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BING ZHANG

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
AddressOne Baylor Plaza
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    Other Positions
    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentBreast Center
    DivisionBreast Cancer Center


    Collapse Research 
    Collapse research activities and funding
    U01CA299401     (ZHANG, BING)Aug 1, 2025 - Jul 31, 2028
    NIH
    Advancing Protein Isoform Analysis through an Integrated Computational Framework.
    Role: Principal Investigator
    U01CA271247     (ZHANG, BING)Jul 26, 2022 - Jun 30, 2024
    NIH
    Illuminating understudied druggable proteins using pan-cancer proteogenomics data
    Role: Principal Investigator
    U24CA271076     (ZHANG, BING)Jun 1, 2022 - May 31, 2027
    NIH
    iPGDAC, An Integrative Proteogenomic Data Analysis Center for CPTAC
    Role: Principal Investigator
    R01CA245903     (ZHANG, BING)Apr 1, 2020 - Mar 31, 2025
    NIH
    Proteogenomics-driven therapeutic discovery in hepatocellular carcinoma
    Role: Principal Investigator
    U24CA210954     (ZHANG, BING)Sep 20, 2016 - Aug 31, 2021
    NIH
    iPGDAC, An Integrative Proteogenomic Data Analysis Center for CPTAC
    Role: Principal Investigator
    U24CA159988     (ZHANG, BING)Aug 26, 2011 - Jul 31, 2017
    NIH
    Vanderbilt Proteome Characterization Center
    Role: Principal Investigator
    R01GM088822     (ZHANG, BING)Aug 20, 2009 - Jun 30, 2014
    NIH
    Systems Approach to the Biological Basis of Colon Cancer Metastases
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Wen B, Wang C, Li K, Han P, Holt MV, Savage SR, Lei JT, Dou Y, Shi Z, Li Y, Zhang B. DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations. Nat Methods. 2025 Sep; 22(9):1857-1867. PMID: 40859022; PMCID: PMC12446062.
      Citations:    Fields:    Translation:HumansCells
    2. M?ller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani DR, Zhang B, Saez-Rodriguez J. Publisher Correction: Comprehensive evaluation of phosphoproteomic-based kinase activity inference. Nat Commun. 2025 Jul 17; 16(1):6591. PMID: 40675995; PMCID: PMC12271350.
      Citations:    Fields:    
    3. M?ller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani DR, Zhang B, Saez-Rodriguez J. Comprehensive evaluation of phosphoproteomic-based kinase activity inference. Nat Commun. 2025 May 22; 16(1):4771. PMID: 40404650; PMCID: PMC12098709.
      Citations:    Fields:    Translation:HumansCells
    4. Jiang W, Jaehnig EJ, Liao Y, Shi Z, Yaron-Barir TM, Johnson JL, Cantley LC, Zhang B. Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites. Nat Commun. 2025 Mar 20; 16(1):2766. PMID: 40113755; PMCID: PMC11926083.
      Citations: 1     Fields:    Translation:HumansCells
    5. Shi Z, Lei JT, Elizarraras JM, Zhang B. Mapping the functional network of human cancer through machine learning and pan-cancer proteogenomics. Nat Cancer. 2025 Jan; 6(1):205-222. PMID: 39663389; PMCID: PMC12036749.
      Citations: 3     Fields:    Translation:Humans
    6. Yi X, Zhao H, Hu S, Dong L, Dou Y, Li J, Gao Q, Zhang B. Tumor-associated antigen prediction using a single-sample gene expression state inference algorithm. Cell Rep Methods. 2024 Nov 18; 4(11):100906. PMID: 39561714; PMCID: PMC11705763.
      Citations: 2     Fields:    Translation:Humans
    7. Savage SR, Yi X, Lei JT, Wen B, Zhao H, Liao Y, Jaehnig EJ, Somes LK, Shafer PW, Lee TD, Fu Z, Dou Y, Shi Z, Gao D, Hoyos V, Gao Q, Zhang B. Pan-cancer proteogenomics expands the landscape of therapeutic targets. Cell. 2024 Aug 08; 187(16):4389-4407.e15. PMID: 38917788; PMCID: PMC12010439.
      Citations: 8     Fields:    Translation:HumansCells
    8. Savage SR, Zhang B. Correction to: Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. Clin Proteomics. 2024 Mar 07; 21(1):20. PMID: 38454337; PMCID: PMC10918992.
      Citations:    
    9. Yi X, Wen B, Ji S, Saltzman AB, Jaehnig EJ, Lei JT, Gao Q, Zhang B. Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification. Mol Cell Proteomics. 2024 Feb; 23(2):100707. PMID: 38154692; PMCID: PMC10831110.
      Citations: 2     Fields:    Translation:HumansCells
    10. Savage SR, Zhang Y, Jaehnig EJ, Liao Y, Shi Z, Pham HA, Xu H, Zhang B. IDPpub: Illuminating the Dark Phosphoproteome Through PubMed Mining. Mol Cell Proteomics. 2024 Jan; 23(1):100682. PMID: 37993103; PMCID: PMC10716774.
      Citations:    
    11. Lei JT, Jaehnig EJ, Smith H, Holt MV, Li X, Anurag M, Ellis MJ, Mills GB, Zhang B, Labrie M. The Breast Cancer Proteome and Precision Oncology. Cold Spring Harb Perspect Med. 2023 10 03; 13(10). PMID: 37137501; PMCID: PMC10547392.
      Citations:    Fields:    Translation:Humans
    12. Zhang B, Bassani-Sternberg M. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery. J Immunother Cancer. 2023 10; 11(10). PMID: 37899131; PMCID: PMC10619091.
      Citations: 1     Fields:    Translation:Humans
    13. Dou Y, Liu Y, Yi X, Olsen LK, Zhu H, Gao Q, Zhou H, Zhang B. SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics. Nat Commun. 2023 09 19; 14(1):5809. PMID: 37726316; PMCID: PMC10509223.
      Citations: 2     Fields:    Translation:Humans
    14. Liao Y, Savage SR, Dou Y, Shi Z, Yi X, Jiang W, Lei JT, Zhang B. A proteogenomics data-driven knowledge base of human cancer. Cell Syst. 2023 09 20; 14(9):777-787.e5. PMID: 37619559; PMCID: PMC10530292.
      Citations: 1     Fields:    Translation:Humans
    15. Li Y, Dou Y, Da Veiga Leprevost F, Geffen Y, Calinawan AP, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Feny? D, Foltz SM, Francis A, Gonzalez-Robles T, G?m?s ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI, Zhang B, Payne SH, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic data and resources for pan-cancer analysis. Cancer Cell. 2023 08 14; 41(8):1397-1406. PMID: 37582339; PMCID: PMC10506762.
      Citations: 4     Fields:    Translation:Humans
    16. Dou Y, Katsnelson L, Gritsenko MA, Hu Y, Reva B, Hong R, Wang YT, Kolodziejczak I, Lu RJ, Tsai CF, Bu W, Liu W, Guo X, An E, Arend RC, Bavarva J, Chen L, Chu RK, Czekanski A, Davoli T, Demicco EG, DeLair D, Devereaux K, Dhanasekaran SM, Dottino P, Dover B, Fillmore TL, Foxall M, Hermann CE, Hiltke T, Hostetter G, Jedryka M, Jewell SD, Johnson I, Kahn AG, Ku AT, Kumar-Sinha C, Kurzawa P, Lazar AJ, Lazcano R, Lei JT, Li Y, Liao Y, Lih TM, Lin TT, Martignetti JA, Masand RP, Matkowski R, McKerrow W, Mesri M, Monroe ME, Moon J, Moore RJ, Nestor MD, Newton C, Omelchenko T, Omenn GS, Payne SH, Petyuk VA, Robles AI, Rodriguez H, Ruggles KV, Rykunov D, Savage SR, Schepmoes AA, Shi T, Shi Z, Tan J, Taylor M, Thiagarajan M, Wang JM, Weitz KK, Wen B, Williams CM, Wu Y, Wyczalkowski MA, Yi X, Zhang X, Zhao R, Mutch D, Chinnaiyan AM, Smith RD, Nesvizhskii AI, Wang P, Wiznerowicz M, Ding L, Mani DR, Zhang H, Anderson ML, Rodland KD, Zhang B, Liu T, Feny? D, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic insights suggest druggable pathways in endometrial carcinoma. Cancer Cell. 2023 09 11; 41(9):1586-1605.e15. PMID: 37567170; PMCID: PMC10631452.
      Citations: 1     Fields:    
    17. Wen B, Zhang B. PepQuery2 democratizes public MS proteomics data for rapid peptide searching. Nat Commun. 2023 04 18; 14(1):2213. PMID: 37072382; PMCID: PMC10113256.
      Citations:    
    18. Jiang W, Wen B, Li K, Zeng WF, da Veiga Leprevost F, Moon J, Petyuk VA, Edwards NJ, Liu T, Nesvizhskii AI, Zhang B. Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification. Mol Cell Proteomics. 2021; 20:100171. PMID: 34737085; PMCID: PMC8609164.
      Citations:    
    19. Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Feny? D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021 09 16; 184(19):5031-5052.e26. PMID: 34534465; PMCID: PMC8654574.
      Citations:    
    20. Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA, Clinical Proteomic Tumor Analysis Consortium, G?m?s ZH, Babur ?, Feny? D. A proteogenomic portrait of lung squamous cell carcinoma. Cell. 2021 08 05; 184(16):4348-4371.e40. PMID: 34358469; PMCID: PMC8475722.
      Citations: 9     Fields:    Translation:HumansCells
    21. Shi Z, Wen B, Gao Q, Zhang B. Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multiomics Data. Mol Cell Proteomics. 2021; 20:100083. PMID: 33887487; PMCID: PMC8165452.
      Citations:    
    22. Lei JT, Zhang B. Proteogenomics drives therapeutic hypothesis generation for precision oncology. Br J Cancer. 2021 07; 125(1):1-3. PMID: 33767418; PMCID: PMC8257710.
      Citations: 1     Fields:    Translation:Humans
    23. Huang C, Chen L, Savage SR, Eguez RV, Dou Y, Li Y, da Veiga Leprevost F, Jaehnig EJ, Lei JT, Wen B, Schnaubelt M, Krug K, Song X, Cieslik M, Chang HY, Wyczalkowski MA, Li K, Colaprico A, Li QK, Clark DJ, Hu Y, Cao L, Pan J, Wang Y, Cho KC, Shi Z, Liao Y, Jiang W, Anurag M, Ji J, Yoo S, Zhou DC, Liang WW, Wendl M, Vats P, Carr SA, Mani DR, Zhang Z, Qian J, Chen XS, Pico AR, Wang P, Chinnaiyan AM, Ketchum KA, Kinsinger CR, Robles AI, An E, Hiltke T, Mesri M, Thiagarajan M, Weaver AM, Sikora AG, Lubinski J, Wierzbicka M, Wiznerowicz M, Satpathy S, Gillette MA, Miles G, Ellis MJ, Omenn GS, Rodriguez H, Boja ES, Dhanasekaran SM, Ding L, Nesvizhskii AI, El-Naggar AK, Chan DW, Zhang H, Zhang B, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell. 2021 03 08; 39(3):361-379.e16. PMID: 33417831; PMCID: PMC7946781.
      Citations: 42     Fields:    Translation:Humans
    24. O'Reilly KC, Anacker AMJ, Rogers TD, Forsberg CG, Wang J, Zhang B, Blakely RD, Veenstra-VanderWeele J. A social encounter drives gene expression changes linked to neuronal function, brain development, and related disorders in mice expressing the serotonin transporter Ala56 variant. Neurosci Lett. 2020 06 21; 730:135027. PMID: 32437898; PMCID: PMC7440397.
      Citations:    
    25. Wen B, Li K, Zhang Y, Zhang B. Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis. Nat Commun. 2020 04 09; 11(1):1759. PMID: 32273506; PMCID: PMC7145864.
      Citations:    
    26. Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekanski A, Jedryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Clinical Proteomic Tumor Analysis Consortium, Feny? D. Proteogenomic Characterization of Endometrial Carcinoma. Cell. 2020 02 20; 180(4):729-748.e26. PMID: 32059776; PMCID: PMC7233456.
      Citations: 96     Fields:    Translation:HumansAnimalsCells
    27. Thangavel H, De Angelis C, Vasaikar S, Bhat R, Jolly MK, Nagi C, Creighton CJ, Chen F, Dobrolecki LE, George JT, Kumar T, Abdulkareem NM, Mao S, Nardone A, Rimawi M, Osborne CK, Lewis MT, Levine H, Zhang B, Schiff R, Giuliano M, Trivedi MV. A CTC-Cluster-Specific Signature Derived from OMICS Analysis of Patient-Derived Xenograft Tumors Predicts Outcomes in Basal-Like Breast Cancer. J Clin Med. 2019 10 24; 8(11). PMID: 31652963; PMCID: PMC6912280.
      Citations: 14     
    28. Zhang B, Kuster B. Proteomics Is Not an Island: Multi-omics Integration Is the Key to Understanding Biological Systems. Mol Cell Proteomics. 2019 08 09; 18(8 suppl 1):S1-S4. PMID: 31399542; PMCID: PMC6692779.
      Citations:    
    29. Savage SR, Shi Z, Liao Y, Zhang B. Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results. Mol Cell Proteomics. 2019 08 09; 18(8 suppl 1):S141-S152. PMID: 31142576; PMCID: PMC6692773.
      Citations:    
    30. Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities. Cell. 2019 05 02; 177(4):1035-1049.e19. PMID: 31031003; PMCID: PMC6768830.
      Citations: 165     Fields:    Translation:HumansCells
    31. Shen J, Vasaikar S, Zhang B. DLAD4U: deriving and prioritizing disease lists from PubMed literature. BMC Bioinformatics. 2018 Dec 28; 19(Suppl 17):495. PMID: 30591010; PMCID: PMC6309061.
      Citations:    
    32. Li K, Wang X, Codreanu SG, Wen B, Chambers MC, Liebler DC, Zhang B. Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity. Mol Cell Proteomics. 2018 03; 17(3):422-430. PMID: 29222161; PMCID: PMC5836368.
      Citations: 25     Fields:    Translation:HumansCells
    33. Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B, Sieber OM, Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B, Sieber OM. Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. Gastroenterology. 2017 10; 153(4):1082-1095. PMID: 28625833; PMCID: PMC5623120.
      Citations:    
    34. Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Feny? D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics. 2017 06; 16(6):959-981. PMID: 28456751; PMCID: PMC5461547.
      Citations:    
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