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CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.
Krysiak K, Danos AM, Saliba J, McMichael JF, Coffman AC, Kiwala S, Barnell EK, Sheta L, Grisdale CJ, Kujan L, Pema S, Lever J, Ridd S, Spies NC, Andric V, Chiorean A, Rieke DT, Clark KA, Reisle C, Venigalla AC, Evans M, Jani P, Takahashi H, Suda A, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Kesserwan C, Lamping M, Shen H, Marr AR, Hoang MH, Singhal K, Khanfar M, Li BV, Lin WH, Terraf P, Corson LB, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith M, Griffith OL. Krysiak K, et al. Among authors: milosavljevic a. Nucleic Acids Res. 2023 Jan 6;51(D1):D1230-D1241. doi: 10.1093/nar/gkac979. Nucleic Acids Res. 2023. PMID: 36373660 Free PMC article.
Integrative analysis of 111 reference human epigenomes.
Roadmap Epigenomics Consortium; Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Roadmap Epigenomics Consortium, et al. Among authors: milosavljevic a. Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248. Nature. 2015. PMID: 25693563 Free PMC article.
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. Rozowsky J, et al. Among authors: milosavljevic a. Cell. 2023 Mar 30;186(7):1493-1511.e40. doi: 10.1016/j.cell.2023.02.018. Cell. 2023. PMID: 37001506 Free PMC article.
The NanoFlow Repository.
Arce JE, Welsh JA, Cook S, Tigges J, Ghiran I, Jones JC, Jackson A, Roth M, Milosavljevic A. Arce JE, et al. Among authors: milosavljevic a. Bioinformatics. 2023 Jun 1;39(6):btad368. doi: 10.1093/bioinformatics/btad368. Bioinformatics. 2023. PMID: 37285317 Free PMC article.
Deconvolution of cancer cell states by the XDec-SM method.
Murillo OD, Petrosyan V, LaPlante EL, Dobrolecki LE, Lewis MT, Milosavljevic A. Murillo OD, et al. Among authors: milosavljevic a. PLoS Comput Biol. 2023 Aug 14;19(8):e1011365. doi: 10.1371/journal.pcbi.1011365. eCollection 2023 Aug. PLoS Comput Biol. 2023. PMID: 37578979 Free PMC article.
Generating Clinical-Grade Gene-Disease Validity Classifications Through the ClinGen Data Platforms.
Wright MW, Thaxton CL, Nelson T, DiStefano MT, Savatt JM, Brush MH, Cheung G, Mandell ME, Wulf B, Ward TJ, Goehringer S, O'Neill T, Weller P, Preston CG, Keseler IM, Goldstein JL, Strande NT, McGlaughon J, Azzariti DR, Cordova I, Dziadzio H, Babb L, Riehle K, Milosavljevic A, Martin CL, Rehm HL, Plon SE, Berg JS, Riggs ER, Klein TE. Wright MW, et al. Among authors: milosavljevic a. Annu Rev Biomed Data Sci. 2024 Aug;7(1):31-50. doi: 10.1146/annurev-biodatasci-102423-112456. Epub 2024 Jul 24. Annu Rev Biomed Data Sci. 2024. PMID: 38663031 Review.
exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers.
LaPlante EL, Stürchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. LaPlante EL, et al. Among authors: milosavljevic a. Cell Genom. 2023 Apr 20;3(5):100303. doi: 10.1016/j.xgen.2023.100303. eCollection 2023 May 10. Cell Genom. 2023. PMID: 37228754 Free PMC article.
Identifying biomarkers of differential chemotherapy response in TNBC patient-derived xenografts with a CTD/WGCNA approach.
Petrosyan V, Dobrolecki LE, Thistlethwaite L, Lewis AN, Sallas C, Srinivasan RR, Lei JT, Kovacevic V, Obradovic P, Ellis MJ, Osborne CK, Rimawi MF, Pavlick A, Shafaee MN, Dowst H, Jain A, Saltzman AB, Malovannaya A, Marangoni E, Welm AL, Welm BE, Li S, Wulf GM, Sonzogni O, Huang C, Vasaikar S, Hilsenbeck SG, Zhang B, Milosavljevic A, Lewis MT. Petrosyan V, et al. Among authors: milosavljevic a. iScience. 2022 Dec 12;26(1):105799. doi: 10.1016/j.isci.2022.105799. eCollection 2023 Jan 20. iScience. 2022. PMID: 36619972 Free PMC article.
243 results