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Items: 1 to 20 of 207

1.

The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758.

Mead D, Hailer F, Chadwick E, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan JD, Dudchenko O, Omer A, Weisz D, Lieberman Aiden E, McCarthy S, Howe K, Sims Y, Torrance J, Tracey A, Challis R, Durbin R, Blaxter M.

Wellcome Open Res. 2020 Feb 19;5:33. doi: 10.12688/wellcomeopenres.15722.1. eCollection 2020.

2.

Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN; HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O.

Nat Commun. 2020 Mar 23;11(1):1572. doi: 10.1038/s41467-020-15098-y.

3.

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.

McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R; HipSci Consortium, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA.

Nat Methods. 2020 Apr;17(4):414-421. doi: 10.1038/s41592-020-0766-3. Epub 2020 Mar 16.

PMID:
32203388
4.

Insights into human genetic variation and population history from 929 diverse genomes.

Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P, Chen Y, Felkel S, Hallast P, Kamm J, Blanché H, Deleuze JF, Cann H, Mallick S, Reich D, Sandhu MS, Skoglund P, Scally A, Xue Y, Durbin R, Tyler-Smith C.

Science. 2020 Mar 20;367(6484). pii: eaay5012. doi: 10.1126/science.aay5012.

PMID:
32193295
5.

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN; HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O.

Nat Commun. 2020 Feb 10;11(1):810. doi: 10.1038/s41467-020-14457-z. Erratum in: Nat Commun. 2020 Mar 23;11(1):1572.

6.

Identifying and removing haplotypic duplication in primary genome assemblies.

Guan D, McCarthy SA, Wood J, Howe K, Wang Y, Durbin R.

Bioinformatics. 2020 Jan 23. pii: btaa025. doi: 10.1093/bioinformatics/btaa025. [Epub ahead of print]

PMID:
31971576
7.

A haplotype-aware de novo assembly of related individuals using pedigree sequence graph.

Garg S, Aach J, Li H, Durbin R, Church G.

Bioinformatics. 2019 Dec 20. pii: btz942. doi: 10.1093/bioinformatics/btz942. [Epub ahead of print]

PMID:
31860070
8.

Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation.

Svardal H, Quah FX, Malinsky M, Ngatunga BP, Miska EA, Salzburger W, Genner MJ, Turner GF, Durbin R.

Mol Biol Evol. 2020 Apr 1;37(4):1100-1113. doi: 10.1093/molbev/msz294.

9.

GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats.

Dawson ET, Durbin R.

J Open Source Softw. 2019;4(33). pii: 1083. doi: 10.21105/joss.01083.

10.

Haplotype-aware graph indexes.

Sirén J, Garrison E, Novak AM, Paten B, Durbin R.

Bioinformatics. 2020 Jan 15;36(2):400-407. doi: 10.1093/bioinformatics/btz575.

PMID:
31406990
11.

Viral coinfection analysis using a MinHash toolkit.

Dawson ET, Wagner S, Roberson D, Yeager M, Boland J, Garrison E, Chanock S, Schiffman M, Raine-Bennett T, Lorey T, Castle PE, Mirabello L, Durbin R.

BMC Bioinformatics. 2019 Jul 12;20(1):389. doi: 10.1186/s12859-019-2918-y.

12.

Induction of Neural Crest Stem Cells From Bardet-Biedl Syndrome Patient Derived hiPSCs.

Barrell WB, Griffin JN, Harvey JL; HipSci Consortium, Danovi D, Beales P, Grigoriadis AE, Liu KJ.

Front Mol Neurosci. 2019 Jun 21;12:139. doi: 10.3389/fnmol.2019.00139. eCollection 2019.

13.

The population history of northeastern Siberia since the Pleistocene.

Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G, Yang MA, Fu Q, Dupanloup I, Giampoudakis K, Nogués-Bravo D, Rahbek C, Kroonen G, Peyrot M, McColl H, Vasilyev SV, Veselovskaya E, Gerasimova M, Pavlova EY, Chasnyk VG, Nikolskiy PA, Gromov AV, Khartanovich VI, Moiseyev V, Grebenyuk PS, Fedorchenko AY, Lebedintsev AI, Slobodin SB, Malyarchuk BA, Martiniano R, Meldgaard M, Arppe L, Palo JU, Sundell T, Mannermaa K, Putkonen M, Alexandersen V, Primeau C, Baimukhanov N, Malhi RS, Sjögren KG, Kristiansen K, Wessman A, Sajantila A, Lahr MM, Durbin R, Nielsen R, Meltzer DJ, Excoffier L, Willerslev E.

Nature. 2019 Jun;570(7760):182-188. doi: 10.1038/s41586-019-1279-z. Epub 2019 Jun 5.

PMID:
31168093
14.

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.

Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A, Wiseman E, Tewary M, Zandstra PW; HipSci Consortium, Durbin R, Fraternali F, Stegle O, Birney E, Luscombe NM, Danovi D, Watt FM.

Cell Rep. 2019 Feb 19;26(8):2078-2087.e3. doi: 10.1016/j.celrep.2019.01.094.

15.

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing.

Kingan SB, Heaton H, Cudini J, Lambert CC, Baybayan P, Galvin BD, Durbin R, Korlach J, Lawniczak MKN.

Genes (Basel). 2019 Jan 18;10(1). pii: E62. doi: 10.3390/genes10010062.

16.

Low-frequency variation in TP53 has large effects on head circumference and intracranial volume.

Haworth S, Shapland CY, Hayward C, Prins BP, Felix JF, Medina-Gomez C, Rivadeneira F, Wang C, Ahluwalia TS, Vrijheid M, Guxens M, Sunyer J, Tachmazidou I, Walter K, Iotchkova V, Jackson A, Cleal L, Huffmann J, Min JL, Sass L, Timmers PRHJ; UK10K consortium, Davey Smith G, Fisher SE, Wilson JF, Cole TJ, Fernandez-Orth D, Bønnelykke K, Bisgaard H, Pennell CE, Jaddoe VWV, Dedoussis G, Timpson N, Zeggini E, Vitart V, St Pourcain B.

Nat Commun. 2019 Jan 21;10(1):357. doi: 10.1038/s41467-018-07863-x.

17.

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow.

Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF, Durbin R.

Nat Ecol Evol. 2018 Dec;2(12):1940-1955. doi: 10.1038/s41559-018-0717-x. Epub 2018 Nov 19.

18.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM.

Nat Genet. 2018 Nov;50(11):1574-1583. doi: 10.1038/s41588-018-0223-8. Epub 2018 Oct 1.

19.

Detecting archaic introgression using an unadmixed outgroup.

Skov L, Hui R, Shchur V, Hobolth A, Scally A, Schierup MH, Durbin R.

PLoS Genet. 2018 Sep 18;14(9):e1007641. doi: 10.1371/journal.pgen.1007641. eCollection 2018 Sep.

20.

Variation graph toolkit improves read mapping by representing genetic variation in the reference.

Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R.

Nat Biotechnol. 2018 Oct;36(9):875-879. doi: 10.1038/nbt.4227. Epub 2018 Aug 20.

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