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Page 1
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Earl D, et al. Among authors: shaw ti. Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16. Genome Res. 2011. PMID: 21926179 Free PMC article.
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Bradnam KR, et al. Among authors: shaw ti. Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10. Gigascience. 2013. PMID: 23870653 Free PMC article.
Jagged2 targeting in lung cancer activates anti-tumor immunity via Notch-induced functional reprogramming of tumor-associated macrophages.
Mandula JK, Sierra-Mondragon RA, Jimenez RV, Chang D, Mohamed E, Chang S, Vazquez-Martinez JA, Cao Y, Anadon CM, Lee SB, Das S, Rocha-Munguba L, Pham VM, Li R, Tarhini AA, Furqan M, Dalton W, Churchman M, Moran-Segura CM, Nguyen J, Perez B, Kojetin DJ, Obermayer A, Yu X, Chen A, Shaw TI, Conejo-Garcia JR, Rodriguez PC. Mandula JK, et al. Among authors: shaw ti. Immunity. 2024 May 14;57(5):1124-1140.e9. doi: 10.1016/j.immuni.2024.03.020. Epub 2024 Apr 17. Immunity. 2024. PMID: 38636522
Comprehensive genomic analysis reveals molecular heterogeneity in pediatric ALK-positive anaplastic large cell lymphoma.
Shaw TI, Pounds S, Cao X, Ma J, Palacios G, Mason J, Perkins S, Wu G, Fan Y, Wang J, Zhou X, Obermayer A, Kinney MC, Kraveka J, Gross T, Sandlund J, Zhang J, Mullighan C, Lim MS, Leventaki V. Shaw TI, et al. Res Sq [Preprint]. 2024 Mar 28:rs.3.rs-4145750. doi: 10.21203/rs.3.rs-4145750/v1. Res Sq. 2024. PMID: 38585847 Free PMC article. Preprint.
Genetic and epigenetic features of bilateral Wilms tumor predisposition in patients from the Children's Oncology Group AREN18B5-Q.
Murphy AJ, Cheng C, Williams J, Shaw TI, Pinto EM, Dieseldorff-Jones K, Brzezinski J, Renfro LA, Tornwall B, Huff V, Hong AL, Mullen EA, Crompton B, Dome JS, Fernandez CV, Geller JI, Ehrlich PF, Mulder H, Oak N, Maciezsek J, Jablonowski CM, Fleming AM, Pichavaram P, Morton CL, Easton J, Nichols KE, Clay MR, Santiago T, Zhang J, Yang J, Zambetti GP, Wang Z, Davidoff AM, Chen X. Murphy AJ, et al. Among authors: shaw ti. Nat Commun. 2023 Dec 18;14(1):8006. doi: 10.1038/s41467-023-43730-0. Nat Commun. 2023. PMID: 38110397 Free PMC article.
CBFA2T3-GLIS2-dependent pediatric acute megakaryoblastic leukemia is driven by GLIS2 and sensitive to navitoclax.
Neault M, Lebert-Ghali CÉ, Fournier M, Capdevielle C, Garfinkle EAR, Obermayer A, Cotton A, Boulay K, Sawchyn C, St-Amand S, Nguyen KH, Assaf B, Mercier FE, Delisle JS, Drobetsky EA, Hulea L, Shaw TI, Zuber J, Gruber TA, Melichar HJ, Mallette FA. Neault M, et al. Among authors: shaw ti. Cell Rep. 2023 Sep 26;42(9):113084. doi: 10.1016/j.celrep.2023.113084. Epub 2023 Sep 15. Cell Rep. 2023. PMID: 37716355 Free article.
PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing.
Obermayer AN, Chang D, Nobles G, Teng M, Tan AC, Wang X, Chen YA, Eschrich S, Rodriguez PC, Grass GD, Meshinchi S, Tarhini A, Chen DT, Shaw TI. Obermayer AN, et al. Among authors: shaw ti. BMC Bioinformatics. 2023 Jun 28;24(1):266. doi: 10.1186/s12859-023-05393-y. BMC Bioinformatics. 2023. PMID: 37380943 Free PMC article.
86 results