Travis Zack, MD, PhD

Assistant Professor

Publications

  1. Sushil M, Zack T, Mandair D, Zheng Z, Wali A, Yu YN, Quan Y, Lituiev D, Butte AJ. A comparative study of large language model-based zero-shot inference and task-specific supervised classification of breast cancer pathology reports. Volume 31 of Issue 10. Journal of the American Medical Informatics Association : JAMIA 2024. PMID: 38900207


  2. Williams CYK, Zack T, Miao BY, Sushil M, Wang M, Kornblith AE, Butte AJ. Use of a Large Language Model to Assess Clinical Acuity of Adults in the Emergency Department. Volume 7 of Issue 5. JAMA network open 2024. PMID: 38713466


  3. Patel A, Doernberg SB, Zack T, Butte AJ, Radtke KK. Predictive Modeling of Drug-Related Adverse Events with Real-World Data: A Case Study of Linezolid Hematologic Outcomes. Clinical pharmacology and therapeutics 2024. PMID: 38345264


  4. Sushil M, Zack T, Mandair D, Zheng Z, Wali A, Yu YN, Quan Y, Butte AJ. A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification. Research square 2024. PMID: 38405831


  5. Zack T, Warner JL. Introducing a Comprehensive Score of Systemic Anticancer Treatment Relevance. Volume 310. Studies in health technology and informatics 2024. PMID: 38269846


  6. Sun S, Zack T, Williams CYK, Sushil M, Butte AJ. Topic modeling on clinical social work notes for exploring social determinants of health factors. Volume 7 of Issue 1. JAMIA Open 2024. PMID: 38223407


  7. Zack T, Lehman E, Suzgun M, Rodriguez JA, Celi LA, Gichoya J, Jurafsky D, Szolovits P, Bates DW, Abdulnour RE, Butte AJ, Alsentzer E. Assessing the potential of GPT-4 to perpetuate racial and gender biases in health care: a model evaluation study. Volume 6 of Issue 1. The Lancet. Digital health 2024. PMID: 38123252


  8. Zack T, Losert KP, Maisel SM, Wild J, Yaqubie A, Herman M, Knox JJ, Mayer RJ, Venook AP, Butte A, O'Neill AF, Abou-Alfa GK, Gordan JD. Defining incidence and complications of fibrolamellar liver cancer through tiered computational analysis of clinical data. NPJ precision oncology 2023. PMID: 36959495


  9. Zack T, Dhaliwal G, Geha R, Margaretten M, Murray S, Hong JC. A Clinical Reasoning-Encoded Case Library Developed through Natural Language Processing. Journal of general internal medicine 2022. PMID: 36071325


  10. Dubois FPB, Shapira O, Greenwald NF, Zack T, Wala J, Tsai JW, Crane A, Baguette A, Hadjadj D, Harutyunyan AS, Kumar KH, Blattner-Johnson M, Vogelzang J, Sousa C, Kang KS, Sinai C, Wang DK, Khadka P, Lewis K, Nguyen L, Malkin H, Ho P, O'Rourke R, Zhang S, Gold R, Deng D, Serrano J, Snuderl M, Jones C, Wright KD, Chi SN, Grill J, Kleinman CL, Goumnerova LC, Jabado N, Jones DTW, Kieran MW, Ligon KL, Beroukhim R, Bandopadhayay P. Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. Volume 3 of Issue 8. Nature cancer 2022. PMID: 35788723


  11. Khadka P, Reitman ZJ, Lu S, Buchan G, Gionet G, Dubois F, Carvalho DM, Shih J, Zhang S, Greenwald NF, Zack T, Shapira O, Pelton K, Hartley R, Bear H, Georgis Y, Jarmale S, Melanson R, Bonanno K, Schoolcraft K, Miller PG, Condurat AL, Gonzalez EM, Qian K, Morin E, Langhnoja J, Lupien LE, Rendo V, Digiacomo J, Wang D, Zhou K, Kumbhani R, Guerra Garcia ME, Sinai CE, Becker S, Schneider R, Vogelzang J, Krug K, Goodale A, Abid T, Kalani Z, Piccioni F, Beroukhim R, Persky NS, Root DE, Carcaboso AM, Ebert BL, Fuller C, Babur O, Kieran MW, Jones C, Keshishian H, Ligon KL, Carr SA, Phoenix TN, Bandopadhayay P. PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. Volume 13 of Issue 1. Nature communications 2022. PMID: 35105861


  12. Arneson D, Elliott M, Mosenia A, Oskotsky B, Solodar S, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties. 2020. PMID: 33199721


  13. Jaimes C, Vajapeyam S, Brown D, Kao PC, Ma C, Greenspan L, Gupta N, Goumnerova L, Bandopahayay P, Dubois F, Greenwald NF, Zack T, Shapira O, Beroukhim R, Ligon KL, Chi S, Kieran MW, Wright KD, Poussaint TY. MR Imaging Correlates for Molecular and Mutational Analyses in Children with Diffuse Intrinsic Pontine Glioma. Volume 41 of Issue 5. AJNR. American journal of neuroradiology 2020. PMID: 32381545


  14. Arneson D, Elliott M, Mosenia A, Oskotsky B, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties. medRxiv : the preprint server for health sciences 2020. PMID: 32511606


  15. Chan P, Halfar J, Adey W, Hetzinger S, Zack T, Moore GWK, Wortmann UG, Williams B, Hou A. Multicentennial record of Labrador Sea primary productivity and sea-ice variability archived in coralline algal barium. Volume 8. Nature communications 2017. PMID: 28569839


  16. Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. Volume 6. eLife 2017. PMID: 28177281


  17. Taylor-Weiner A, Zack T, O'Donnell E, Guerriero JL, Bernard B, Reddy A, Han GC, AlDubayan S, Amin-Mansour A, Schumacher SE, Litchfield K, Turnbull C, Gabriel S, Beroukhim R, Getz G, Carter SL, Hirsch MS, Letai A, Sweeney C, Van Allen EM. Genomic evolution and chemoresistance in germ-cell tumours. Volume 540 of Issue 7631. Nature 2016. PMID: 27905446


  18. Gibson WJ, Ruan DT, Paulson VA, Barletta JA, Hanna GJ, Kraft S, Calles A, Nehs MA, Moore FD, Taylor-Weiner A, Wala JA, Zack TI, Lee TC, Fennessy FM, Alexander EK, Thomas T, Janne PA, Garraway LA, Carter SL, Beroukhim R, Lorch JH, Van Allen EM. Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer. Volume 23 of Issue 9. Clinical cancer research : an official journal of the American Association for Cancer Research 2016. PMID: 27797976


  19. Gibson WJ, Hoivik EA, Halle MK, Taylor-Weiner A, Cherniack AD, Berg A, Holst F, Zack TI, Werner HM, Staby KM, Rosenberg M, Stefansson IM, Kusonmano K, Chevalier A, Mauland KK, Trovik J, Krakstad C, Giannakis M, Hodis E, Woie K, Bjorge L, Vintermyr OK, Wala JA, Lawrence MS, Getz G, Carter SL, Beroukhim R, Salvesen HB. The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis. Volume 48 of Issue 8. Nature genetics 2016. PMID: 27348297


  20. Kim JW, Botvinnik OB, Abudayyeh O, Birger C, Rosenbluh J, Shrestha Y, Abazeed ME, Hammerman PS, DiCara D, Konieczkowski DJ, Johannessen CM, Liberzon A, Alizad-Rahvar AR, Alexe G, Aguirre A, Ghandi M, Greulich H, Vazquez F, Weir BA, Van Allen EM, Tsherniak A, Shao DD, Zack TI, Noble M, Getz G, Beroukhim R, Garraway LA, Ardakani M, Romualdi C, Sales G, Barbie DA, Boehm JS, Hahn WC, Mesirov JP, Tamayo P. Characterizing genomic alterations in cancer by complementary functional associations. Volume 34 of Issue 5. Nature biotechnology 2016. PMID: 27088724


  21. . Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. The New England journal of medicine 2015. PMID: 26061751


  22. Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Volume 28 of Issue 17. Genes & development 2014. PMID: 25184681


  23. Gong Y, Zack TI, Morris LG, Lin K, Hukkelhoven E, Raheja R, Tan IL, Turcan S, Veeriah S, Meng S, Viale A, Schumacher SE, Palmedo P, Beroukhim R, Chan TA. Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins. Volume 46 of Issue 6. Nature genetics 2014. PMID: 24793136


  24. Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhsng CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R. Pan-cancer patterns of somatic copy number alteration. Volume 45 of Issue 10. Nature genetics 2013. PMID: 24071852


  25. Raeder MB, Birkeland E, Trovik J, Krakstad C, Shehata S, Schumacher S, Zack TI, Krohn A, Werner HM, Moody SE, Wik E, Stefansson IM, Holst F, Oyan AM, Tamayo P, Mesirov JP, Kalland KH, Akslen LA, Simon R, Beroukhim R, Salvesen HB. Integrated genomic analysis of the 8q24 amplification in endometrial cancers identifies ATAD2 as essential to MYC-dependent cancers. Volume 8 of Issue 2. PloS one 2013. PMID: 23393560


  26. Hamilton MP, Rajapakshe K, Hartig SM, Reva B, McLellan MD, Kandoth C, Ding L, Zack TI, Gunaratne PH, Wheeler DA, Coarfa C, McGuire SE. Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Volume 4. Nature communications 2013. PMID: 24220575


  27. Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP. ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Volume 23 of Issue 4. Genome research 2012. PMID: 23269662


  28. Rosenbluh J, Nijhawan D, Cox AG, Li X, Neal JT, Schafer EJ, Zack TI, Wang X, Tsherniak A, Schinzel AC, Shao DD, Schumacher SE, Weir BA, Vazquez F, Cowley GS, Root DE, Mesirov JP, Beroukhim R, Kuo CJ, Goessling W, Hahn WC. β-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. Volume 151 of Issue 7. Cell 2012. PMID: 23245941


  29. Nijhawan D, Zack TI, Ren Y, Strickland MR, Lamothe R, Schumacher SE, Tsherniak A, Besche HC, Rosenbluh J, Shehata S, Cowley GS, Weir BA, Goldberg AL, Mesirov JP, Root DE, Bhatia SN, Beroukhim R, Hahn WC. Cancer vulnerabilities unveiled by genomic loss. Volume 150 of Issue 4. Cell 2012. PMID: 22901813


  30. Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G. Absolute quantification of somatic DNA alterations in human cancer. Volume 30 of Issue 5. Nature biotechnology 2012. PMID: 22544022