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Jeremiah Wala, MD, PhD

Title(s)Resident Physician, Medicine
SchoolSchool of Medicine
Address505 Parnassus Avenue
San Francisco CA 94117
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    Harvard Medical School, Boston, MAMD-PhD05/2019Biomedical Informatics
    Cornell University, Ithaca, NYMS05/2010Applied Physics
    University of California, San Francisco, CAInternal 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. to make corrections and additions.
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    Altmetrics Details 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. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. 2020 Oct 01; 183(1):197-210.e32. Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczynski KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. PMID: 33007263.
      View in: PubMed   Mentions: 2     Fields:    
    2. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 11; 38(11):1347-1355. Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. PMID: 32541955.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    3. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 03; 52(3):306-319. 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. PMID: 32024998.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    4. Patterns of somatic structural variation in human cancer genomes. Nature. 2020 02; 578(7793):112-121. 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. PMID: 32025012.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    5. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 02; 578(7793):102-111. 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. PMID: 32025015.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    6. Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition. Elife. 2019 03 12; 8. 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. PMID: 30860482.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    7. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018 07 12; 174(2):433-447.e19. 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. PMID: 29909985.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    8. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 05; 24(5):679-690. 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. PMID: 29713087.
      View in: PubMed   Mentions: 156     Fields:    Translation:Humans
    9. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 2018 04; 28(4):581-591. 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. PMID: 29535149.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    10. Genomic landscape of high-grade meningiomas. NPJ Genom Med. 2017; 2. 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. PMID: 28713588.
      View in: PubMed   Mentions:
    11. SeqLib: a C?++ API for rapid BAM manipulation, sequence alignment and sequence assembly. Bioinformatics. 2017 03 01; 33(5):751-753. Wala J, Beroukhim R. PMID: 28011768.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    12. Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer. Clin Cancer Res. 2017 May 01; 23(9):2367-2373. 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. PMID: 27797976.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    13. The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis. Nat Genet. 2016 08; 48(8):848-55. 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. PMID: 27348297.
      View in: PubMed   Mentions: 51     Fields:    Translation:Humans
    14. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet. 2016 06; 48(6):607-16. 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. PMID: 27158780.
      View in: PubMed   Mentions: 225     Fields:    Translation:Humans
    15. CANCER. The oncogene makes its escape. Science. 2016 Mar 25; 351(6280):1398-9. Wala J, Beroukhim R. PMID: 27013717.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    16. VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules. Bioinformatics. 2016 07 01; 32(13):2029-31. Wala J, Zhang CZ, Meyerson M, Beroukhim R. PMID: 27153727.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    17. MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. Nat Genet. 2016 Mar; 48(3):273-82. 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. PMID: 26829751.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansCells
    18. 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). 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. .
      View in: Publisher Site   Mentions:
    19. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013 Oct; 45(10):1134-40. PMID: 24071852.
      View in: PubMed   Mentions: 544     Fields:    Translation:Humans
    20. 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.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    21. Optimal partial-arcs in VMAT treatment planning. Phys Med Biol. 2012 Sep 21; 57(18):5861-74. PMID: 22951381.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    22. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    23. Multicriteria VMAT optimization. Med Phys. 2012 Feb; 39(2):686-96. PMID: 22320778.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    24. Multi-criteria Optimization of IMRT Plans in Prostate Cancer. International Journal of Radiation Oncology • Biology • Physics. 2011 Oct 1; 81(2):s419-s420. J.A. Wala, D. Craft, J.J. Paly, J.A. Efstathiou. .
      View in: Publisher Site   Mentions:
    25. 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. A. Trofimov, L. Song, J.A. Wala, D. Craft, H. Lu, S. Mutic, J.A. Efstathiou. .
      View in: Publisher Site   Mentions:
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