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Items: 1 to 50 of 89

1.

Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles.

Helbing CC, Hammond SA, Jackman SH, Houston S, Warren RL, Cameron CE, Birol I.

Sci Rep. 2019 Feb 6;9(1):1529. doi: 10.1038/s41598-018-38442-1.

2.

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.

3.

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.

4.

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data.

Chiu R, Nip KM, Chu J, Birol I.

BMC Med Genomics. 2018 Sep 10;11(1):79. doi: 10.1186/s12920-018-0402-6.

5.

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

Xue Z, Warren RL, Gibb EA, MacMillan D, Wong J, Chiu R, Hammond SA, Yang C, Nip KM, Ennis CA, Hahn A, Reynolds S, Birol I.

BMC Genomics. 2018 Jul 13;19(1):536. doi: 10.1186/s12864-018-4903-7.

6.

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.

7.

Genome-Enhanced Detection and Identification (GEDI) of plant pathogens.

Feau N, Beauseigle S, Bergeron MJ, Bilodeau GJ, Birol I, Cervantes-Arango S, Dhillon B, Dale AL, Herath P, Jones SJM, Lamarche J, Ojeda DI, Sakalidis ML, Taylor G, Tsui CKM, Uzunovic A, Yueh H, Tanguay P, Hamelin RC.

PeerJ. 2018 Feb 22;6:e4392. doi: 10.7717/peerj.4392. eCollection 2018.

8.

A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations.

Campbell LJ, Hammond SA, Price SJ, Sharma MD, Garner TWJ, Birol I, Helbing CC, Wilfert L, Griffiths AGF.

Mol Ecol. 2018 Mar;27(6):1413-1427. doi: 10.1111/mec.14528. Epub 2018 Mar 29.

PMID:
29420865
9.

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Khan H, Mohamadi H, Vandervalk BP, Warren RL, Chu J, Birol I.

Bioinformatics. 2018 May 15;34(10):1697-1704. doi: 10.1093/bioinformatics/btx839.

10.

The Genome of the Beluga Whale (Delphinapterus leucas).

Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA, Bilobram S, Mordecai G, Suttle CA, Miller KM, Schulze A, Chan AM, Jones SJ, Tse K, Li I, Cheung D, Mungall KL, Choo C, Ally A, Dhalla N, Tam AKY, Troussard A, Kirk H, Pandoh P, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Haulena M.

Genes (Basel). 2017 Dec 11;8(12). pii: E378. doi: 10.3390/genes8120378.

11.

The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).

Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Jones SJM.

Genes (Basel). 2017 Dec 11;8(12). pii: E379. doi: 10.3390/genes8120379.

12.

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.

Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H, Gibb EA, Pandoh P, Kirk H, Zhao Y, Jones M, Mungall AJ, Coope R, Pleasance S, Moore RA, Holt RA, Round JM, Ohora S, Walle BV, Veldhoen N, Helbing CC, Birol I.

Nat Commun. 2017 Nov 10;8(1):1433. doi: 10.1038/s41467-017-01316-7.

13.

ARCS: scaffolding genome drafts with linked reads.

Yeo S, Coombe L, Warren RL, Chu J, Birol I.

Bioinformatics. 2018 Mar 1;34(5):725-731. doi: 10.1093/bioinformatics/btx675.

14.

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.

15.

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;152(3):117-121. doi: 10.1159/000479463. Epub 2017 Aug 31.

PMID:
28854430
16.

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.

17.

NanoSim: nanopore sequence read simulator based on statistical characterization.

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

Gigascience. 2017 Apr 1;6(4):1-6. doi: 10.1093/gigascience/gix010.

18.

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.

19.

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
20.

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. Erratum in: Bioinformatics. 2017 Sep 1;33(17 ):2789.

21.

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.

22.

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.

23.

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.

24.

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.

25.

ntHash: recursive nucleotide hashing.

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

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

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes.

Birol I, Behsaz B, Hammond SA, Kucuk E, Veldhoen N, Helbing CC.

PLoS One. 2015 Jun 29;10(6):e0130720. doi: 10.1371/journal.pone.0130720. eCollection 2015.

34.

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.

35.

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.

36.

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.

37.

Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis.

Shoshan E, Mobley AK, Braeuer RR, Kamiya T, Huang L, Vasquez ME, Salameh A, Lee HJ, Kim SJ, Ivan C, Velazquez-Torres G, Nip KM, Zhu K, Brooks D, Jones SJ, Birol I, Mosqueda M, Wen YY, Eterovic AK, Sood AK, Hwu P, Gershenwald JE, Robertson AG, Calin GA, Markel G, Fidler IJ, Bar-Eli M.

Nat Cell Biol. 2015 Mar;17(3):311-21. doi: 10.1038/ncb3110. Epub 2015 Feb 16.

38.

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.

39.

Insights into conifer giga-genomes.

De La Torre AR, Birol I, Bousquet J, Ingvarsson PK, Jansson S, Jones SJ, Keeling CI, MacKay J, Nilsson O, Ritland K, Street N, Yanchuk A, Zerbe P, Bohlmann J.

Plant Physiol. 2014 Dec;166(4):1724-32. doi: 10.1104/pp.114.248708. Epub 2014 Oct 27. Review.

40.

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.

41.

JAGuaR: junction alignments to genome for RNA-seq reads.

Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, Pang J, Ma YP, Jones SJ, Birol İ.

PLoS One. 2014 Jul 25;9(7):e102398. doi: 10.1371/journal.pone.0102398. eCollection 2014.

42.

Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size.

Stival Sena J, Giguère I, Boyle B, Rigault P, Birol I, Zuccolo A, Ritland K, Ritland C, Bohlmann J, Jones S, Bousquet J, Mackay J.

BMC Plant Biol. 2014 Apr 16;14:95. doi: 10.1186/1471-2229-14-95.

43.

A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations.

Bosdet IE, Docking TR, Butterfield YS, Mungall AJ, Zeng T, Coope RJ, Yorida E, Chow K, Bala M, Young SS, Hirst M, Birol I, Moore RA, Jones SJ, Marra MA, Holt R, Karsan A.

J Mol Diagn. 2013 Nov;15(6):796-809. doi: 10.1016/j.jmoldx.2013.07.004. Epub 2013 Oct 4. Erratum in: J Mol Diagn. 2014 May;16(3):378.

PMID:
24094589
44.

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.

45.

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.

46.

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.

47.

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.

48.

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline.

Hadj Khodabakhshi A, Fejes AP, Birol I, Jones SJ.

BMC Bioinformatics. 2013 May 28;14:167. doi: 10.1186/1471-2105-14-167.

49.

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing.

Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA.

Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22.

50.

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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