D, He Y, Zhang J, Lu D, Liu X, Yu L, Zhao S, Li Y, Lin D, Wang Y, Wang L, Chen Y, Sun Y, Wang C, Huang H. Intrinsic BET inhibitor resistance in SPOP-mutated prostate cancer is mediated by BET protein stabilization and AKT-mTORC1 activation. Nat Med. 2017 Sep;23(9):1055-1062. doi: 10.1038/nm.4379.

  3. Jin X, Pan Y, Wang L, Ma T, Zhang L, Tang AH, Billadeau DD, Wu H, Huang H. Fructose-1,6-bisphosphatase Inhibits ERK Activation and Bypasses Gemcitabine Resistance in Pancreatic Cancer by Blocking IQGAP1-MAPK Interaction. Cancer Res. 2017 Aug 15;77(16):4328-4341. doi: 10.1158/0008-5472.CAN-16-3143.

  4. Kohli M, Ho Y, Ho Y, Hillman DW, Van Etten JL, Henzler C, Yang R, Sperger JM, Li Y, Tseng E, Hon T, Clark T, Tan W, Carlson RE, Wang L, Sicotte H, Thai H, Jimenez R, Huang H, Vedell PT, Eckloff BW, Quevedo JF, Pitot HC, Costello BA, Jen J, Wieben ED, Silverstein KAT, Lang JM, Wang L, Dehm SM. Androgen Receptor Variant AR-V9 Is Coexpressed with AR-V7 in Prostate Cancer Metastases and Predicts Abiraterone Resistance. Clin Cancer Res. 2017 Aug 15;23(16):4704-4715. doi: 10.1158/1078-0432.CCR-17-0017.

  5. Ye Z, Ma T, Kalmbach MT, Dasari S, Kocher JA, Wang L#. CircularLogo: A lightweight web application to visualize intra-motif dependencies. BMC Bioinformatics. 2017 May 22;18(1):269. doi: 10.1186/s12859-017-1680-2.

  6. Pan CW, Jin X, Zhao Y, Pan Y, Yang J, Karnes RJ, Zhang J, Wang L, Huang H. AKT-phosphorylated FOXO1 suppresses ERK activation and chemoresistance by disrupting IQGAP1-MAPK interaction. EMBO J. 2017 Apr 13;36(8):995-1010. doi: 10.15252/embj.201695534.

  7. Jin X, Pan Y, Wang L, Zhang L, Ravichandran R, Potts PR, Jiang J, Wu H, Huang H. MAGE-TRIM28 complex promotes the Warburg effect and hepatocellular carcinoma progression by targeting FBP1 for degradation. Oncogenesis. 2017 Apr 10;6(4):e312. doi: 10.1038/oncsis.2017.21.

  8. McNair C, Urbanucci A, Comstock CE, Augello MA, Goodwin JF, Launchbury R, Zhao SG, Schiewer MJ, Ertel A, Karnes J, Davicioni E, Wang L, Wang Q, Mills IG, Feng FY, Li W, Carroll JS, Knudsen KE. Cell cycle-coupled expansion of AR activity promotes cancer progression. Oncogene. 2017 Mar 23;36(12):1655-1668. doi: 10.1038/onc.2016.334.

  9. Ho TH, Serie DJ, Parasramka M, Cheville JC, Bot BM, Tan W, Wang L, Joseph RW, Hilton T, Leibovich BC, Parker AS, Eckel-Passow JE. Differential gene expression profiling of matched primary renal cell carcinoma and metastases reveals upregulation of extracellular matrix genes. Ann Oncol. 2017 Mar 1;28(3):604-610. doi: 10.1093/annonc/mdw652.

2016

  1. He Y, Peng S, Wang J, Chen H, Cong X, Chen A, Hu M, Qin M, Wu H, Gao S, Wang L, Wang X, Yi Z, Liu M. Ailanthone targets p23 to overcome MDV3100 resistance in castration-resistant prostate cancer. Nat Commun. 2016 Dec 13;7:13122. doi: 10.1038/ncomms13122.

  2. Zhao J, Zhao Y, Wang L, Wang L, Zhang J, Karnes RJ, Kohli M, Wang G, Huang H. Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer. Oncotarget. 2016 Jun 21;7(25):38551-38565. doi: 10.18632/oncotarget.9535.

  3. Blee AM, Liu S, Wang L, Huang H. BET bromodomain-mediated interaction between ERG and BRD4 promotes prostate cancer cell invasion. Oncotarget. 2016 Jun 21;7(25):38319-38332. doi: 10.18632/oncotarget.9513.

  4. Pan CW, Liu H, Zhao Y, Qian C, Wang L, Qi J. JNK2 downregulation promotes tumorigenesis and chemoresistance by decreasing p53 stability in bladder cancer. Oncotarget. 2016 Jun 7;7(23):35119-31. doi: 10.18632/oncotarget.9046.

  5. Zhao Y, Wang L, Ren S, Wang L, Blackburn PR, McNulty MS, Gao X, Qiao M, Vessella RL, Kohli M, Zhang J, Karnes RJ, Tindall DJ, Kim Y, MacLeod R, Ekker SC, Kang T, Sun Y, Huang H. Activation of P-TEFb by Androgen Receptor-Regulated Enhancer RNAs in Castration-Resistant Prostate Cancer. Cell Rep. 2016 Apr 19;15(3):599-610. doi: 10.1016/j.celrep.2016.03.038.

  6. Hart SN, Ellingson MS, Schahl K, Vedell PT, Carlson RE, Sinnwell JP, Barman P, Sicotte H, Eckel-Passow JE, Wang L, Kalari KR, Qin R, Kruisselbrink TM, Jimenez RE, Bryce AH, Tan W, Weinshilboum R, Wang L, Kohli M. Determining the frequency of pathogenic germline variants from exome sequencing in patients with castrate-resistant prostate cancer. BMJ Open. 2016 Apr 15;6(4):e010332. doi: 10.1136/bmjopen-2015-010332.

  7. Wang L*, Nie J*, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JP. Measure transcript integrity using RNA-seq data. BMC Bioinformatics. 2016 Feb 3;17:58. doi: 10.1186/s12859-016-0922-z.

2015

  1. Wang D, Ding L, Wang L, Zhao Y, Sun Z, Karnes RJ, Zhang J, Huang H. LncRNA MALAT1 enhances oncogenic activities of EZH2 in castration-resistant prostate cancer. Oncotarget. 2015 Dec 1;6(38):41045-55. doi: 10.18632/oncotarget.5728.

  2. An J, Ren S, Murphy SJ, Dalangood S, Chang C, Pang X, Cui Y, Wang L, Pan Y, Zhang X, Zhu Y, Wang C, Halling GC, Cheng L, Sukov WR, Karnes RJ, Vasmatzis G, Zhang Q, Zhang J, Cheville JC, Yan J, Sun Y, Huang H. Truncated ERG Oncoproteins from TMPRSS2-ERG Fusions Are Resistant to SPOP-Mediated Proteasome Degradation. Mol Cell. 2015 Sep 17;59(6):904-16. doi: 10.1016/j.molcel.2015.07.025.

  3. Wang L*, Nie JJ, Kocher JP. PVAAS: identify variants associated with aberrant splicing from RNA-seq. Bioinformatics. 2015 May 15;31(10):1668-70. doi: 10.1093/bioinformatics/btv001.

  4. Chen Z, Lan X, Thomas-Ahner JM, Wu D, Liu X, Ye Z, Wang L, Sunkel B, Grenade C, Chen J, Zynger DL, Yan PS, Huang J, Nephew KP, Huang TH, Lin S, Clinton SK, Li W, Jin VX, Wang Q. Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer. EMBO J. 2015 Feb 12;34(4):502-16. doi: 10.15252/embj.201490306.

  5. Lu J, Lonergan PE, Nacusi LP, Wang L, Schmidt LJ, Sun Z, Van der Steen T, Boorjian SA, Kosari F, Vasmatzis G, Klee GG, Balk SP, Huang H, Wang C, Tindall DJ. The cistrome and gene signature of androgen receptor splice variants in castration resistant prostate cancer cells. J Urol. 2015 Feb;193(2):690-8. doi: 10.1016/j.juro.2014.08.043.

  6. Kohli M*#, Wang L*#, Xie F, Sicotte H, Yin P, Dehm SM, Hart SN, Vedell PT, Barman P, Qin R, Mahoney DW, Carlson RE, Eckel-Passow JE, Atwell TD, Eiken PW, McMenomy BP, Wieben ED, Jha G, Jimenez RE, Weinshilboum R, Wang L. Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy. PLoS One. 2015 Dec 22;10(12):e0145176. doi: 10.1371/journal.pone.0145176.

  7. Wang L*, Huang H*, Dougherty G, Zhao Y, Hossain A, Kocher JP. Epidaurus: aggregation and integration analysis of prostate cancer epigenome. Nucleic Acids Res. 2015 Jan;43(2):e7. doi: 10.1093/nar/gku1079.

  8. Sowalsky AG, Xia Z, Wang L, Zhao H, Chen S, Bubley GJ, Balk SP, Li W. Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer. Mol Cancer Res. 2015 Jan;13(1):98-106. doi: 10.1158/1541-7786.MCR-14-0273.

2014

  1. Wang L*#, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Nov 10;42(20):e156. doi: 10.1093/nar/gku846.

  2. Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. BMC Bioinformatics. 2014 Aug 15;15(1):280. doi: 10.1186/1471-2105-15-280.

  3. Blackmore JK, Karmakar S, Gu G, Chaubal V, Wang L, Li W, Smith CL. The SMRT Coregulator Enhances Growth of Estrogen Receptor-alpha-Positive Breast Cancer Cells by Promotion of Cell Cycle Progression and Inhibition of Apoptosis. Endocrinology. 2014 Sep;155(9):3251-61. doi: 10.1210/en.2014-1002.

  4. Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L#. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730.

  5. Adikesavan AK, Karmakar S, Pardo P, Wang L, Liu S, Li W, Smith CL. Activation of p53 transcriptional activity by SMRT: a histone deacetylase 3-independent function of a transcriptional corepressor. Mol Cell Biol. 2014 Apr;34(7):1246-61. doi: 10.1128/MCB.01216-13.

  6. Ding L, Chen S, Liu P, Pan Y, Zhong J, Regan KM, Wang L, Yu C, Rizzardi A, Cheng L, Zhang J, Schmechel SC, Cheville JC, Van Deursen J, Tindall DJ, Huang H. CBP loss cooperates with PTEN haploinsufficiency to drive prostate cancer: implications for epigenetic therapy. Cancer Res. 2014 Apr 1;74(7):2050-61. doi: 10.1158/0008-5472.CAN-13-1659.

2013

  1. Wang L, Zeng X, Chen S, Ding L, Zhong J, Zhao JC, Wang L, Sarver A, Koller A, Zhi J, Ma Y, Yu J, Chen J, Huang H. BRCA1 is a negative modulator of the PRC2 complex. EMBO J. 2013 May 29;32(11):1584-97. doi: 10.1038/emboj.2013.95.

  2. Wang L*, Park HJ*, Dasari S, Wang S, Kocher JP, Li W. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013 Apr 1;41(6):e74. doi: 10.1093/nar/gkt006.

  3. Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA. Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. PLoS One. 2013 Aug 19;8(8):e71745. doi: 10.1371/journal.pone.0071745.

  4. Rijnkels M, Freeman-Zadrowski C, Hernandez J, Potluri V, Wang L, Li W, Lemay DG. Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation. PLoS One. 2013;8(1):e53270. doi: 10.1371/journal.pone.0053270.

2012

  1. Wang L*, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356.

2011

  1. Zhang C*, Wang L*, Wu D, Chen H, Chen Z, Thomas-Ahner JM, Zynger DL, Eeckhoute J, Yu J, Luo J, Brown M, Clinton SK, Nephew KP, Huang TH, Li W, Wang Q. Definition of a FoxA1 Cistrome that is crucial for G1 to S-phase cell-cycle transit in castration-resistant prostate cancer. Cancer Res. 22011 Nov 1;71(21):6738-6748. doi: 10.1158/0008-5472.CAN-11-1882.

  2. Kannan K*, Wang L*, Wang J, Ittmann MM, Li W, Yen L. Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing. Proc Natl Acad Sci U S A. 2011 May 31;108(22):9172-7. doi: 10.1073/pnas.1100489108.

  3. Klisch TJ, Xi Y, Flora A, Wang L, Li W, Zoghbi HY. In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development. Proc Natl Acad Sci U S A. 2011 Feb 22;108(8):3288-93. doi: 10.1073/pnas.1100230108.

  4. Daines B*, Wang H*, Wang L*, Li Y, Han Y, Emmert D, Gelbart W, Wang X, Li W, Gibbs R, Chen R. The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res. 2011 Feb;21(2):315-24. doi: 10.1101/gr.107854.110.

2010

  1. Chen Z*, Wang L*, Wang Q, Li W. Histone modifications and chromatin organization in prostate cancer. Epigenomics. 2010 Aug;2(4):551-60. doi: 10.2217/epi.10.31.

  2. Lanz RB, Bulynko Y, Malovannaya A, Labhart P, Wang L, Li W, Qin J, Harper M, O’Malley BW. Global characterization of transcriptional impact of the SRC-3 coregulator. Mol Endocrinol. 2010 Apr;24(4):859-72. doi: 10.1210/me.2009-0499.

  3. Wang L*, Xi Y, Yu J, Dong L, Yen L, Li W. A statistical method for the detection of alternative splicing using RNA-seq . PLoS One. 2010 Jan 8;5(1):e8529. doi: 10.1371/journal.pone.0008529.

2009

  1. Wang L*, Hao L, Li X, Hu S, Ge S, Yu J. SNP deserts of Asian cultivated rice: genomic regions under domestication. J Evol Biol. 2009 Apr;22(4):751-61. doi: 10.1111/j.1420-9101.2009.01698.x.

  2. Li X, Tan L, Wang L, Hu S, Sun C. Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions. Mol Genet Genomics. 2009 Jan;281(1):11-8. doi: 10.1007/s00438-008-0388-4. Epub 2008 Sep 30.

2008

  1. Wang W, Meng B, Ge X, Song S, Yang Y, Yu X, Wang L, Hu S, Liu S, Yu J. Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines. Proteomics. 2008 Nov;8(22):4808-21. doi: 10.1002/pmic.200701164.

Book Chapter

  1. Li X, Nair A, Wang S, Wang L#. Quality control of RNA-seq experiments. Methods Mol Biol. (Springer). 2015;1269:137-46. doi: 10.1007/978-1-4939-2291-8_8.

  2. L. Y, Wang L#. RNA coding potential prediction using alignment-free logistic regression model. Methods Mol Biol. (Springer). 2021;2254:27-39. doi: 10.1007/978-1-0716-1158-6_3

Other resources