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Jeremiah Wala, MD, PhD

Title(s)Resident Physician, Medicine
SchoolSchool of Medicine
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Weischenfeldt J, Beroukhim R, Campbell PJ. Patterns of somatic structural variation in human cancer genomes. Nature. 2020 02; 578(7793):112-121. PMID: 32025012.
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    2. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 02; 578(7793):102-111. PMID: 32025015.
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    3. Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, Campbell PJ, Tubio JMC. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 03; 52(3):306-319. PMID: 32024998.
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    4. Hong AL, Tseng YY, Wala JA, Kim WJ, Kynnap BD, Doshi MB, Kugener G, Sandoval GJ, Howard TP, Li J, Yang X, Tillgren M, Ghandi M, Sayeed A, Deasy R, Ward A, McSteen B, Labella KM, Keskula P, Tracy A, Connor C, Clinton CM, Church AJ, Crompton BD, Janeway KA, Van Hare B, Sandak D, Gjoerup O, Bandopadhayay P, Clemons PA, Schreiber SL, Root DE, Gokhale PC, Chi SN, Mullen EA, Roberts CW, Kadoch C, Beroukhim R, Ligon KL, Boehm JS, Hahn WC. Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition. Elife. 2019 03 12; 8. PMID: 30860482.
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    5. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 Aug; 24(8):1292. PMID: 29955181.
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    6. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 Aug; 24(8):1290-1291. PMID: 29955182.
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    7. Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D, Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018 07 12; 174(2):433-447.e19. PMID: 29909985.
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    8. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 05; 24(5):679-690. PMID: 29713087.
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    9. Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 2018 04; 28(4):581-591. PMID: 29535149.
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    10. Bi WL, Greenwald NF, Abedalthagafi M, Wala J, Gibson WJ, Agarwalla PK, Horowitz P, Schumacher SE, Esaulova E, Mei Y, Chevalier A, A Ducar M, Thorner AR, van Hummelen P, O Stemmer-Rachamimov A, Artyomov M, Al-Mefty O, Dunn GP, Santagata S, Dunn IF, Beroukhim R. Erratum: Genomic landscape of high-grade meningiomas. NPJ Genom Med. 2017; 2:26. PMID: 29263836.
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    11. Pratiti Bandopadhayay, Noah F. Greenwald, Jeremiah Wala, Ofer Sharpira, Adam Tracy, Mariella Filbin, Ryan O’Rourke, Patricia Ho, Claire Sinai, Hayley Malkin, Lianne Greenspan, Kristen Lawler, Kristine Pelton, Anu Banerjee, Oren Becher, Kaynalakshmi Ayyanar, William Gump, Anne Bendel, Daniel C. Bowers, Mahmoud Nagib, Bradley Weprin, Amy-Lee Bredlau, Sridharan Gururangan, Herbert Fuchs, Kenneth Cohen, Melanie Comito, Mark Dias, Jason Fangusaro, Stewart Goldman, Jennifer D. Elster, Paul G. Fisher, Tadanori Tomita, Tord Alden, Arthur DiPatri, Sharon Gardner, Matthias Karajannis, David Harter, Michael H. Handler, Karen Gauvain, David Limbrick, Jeffrey Leonard, Russ Geyer, Sarah E.S. Leary, Ziab Khatib, Samuel Browd, John Ragheb, Sanjiv Bhatia, Tobey McDonald, Dolly Aguilera, Barun Brahma, Peter Manley, Karen D. Wright, Susan Chi, Sabine Mueller, Jeff Murray, Kellie Nazemi, Lissa Baird, Michelle Monje, Nathan Robison, Erin Kiehna, Mark Krieger, Eric Sandler, Philipp Aldana, Joshua Rubin, Matija Snuderl, Zhihong Joanne Wang, Sandeep Sood, Donna Neuberg, Mario Suva, Rosalind Segal, Nada Jabado, Maneka Puligandla, Michael D. Prados, Karen Marcus, Daphne A. Haas-Kogan, Liliana Goumnerova, Nalin Gupta, Keith Ligon, Rameen Beroukhim, Mark Kieran. DIPG-29. GENOMIC LANDSCAPE OF DIFFUSE INTRINSIC PONTINE GLIOMA: AN ANALYSIS OF THE DIPG-BATS COHORT. Neuro-Oncology. 2017 Jun 1; 19(suppl_4):iv11-iv11.
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    12. Bi WL, Greenwald NF, Abedalthagafi M, Wala J, Gibson WJ, Agarwalla PK, Horowitz P, Schumacher SE, Esaulova E, Mei Y, Chevalier A, Ducar M, Thorner AR, van Hummelen P, Stemmer-Rachamimov A, Artyomov M, Al-Mefty O, Dunn GP, Santagata S, Dunn IF, Beroukhim R. Genomic landscape of high-grade meningiomas. NPJ Genom Med. 2017; 2. PMID: 28713588.
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    13. Wala J, Beroukhim R. SeqLib: a C?++ API for rapid BAM manipulation, sequence alignment and sequence assembly. Bioinformatics. 2017 03 01; 33(5):751-753. PMID: 28011768.
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    14. 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. Clin Cancer Res. 2017 May 01; 23(9):2367-2373. PMID: 27797976.
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    15. 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. Nat Genet. 2016 08; 48(8):848-55. PMID: 27348297.
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    16. Guillaume Bergthold, Pratiti Bandopadhayay, Lori Ramkissoon, Payal Jain, Jeremiah Wala, Steven Schumacher, Shakti Ramkissoon, Pascale Varlet, Mélanie Pages, Matthew Ducar, Paul Van Hummelen, Daniel Bowers, Caterina Giannini, Stephanie Puget, Cynthia Hawkins, Uri Tabori, Almos Klekner, Laszlo Bognar, Peter Burger, Charles Eberhart, Fausto Rodriguez, D. Ashley Hill, Sabine Muller, Daphne Haas-Kogan, Joanna Phillips, Sandro Santagata, Charles Stiles, James Bradner, Nada Jabado, Alon Goren, Jacques Grill, Azra Ligon, Liliana Goumnerova, Angela Waanders, Philip Storm, Mark Kieran, Adam Resnick, Keith Ligon, Rameen Beroukhim. LG-02MYB-QKI REARRANGEMENTS IN ANGIOCENTRIC GLIOMA DRIVE TUMORIGENICITY THROUGH A TRIPARTITE MECHANISM. Neuro-Oncology. 2016 Jun 1; 18(suppl 3):iii78.2-iii78.
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    17. Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G, Artyomov MN, Schreiber R, Govindan R, Meyerson M. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet. 2016 06; 48(6):607-16. PMID: 27158780.
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    18. Wala J, Beroukhim R. CANCER. The oncogene makes its escape. Science. 2016 Mar 25; 351(6280):1398-9. PMID: 27013717.
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    19. Wala J, Zhang CZ, Meyerson M, Beroukhim R. VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules. Bioinformatics. 2016 07 01; 32(13):2029-31. PMID: 27153727.
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    20. Pankaj Agarwalla, Wenya Bi, William Gibson, Shakti Ramkissoon, Steven Schumacher, Jeremiah Wala, Michael Biggs, Anat Stemmer-Rachamimov, Frederick Barker, Robert Martuza, Peleg Horowitz, Ian Dunn, Rameen Beroukhim. Next-Generation Sequencing of Sporadic Schwannomas Reveals Critical Importance of NF2 Alteration. Journal of Neurological Surgery Part B Skull Base. 2016 Feb 1; 77(S 01).
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    21. Bandopadhayay P, Ramkissoon LA, Jain P, Bergthold G, Wala J, Zeid R, Schumacher SE, Urbanski L, O'Rourke R, Gibson WJ, Pelton K, Ramkissoon SH, Han HJ, Zhu Y, Choudhari N, Silva A, Boucher K, Henn RE, Kang YJ, Knoff D, Paolella BR, Gladden-Young A, Varlet P, Pages M, Horowitz PM, Federation A, Malkin H, Tracy AA, Seepo S, Ducar M, Van Hummelen P, Santi M, Buccoliero AM, Scagnet M, Bowers DC, Giannini C, Puget S, Hawkins C, Tabori U, Klekner A, Bognar L, Burger PC, Eberhart C, Rodriguez FJ, Hill DA, Mueller S, Haas-Kogan DA, Phillips JJ, Santagata S, Stiles CD, Bradner JE, Jabado N, Goren A, Grill J, Ligon AH, Goumnerova L, Waanders AJ, Storm PB, Kieran MW, Ligon KL, Beroukhim R, Resnick AC. MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. Nat Genet. 2016 Mar; 48(3):273-82. PMID: 26829751.
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    22. Alice H. Berger, Fujiko Duke, Marcin Imielinski, Nathan Kaplan, Jeremiah Wala, Geng-Xian Shi, Douglas A. Andres, Matthew Meyerson. Abstract PR02: Recurrent oncogenic mutations in the small GTPase RIT1 activate PI3K and MEK. Clinical Cancer Research. 2014 Jan 15; 20(2 Supplement):pr02-pr02.
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    23. Alice H. Berger, Fujiko Duke, Marcin Imielinski, Nathan Kaplan, Jeremiah Wala, Geng-Xian Shi, Douglas A. Andres, Matthew Meyerson. Abstract A04: Recurrent oncogenic mutations in the small GTPase RIT1 activate PI3K and MEK. Clinical Cancer Research. 2014 Jan 15; 20(2 Supplement):a04-a04.
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    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. Nat Genet. 2013 Oct; 45(10):1134-40. PMID: 24071852.
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    25. Wala J, Craft D, Paly J, Zietman A, Efstathiou J. Maximizing dosimetric benefits of IMRT in the treatment of localized prostate cancer through multicriteria optimization planning. Med Dosim. 2013; 38(3):298-303. PMID: 23540492.
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    26. Wala J, Salari E, Chen W, Craft D. Optimal partial-arcs in VMAT treatment planning. Phys Med Biol. 2012 Sep 21; 57(18):5861-74. PMID: 22951381.
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    27. Salari E, Wala J, Craft D. Exploring trade-offs between VMAT dose quality and delivery efficiency using a network optimization approach. Phys Med Biol. 2012 Sep 07; 57(17):5587-600. PMID: 22892588.
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    28. T. Bortfeld, H. Shih, T. Hong, J. Wo, J. Efstathiou, J. Wala, C. Craft. 337 BETTER IMRT: FIRST CLINICAL EXPERIENCE WITH MULTI-CRITERIA OPTIMIZATION. Radiotherapy and Oncology. 2012 Mar 1; 102:s177-s178.
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    29. Craft D, McQuaid D, Wala J, Chen W, Salari E, Bortfeld T. Multicriteria VMAT optimization. Med Phys. 2012 Feb; 39(2):686-96. PMID: 22320778.
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    30. J.A. Wala, D. Craft, J.J. Paly, J.A. Efstathiou. Multi-criteria Optimization of IMRT Plans in Prostate Cancer. International Journal of Radiation Oncology • Biology • Physics. 2011 Oct 1; 81(2):s419-s420.
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    31. A. Trofimov, L. Song, J.A. Wala, D. Craft, H. Lu, S. Mutic, J.A. Efstathiou. Evaluation of the Utility of Parameterized Expectation Values of Dose-Volume Metrics for Quality Control in IMRT and Proton Therapy Planning for Prostate Carcinoma. International Journal of Radiation Oncology • Biology • Physics. 2011 Oct 1; 81(2):s822-s823.
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