Tao Wang, PHD

Peer-Reviewed Articles

1. Yang Y, Wang K, Lu Z, Wang T, Wang X. Cytomulate: accurate and efficient simulation of CyTOF data. Genome Biol 24(1):262, 2023. e-Pub 2023. PMID: 37974276.
2. Johnson KC, Johnson ST, Liu J, Chu Y, Arana C, Han Y, Wang T, Corey DR. Consequences of depleting TNRC6, AGO, and DROSHA proteins on expression of microRNAs. RNA 29(8):1166-1184, 2023. e-Pub 2023. PMID: 37169394.
3. Rong R, Wei Y, Li L, Wang T, Zhu H, Xiao G, Wang Y. Image-based quantification of histological features as a function of spatial location using the Tissue Positioning System. EBioMedicine 94:104698, 2023. e-Pub 2023. PMID: 37453365.
4. Lin YH, Wei Y, Zeng Q, Wang Y, Pagani CA, Li L, Zhu M, Wang Z, Hsieh MH, Corbitt N, Zhang Y, Sharma T, Wang T, Zhu H. IGFBP2 expressing midlobular hepatocytes preferentially contribute to liver homeostasis and regeneration. Cell Stem Cell 30(5):665-676.e4, 2023. e-Pub 2023. PMID: 37146585.
5. Wang Z, Zhu S, Jia Y, Wang Y, Kubota N, Fujiwara N, Gordillo R, Lewis C, Zhu M, Sharma T, Li L, Zeng Q, Lin YH, Hsieh MH, Gopal P, Wang T, Hoare M, Campbell P, Hoshida Y, Zhu H. Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease. Cell 186(9):1968-1984.e20, 2023. e-Pub 2023. PMID: 37040760.
6. Wang K, Yang Y, Wu F, Song B, Wang X, Wang T. Comparative analysis of dimension reduction methods for cytometry by time-of-flight data. Nat Commun 14(1):1836, 2023. e-Pub 2023. PMID: 37005472.
7. Frank ML, Lu K, Erdogan C, Han Y, Hu J, Wang T, Heymach JV, Zhang J, Reuben A. T-Cell Receptor Repertoire Sequencing in the Era of Cancer Immunotherapy. Clin Cancer Res 29(6):994-1008, 2023. e-Pub 2023. PMID: 36413126.
8. Kim Y, Wang T, Xiong D, Wang X, Park S. Multiple instance neural networks based on sparse attention for cancer detection using T-cell receptor sequences. BMC Bioinformatics 23(1):469, 2022. e-Pub 2022. PMID: 36348271.
9. Celen C, Chuang JC, Shen S, Li L, Maggiore G, Jia Y, Luo X, Moore A, Wang Y, Otto JE, Collings CK, Wang Z, Sun X, Nassour I, Park J, Ghaben A, Wang T, Wang SC, Scherer PE, Kadoch C, Zhu H. Arid1a loss potentiates pancreatic beta-cell regeneration through activation of EGF signaling. Cell Rep 41(5):111581, 2022. e-Pub 2022. PMID: 36323264.
10. Lu T, Park S, Han Y, Wang Y, Hubert SM, Futreal PA, Wistuba I, Heymach JV, Reuben A, Zhang J, Wang T. Netie: inferring the evolution of neoantigen-T cell interactions in tumors. Nat Methods 19(11):1480-1489, 2022. e-Pub 2022. PMID: 36303017.
11. Deng S, Wang C, Wang Y, Xu Y, Li X, Johnson NA, Mukherji A, Lo UG, Xu L, Gonzalez J, Metang LA, Ye J, Tirado CR, Rodarte K, Zhou Y, Xie Z, Arana C, Annamalai V, Liu X, Vander Griend DJ, Strand D, Hsieh JT, Li B, Raj G, Wang T, Mu P. Ectopic JAK-STAT activation enables the transition to a stem-like and multilineage state conferring AR-targeted therapy resistance. Nat Cancer 3(9):1071-1087, 2022. e-Pub 2022. PMID: 36065066.
12. Wang Y, Song B, Wang S, Chen M, Xie Y, Xiao G, Wang L, Wang T. Sprod for de-noising spatially resolved transcriptomics data based on position and image information. Nat Methods 19(8):950-958, 2022. e-Pub 2022. PMID: 35927477.
13. Zhu J, Gouru A, Wu F, Berzofsky JA, Xie Y, Wang T. BepiTBR: T-B reciprocity enhances B cell epitope prediction. iScience 25(2):103764, 2022. e-Pub 2022. PMID: 35128358.
14. Hannan R, Mohamad O, Diaz de Leon A, Manna S, Pop LM, Zhang Z, Mannala S, Christie A, Christley S, Monson N, Ishihara D, Hsu EJ, Ahn C, Kapur P, Chen M, Arriaga Y, Courtney K, Cantarel B, Wakeland EK, Fu YX, Pedrosa I, Cowell L, Wang T, Margulis V, Choy H, Timmerman RD, Brugarolas J. Outcome and Immune Correlates of a Phase II Trial of High-Dose Interleukin-2 and Stereotactic Ablative Radiotherapy for Metastatic Renal Cell Carcinoma. Clin Cancer Res 27(24):6716-6725, 2021. e-Pub 2021. PMID: 34551906.
15. Foray AP, Candon S, Hildebrand S, Marquet C, Valette F, Pecquet C, Lemoine S, Langa-Vives F, Dumas M, Hu P, Santamaria P, You S, Lyon S, Scott L, Bu CH, Wang T, Xu D, Moresco EMY, Scazzocchio C, Bach JF, Beutler B, Chatenoud L. De novo germline mutation in the dual specificity phosphatase 10 gene accelerates autoimmune diabetes. Proc Natl Acad Sci U S A 118(47), 2021. e-Pub 2021. PMID: 34782469.
16. Kim K, Zhou Q, Christie A, Stevens C, Ma Y, Onabolu O, Chintalapati S, Mckenzie T, Tcheuyap VT, Woolford L, Zhang H, Singla N, Parida PK, Marquez-Palencia M, Pedrosa I, Margulis V, Sagalowsky A, Xie Z, Wang T, Durinck S, Modrusan Z, Seshagiri S, Kapur P, Brugarolas J, Malladi S. Determinants of renal cell carcinoma invasion and metastatic competence. Nat Commun 12(1):5760, 2021. e-Pub 2021. PMID: 34608135.
17. Lu T, Zhang Z, Zhu J, Wang Y, Jiang P, Xiao X, Bernatchez C, Heymach JV, Gibbons DL, Wang J, Xu L, Reuben A, Wang T. Deep learning-based prediction of the T cell receptor-antigen binding specificity. Nat Mach Intell 3(10):864-875, 2021. e-Pub 2021. PMID: 36003885.
18. Udayakumar D, Zhang Z, Xi Y, Dwivedi DK, Fulkerson M, Haldeman S, McKenzie T, Yousuf Q, Joyce A, Hajibeigi A, Notgrass H, de Leon AD, Yuan Q, Lewis MA, Madhuranthakam AJ, Sibley RC, Elias R, Guo J, Christie A, McKay RM, Cadeddu JA, Bagrodia A, Margulis V, Brugarolas J, Wang T, Kapur P, Pedrosa I. Deciphering Intratumoral Molecular Heterogeneity in Clear Cell Renal Cell Carcinoma with a Radiogenomics Platform. Clin Cancer Res 27(17):4794-4806, 2021. e-Pub 2021. PMID: 34210685.
19. Lu Q, Liu J, Zhao S, Gomez Castro MF, Laurent-Rolle M, Dong J, Ran X, Damani-Yokota P, Tang H, Karakousi T, Son J, Kaczmarek ME, Zhang Z, Yeung ST, McCune BT, Chen RE, Tang F, Ren X, Chen X, Hsu JCC, Teplova M, Huang B, Deng H, Long Z, Mudianto T, Jin S, Lin P, Du J, Zang R, Su TT, Herrera A, Zhou M, Yan R, Cui J, Zhu J, Zhou Q, Wang T, Ma J, Koralov SB, Zhang Z, Aifantis I, Segal LN, Diamond MS, Khanna KM, Stapleford KA, Cresswell P, Liu Y, Ding S, Xie Q, Wang J. SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through C-type lectin receptors and Tweety family member 2. Immunity 54(6):1304-1319.e9, 2021. e-Pub 2021. PMID: 34048708.
20. SoRelle JA, Chen Z, Wang J, Yue T, Choi JH, Wang KW, Zhong X, Hildebrand S, Russell J, Scott L, Xu D, Zhan X, Bu CH, Wang T, Choi M, Tang M, Ludwig S, Zhan X, Li X, Moresco EMY, Beutler B. Dominant atopy risk mutations identified by mouse forward genetic analysis. Allergy 76(4):1095-1108, 2021. e-Pub 2021. PMID: 32810290.
21. Cai L, Liu H, Huang F, Fujimoto J, Girard L, Chen J, Li Y, Zhang YA, Deb D, Stastny V, Pozo K, Kuo CS, Jia G, Yang C, Zou W, Alomar A, Huffman K, Papari-Zareei M, Yang L, Drapkin B, Akbay EA, Shames DS, Wistuba II, Wang T, Johnson JE, Xiao G, DeBerardinis RJ, Minna JD, Xie Y, Gazdar AF. Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. Commun Biol 4(1):314, 2021. e-Pub 2021. PMID: 33750914.
22. Wei Y, Wang YG, Jia Y, Li L, Yoon J, Zhang S, Wang Z, Zhang Y, Zhu M, Sharma T, Lin YH, Hsieh MH, Albrecht JH, Le PT, Rosen CJ, Wang T, Zhu H. Liver homeostasis is maintained by midlobular zone 2 hepatocytes. Science 371(6532), 2021. e-Pub 2021. PMID: 33632817.
23. Lu C, Guan J, Lu S, Jin Q, Rousseau B, Lu T, Stephens D, Zhang H, Zhu J, Yang M, Ren Z, Liang Y, Liu Z, Han C, Liu L, Cao X, Zhang A, Qiao J, Batten K, Chen M, Castrillon DH, Wang T, Li B, Diaz LA Jr, Li GM, Fu YX. DNA Sensing in Mismatch Repair-Deficient Tumor Cells Is Essential for Anti-tumor Immunity. Cancer Cell 39(1):96-108.e6, 2021. e-Pub 2021. PMID: 33338425.
24. Lu T, Park S, Zhu J, Wang Y, Zhan X, Wang X, Wang L, Zhu H, Wang T. Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data. Cell Rep 34(1):108589, 2021. e-Pub 2021. PMID: 33406427.
25. Zhang Z, Xiong D, Wang X, Liu H, Wang T. Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics. Nat Methods 18(1):92-99, 2021. e-Pub 2021. PMID: 33408405.
26. Reese B, Silwal A, Daugherity E, Daugherity M, Arabi M, Daly P, Paterson Y, Woolford L, Christie A, Elias R, Brugarolas J, Wang T, Karbowniczek M, Markiewski MM. Complement as Prognostic Biomarker and Potential Therapeutic Target in Renal Cell Carcinoma. J Immunol 205(11):3218-3229, 2020. e-Pub 2020. PMID: 33158953.
27. Chung AS, Mettlen M, Ganguly D, Lu T, Wang T, Brekken RA, Hsiehchen D, Zhu H. Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma. Cancer Prev Res (Phila) 13(11):911-922, 2020. e-Pub 2020. PMID: 32839204.
28. Park S, Wang X, Lim J, Xiao G, Lu T, Wang T. Bayesian multiple instance regression for modeling immunogenic neoantigens. Stat Methods Med Res 29(10):3032-3047, 2020. e-Pub 2020. PMID: 32401701.
29. Wang Z, Chen K, Jia Y, Chuang JC, Sun X, Lin YH, Celen C, Li L, Huang F, Liu X, Castrillon DH, Wang T, Zhu H. Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes. Nat Cancer 1(9):909-922, 2020. e-Pub 2020. PMID: 34386776.
30. Zhu M, Li L, Lu T, Yoo H, Zhu J, Gopal P, Wang SC, Porembka MR, Rich NE, Kagan S, Odewole M, Renteria V, Waljee AK, Wang T, Singal AG, Yopp AC, Zhu H. Uncovering Biological Factors That Regulate Hepatocellular Carcinoma Growth Using Patient-Derived Xenograft Assays. Hepatology 72(3):1085-1101, 2020. e-Pub 2020. PMID: 31899548.
31. Hsiehchen D, Hsieh A, Samstein RM, Lu T, Beg MS, Gerber DE, Wang T, Morris LGT, Zhu H. DNA Repair Gene Mutations as Predictors of Immune Checkpoint Inhibitor Response beyond Tumor Mutation Burden. Cell Rep Med 1(3), 2020. e-Pub 2020. PMID: 32676589.
32. Wang S, Rong R, Yang DM, Fujimoto J, Yan S, Cai L, Yang L, Luo D, Behrens C, Parra ER, Yao B, Xu L, Wang T, Zhan X, Wistuba II, Minna J, Xie Y, Xiao G. Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer. Cancer Res 80(10):2056-2066, 2020. e-Pub 2020. PMID: 31915129.
33. Lin YH, Zhang S, Zhu M, Lu T, Chen K, Wen Z, Wang S, Xiao G, Luo D, Jia Y, Li L, MacConmara M, Hoshida Y, Singal AG, Yopp A, Wang T, Zhu H. Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury. Gastroenterology 158(6):1698-1712.e14, 2020. e-Pub 2020. PMID: 31972235.
34. Singla N, Xie Z, Zhang Z, Gao M, Yousuf Q, Onabolu O, McKenzie T, Tcheuyap VT, Ma Y, Choi J, McKay R, Christie A, Torras OR, Bowman IA, Margulis V, Pedrosa I, Przybycin C, Wang T, Kapur P, Rini B, Brugarolas J. Pancreatic tropism of metastatic renal cell carcinoma. JCI Insight 5(7), 2020. e-Pub 2020. PMID: 32271170.
35. Lu T, Wang S, Xu L, Zhou Q, Singla N, Gao J, Manna S, Pop L, Xie Z, Chen M, Luke JJ, Brugarolas J, Hannan R, Wang T. Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes. Sci Immunol 5(44), 2020. e-Pub 2020. PMID: 32086382.
36. Courtney KD, Ma Y, Diaz de Leon A, Christie A, Xie Z, Woolford L, Singla N, Joyce A, Hill H, Madhuranthakam AJ, Yuan Q, Xi Y, Zhang Y, Chang J, Fatunde O, Arriaga Y, Frankel AE, Kalva S, Zhang S, McKenzie T, Reig Torras O, Figlin RA, Rini BI, McKay RM, Kapur P, Wang T, Pedrosa I, Brugarolas J. HIF-2 Complex Dissociation, Target Inhibition, and Acquired Resistance with PT2385, a First-in-Class HIF-2 Inhibitor, in Patients with Clear Cell Renal Cell Carcinoma. Clin Cancer Res 26(4):793-803, 2020. e-Pub 2020. PMID: 31727677.
37. Zhang M, Wang T, Xiao G, Xie Y. Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Genes (Basel) 11(1), 2020. e-Pub 2020. PMID: 31947823.
38. Wang S, Wang T, Yang L, Yang DM, Fujimoto J, Yi F, Luo X, Yang Y, Yao B, Lin S, Moran C, Kalhor N, Weissferdt A, Minna J, Xie Y, Wistuba II, Mao Y, Xiao G. ConvPath: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network. EBioMedicine 50:103-110, 2019. e-Pub 2019. PMID: 31767541.
39. Zhang Z, Luo D, Zhong X, Choi JH, Ma Y, Wang S, Mahrt E, Guo W, Stawiski EW, Modrusan Z, Seshagiri S, Kapur P, Hon GC, Brugarolas J, Wang T. SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples. Genes (Basel) 10(7), 2019. e-Pub 2019. PMID: 31336988.
40. Choi JH, Zhong X, McAlpine W, Liao TC, Zhang D, Fang B, Russell J, Ludwig S, Nair-Gill E, Zhang Z, Wang KW, Misawa T, Zhan X, Choi M, Wang T, Li X, Tang M, Sun Q, Yu L, Murray AR, Moresco EMY, Beutler B. LMBR1L regulates lymphopoiesis through Wnt/beta-catenin signaling. Science 364(6440), 2019. e-Pub 2019. PMID: 31073040.
41. Zhu M, Lu T, Jia Y, Luo X, Gopal P, Li L, Odewole M, Renteria V, Singal AG, Jang Y, Ge K, Wang SC, Sorouri M, Parekh JR, MacConmara MP, Yopp AC, Wang T, Zhu H. Somatic Mutations Increase Hepatic Clonal Fitness and Regeneration in Chronic Liver Disease. Cell 177(3):608-621.e12, 2019. e-Pub 2019. PMID: 30955891.
42. Lodhi HA, Peri-Okonny PA, Schesing K, Phelps K, Ngo C, Evans H, Arbique D, Price AL, Vernino S, Phillips L, Mitchell JH, Smith SA, Yano Y, Das SR, Wang T, Vongpatanasin W. Usefulness of Blood Pressure Variability Indices Derived From 24-Hour Ambulatory Blood Pressure Monitoring in Detecting Autonomic Failure. J Am Heart Assoc 8(7):e010161, 2019. e-Pub 2019. PMID: 30905258.
43. Zhang M, Wang T, Sirianni R, Shaul PW, Xie Y. Identifying genes with tri-modal association with survival and tumor grade in cancer patients. BMC Bioinformatics 20(1):13, 2019. e-Pub 2019. PMID: 30621577.
44. Wang T, Lu R, Lai S, Schiller JH, Zhou FL, Ci B, Wang S, Gao X, Yao B, Gerber DE, Johnson DH, Xiao G, Xie Y. Development and Validation of a Nomogram Prognostic Model for Patients With Advanced Non-Small-Cell Lung Cancer. Cancer Inform 18:1176935119837547, 2019. e-Pub 2019. PMID: 31057324.
45. McAlpine W, Wang KW, Choi JH, San Miguel M, McAlpine SG, Russell J, Ludwig S, Li X, Tang M, Zhan X, Choi M, Wang T, Bu CH, Murray AR, Moresco EMY, Turer EE, Beutler B. The class I myosin MYO1D binds to lipid and protects against colitis. Dis Model Mech 11(9), 2018. e-Pub 2018. PMID: 30279225.
46. Wang T, Lu R, Kapur P, Jaiswal BS, Hannan R, Zhang Z, Pedrosa I, Luke JJ, Zhang H, Goldstein LD, Yousuf Q, Gu YF, McKenzie T, Joyce A, Kim MS, Wang X, Luo D, Onabolu O, Stevens C, Xie Z, Chen M, Filatenkov A, Torrealba J, Luo X, Guo W, He J, Stawiski E, Modrusan Z, Durinck S, Seshagiri S, Brugarolas J. An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors. Cancer Discov 8(9):1142-1155, 2018. e-Pub 2018. PMID: 29884728.
47. Wang S, Khera R, Das SR, Vigen R, Wang T, Luo X, Lu R, Zhan X, Xiao G, Vongpatanasin W, Xie Y. Usefulness of a Simple Algorithm to Identify Hypertensive Patients Who Benefit from Intensive Blood Pressure Lowering. Am J Cardiol 122(2):248-254, 2018. e-Pub 2018. PMID: 29880288.
48. Wang Y, Cao L, Lee CY, Matsuo T, Wu K, Asher G, Tang L, Saitoh T, Russell J, Klewe-Nebenius D, Wang L, Soya S, Hasegawa E, Cherasse Y, Zhou J, Li Y, Wang T, Zhan X, Miyoshi C, Irukayama Y, Cao J, Meeks JP, Gautron L, Wang Z, Sakurai K, Funato H, Sakurai T, Yanagisawa M, Nagase H, Kobayakawa R, Kobayakawa K, Beutler B, Liu Q. Large-scale forward genetics screening identifies Trpa1 as a chemosensor for predator odor-evoked innate fear behaviors. Nat Commun 9(1):2041, 2018. e-Pub 2018. PMID: 29795268.
49. Wang T, Bu CH, Hildebrand S, Jia G, Siggs OM, Lyon S, Pratt D, Scott L, Russell J, Ludwig S, Murray AR, Moresco EMY, Beutler B. Probability of phenotypically detectable protein damage by ENU-induced mutations in the Mutagenetix database. Nat Commun 9(1):441, 2018. e-Pub 2018. PMID: 29382827.
50. Gu YF, Cohn S, Christie A, McKenzie T, Wolff N, Do QN, Madhuranthakam AJ, Pedrosa I, Wang T, Dey A, Busslinger M, Xie XJ, Hammer RE, McKay RM, Kapur P, Brugarolas J. Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade. Cancer Discov 7(8):900-917, 2017. e-Pub 2017. PMID: 28473526.
51. Choi JH, Wang KW, Zhang D, Zhan X, Wang T, Bu CH, Behrendt CL, Zeng M, Wang Y, Misawa T, Li X, Tang M, Zhan X, Scott L, Hildebrand S, Murray AR, Moresco EM, Hooper LV, Beutler B. IgD class switching is initiated by microbiota and limited to mucosa-associated lymphoid tissue in mice. Proc Natl Acad Sci U S A 114(7):E1196-E1204, 2017. e-Pub 2017. PMID: 28137874.
52. Turer E, McAlpine W, Wang KW, Lu T, Li X, Tang M, Zhan X, Wang T, Zhan X, Bu CH, Murray AR, Beutler B. Creatine maintains intestinal homeostasis and protects against colitis. Proc Natl Acad Sci U S A 114(7):E1273-E1281, 2017. e-Pub 2017. PMID: 28137860.
53. Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. Lancet Oncol 18(1):132-142, 2017. e-Pub 2017. PMID: 27864015.
54. Li Q, Yi F, Wang T, Xiao G, Liang F. Lung Cancer Pathological Image Analysis Using a Hidden Potts Model. Cancer Inform 16:1176935117711910, 2017. e-Pub 2017. PMID: 28615918.
55. Sieberts SK, Zhu F, Garcia-Garcia J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornes O, Guney E, Li H, Marin MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellon V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun 7:12460, 2016. e-Pub 2016. PMID: 27549343.
56. Zang C, Wang T, Deng K, Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He HH, Brown M, Liu JS, Xie Y, Liu XS. High-dimensional genomic data bias correction and data integration using MANCIE. Nat Commun 7:11305, 2016. e-Pub 2016. PMID: 27072482.
57. Zhou M, Wang T, Fu J, Xiao G, Liu Y. Nonoptimal codon usage influences protein structure in intrinsically disordered regions. Mol Microbiol 97(5):974-87, 2015. e-Pub 2015. PMID: 26032251.
58. Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J. Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol 33(9):933-40, 2015. e-Pub 2015. PMID: 26258538.
59. Chu Y, Wang T, Dodd D, Xie Y, Janowski BA, Corey DR. Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells. Nucleic Acids Res 43(11):e75, 2015. e-Pub 2015. PMID: 25813040.
60. Wang T, Zhan X, Bu CH, Lyon S, Pratt D, Hildebrand S, Choi JH, Zhang Z, Zeng M, Wang KW, Turer E, Chen Z, Zhang D, Yue T, Wang Y, Shi H, Wang J, Sun L, SoRelle J, McAlpine W, Hutchins N, Zhan X, Fina M, Gobert R, Quan J, Kreutzer M, Arnett S, Hawkins K, Leach A, Tate C, Daniel C, Reyna C, Prince L, Davis S, Purrington J, Bearden R, Weatherly J, White D, Russell J, Sun Q, Tang M, Li X, Scott L, Moresco EM, McInerney GM, Karlsson Hedestam GB, Xie Y, Beutler B. Real-time resolution of point mutations that cause phenovariance in mice. Proc Natl Acad Sci U S A 112(5):E440-9, 2015. e-Pub 2015. PMID: 25605905.
61. Sei E, Wang T, Hunter OV, Xie Y, Conrad NK. HITS-CLIP analysis uncovers a link between the Kaposi's sarcoma-associated herpesvirus ORF57 protein and host pre-mRNA metabolism. PLoS Pathog 11(2):e1004652, 2015. e-Pub 2015. PMID: 25710169.
62. Yang J, Tang H, Li Y, Zhong R, Wang T, Wong S, Xiao G, Xie Y. DIGRE: Drug-Induced Genomic Residual Effect Model for Successful Prediction of Multidrug Effects. CPT Pharmacometrics Syst Pharmacol 4(2):e1, 2015. e-Pub 2015. PMID: 26225227.
63. Chen X, Zhao C, Li X, Wang T, Li Y, Cao C, Ding Y, Dong M, Finci L, Wang JH, Li X, Liu L. Terazosin activates Pgk1 and Hsp90 to promote stress resistance. Nat Chem Biol 11(1):19-25, 2015. e-Pub 2015. PMID: 25383758.
64. Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A. A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol 32(12):1213-22, 2014. e-Pub 2014. PMID: 25419740.
65. Augustyn A, Borromeo M, Wang T, Fujimoto J, Shao C, Dospoy PD, Lee V, Tan C, Sullivan JP, Larsen JE, Girard L, Behrens C, Wistuba II, Xie Y, Cobb MH, Gazdar AF, Johnson JE, Minna JD. ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers. Proc Natl Acad Sci U S A 111(41):14788-93, 2014. e-Pub 2014. PMID: 25267614.
66. Kwon I, Xiang S, Kato M, Wu L, Theodoropoulos P, Wang T, Kim J, Yun J, Xie Y, McKnight SL. Poly-dipeptides encoded by the C9orf72 repeats bind nucleoli, impede RNA biogenesis, and kill cells. Science 345(6201):1139-45, 2014. e-Pub 2014. PMID: 25081482.
67. Yun J, Wang T, Xiao G. Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP. Biometrics 70(2):430-40, 2014. e-Pub 2014. PMID: 24571656.
68. Wang T, Xie Y, Xiao G. dCLIP: a computational approach for comparative CLIP-seq analyses. Genome Biol 15(1):R11, 2014. e-Pub 2014. PMID: 24398258.
69. Wang T, Chen B, Kim M, Xie Y, Xiao G. A model-based approach to identify binding sites in CLIP-Seq data. PLoS One 9(4):e93248, 2014. e-Pub 2014. PMID: 24714572.

Review Articles

1. Zhang M, Sheffield T, Zhan X, Li Q, Yang DM, Wang Y, Wang S, Xie Y, Wang T, Xiao G. Spatial molecular profiling: platforms, applications and analysis tools. Brief Bioinform 22(3), 2021. e-Pub 2021. PMID: 32770205.
2. Xiong D, Zhang Z, Wang T, Wang X. A comparative study of multiple instance learning methods for cancer detection using T-cell receptor sequences. Comput Struct Biotechnol J 19:3255-3268, 2021. e-Pub 2021. PMID: 34141144.
3. Wang T, Xiao G, Chu Y, Zhang MQ, Corey DR, Xie Y. Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Res 43(11):5263-74, 2015. e-Pub 2015. PMID: 25958398.

Other Articles

1. Zhu M, Wang Y, Lu T, Guo J, Li L, Hsieh MH, Gopal P, Han Y, Fujiwara N, Wallace DP, Yu ASL, Fang X, Ransom C, Verschleisser S, Hsiehchen D, Hoshida Y, Singal AG, Yopp A, Wang T, Zhu H PKD1 mutant clones within cirrhotic livers inhibit steatohepatitis without promoting cancer. Cell Metab, 2024. PMID: 38901424.
2. Xu Y, Yang Y, Wang Z, Sjöström M, Jiang Y, Tang Y, Cheng S, Deng S, Wang C, Gonzalez J, Johnson NA, Li X, Li X, Metang LA, Mukherji A, Xu Q, Tirado CR, Wainwright G, Yu X, Barnes S, Hofstad M, Chen Y, Zhu H, Hanker AB, Raj GV, Zhu G, He HH, Wang Z, Arteaga CL, Liang H, Feng FY, Wang Y, Wang T, Mu P ZNF397 Deficiency Triggers TET2-Driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer. Cancer Discov, 2024. PMID: 38591846.
3. Wang T, Guo Y, Ma H, Na S, Zhong W, Han Y, Wang T, Huang J GTE: a graph learning framework for prediction of T-cell receptors and epitopes binding specificity. Brief Bioinform, 2024. PMID: 39007599.
4. von Itzstein MS, Yang Y, Wang Y, Hsiehchen D, Sheffield TY, Fattah F, Popat V, Ahmed M, Homsi J, Dowell JE, Rashdan S, Lohrey J, Hammers HJ, Hughes RS, Wang T, Xie Y, Gerber DE Highly variable timing renders immunotherapy efficacy and toxicity impractical biomarkers of one another in clinical practice. Front Immunol, 2024. PMID: 38690281.
5. Johnson KC, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S, Graswich J, Han Y, Wang T, Westcott JM, Brekken RA, Peng L, Karagkounis G, Corey DR Nuclear localization of Argonaute 2 is affected by cell density and may relieve repression by microRNAs. Nucleic Acids Res, 2024. PMID: 38109320.
6. Prakasam G, Mishra A, Christie A, Miyata J, Carrillo D, Tcheuyap VT, Ye H, Do QN, Wang Y, Reig Torras O, Butti R, Zhong H, Gagan J, Jones KB, Carroll TJ, Modrusan Z, Durinck S, Requena-Komuro MC, Williams NS, Pedrosa I, Wang T, Rakheja D, Kapur P, Brugarolas J Comparative genomics incorporating translocation renal cell carcinoma mouse model reveals molecular mechanisms of tumorigenesis. J Clin Invest , 2024. PMID: 38386415.
7. Zhang F, Mulvaney O, Salcedo E, Manna S, Zhu JZ, Wang T, Ahn C, Pop LM, Hannan R Radiation-Induced Innate Neutrophil Response in Tumor Is Mediated by the CXCLs/CXCR2 Axis. Cancers (Basel), 2023. PMID: 38067390.
8. Rodriguez Tirado C, Wang C, Li X, Deng S, Gonzalez J, Johnson NA, Xu Y, Metang LA, Sundar Rajan M, Yang Y, Yin Y, Hofstad M, Raj GV, Zhang S, Lemoff A, He W, Fan J, Wang Y, Wang T, Mu P UBE2J1 is the E2 ubiquitin-conjugating enzyme regulating androgen receptor degradation and antiandrogen resistance. Oncogene, 2023. PMID: 38030789.
9. Zhu Z, Lou G, Teng XL, Wang H, Luo Y, Shi W, Yihunie K, Hao S, DeGolier K, Liao C, Huang H, Zhang Q, Fry T, Wang T, Yao C, Wu T FOXP1 and KLF2 reciprocally regulate checkpoints of stem-like to effector transition in CAR T cells. Nature Immunology, 2023. PMID: 38012417.
10. Yang Y, Wang K, Lu Z, Wang T, Wang X Cytomulate: accurate and efficient simulation of CyTOF data. Genome Biol, 2023. PMID: 7974279.
11. Hannan R, McLaughlin MF, Pop LM, Pedrosa I, Kapur P, Garant A, Ahn C, Christie A, Zhu J, Wang T, Robles L, Durakoglugil D, Woldu S, Margulis V, Gahan J, Brugarolas J, Timmerman R, Cadeddu J Phase 2 Trial of Stereotactic Ablative Radiotherapy for Patients with Primary Renal Cancer. Eur Urol, 2023. PMID: 36898872.
12. Li X, Wang Y, Deng S, Zhu G, Wang C, Johnson NA, Zhang Z, Tirado CR, Xu Y, Metang LA, Gonzalez J, Mukherji A, Ye J, Yang Y, Peng W, Tang Y, Hofstad M, Xie Z, Yoon H, Chen L, Liu X, Chen S, Zhu H, Strand D, Liang H, Raj G, He HH, Mendell JT, Li B, Wang T, Mu P Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer. Cancer Cell, 2023. PMID: 37478850.
13. Zhang C, Wang X, Chen M, Wang T A comparison of hypothesis tests for homogeneity in meta-analysis with focus on rare binary events. Res Synth Methods 12(4):408-428, 2021. PMID: 34231330.

Book Chapters

1. Wang T, Xiao G, Chu Y, Zhang MQ, Corey DR, Xie Y. Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Res, 2015.

Books (edited and written)

1. Wang T. Finding RNA-Protein Interactions Sites Using HMMs. In Hidden Markov Models - Methods and Protocols. Humana Press, 2017.