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Jeremiah Wala - Publications

Affiliations: 
Dana-Farber Cancer Institute and Harvard Medical School, USA 
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 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, ... ... Wala JA, et al. Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics. PMID 36944736 DOI: 10.1038/s41588-023-01319-9  0.535
2023 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. Author Correction: Patterns of somatic structural variation in human cancer genomes. Nature. PMID 36697835 DOI: 10.1038/s41586-022-05597-x  0.507
2023 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, et al. Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. PMID 36697832 DOI: 10.1038/s41586-022-05599-9  0.664
2022 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, et al. Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. Nature Cancer. PMID 35788723 DOI: 10.1038/s43018-022-00403-z  0.697
2021 Tan KT, Kim H, Carrot-Zhang J, Zhang Y, Kim WJ, Kugener G, Wala JA, Howard TP, Chi YY, Beroukhim R, Li H, Ha G, Alper SL, Perlman EJ, Mullen EA, et al. Haplotype-resolved germline and somatic alterations in renal medullary carcinomas. Genome Medicine. 13: 114. PMID 34261517 DOI: 10.1186/s13073-021-00929-4  0.583
2020 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, ... ... Wala JA, et al. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. 183: 197-210.e32. PMID 33007263 DOI: 10.1016/j.cell.2020.08.006  0.573
2020 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, et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 578: 102-111. PMID 32025015 DOI: 10.1038/s41586-020-1965-x  0.699
2020 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, et al. Patterns of somatic structural variation in human cancer genomes. Nature. 578: 112-121. PMID 32025012 DOI: 10.1038/S41586-019-1913-9  0.566
2020 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, ... ... Wala JA, et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics. PMID 32024998 DOI: 10.1038/S41588-019-0562-0  0.576
2019 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, et al. Renal medullary carcinomas depend upon loss and are sensitive to proteasome inhibition. Elife. 8. PMID 30860482 DOI: 10.7554/Elife.44161  0.653
2019 Hong AL, Tseng Y, Wala JA, Kim W, Kynnap BD, Doshi MB, Kugener G, Sandoval GJ, Howard TP, Li J, Yang X, Tillgren M, Ghandi M, Sayeed A, Deasy R, et al. Author response: Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition Elife. DOI: 10.7554/Elife.44161.051  0.587
2018 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, et al. Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nature Medicine. PMID 29955182 DOI: 10.1038/S41591-018-0097-4  0.534
2018 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, et al. Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nature Medicine. PMID 29955181 DOI: 10.1038/S41591-018-0098-3  0.553
2018 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, et al. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. PMID 29909985 DOI: 10.1016/J.Cell.2018.05.036  0.62
2018 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, et al. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nature Medicine. PMID 29713087 DOI: 10.1038/S41591-018-0016-8  0.61
2018 Wala JA, Bandopadhayay P, Greenwald N, 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, et al. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Research. PMID 29535149 DOI: 10.1101/Gr.221028.117  0.722
2018 Hong AL, Tseng Y, Kynnap BD, Doshi MB, Wala J, Sandoval G, Church AJ, Mullen E, Kadoch C, Roberts CWM, Beroukhim R, Boehm JS, Hahn WC. Abstract B18: Modeling renal medullary carcinomas identifies druggable vulnerabilities in SMARCB1-deficient cancers Cancer Research. 78. DOI: 10.1158/1538-7445.Pedca17-B18  0.537
2017 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, et al. Erratum: Genomic landscape of high-grade meningiomas. Npj Genomic Medicine. 2: 26. PMID 29263836 DOI: 10.1038/S41525-017-0023-6  0.736
2017 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, et al. Genomic landscape of high-grade meningiomas. Npj Genomic Medicine. 2. PMID 28713588 DOI: 10.1038/S41525-017-0014-7  0.771
2017 Chapuy B, Stewart C, Dunford A, Kim J, Kamburow A, Redd RA, Lawrence M, Roemer MGM, Li A, Ziepert M, Staiger AM, Wala J, Ducar MD, Leshchiner I, Rheinbay E, et al. Genetically-Defined Diffuse Large B-Cell Lymphoma Subsets Arise By Distinct Pathogenetic Mechanisms and Predict Outcome Blood. 130: 38-38. DOI: 10.1182/Blood.V130.Suppl_1.38.38  0.552
2017 Bandopadhayay P, Greenwald NF, Wala J, Sharpira O, Tracy A, Filbin M, O’Rourke R, Ho P, Sinai C, Malkin H, Greenspan L, Lawler K, Pelton K, Banerjee A, Becher O, et al. DIPG-29. GENOMIC LANDSCAPE OF DIFFUSE INTRINSIC PONTINE GLIOMA: AN ANALYSIS OF THE DIPG-BATS COHORT Neuro-Oncology. 19: iv11-iv11. DOI: 10.1093/Neuonc/Nox083.044  0.659
2016 Wala J, Beroukhim R. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly. Bioinformatics (Oxford, England). PMID 28011768 DOI: 10.1093/Bioinformatics/Btw741  0.437
2016 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, et al. Genomic heterogeneity and exceptional response to dual pathway inhibition in anaplastic thyroid cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 27797976 DOI: 10.1158/1078-0432.Ccr-16-2154-T  0.76
2016 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, ... ... Wala JA, et al. The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis. Nature Genetics. PMID 27348297 DOI: 10.1038/Ng.3602  0.802
2016 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, et al. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nature Genetics. PMID 27158780 DOI: 10.1038/Ng.3564  0.383
2016 Wala J, Zhang CZ, Meyerson M, Beroukhim R. VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules. Bioinformatics (Oxford, England). PMID 27153727 DOI: 10.1093/Bioinformatics/Btw111  0.584
2016 Wala J, Beroukhim R. CANCER. The oncogene makes its escape. Science (New York, N.Y.). 351: 1398-9. PMID 27013717 DOI: 10.1126/Science.Aaf5542  0.535
2016 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, et al. MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. Nature Genetics. PMID 26829751 DOI: 10.1038/Ng.3500  0.743
2016 Gibson WJ, Ruan DT, Paulson VA, Barletta JA, Hanna GJ, Kraft S, Calles A, Nehs M, Moore F, Taylor-Weiner A, Wala J, Zack T, Lee T, Fennessy F, Alexander E, et al. Abstract LB-227: Truncal activating MAPK and PI3K pathway alterations and exceptional response to dual pathway inhibition in anaplastic thyroid cancer Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Lb-227  0.663
2016 Bergthold G, Bandopadhayay P, Ramkissoon L, Jain P, Wala J, Schumacher S, Ramkissoon S, Varlet P, Pages M, Ducar M, Van Hummelen P, Bowers D, Giannini C, Puget S, Hawkins C, et al. LG-02MYB-QKI REARRANGEMENTS IN ANGIOCENTRIC GLIOMA DRIVE TUMORIGENICITY THROUGH A TRIPARTITE MECHANISM Neuro-Oncology. 18: iii78.2-iii78. DOI: 10.1093/Neuonc/Now075.02  0.751
2016 Agarwalla P, Bi W, Gibson W, Ramkissoon S, Schumacher S, Wala J, Biggs M, Stemmer-Rachamimov A, Barker F, Martuza R, Horowitz P, Dunn I, Beroukhim R. Next-Generation Sequencing of Sporadic Schwannomas Reveals Critical Importance of NF2 Alteration Journal of Neurological Surgery Part B: Skull Base. 77. DOI: 10.1055/S-0036-1579807  0.716
2014 Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi GX, Andres DA, Meyerson M. Oncogenic RIT1 mutations in lung adenocarcinoma. Oncogene. 33: 4418-23. PMID 24469055 DOI: 10.1038/onc.2013.581  0.43
2014 Berger AH, Brooks AN, Imielinski M, Cherniack A, Duke F, Kaplan N, Wala J, Meyerson M. Abstract PR08:NF1,MET, andRIT1mutations are RAS-pathway driver events in lung adenocarcinoma Molecular Cancer Research. 12. DOI: 10.1158/1557-3125.Rasonc14-Pr08  0.487
2013 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, et al. Pan-cancer patterns of somatic copy number alteration. Nature Genetics. 45: 1134-40. PMID 24071852 DOI: 10.1038/Ng.2760  0.788
2013 Berger A, Imielinski M, Duke F, Wala J, Kaplan N, Shi G, Andres D, Meyerson M. Abstract C140: RIT1 mutations define a new genetic subset of lung adenocarcinoma. Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Targ-13-C140  0.451
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