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Mahmoud Ghandi, Ph.D. - Publications

Affiliations: 
2012 Johns Hopkins University, Baltimore, MD 
Area:
Biomedical Engineering
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29 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
2020 McFarland JM, Paolella BR, Warren A, Geiger-Schuller K, Shibue T, Rothberg M, Kuksenko O, Colgan WN, Jones A, Chambers E, Dionne D, Bender S, Wolpin BM, Ghandi M, Tirosh I, et al. Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action. Nature Communications. 11: 4296. PMID 32855387 DOI: 10.1038/S41467-020-17440-W  0.357
2020 Nusinow DP, Szpyt J, Ghandi M, Rose CM, McDonald ER, Kalocsay M, Jané-Valbuena J, Gelfand E, Schweppe DK, Jedrychowski M, Golji J, Porter DA, Rejtar T, Wang YK, Kryukov GV, et al. Quantitative Proteomics of the Cancer Cell Line Encyclopedia. Cell. 180: 387-402.e16. PMID 31978347 DOI: 10.1016/J.Cell.2019.12.023  0.367
2019 Oberlick EM, Rees MG, Seashore-Ludlow B, Vazquez F, Nelson GM, Dharia NV, Weir BA, Tsherniak A, Ghandi M, Krill-Burger JM, Meyers RM, Wang X, Montgomery P, Root DE, Bieber JM, et al. Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors. Cell Reports. 28: 2331-2344.e8. PMID 31461650 DOI: 10.1016/J.Celrep.2019.07.021  0.372
2019 Togami K, Pastika T, Stephansky J, Ghandi M, Christie AL, Jones KL, Johnson CA, Lindsay RW, Brooks CL, Letai A, Craig JW, Pozdnyakova O, Weinstock DM, Montero J, Aster JC, et al. DNA methyltransferase inhibition overcomes diphthamide pathway deficiencies underlying CD123-targeted treatment resistance. The Journal of Clinical Investigation. PMID 31437130 DOI: 10.1172/Jci128571  0.313
2019 Li H, Ning S, Ghandi M, Kryukov GV, Gopal S, Deik A, Souza A, Pierce K, Keskula P, Hernandez D, Ann J, Shkoza D, Apfel V, Zou Y, Vazquez F, et al. The landscape of cancer cell line metabolism. Nature Medicine. 25: 850-860. PMID 31068703 DOI: 10.1038/S41591-019-0404-8  0.364
2019 Ghandi M, Huang FW, Jané-Valbuena J, Kryukov GV, Lo CC, McDonald ER, Barretina J, Gelfand ET, Bielski CM, Li H, Hu K, Andreev-Drakhlin AY, Kim J, Hess JM, Haas BJ, et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature. PMID 31068700 DOI: 10.1038/S41586-019-1186-3  0.403
2019 Chan EM, Shibue T, McFarland JM, Gaeta B, Ghandi M, Dumont N, Gonzalez A, McPartlan JS, Li T, Zhang Y, Bin Liu J, Lazaro JB, Gu P, Piett CG, Apffel A, et al. WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature. PMID 30971823 DOI: 10.1038/S41586-019-1102-X  0.368
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  0.323
2018 Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, ... ... Ghandi M, et al. Genetic and transcriptional evolution alters cancer cell line drug response. Nature. PMID 30089904 DOI: 10.1038/S41586-018-0409-3  0.358
2017 Stern JL, Paucek RD, Huang FW, Ghandi M, Nwumeh R, Costello JC, Cech TR. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes. Cell Reports. 21: 3700-3707. PMID 29281820 DOI: 10.1016/J.Celrep.2017.12.001  0.33
2017 Kim JW, Abudayyeh OO, Yeerna H, Yeang CH, Stewart M, Jenkins RW, Kitajima S, Konieczkowski DJ, Medetgul-Ernar K, Cavazos T, Mah C, Ting S, Van Allen EM, Cohen O, Mcdermott J, ... ... Ghandi M, et al. Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Systems. 5: 105-118.e9. PMID 28837809 DOI: 10.1016/J.Cels.2017.08.002  0.358
2017 Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, Gill S, Harrington WF, Pantel S, Krill-Burger JM, Meyers RM, Ali L, Goodale A, Lee Y, Jiang G, ... ... Ghandi M, et al. Defining a Cancer Dependency Map. Cell. 170: 564-576.e16. PMID 28753430 DOI: 10.1016/J.Cell.2017.06.010  0.381
2017 Stephansky J, Togami K, Ghandi M, Montero J, vonEgypt N, Lindsay R, Brooks C, Aster JC, Johannessen C, Lane AA. Resistance to SL-401 in AML and BPDCN Is Associated with Loss of the Diphthamide Synthesis Pathway Enzyme DPH1 and Is Reversible By Azacitidine Blood. 130: 797-797. DOI: 10.1182/Blood.V130.Suppl_1.797.797  0.327
2017 Yeerna H, Rangan R, Aguirre A, Kim W, Vazquez F, Weir B, Ghandi M, Tsherniak A, Boehm J, Hahn W, Mesirov J, Tamayo P. Abstract 1555: Pan-cancer patterns of synthetic lethality: statistical modeling of gene dependency profiles Cancer Research. 77: 1555-1555. DOI: 10.1158/1538-7445.Am2017-1555  0.39
2016 Tsvetkov P, Sokol E, Jin D, Brune Z, Thiru P, Ghandi M, Garraway LA, Gupta PB, Santagata S, Whitesell L, Lindquist S. Suppression of 19S proteasome subunits marks emergence of an altered cell state in diverse cancers. Proceedings of the National Academy of Sciences of the United States of America. PMID 28028240 DOI: 10.1073/Pnas.1619067114  0.373
2016 Le X, Antony R, Razavi P, Treacy DJ, Luo F, Ghandi M, Castel P, Scaltriti M, Baselga J, Garraway LA. Systematic functional characterization of resistance to PI3K inhibition in breast cancer. Cancer Discovery. PMID 27604488 DOI: 10.1158/2159-8290.Cd-16-0305  0.328
2016 Ghandi M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, Beer MA. gkmSVM: an R package for gapped-kmer SVM. Bioinformatics (Oxford, England). PMID 27153639 DOI: 10.1093/Bioinformatics/Btw203  0.503
2016 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, et al. Characterizing genomic alterations in cancer by complementary functional associations. Nature Biotechnology. PMID 27088724 DOI: 10.1038/Nbt.3527  0.408
2016 Togami K, Madan V, Li J, Villani A, Sarkizova S, Ghandi M, Buczkowski K, Li Y, Biichle S, Angelot-Delettre F, Seiler M, Buonamici S, Taylor J, Abdel-Wahab O, Hammerman PS, et al. Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN) Harbors Frequent Splicesosome Mutations That Cause Aberrant RNA Splicing Affecting Genes Critical in pDC Differentiation and Function Blood. 128: 738-738. DOI: 10.1182/Blood.V128.22.738.738  0.32
2015 Stransky N, Ghandi M, Kryukov GV, Garraway LA, Lehár J, Liu M, Sonkin D, Kauffmann A, Venkatesan K, Edelman EJ, Riester M, Barretina J, Caponigro G, Schlegel R, Sellers WR, et al. Pharmacogenomic agreement between two cancer cell line data sets Nature. 528: 84-87. PMID 26570998 DOI: 10.1038/Nature15736  0.385
2014 Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, et al. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell. 26: 813-25. PMID 25490447 DOI: 10.1016/J.Ccell.2014.10.012  0.321
2014 Ghandi M, Lee D, Mohammad-Noori M, Beer MA. Enhanced regulatory sequence prediction using gapped k-mer features. Plos Computational Biology. 10: e1003711. PMID 25033408 DOI: 10.1371/Journal.Pcbi.1003711  0.538
2014 Helming KC, Wang X, Wilson BG, Vazquez F, Haswell JR, Manchester HE, Kim Y, Kryukov GV, Ghandi M, Aguirre AJ, Jagani Z, Wang Z, Garraway LA, Hahn WC, Roberts CW. ARID1B is a specific vulnerability in ARID1A-mutant cancers. Nature Medicine. 20: 251-4. PMID 24562383 DOI: 10.1038/Nm.3480  0.381
2014 Ghandi M, Mohammad-Noori M, Beer MA. Robust k-mer frequency estimation using gapped k-mers. Journal of Mathematical Biology. 69: 469-500. PMID 23861010 DOI: 10.1007/S00285-013-0705-3  0.525
2014 Helming K, Wang X, Wilson B, Vazquez F, Haswell J, Manchester H, Kim Y, Kryukov GV, Ghandi M, Aguirre AJ, Jagani Z, Wang Z, Garraway L, Hahn W, Roberts C. Abstract LB-126: ARID1B is a specific vulnerability in ARID1A-mutant cancers Cancer Research. 74. DOI: 10.1158/1538-7445.Am2014-Lb-126  0.391
2013 Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, et al. Punctuated evolution of prostate cancer genomes. Cell. 153: 666-77. PMID 23622249 DOI: 10.1016/J.Cell.2013.03.021  0.345
2013 Landau D, Clement K, Boyle P, Ziller M, Stevenson KE, Kotliar D, Saksena G, Eng M, Sougnez C, Zhang W, Ghandi M, Garraway L, Gabriel S, Lander ES, Brown JR, et al. Increased Local Disorder of DNA Methylation Forms the Basis of High Intra-Leukemic Epigenetic Heterogeneity and Enhances CLL Evolution Blood. 122: 596-596. DOI: 10.1182/Blood.V122.21.596.596  0.34
2012 Ghandi M, Beer MA. Group normalization for genomic data. Plos One. 7: e38695. PMID 22912661 DOI: 10.1371/Journal.Pone.0038695  0.533
2012 Jing Y, Qian Y, Ghandi M, He A, Borys MC, Pan SH, Li ZJ. A mechanistic study on the effect of dexamethasone in moderating cell death in Chinese Hamster Ovary cell cultures. Biotechnology Progress. 28: 490-6. PMID 22140034 DOI: 10.1002/Btpr.747  0.302
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