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A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization.
Pacini C, Duncan E, Gonçalves E, Gilbert J, Bhosle S, Horswell S, Karakoc E, Lightfoot H, Curry E, Muyas F, Bouaboula M, Pedamallu CS, Cortes-Ciriano I, Behan FM, Zalmas LP, Barthorpe A, Francies H, Rowley S, Pollard J, Beltrao P, Parts L, Iorio F, Garnett MJ. Pacini C, et al. Among authors: bhosle s. Cancer Cell. 2024 Feb 12;42(2):301-316.e9. doi: 10.1016/j.ccell.2023.12.016. Epub 2024 Jan 11. Cancer Cell. 2024. PMID: 38215750 Free article.
Curation of viral genomes: challenges, applications and the way forward.
Kulkarni-Kale U, Bhosle SG, Manjari GS, Joshi M, Bansode S, Kolaskar AS. Kulkarni-Kale U, et al. Among authors: bhosle sg. BMC Bioinformatics. 2006 Dec 18;7 Suppl 5(Suppl 5):S12. doi: 10.1186/1471-2105-7-S5-S12. BMC Bioinformatics. 2006. PMID: 17254296 Free PMC article.
VirGen: a comprehensive viral genome resource.
Kulkarni-Kale U, Bhosle S, Manjari GS, Kolaskar AS. Kulkarni-Kale U, et al. Among authors: bhosle s. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D289-92. doi: 10.1093/nar/gkh098. Nucleic Acids Res. 2004. PMID: 14681415 Free PMC article.
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.
Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. Iorio F, et al. Among authors: bhosle sg. BMC Genomics. 2018 Aug 13;19(1):604. doi: 10.1186/s12864-018-4989-y. BMC Genomics. 2018. PMID: 30103702 Free PMC article.
Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis.
Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, Dawson KJ, Ju YS, Iorio F, Tubio JMC, Koh CC, Georgakopoulos-Soares I, Rodríguez-Martín B, Otlu B, O'Meara S, Butler AP, Menzies A, Bhosle SG, Raine K, Jones DR, Teague JW, Beal K, Latimer C, O'Neill L, Zamora J, Anderson E, Patel N, Maddison M, Ng BL, Graham J, Garnett MJ, McDermott U, Nik-Zainal S, Campbell PJ, Stratton MR. Petljak M, et al. Among authors: bhosle sg. Cell. 2019 Mar 7;176(6):1282-1294.e20. doi: 10.1016/j.cell.2019.02.012. Cell. 2019. PMID: 30849372 Free PMC article.
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group; Creighton CJ; PCAWG Consortium. Zhang Y, et al. Nat Commun. 2020 Feb 5;11(1):736. doi: 10.1038/s41467-019-13885-w. Nat Commun. 2020. PMID: 32024823 Free PMC article.
Pathway and network analysis of more than 2500 whole cancer genomes.
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; PCAWG Drivers and Functional Interpretation Working Group; Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium. Reyna MA, et al. Nat Commun. 2020 Feb 5;11(1):729. doi: 10.1038/s41467-020-14367-0. Nat Commun. 2020. PMID: 32024854 Free PMC article.
Patterns of somatic structural variation in human cancer genomes.
Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M; PCAWG Structural Variation Working Group; Weischenfeldt J, Beroukhim R, Campbell PJ; PCAWG Consortium. Li Y, et al. Nature. 2020 Feb;578(7793):112-121. doi: 10.1038/s41586-019-1913-9. Epub 2020 Feb 5. Nature. 2020. PMID: 32025012 Free PMC article.
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
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; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group; Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium. Rheinbay E, et al. Nature. 2020 Feb;578(7793):102-111. doi: 10.1038/s41586-020-1965-x. Epub 2020 Feb 5. Nature. 2020. PMID: 32025015 Free PMC article.
120 results