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Items: 1 to 20 of 78

1.

Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease.

Hasan NA, Warren RL, Epperson LE, Malecha A, Alexander DC, Turenne CY, MacMillan D, Birol I, Pleasance S, Coope R, Jones SJM, Romney MG, Ng M, Chan T, Rodrigues M, Tang P, Gardy JL, Strong M.

Genome Announc. 2017 Sep 14;5(37). pii: e00963-17. doi: 10.1128/genomeA.00963-17.

PMID:
28912319
2.

Kollector: transcript-informed, targeted de novo assembly of gene loci.

Kucuk E, Chu J, Vandervalk BP, Austin Hammond S, Warren RL, Birol I.

Bioinformatics. 2017 Sep 1;33(17):2789. doi: 10.1093/bioinformatics/btx405. No abstract available.

PMID:
28903539
3.

Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98.

Thibodeau ML, Steinraths M, Brown L, Zong Z, Shomer N, Taubert S, Mungall KL, Ma YP, Mueller R, Birol I, Lehman A.

Cytogenet Genome Res. 2017 Aug 31. doi: 10.1159/000479463. [Epub ahead of print]

PMID:
28854430
4.

ntCard: a streaming algorithm for cardinality estimation in genomics data.

Mohamadi H, Khan H, Birol I.

Bioinformatics. 2017 May 1;33(9):1324-1330. doi: 10.1093/bioinformatics/btw832.

5.

NanoSim: nanopore sequence read simulator based on statistical characterization.

Yang C, Chu J, Warren RL, Birol I.

Gigascience. 2017 Feb 24. doi: 10.1093/gigascience/gix010. [Epub ahead of print]

6.

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.

7.

De novo assembly of the ringed seal (Pusa hispida) blubber transcriptome: A tool that enables identification of molecular health indicators associated with PCB exposure.

Brown TM, Hammond SA, Behsaz B, Veldhoen N, Birol I, Helbing CC.

Aquat Toxicol. 2017 Apr;185:48-57. doi: 10.1016/j.aquatox.2017.02.004. Epub 2017 Feb 3.

PMID:
28187360
8.

Kollector: transcript-informed, targeted de novo assembly of gene loci.

Kucuk E, Chu J, Vandervalk BP, Hammond SA, Warren RL, Birol I.

Bioinformatics. 2017 Jun 15;33(12):1782-1788. doi: 10.1093/bioinformatics/btx078.

9.

A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance.

Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J, Mackay J, Isabel N, Bousquet J.

Plant J. 2017 Apr;90(1):189-203. doi: 10.1111/tpj.13478. Epub 2017 Mar 6.

PMID:
28090692
10.

ntCard: a streaming algorithm for cardinality estimation in genomics data.

Mohamadi H, Khan H, Birol I.

Bioinformatics. 2017 Jan 5. pii: btw832. doi: 10.1093/bioinformatics/btw832. [Epub ahead of print]

PMID:
28057681
11.

Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art.

Chu J, Mohamadi H, Warren RL, Yang C, Birol I.

Bioinformatics. 2017 Apr 15;33(8):1261-1270. doi: 10.1093/bioinformatics/btw811. Review.

12.

Genome sequences of six Phytophthora species threatening forest ecosystems.

Feau N, Taylor G, Dale AL, Dhillon B, Bilodeau GJ, Birol I, Jones SJ, Hamelin RC.

Genom Data. 2016 Oct 3;10:85-88. eCollection 2016 Dec.

13.

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.

14.

ntHash: recursive nucleotide hashing.

Mohamadi H, Chu J, Vandervalk BP, Birol I.

Bioinformatics. 2016 Nov 15;32(22):3492-3494. Epub 2016 Jul 16.

15.

Divergent clonal selection dominates medulloblastoma at recurrence.

Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH Jr, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD.

Nature. 2016 Jan 21;529(7586):351-7. doi: 10.1038/nature16478. Epub 2016 Jan 13.

16.

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.

17.

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.

18.

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.

19.

Large-scale profiling of microRNAs for The Cancer Genome Atlas.

Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, Ma Y, Jones S, Marra MA.

Nucleic Acids Res. 2016 Jan 8;44(1):e3. doi: 10.1093/nar/gkv808. Epub 2015 Aug 13.

20.

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.

Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJ, Birol I.

Gigascience. 2015 Aug 4;4:35. doi: 10.1186/s13742-015-0076-3. eCollection 2015.

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