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Jonathan Thomas Lei

TitlePostdoc Fellows and Associates
InstitutionBaylor College of Medicine
DepartmentPostDoc
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    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.
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    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. Moon CI, Elizarraras JM, Lei JT, Jia B, Zhang B. ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials. Nucleic Acids Res. 2024 Jan 05; 52(D1):D1201-D1209. PMID: 37811874; PMCID: PMC10767859.
      Citations: 1     Fields:    Translation:Humans
    2. Yi X, Wen B, Ji S, Saltzman A, Jaehnig EJ, Lei JT, Gao Q, Zhang B, 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:    Fields:    Translation:HumansCells
    3. 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
    4. Gou X, Kim BJ, Anurag M, Lei JT, Young MN, Holt MV, Fandino D, Vollert CT, Singh P, Alzubi MA, Malovannaya A, Dobrolecki LE, Lewis MT, Li S, Foulds CE, Ellis MJ. Kinome Reprogramming Is a Targetable Vulnerability in ESR1 Fusion-Driven Breast Cancer. Cancer Res. 2023 10 02; 83(19):3237-3251. PMID: 37071495; PMCID: PMC10543968.
      Citations:    Fields:    Translation:HumansAnimals
    5. 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
    6. Wang J, Saltzman AB, Jaehnig EJ, Lei JT, Malovannaya A, Holt MV, Young MN, Rimawi MF, Ademuyiwa FO, Anurag M, Kim BJ, Ellis MJ. Kinase Inhibitor Pulldown Assay Identifies a Chemotherapy Response Signature in Triple-negative Breast Cancer Based on Purine-binding Proteins. Cancer Res Commun. 2023 08; 3(8):1551-1563. PMID: 37587913; PMCID: PMC10426551.
      Citations:    Translation:Humans
    7. 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
    8. 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:    
    9. Kim BJ, Zheng ZY, Lei JT, Holt MV, Chen A, Peng J, Fandino D, Singh P, Kennedy H, Dou Y, Chica-Parrado MDR, Bikorimana E, Ye D, Wang Y, Hanker AB, Mohamed N, Hilsenbeck SG, Lim B, Asirvatham JR, Sreekumar A, Zhang B, Miles G, Anurag M, Ellis MJ, Chang EC. Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor-positive Breast Cancers for Targeted Treatment. Cancer Res Commun. 2023 07; 3(7):1366-1377. PMID: 37501682; PMCID: PMC10370361.
      Citations:    Translation:Humans
    10. Oropeza E, Seker S, Carrel S, Mazumder A, Lozano D, Jimenez A, VandenHeuvel SN, Noltensmeyer DA, Punturi NB, Lei JT, Lim B, Waltz SE, Raghavan SA, Bainbridge MN, Haricharan S. Molecular portraits of cell cycle checkpoint kinases in cancer evolution, progression, and treatment responsiveness. Sci Adv. 2023 06 30; 9(26):eadf2860. PMID: 37390209; PMCID: PMC10313178.
      Citations:    Fields:    Translation:Humans
    11. Yi X, Wen B, Ji S, Saltzman A, Jaehnig EJ, Lei JT, Gao Q, Zhang B. Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification. bioRxiv. 2023 Jan 12. PMID: 36711982; PMCID: PMC9882090.
      Citations:    
    12. Petrosyan V, Dobrolecki LE, Thistlethwaite L, Lewis AN, Sallas C, Srinivasan RR, Lei JT, Kovacevic V, Obradovic P, Ellis MJ, Osborne CK, Rimawi MF, Pavlick A, Shafaee MN, Dowst H, Jain A, Saltzman AB, Malovannaya A, Marangoni E, Welm AL, Welm BE, Li S, Wulf GM, Sonzogni O, Huang C, Vasaikar S, Hilsenbeck SG, Zhang B, Milosavljevic A, Lewis MT. Identifying biomarkers of differential chemotherapy response in TNBC patient-derived xenografts with a CTD/WGCNA approach. iScience. 2023 Jan 20; 26(1):105799. PMID: 36619972; PMCID: PMC9813793.
      Citations: 4     
    13. Anurag M, Jaehnig EJ, Krug K, Lei JT, Bergstrom EJ, Kim BJ, Vashist TD, Huynh AMT, Dou Y, Gou X, Huang C, Shi Z, Wen B, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Dobrolecki LE, Rodriguez H, Robles AI, Hiltke T, Lewis MT, Nangia JR, Nemati Shafaee M, Li S, Hagemann IS, Hoog J, Lim B, Osborne CK, Mani DR, Gillette MA, Zhang B, Echeverria GV, Miles G, Rimawi MF, Carr SA, Ademuyiwa FO, Satpathy S, Ellis MJ. Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer. Cancer Discov. 2022 11 02; 12(11):2586-2605. PMID: 36001024; PMCID: PMC9627136.
      Citations:    
    14. Zheng ZY, Elsarraj H, Lei JT, Hong Y, Anurag M, Feng L, Kennedy H, Shen Y, Lo F, Zhao Z, Zhang B, Zhang XH, Tawfik OW, Behbod F, Chang EC. Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness. Breast Cancer Res. 2022 10 18; 24(1):68. PMID: 36258226; PMCID: PMC9578182.
      Citations:    Fields:    Translation:Humans
    15. Goldblatt DL, Valverde Ha G, Wali S, Kulkarni VV, Longmire MK, Jaramillo AM, Chittuluru RP, Fouts A, Martinez-Moczygemba M, Lei JT, Huston DP, Tuvim MJ, Dickey BF, Evans SE. Epithelial immunomodulation by aerosolized Toll-like receptor agonists prevents allergic inflammation in airway mucosa in mice. Front Pharmacol. 2022; 13:833380. PMID: 36105216; PMCID: PMC9464972.
      Citations:    
    16. Eteleeb AM, Thunuguntla PK, Gelev KZ, Tang CY, Rozycki EB, Miller A, Lei JT, Jayasinghe RG, Dang HX, White NM, Reis-Filho JS, Mardis ER, Ellis MJ, Ding L, Silva-Fisher JM, Maher CA. LINC00355 regulates p27KIP expression by binding to MENIN to induce proliferation in late-stage relapse breast cancer. NPJ Breast Cancer. 2022 Apr 13; 8(1):49. PMID: 35418131; PMCID: PMC9007952.
      Citations:    
    17. Gou X, Anurag M, Lei JT, Kim BJ, Singh P, Seker S, Fandino D, Han A, Rehman S, Hu J, Korchina V, Doddapaneni H, Dobrolecki LE, Mitsiades N, Lewis MT, Welm AL, Li S, Lee AV, Robinson DR, Foulds CE, Ellis MJ. Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer. Cancer Res. 2021 12 15; 81(24):6259-6272. PMID: 34711608; PMCID: PMC9234971.
      Citations:    Fields:    Translation:HumansAnimalsCells
    18. 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
    19. 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
    20. 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
    21. Krug K, Jaehnig EJ, Satpathy S, Blumenberg L, Karpova A, Anurag M, Miles G, Geffen Y, Tang LC, Heiman DI, Cao S, Maruvka YE, Lei JT, Huang C, Kothadia RB, Colaprico A, Birger C, Wang J, Dou Y, Wen B, Shi Z, Liao Y, Wiznerowicz M, Wyczalkowski MA, Chen XS, Kennedy JJ, Paulovich AG, Thiagarajan M, Kinsinger CR, Hiltke T, Boja ES, Mesri M, Robles AI, Rodriguez H, Westbrook TF, Ding L, Getz G, Clauser KR, Ruggles KV, Zhang B, Mani DR, Carr SA, Ellis MJ, Gillette MA, Clinical Proteomic Tumor Analysis Consortium, Mertins P, Feny? D. Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy. Cell. 2020 11 25; 183(5):1436-1456.e31. PMID: 33212010; PMCID: PMC8077737.
      Citations: 65     Fields:    Translation:HumansCells
    22. Zheng ZY, Anurag M, Lei JT, Cao J, Singh P, Peng J, Kennedy H, Nguyen NC, Chen Y, Lavere P, Li J, Du XH, Cakar B, Song W, Kim BJ, Shi J, Seker S, Chan DW, Zhao GQ, Chen X, Banks KC, Lanman RB, Shafaee MN, Zhang XH, Vasaikar S, Zhang B, Hilsenbeck SG, Li W, Foulds CE, Ellis MJ, Chang EC. Neurofibromin Is an Estrogen Receptor-a Transcriptional Co-repressor in Breast Cancer. Cancer Cell. 2020 03 16; 37(3):387-402.e7. PMID: 32142667; PMCID: PMC7286719.
      Citations: 22     Fields:    Translation:HumansAnimalsCells
    23. Lei JT, Anurag M, Haricharan S, Gou X, Ellis MJ. Endocrine therapy resistance: new insights. Breast. 2019 Nov; 48 Suppl 1:S26-S30. PMID: 31839155; PMCID: PMC6939855.
      Citations: 13     Fields:    Translation:Humans
    24. Rodrigues-Peres RM, de S Carvalho B, Anurag M, Lei JT, Conz L, Ramalho S, de Paiva GR, Derchain SFM, Lopes-Cendes I, Ellis MJ, Sarian LO, Gon?alves R, Cardoso Filho C. Copy number alterations associated with clinical features in an underrepresented population with breast cancer. Mol Genet Genomic Med. 2019 07; 7(7):e00750. PMID: 31099189; PMCID: PMC6625096.
      Citations: 4     Fields:    Translation:Humans
    25. Lei JT, Gou X, Seker S, Ellis MJ. ESR1 alterations and metastasis in estrogen receptor positive breast cancer. J Cancer Metastasis Treat. 2019; 5. PMID: 31106278; PMCID: PMC6519472.
      Citations: 35     
    26. Matsunuma R, Chan DW, Kim BJ, Singh P, Han A, Saltzman AB, Cheng C, Lei JT, Wang J, Roberto da Silva L, Sahin E, Leng M, Fan C, Perou CM, Malovannaya A, Ellis MJ. DPYSL3 modulates mitosis, migration, and epithelial-to-mesenchymal transition in claudin-low breast cancer. Proc Natl Acad Sci U S A. 2018 12 18; 115(51):E11978-E11987. PMID: 30498031; PMCID: PMC6305012.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    27. Lei JT, Gou X, Ellis MJ. ESR1 fusions drive endocrine therapy resistance and metastasis in breast cancer. Mol Cell Oncol. 2018; 5(6):e1526005. PMID: 30525098; PMCID: PMC6276858.
      Citations: 6     
    28. Lei JT, Shao J, Zhang J, Iglesia M, Chan DW, Cao J, Anurag M, Singh P, He X, Kosaka Y, Matsunuma R, Crowder R, Hoog J, Phommaly C, Punturi N, Schmidt C, Bartram A, Jou E, Devarakonda V, Holloway KR, Lai WV, Hampton O, Rogers A, Tobias E, Parikh PA, Davies SR, Li S, Ma CX, Suman VJ, Hunt KK, Watson MA, Hoadley KA, Thompson EA, Chen X, Kavuri SM, Creighton CJ, Maher CA, Perou CM, Haricharan S, Ellis MJ, Goncalves R, Ramalho S, Peres RMR. Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer. Cell Rep. 2018 08 07; 24(6):1434-1444.e7. PMID: 30089255; PMCID: PMC6171747.
      Citations: 35     Fields:    Translation:Humans
    29. Gates LA, Gu G, Chen Y, Rohira AD, Lei JT, Hamilton RA, Yu Y, Lonard DM, Wang J, Wang SP, Edwards DG, Lavere PF, Shao J, Yi P, Jain A, Jung SY, Malovannaya A, Li S, Shao J, Roeder RG, Ellis MJ, Qin J, Fuqua SAW, O'Malley BW, Foulds CE. Proteomic profiling identifies key coactivators utilized by mutant ERa proteins as potential new therapeutic targets. Oncogene. 2018 08; 37(33):4581-4598. PMID: 29748621; PMCID: PMC6095836.
      Citations: 28     Fields:    Translation:HumansCells
    30. Haricharan S, Punturi N, Singh P, Holloway KR, Anurag M, Schmelz J, Schmidt C, Lei JT, Suman V, Hunt K, Olson JA, Hoog J, Li S, Huang S, Edwards DP, Kavuri SM, Bainbridge MN, Ma CX, Ellis MJ. Loss of MutL Disrupts CHK2-Dependent Cell-Cycle Control through CDK4/6 to Promote Intrinsic Endocrine Therapy Resistance in Primary Breast Cancer. Cancer Discov. 2017 10; 7(10):1168-1183. PMID: 28801307; PMCID: PMC5733075.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    31. 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, Ellis MJ, Carr SA, NCI CPTAC, Feny? D. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016 06 02; 534(7605):55-62. PMID: 27251275; PMCID: PMC5102256.
      Citations: 618     Fields:    Translation:HumansCells
    32. Haricharan S, Lei J, Ellis M. Mammary Ductal Environment Is Necessary for Faithful Maintenance of Estrogen Signaling in ER? Breast Cancer. Cancer Cell. 2016 Mar 14; 29(3):249-250. PMID: 26977876; PMCID: PMC5047062.
      Citations: 5     Fields:    Translation:HumansAnimals
    33. Lei JT, Mazumdar T, Martinez-Moczygemba M. Three lysine residues in the common ? chain of the interleukin-5 receptor are required for Janus kinase (JAK)-dependent receptor ubiquitination, endocytosis, and signaling. J Biol Chem. 2011 Nov 18; 286(46):40091-103. PMID: 21965659; PMCID: PMC3220589.
      Citations: 9     Fields:    Translation:HumansCells
    34. Martinez-Moczygemba M, Doan ML, Elidemir O, Fan LL, Cheung SW, Lei JT, Moore JP, Tavana G, Lewis LR, Zhu Y, Muzny DM, Gibbs RA, Huston DP. Pulmonary alveolar proteinosis caused by deletion of the GM-CSFRalpha gene in the X chromosome pseudoautosomal region 1. J Exp Med. 2008 Nov 24; 205(12):2711-6. PMID: 18955567; PMCID: PMC2585851.
      Citations: 77     Fields:    Translation:HumansAnimalsCells
    35. Lei JT, Martinez-Moczygemba M. Separate endocytic pathways regulate IL-5 receptor internalization and signaling. J Leukoc Biol. 2008 Aug; 84(2):499-509. PMID: 18511572; PMCID: PMC2493073.
      Citations: 19     Fields:    Translation:HumansCells
    36. Martinez-Moczygemba M, Huston DP, Lei JT. JAK kinases control IL-5 receptor ubiquitination, degradation, and internalization. J Leukoc Biol. 2007 Apr; 81(4):1137-48. PMID: 17227823.
      Citations: 19     Fields:    Translation:HumansCells
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