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publications.csv
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Title,URL,Description,Details,ShortDetails,Resource,Type,Identifiers,Db,EntrezUID,Properties
"ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research.","/pubmed/31004474","Jackman SD, Mozgacheva T, Chen S, O'Huiginn B, Bailey L, Birol I, Jones SJM.","Bioinformatics. 2019 Apr 20. pii: btz278. doi: 10.1093/bioinformatics/btz278. [Epub ahead of print]","Bioinformatics. 2019","PubMed","citation","PMID:31004474","pubmed","31004474","create date:2019/04/21 | first author:Jackman SD",
"The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.","/pubmed/30513700","Taylor GA, Kirk H, Coombe L, Jackman SD, Chu J, Tse K, Cheng D, Chuah E, Pandoh P, Carlsen R, Zhao Y, Mungall AJ, Moore R, Birol I, Franke M, Marra MA, Dutton C, Jones SJM.","Genes (Basel). 2018 Nov 30;9(12). pii: E598. doi: 10.3390/genes9120598.","Genes (Basel). 2018","PubMed","citation","PMID:30513700 | PMCID:PMC6315469","pubmed","30513700","create date:2018/12/06 | first author:Taylor GA",
"Tigmint: correcting assembly errors using linked reads from large molecules.","/pubmed/30367597","Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, Birol I.","BMC Bioinformatics. 2018 Oct 26;19(1):393. doi: 10.1186/s12859-018-2425-6.","BMC Bioinformatics. 2018","PubMed","citation","PMID:30367597 | PMCID:PMC6204047","pubmed","30367597","create date:2018/10/28 | first author:Jackman SD",
"ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.","/pubmed/29925315","Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL.","BMC Bioinformatics. 2018 Jun 20;19(1):234. doi: 10.1186/s12859-018-2243-x.","BMC Bioinformatics. 2018","PubMed","citation","PMID:29925315 | PMCID:PMC6011487","pubmed","29925315","create date:2018/06/22 | first author:Coombe L",
"ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.","/pubmed/28232478","Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I.","Genome Res. 2017 May;27(5):768-777. doi: 10.1101/gr.214346.116. Epub 2017 Feb 23.","Genome Res. 2017","PubMed","citation","PMID:28232478 | PMCID:PMC5411771","pubmed","28232478","create date:2017/02/25 | first author:Jackman SD"
"Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.","/pubmed/27632164","Coombe L, Warren RL, Jackman SD, Yang C, Vandervalk BP, Moore RA, Pleasance S, Coope RJ, Bohlmann J, Holt RA, Jones SJ, Birol I.","PLoS One. 2016 Sep 15;11(9):e0163059. doi: 10.1371/journal.pone.0163059. eCollection 2016.","PLoS One. 2016","PubMed","citation","PMID:27632164 | PMCID:PMC5025161","pubmed","27632164","create date:2016/09/16 | first author:Coombe L"
"Evolution of Specialization of Cassida rubiginosa on Cirsium arvense (Compositae, Cardueae).","/pubmed/27602042","Cripps MG, Jackman SD, Roquet C, van Koten C, Rostás M, Bourdôt GW, Susanna A.","Front Plant Sci. 2016 Aug 23;7:1261. doi: 10.3389/fpls.2016.01261. eCollection 2016.","Front Plant Sci. 2016","PubMed","citation","PMID:27602042 | PMCID:PMC4994537","pubmed","27602042","create date:2016/09/08 | first author:Cripps MG"
"Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.","/pubmed/26645680","Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJ, Bohlmann J, Birol I.","Genome Biol Evol. 2015 Dec 8;8(1):29-41. doi: 10.1093/gbe/evv244.","Genome Biol Evol. 2015","PubMed","citation","PMID:26645680 | PMCID:PMC4758241","pubmed","26645680","create date:2015/12/10 | first author:Jackman SD"
"Sealer: a scalable gap-closing application for finishing draft genomes.","/pubmed/26209068","Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.","BMC Bioinformatics. 2015 Jul 25;16:230. doi: 10.1186/s12859-015-0663-4.","BMC Bioinformatics. 2015","PubMed","citation","PMID:26209068 | PMCID:PMC4515008","pubmed","26209068","create date:2015/07/26 | first author:Paulino D"
"Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.","/pubmed/26017574","Warren RL, Keeling CI, Yuen MM, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJ, et al.","Plant J. 2015 Jul;83(2):189-212. doi: 10.1111/tpj.12886. Epub 2015 Jun 19.","Plant J. 2015","PubMed","citation","PMID:26017574","pubmed","26017574","create date:2015/05/29 | first author:Warren RL"
"UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation.","/pubmed/26020645","Jackman SD, Bohlmann J, Birol İ.","PLoS One. 2015 May 28;10(5):e0128026. doi: 10.1371/journal.pone.0128026. eCollection 2015.","PLoS One. 2015","PubMed","citation","PMID:26020645 | PMCID:PMC4447347","pubmed","26020645","create date:2015/05/29 | first author:Jackman SD"
"On the representation of de Bruijn graphs.","/pubmed/25629448","Chikhi R, Limasset A, Jackman S, Simpson JT, Medvedev P.","J Comput Biol. 2015 May;22(5):336-52. doi: 10.1089/cmb.2014.0160. Epub 2015 Jan 28.","J Comput Biol. 2015","PubMed","citation","PMID:25629448","pubmed","25629448","create date:2015/01/30 | first author:Chikhi R"
"DIDA: Distributed Indexing Dispatched Alignment.","/pubmed/25923767","Mohamadi H, Vandervalk BP, Raymond A, Jackman SD, Chu J, Breshears CP, Birol I.","PLoS One. 2015 Apr 29;10(4):e0126409. doi: 10.1371/journal.pone.0126409. eCollection 2015.","PLoS One. 2015","PubMed","citation","PMID:25923767 | PMCID:PMC4414605","pubmed","25923767","create date:2015/04/30 | first author:Mohamadi H"
"Konnector v2.0: pseudo-long reads from paired-end sequencing data.","/pubmed/26399504","Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.","BMC Med Genomics. 2015;8 Suppl 3:S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23.","BMC Med Genomics. 2015","PubMed","citation","PMID:26399504 | PMCID:PMC4582294","pubmed","26399504","create date:2015/09/25 | first author:Vandervalk BP"
"Spaced Seed Data Structures for De Novo Assembly.","/pubmed/26539459","Birol I, Chu J, Mohamadi H, Jackman SD, Raghavan K, Vandervalk BP, Raymond A, Warren RL.","Int J Genomics. 2015;2015:196591. doi: 10.1155/2015/196591. Epub 2015 Oct 11.","Int J Genomics. 2015","PubMed","citation","PMID:26539459 | PMCID:PMC4619942","pubmed","26539459","create date:2015/11/06 | first author:Birol I"
"Kleat: cleavage site analysis of transcriptomes.","/pubmed/25592595","Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, Karsan A.","Pac Symp Biocomput. 2015:347-58.","Pac Symp Biocomput. 2015","PubMed","citation","PMID:25592595 | PMCID:PMC4350765","pubmed","25592595","create date:2015/01/17 | first author:Birol I"
"BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.","/pubmed/25143290","Chu J, Sadeghi S, Raymond A, Jackman SD, Nip KM, Mar R, Mohamadi H, Butterfield YS, Robertson AG, Birol I.","Bioinformatics. 2014 Dec 1;30(23):3402-4. doi: 10.1093/bioinformatics/btu558. Epub 2014 Aug 20.","Bioinformatics. 2014","PubMed","citation","PMID:25143290 | PMCID:PMC4816029","pubmed","25143290","create date:2014/08/22 | first author:Chu J"
"Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii.","/pubmed/23977017","Lenassi M, Gostinčar C, Jackman S, Turk M, Sadowski I, Nislow C, Jones S, Birol I, Cimerman NG, Plemenitaš A.","PLoS One. 2013 Aug 15;8(8):e71328. doi: 10.1371/journal.pone.0071328. eCollection 2013.","PLoS One. 2013","PubMed","citation","PMID:23977017 | PMCID:PMC3744574","pubmed","23977017","create date:2013/08/27 | first author:Lenassi M"
"Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.","/pubmed/23941359","Swanson L, Robertson G, Mungall KL, Butterfield YS, Chiu R, Corbett RD, Docking TR, Hogge D, Jackman SD, Moore RA, Mungall AJ, Nip KM, Parker JD, Qian JQ, Raymond A, Sung S, Tam A, Thiessen N, Varhol R, Wang S, Yorukoglu D, Zhao Y, et al.","BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550.","BMC Genomics. 2013","PubMed","citation","PMID:23941359 | PMCID:PMC3751903","pubmed","23941359","create date:2013/08/15 | first author:Swanson L"
"Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.","/pubmed/23870653","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, et al.","Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.","Gigascience. 2013","PubMed","citation","PMID:23870653 | PMCID:PMC3844414","pubmed","23870653","create date:2013/07/23 | first author:Bradnam KR"
"Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.","/pubmed/23698863","Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B, Yanchuk A, Ritland C, Boyle B, Bousquet J, Ritland K, Mackay J, et al.","Bioinformatics. 2013 Jun 15;29(12):1492-7. doi: 10.1093/bioinformatics/btt178. Epub 2013 May 22.","Bioinformatics. 2013","PubMed","citation","PMID:23698863 | PMCID:PMC3673215","pubmed","23698863","create date:2013/05/24 | first author:Birol I"
"The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera.","/pubmed/23725015","Haridas S, Wang Y, Lim L, Massoumi Alamouti S, Jackman S, Docking R, Robertson G, Birol I, Bohlmann J, Breuil C.","BMC Genomics. 2013 Jun 2;14:373. doi: 10.1186/1471-2164-14-373.","BMC Genomics. 2013","PubMed","citation","PMID:23725015 | PMCID:PMC3680317","pubmed","23725015","create date:2013/06/04 | first author:Haridas S"
"Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest.","/pubmed/23537049","Keeling CI, Yuen MM, Liao NY, Docking TR, Chan SK, Taylor GA, Palmquist DL, Jackman SD, Nguyen A, Li M, Henderson H, Janes JK, Zhao Y, Pandoh P, Moore R, Sperling FA, Huber DP, Birol I, Jones SJ, Bohlmann J.","Genome Biol. 2013 Mar 27;14(3):R27. doi: 10.1186/gb-2013-14-3-r27.","Genome Biol. 2013","PubMed","citation","PMID:23537049 | PMCID:PMC4053930","pubmed","23537049","create date:2013/03/30 | first author:Keeling CI"
"The genetic landscape of high-risk neuroblastoma.","/pubmed/23334666","Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, et al.","Nat Genet. 2013 Mar;45(3):279-84. doi: 10.1038/ng.2529. Epub 2013 Jan 20.","Nat Genet. 2013","PubMed","citation","PMID:23334666 | PMCID:PMC3682833","pubmed","23334666","create date:2013/01/22 | first author:Pugh TJ"
"Subgroup-specific structural variation across 1,000 medulloblastoma genomes.","/pubmed/22832581","Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, et al.","Nature. 2012 Aug 2;488(7409):49-56. doi: 10.1038/nature11327.","Nature. 2012","PubMed","citation","PMID:22832581 | PMCID:PMC3683624","pubmed","22832581","create date:2012/07/27 | first author:Northcott PA"
"Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers.","/pubmed/22072542","Yip S, Butterfield YS, Morozova O, Chittaranjan S, Blough MD, An J, Birol I, Chesnelong C, Chiu R, Chuah E, Corbett R, Docking R, Firme M, Hirst M, Jackman S, Karsan A, Li H, Louis DN, Maslova A, Moore R, Moradian A, Mungall KL, et al.","J Pathol. 2012 Jan;226(1):7-16. doi: 10.1002/path.2995. Epub 2011 Nov 10.","J Pathol. 2012","PubMed","citation","PMID:22072542 | PMCID:PMC3246739","pubmed","22072542","create date:2011/11/11 | first author:Yip S"
"Assemblathon 1: a competitive assessment of de novo short read assembly methods.","/pubmed/21926179","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, et al.","Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.","Genome Res. 2011","PubMed","citation","PMID:21926179 | PMCID:PMC3227110","pubmed","21926179","create date:2011/09/20 | first author:Earl D"
"Genome sequence of Mycoplasma capricolum subsp. capripneumoniae strain M1601.","/pubmed/21994928","Chu Y, Gao P, Zhao P, He Y, Liao N, Jackman S, Zhao Y, Birol I, Duan X, Lu Z.","J Bacteriol. 2011 Nov;193(21):6098-9. doi: 10.1128/JB.05980-11.","J Bacteriol. 2011","PubMed","citation","PMID:21994928 | PMCID:PMC3194924","pubmed","21994928","create date:2011/10/14 | first author:Chu Y"
"Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees.","/pubmed/21923906","Chan QW, Cornman RS, Birol I, Liao NY, Chan SK, Docking TR, Jackman SD, Taylor GA, Jones SJ, de Graaf DC, Evans JD, Foster LJ.","BMC Genomics. 2011 Sep 16;12:450. doi: 10.1186/1471-2164-12-450.","BMC Genomics. 2011","PubMed","citation","PMID:21923906 | PMCID:PMC3188533","pubmed","21923906","create date:2011/09/20 | first author:Chan QW"
"Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.","/pubmed/21796119","Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, et al.","Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351.","Nature. 2011","PubMed","citation","PMID:21796119 | PMCID:PMC3210554","pubmed","21796119","create date:2011/07/29 | first author:Morin RD"
"De novo assembly and analysis of RNA-seq data.","/pubmed/20935650","Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, et al.","Nat Methods. 2010 Nov;7(11):909-12. doi: 10.1038/nmeth.1517. Epub 2010 Oct 10.","Nat Methods. 2010","PubMed","citation","PMID:20935650","pubmed","20935650","create date:2010/10/12 | first author:Robertson G"
"Assembling genomes using short-read sequencing technology.","/pubmed/20128932","Jackman SD, Birol I.","Genome Biol. 2010 Jan 28;11(1):202. doi: 10.1186/gb-2010-11-1-202. Review.","Genome Biol. 2010","PubMed","citation","PMID:20128932 | PMCID:PMC2847710","pubmed","20128932","create date:2010/02/05 | first author:Jackman SD"
"De novo transcriptome assembly with ABySS.","/pubmed/19528083","Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ.","Bioinformatics. 2009 Nov 1;25(21):2872-7. doi: 10.1093/bioinformatics/btp367. Epub 2009 Jun 15.","Bioinformatics. 2009","PubMed","citation","PMID:19528083","pubmed","19528083","create date:2009/06/17 | first author:Birol I"
"ABySS-Explorer: visualizing genome sequence assemblies.","/pubmed/19834150","Nielsen CB, Jackman SD, Birol I, Jones SJ.","IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):881-8. doi: 10.1109/TVCG.2009.116.","IEEE Trans Vis Comput Graph. 2009","PubMed","citation","PMID:19834150","pubmed","19834150","create date:2009/10/17 | first author:Nielsen CB"
"ABySS: a parallel assembler for short read sequence data.","/pubmed/19251739","Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.","Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27.","Genome Res. 2009","PubMed","citation","PMID:19251739 | PMCID:PMC2694472","pubmed","19251739","create date:2009/03/03 | first author:Simpson JT"