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417 results

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Page 1
An international report on bacterial communities in esophageal squamous cell carcinoma.
Nomburg J, Bullman S, Nasrollahzadeh D, Collisson EA, Abedi-Ardekani B, Akoko LO, Atkins JR, Buckle GC, Gopal S, Hu N, Kaimila B, Khoshnia M, Malekzadeh R, Menya D, Mmbaga BT, Moody S, Mulima G, Mushi BP, Mwaiselage J, Mwanga A, Newton Y, Ng DL, Radenbaugh A, Rwakatema DS, Selekwa M, Schüz J, Taylor PR, Vaske C, Goldstein A, Stratton MR, McCormack V, Brennan P, DeCaprio JA, Meyerson M, Mmbaga EJ, Van Loon K. Nomburg J, et al. Among authors: stratton mr. Int J Cancer. 2022 Dec 1;151(11):1947-1959. doi: 10.1002/ijc.34212. Epub 2022 Aug 11. Int J Cancer. 2022. PMID: 35837755 Free PMC article.
Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment.
Díaz-Gay M, Vangara R, Barnes M, Wang X, Islam SMA, Vermes I, Narasimman NB, Yang T, Jiang Z, Moody S, Senkin S, Brennan P, Stratton MR, Alexandrov LB. Díaz-Gay M, et al. Among authors: stratton mr. bioRxiv [Preprint]. 2023 Jul 11:2023.07.10.548264. doi: 10.1101/2023.07.10.548264. bioRxiv. 2023. Update in: Bioinformatics. 2023 Dec 1;39(12):btad756. doi: 10.1093/bioinformatics/btad756 PMID: 37502962 Free PMC article. Updated. Preprint.
Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment.
Díaz-Gay M, Vangara R, Barnes M, Wang X, Islam SMA, Vermes I, Duke S, Narasimman NB, Yang T, Jiang Z, Moody S, Senkin S, Brennan P, Stratton MR, Alexandrov LB. Díaz-Gay M, et al. Among authors: stratton mr. Bioinformatics. 2023 Dec 1;39(12):btad756. doi: 10.1093/bioinformatics/btad756. Bioinformatics. 2023. PMID: 38096571 Free PMC article.
The Mutographs biorepository: A unique genomic resource to study cancer around the world.
Perdomo S, Abedi-Ardekani B, de Carvalho AC, Ferreiro-Iglesias A, Gaborieau V, Cattiaux T, Renard H, Chopard P, Carreira C, Spanu A, Nikmanesh A, Cardoso Penha RC, Antwi SO, Ashton-Prolla P, Canova C, Chitapanarux T, Cox R, Curado MP, de Oliveira JC, Dzamalala C, Fabianova E, Ferri L, Fitzgerald R, Foretova L, Gallinger S, Goldstein AM, Holcatova I, Huertas A, Janout V, Jarmalaite S, Kaneva R, Kowalski LP, Kulis T, Lagiou P, Lissowska J, Malekzadeh R, Mates D, McCorrmack V, Menya D, Mhatre S, Mmbaga BT, de Moricz A, Nyirády P, Ognjanovic M, Papadopoulou K, Polesel J, Purdue MP, Rascu S, Rebolho Batista LM, Reis RM, Ribeiro Pinto LF, Rodríguez-Urrego PA, Sangkhathat S, Sangrajrang S, Shibata T, Stakhovsky E, Świątkowska B, Vaccaro C, Vasconcelos de Podesta JR, Vasudev NS, Vilensky M, Yeung J, Zaridze D, Zendehdel K, Scelo G, Chanudet E, Wang J, Fitzgerald S, Latimer C, Moody S, Humphreys L, Alexandrov LB, Stratton MR, Brennan P. Perdomo S, et al. Among authors: stratton mr. Cell Genom. 2024 Mar 13;4(3):100500. doi: 10.1016/j.xgen.2024.100500. Epub 2024 Feb 6. Cell Genom. 2024. PMID: 38325367 Free PMC article. Review.
Integrative pathway enrichment analysis of multivariate omics data.
Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; PCAWG Drivers and Functional Interpretation Working Group; Reimand J; PCAWG Consortium. Paczkowska M, et al. Nat Commun. 2020 Feb 5;11(1):735. doi: 10.1038/s41467-019-13983-9. Nat Commun. 2020. PMID: 32024846 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.
Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group; Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group; Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. PCAWG Transcriptome Core Group, et al. Nature. 2020 Feb;578(7793):129-136. doi: 10.1038/s41586-020-1970-0. Epub 2020 Feb 5. Nature. 2020. PMID: 32025019 Free PMC article.
Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor.
Islam SMA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Islam SMA, et al. Among authors: stratton mr. Cell Genom. 2022 Nov 9;2(11):None. doi: 10.1016/j.xgen.2022.100179. Cell Genom. 2022. PMID: 36388765 Free PMC article.
417 results