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Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops.
Harada T, Kalfon J, Perez MW, Eagle K, Braes FD, Batley R, Heshmati Y, Ferrucio JX, Ewers J, Mehta S, Kossenkov A, Ellegast JM, Bowker A, Wickramasinghe J, Nabet B, Paralkar VR, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. Harada T, et al. Among authors: wickramasinghe j. bioRxiv [Preprint]. 2023 Mar 15:2023.03.13.532438. doi: 10.1101/2023.03.13.532438. bioRxiv. 2023. PMID: 36993171 Free PMC article. Preprint.
A deep learning approach reveals unexplored landscape of viral expression in cancer.
Elbasir A, Ye Y, Schäffer DE, Hao X, Wickramasinghe J, Tsingas K, Lieberman PM, Long Q, Morris Q, Zhang R, Schäffer AA, Auslander N. Elbasir A, et al. Among authors: wickramasinghe j. Nat Commun. 2023 Feb 11;14(1):785. doi: 10.1038/s41467-023-36336-z. Nat Commun. 2023. PMID: 36774364 Free PMC article.
DAXX-ATRX regulation of p53 chromatin binding and DNA damage response.
Gulve N, Su C, Deng Z, Soldan SS, Vladimirova O, Wickramasinghe J, Zheng H, Kossenkov AV, Lieberman PM. Gulve N, et al. Among authors: wickramasinghe j. Nat Commun. 2022 Aug 26;13(1):5033. doi: 10.1038/s41467-022-32680-8. Nat Commun. 2022. PMID: 36028493 Free PMC article.
PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery.
Koc S, Lloyd MW, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson BJ, White B, Lott P, Dobrolecki LE, Dowst H; PDXNet Consortium; Evrard YA, Wallace TA, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Chen MS, Carvajal-Carmona L, Welm AL, Welm BE, Lewis MT, Govindan R, Ding L, Li S, Herlyn M, Davies MA, Roth J, Meric-Bernstam F, Robinson PN, Bult CJ, Davis-Dusenbery B, Dean DA 2nd, Chuang JH. Koc S, et al. NAR Cancer. 2022 Apr 22;4(2):zcac014. doi: 10.1093/narcan/zcac014. eCollection 2022 Jun. NAR Cancer. 2022. PMID: 35475145 Free PMC article.
A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia.
Harada T, Heshmati Y, Kalfon J, Perez MW, Xavier Ferrucio J, Ewers J, Hubbell Engler B, Kossenkov A, Ellegast JM, Yi JS, Bowker A, Zhu Q, Eagle K, Liu T, Kai Y, Dempster JM, Kugener G, Wickramasinghe J, Herbert ZT, Li CH, Vrabič Koren J, Weinstock DM, Paralkar VR, Nabet B, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. Harada T, et al. Among authors: wickramasinghe j. Genes Dev. 2022 Mar 1;36(5-6):368-389. doi: 10.1101/gad.349284.121. Epub 2022 Mar 17. Genes Dev. 2022. PMID: 35301220 Free PMC article.
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