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Page 1
Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.
Lu D, Kalantar KL, Chu VT, Glascock AL, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR. Lu D, et al. Among authors: holmes o. bioRxiv [Preprint]. 2024 Apr 18:2024.04.12.589250. doi: 10.1101/2024.04.12.589250. bioRxiv. 2024. PMID: 38645206 Free PMC article. Preprint.
IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.
Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, Kislyuk A, Lin MF, Mariano M, Morse T, Reynoso LV, Cruz DR, Sheu J, Tang J, Wang J, Zhang MA, Zhong E, Ahyong V, Lay S, Chea S, Bohl JA, Manning JE, Tato CM, DeRisi JL. Kalantar KL, et al. Gigascience. 2020 Oct 15;9(10):giaa111. doi: 10.1093/gigascience/giaa111. Gigascience. 2020. PMID: 33057676 Free PMC article.
Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.
Langelier C, Lu D, Kalantar K, Chu V, Glascock A, Guerrero E, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones A, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani P, Pickering A, Raphenya A, Alcock B, McArthur A. Langelier C, et al. Among authors: holmes o. Res Sq [Preprint]. 2024 May 2:rs.3.rs-4271356. doi: 10.21203/rs.3.rs-4271356/v1. Res Sq. 2024. PMID: 38746293 Free PMC article. Preprint.
Potassium Supplementation and Prevention of Atrial Fibrillation After Cardiac Surgery: The TIGHT K Randomized Clinical Trial.
O'Brien B, Campbell NG, Allen E, Jamal Z, Sturgess J, Sanders J, Opondo C, Roberts N, Aron J, Maccaroni MR, Gould R, Kirmani BH, Gibbison B, Kunst G, Zarbock A, Kleine-Brüggeney M, Stoppe C, Pearce K, Hughes M, Van Dyck L, Evans R, Montgomery HE, Elbourne D; TIGHT K investigators. O'Brien B, et al. JAMA. 2024 Sep 24;332(12):979-988. doi: 10.1001/jama.2024.17888. JAMA. 2024. PMID: 39215972 Clinical Trial.
Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing.
Fielding D, Lakis V, Dalley AJ, Chittoory H, Newell F, Koufariotis LT, Patch AM, Kazakoff S, Bashirzadeh F, Son JH, Ryan K, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Pattison A, Fairbairn D, Gune S, Christie J, Holmes O, Leonard C, Wood S, Pearson JV, Lakhani SR, Waddell N, Simpson PT, Nones K. Fielding D, et al. Among authors: holmes o. Cancers (Basel). 2024 Feb 15;16(4):785. doi: 10.3390/cancers16040785. Cancers (Basel). 2024. PMID: 38398180 Free PMC article.
The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants-a multi-site prospective cohort study.
Davidson AL, Dressel U, Norris S, Canson DM, Glubb DM, Fortuno C, Hollway GE, Parsons MT, Vidgen ME, Holmes O, Koufariotis LT, Lakis V, Leonard C, Wood S, Xu Q, McCart Reed AE, Pickett HA, Al-Shinnag MK, Austin RL, Burke J, Cops EJ, Nichols CB, Goodwin A, Harris MT, Higgins MJ, Ip EL, Kiraly-Borri C, Lau C, Mansour JL, Millward MW, Monnik MJ, Pachter NS, Ragunathan A, Susman RD, Townshend SL, Trainer AH, Troth SL, Tucker KM, Wallis MJ, Walsh M, Williams RA, Winship IM, Newell F, Tudini E, Pearson JV, Poplawski NK, Mar Fan HG, James PA, Spurdle AB, Waddell N, Ward RL. Davidson AL, et al. Among authors: holmes o. Genome Med. 2023 Sep 19;15(1):74. doi: 10.1186/s13073-023-01223-1. Genome Med. 2023. PMID: 37723522 Free PMC article.
A first-in-class pan-lysyl oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancer.
Chitty JL, Yam M, Perryman L, Parker AL, Skhinas JN, Setargew YFI, Mok ETY, Tran E, Grant RD, Latham SL, Pereira BA, Ritchie SC, Murphy KJ, Trpceski M, Findlay AD, Melenec P, Filipe EC, Nadalini A, Velayuthar S, Major G, Wyllie K, Papanicolaou M, Ratnaseelan S, Phillips PA, Sharbeen G, Youkhana J, Russo A, Blackwell A, Hastings JF, Lucas MC, Chambers CR, Reed DA, Stoehr J, Vennin C, Pidsley R, Zaratzian A, Da Silva AM, Tayao M, Charlton B, Herrmann D, Nobis M, Clark SJ, Biankin AV, Johns AL, Croucher DR, Nagrial A, Gill AJ, Grimmond SM; Australian Pancreatic Cancer Genome Initiative (APGI); Australian Pancreatic Cancer Matrix Atlas (APMA); Pajic M, Timpson P, Jarolimek W, Cox TR. Chitty JL, et al. Nat Cancer. 2023 Sep;4(9):1326-1344. doi: 10.1038/s43018-023-00614-y. Epub 2023 Aug 28. Nat Cancer. 2023. PMID: 37640930 Free PMC article.
Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy.
M Naeini M, Newell F, Aoude LG, Bonazzi VF, Patel K, Lampe G, Koufariotis LT, Lakis V, Addala V, Kondrashova O, Johnston RL, Sharma S, Brosda S, Holmes O, Leonard C, Wood S, Xu Q, Thomas J, Walpole E, Tao Mai G, Ackland SP, Martin J, Burge M, Finch R, Karapetis CS, Shannon J, Nott L, Bohmer R, Wilson K, Barnes E, Zalcberg JR, Mark Smithers B, Simes J, Price T, Gebski V, Nones K, Watson DI, Pearson JV, Barbour AP, Waddell N. M Naeini M, et al. Among authors: holmes o. Nat Commun. 2023 May 31;14(1):3155. doi: 10.1038/s41467-023-38891-x. Nat Commun. 2023. PMID: 37258531 Free PMC article.
173 results