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Items: 1 to 20 of 33

1.

The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.

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.

2.

Tigmint: correcting assembly errors using linked reads from large molecules.

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.

3.

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

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.

4.

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.

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.

5.

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

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.

6.

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

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.

7.

Spaced Seed Data Structures for De Novo Assembly.

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.

8.

Konnector v2.0: pseudo-long reads from paired-end sequencing data.

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.

9.

Sealer: a scalable gap-closing application for finishing draft genomes.

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.

10.

UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation.

Jackman SD, Bohlmann J, Birol İ.

PLoS One. 2015 May 28;10(5):e0128026. doi: 10.1371/journal.pone.0128026. eCollection 2015.

11.

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

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, MacKay J, Birol I, Bohlmann J.

Plant J. 2015 Jul;83(2):189-212. doi: 10.1111/tpj.12886. Epub 2015 Jun 19.

12.

DIDA: Distributed Indexing Dispatched Alignment.

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.

13.

On the representation of de Bruijn graphs.

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.

PMID:
25629448
14.

Kleat: cleavage site analysis of transcriptomes.

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.

15.

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.

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.

16.

Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii.

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.

17.

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.

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, Hoodless PA, Sahinalp SC, Karsan A, Birol I.

BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550.

18.

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.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

19.

The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera.

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.

20.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.

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, Bohlmann J, Jones SJ.

Bioinformatics. 2013 Jun 15;29(12):1492-7. doi: 10.1093/bioinformatics/btt178. Epub 2013 May 22.

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