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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: haimel m. 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: haimel m. Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10. Gigascience. 2013. PMID: 23870653 Free PMC article.
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.
Watson-Haigh NS, Shang CA, Haimel M, Kostadima M, Loos R, Deshpande N, Duesing K, Li X, McGrath A, McWilliam S, Michnowicz S, Moolhuijzen P, Quenette S, Revote JN, Tyagi S, Schneider MV. Watson-Haigh NS, et al. Among authors: haimel m. Brief Bioinform. 2013 Sep;14(5):563-74. doi: 10.1093/bib/bbt022. Epub 2013 Mar 29. Brief Bioinform. 2013. PMID: 23543352 Free PMC article.
A single-center cohort study of patients with hereditary spherocytosis in Central Europe reveals a high frequency of novel disease-causing genotypes.
Kager L, Jimenez-Heredia R, Zeitlhofer P, Novak W, Eder SK, Segarra-Roca A, Frohne A, Nebral K, Haimel M, Geyeregger R, Roetzer-Londgin K, Haas OA, Boztug K. Kager L, et al. Among authors: haimel m. Hemasphere. 2024 Jan 26;8(1):e31. doi: 10.1002/hem3.31. eCollection 2024 Jan. Hemasphere. 2024. PMID: 38434532 Free PMC article. No abstract available.
Curation and expansion of the Human Phenotype Ontology for systemic autoinflammatory diseases improves phenotype-driven disease-matching.
Maassen W, Legger G, Kul Cinar O, van Daele P, Gattorno M, Bader-Meunier B, Wouters C, Briggs T, Johansson L, van der Velde J, Swertz M, Omoyinmi E, Hoppenreijs E, Belot A, Eleftheriou D, Caorsi R, Aeschlimann F, Boursier G, Brogan P, Haimel M, van Gijn M. Maassen W, et al. Among authors: haimel m. Front Immunol. 2023 Sep 12;14:1215869. doi: 10.3389/fimmu.2023.1215869. eCollection 2023. Front Immunol. 2023. PMID: 37781402 Free PMC article.
Autosomal Dominant STAT6 Gain of Function Causes Severe Atopy Associated with Lymphoma.
Minskaia E, Maimaris J, Jenkins P, Albuquerque AS, Hong Y, Eleftheriou D, Gilmour KC, Grace R, Moreira F, Grimbacher B; NIHR Bioresource-Rare Diseases Consortium; Morris EC, Burns SO. Minskaia E, et al. J Clin Immunol. 2023 Oct;43(7):1611-1622. doi: 10.1007/s10875-023-01530-7. Epub 2023 Jun 14. J Clin Immunol. 2023. PMID: 37316763 Free PMC article.
Practical challenges for functional validation of STAT1 gain of function genetic variants.
Albuquerque AS, Maimaris J, McKenna AJ, Lambourne J, Moreira F, Workman S, Megy K, Simeoni I, Lango Allen H; NIHR BioResource-Rare Disease Consortium; Morris EC, Burns SO. Albuquerque AS, et al. Clin Exp Immunol. 2023 Apr 25;212(2):166-169. doi: 10.1093/cei/uxad008. Clin Exp Immunol. 2023. PMID: 36722341 Free PMC article. No abstract available.
A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing.
Denommé-Pichon AS, Matalonga L, de Boer E, Jackson A, Benetti E, Banka S, Bruel AL, Ciolfi A, Clayton-Smith J, Dallapiccola B, Duffourd Y, Ellwanger K, Fallerini C, Gilissen C, Graessner H, Haack TB, Havlovicova M, Hoischen A, Jean-Marçais N, Kleefstra T, López-Martín E, Macek M, Mencarelli MA, Moutton S, Pfundt R, Pizzi S, Posada M, Radio FC, Renieri A, Rooryck C, Ryba L, Safraou H, Schwarz M, Tartaglia M, Thauvin-Robinet C, Thevenon J, Tran Mau-Them F, Trimouille A, Votypka P, de Vries BBA, Willemsen MH, Zurek B, Verloes A, Philippe C; Solve-RD DITF-ITHACA; Solve-RD SNV-indel Working Group; Solve-RD Consortia; Orphanomix Group; Vitobello A, Vissers LELM, Faivre L. Denommé-Pichon AS, et al. Genet Med. 2023 Apr;25(4):100018. doi: 10.1016/j.gim.2023.100018. Epub 2023 Jan 20. Genet Med. 2023. PMID: 36681873 Free article.
49 results