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Shaun D. Jackman - Publications

Affiliations: 
2012- Bioinformatics University of British Columbia, Vancouver, Vancouver, BC, Canada 
Area:
Bioinformatics, Genome sequence assembly
Website:
http://sjackman.ca
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54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Shalev TJ, Gamal El-Dien O, Yuen MMS, Shengqiang S, Jackman SD, Warren RL, Coombe L, van der Merwe L, Stewart A, Boston LB, Plott C, Jenkins J, He G, Yan J, Yan M, et al. The western redcedar genome reveals low genetic diversity in a self-compatible conifer. Genome Research. PMID 36109148 DOI: 10.1101/gr.276358.121  0.564
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Jackman S, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8  0.521
2020 Jackman SD, Coombe L, Warren RL, Kirk H, Trinh E, MacLeod T, Pleasance S, Pandoh P, Zhao Y, Coope RJ, Bousquet J, Bohlmann J, Jones SJM, Birol I. Complete mitochondrial genome of a gymnosperm, Sitka spruce (Picea sitchensis), indicates a complex physical structure. Genome Biology and Evolution. PMID 32449750 DOI: 10.1093/Gbe/Evaa108  0.681
2019 Kwan HH, Culibrk L, Taylor GA, Leelakumari S, Tan R, Jackman SD, Tse K, MacLeod T, Cheng D, Chuah E, Kirk H, Pandoh P, Carlsen R, Zhao Y, Mungall AJ, et al. The Genome of the Steller Sea Lion (). Genes. 10. PMID 31248052 DOI: 10.3390/Genes10070486  0.702
2019 Lin D, Coombe L, Jackman SD, Gagalova KK, Warren RL, Hammond SA, McDonald H, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Doerksen T, Jaquish B, et al. Complete Chloroplast Genome Sequence of an Engelmann Spruce (, Genotype Se404-851) from Western Canada. Microbiology Resource Announcements. 8. PMID 31196920 DOI: 10.1128/MRA.00382-19  0.676
2019 Lin D, Coombe L, Jackman SD, Gagalova KK, Warren RL, Hammond SA, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Jaquish B, Isabel N, Bousquet J, et al. Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada. Microbiology Resource Announcements. 8. PMID 31171622 DOI: 10.1128/MRA.00381-19  0.666
2019 Jackman SD, Mozgacheva T, Chen S, O'Huiginn B, Bailey L, Birol I, Jones SJM. ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research. Bioinformatics (Oxford, England). PMID 31004474 DOI: 10.1093/Bioinformatics/Btz278  0.541
2019 Jackman S, Chu J, Nikolić V, Afshinfard A, Coombe L, Dilek G, Palchowdhury S, Mohamadi H, Warren R, Bohlmann J, Birol İ. Physlr: Construct a physical map from linked reads F1000research. 8. DOI: 10.7490/F1000Research.1117235.1  0.509
2018 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, et al. The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis. Genes. 9. PMID 30513700 DOI: 10.3390/Genes9120598  0.733
2018 Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, Birol I. Tigmint: correcting assembly errors using linked reads from large molecules. Bmc Bioinformatics. 19: 393. PMID 30367597 DOI: 10.1186/s12859-018-2425-6  0.702
2018 Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL. ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. Bmc Bioinformatics. 19: 234. PMID 29925315 DOI: 10.1186/S12859-018-2243-X  0.721
2018 Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, Birol İ. Tigmint: correct assembly errors using linked reads from large molecules F1000research. 7. DOI: 10.7490/F1000Research.1115395.1  0.547
2017 Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I. ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter. Genome Research. PMID 28232478 DOI: 10.1101/Gr.214346.116  0.728
2017 Jackman SD, Vandervalk BP, Warren RL, Mohamadi H, Chu J, Yeo S, Coombe L, Bohlmann J, Jones SJM, Birol I. Tigmint: correct misassemblies using linked reads from large molecules F1000research. 6. DOI: 10.7490/F1000Research.1114646.1  0.543
2017 Chu J, Coombe L, Yeo S, Vandervalk B, Warren R, Jackman S, Küçük E, Birol I. 10x genomics chromium targetted molecule assembly and genome scaffolding F1000research. 6. DOI: 10.7490/F1000Research.1113689.1  0.668
2017 Jackman SD, Vandervalk BP, Warren RL, Mohamadi H, Chu J, Yeo S, Coombe L, Pleasance S, Coope RJ, Bohlmann J, Jones SJ, Birol İ. Mitochondrial genome of Sitka spruce assembled using chromium reads F1000research. 6. DOI: 10.7490/F1000Research.1113648.1  0.653
2016 Coombe L, Warren RL, Jackman SD, Yang C, Vandervalk BP, Moore RA, Pleasance S, Coope RJ, Bohlmann J, Holt RA, Jones SJ, Birol I. Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data. Plos One. 11: e0163059. PMID 27632164 DOI: 10.1371/Journal.Pone.0163059  0.73
2016 Jackman S, Birol I. Linuxbrew and Homebrew for cross-platform package management F1000research. 5. DOI: 10.7490/F1000Research.1112681.1  0.477
2015 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. Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation. Genome Biology and Evolution. PMID 26645680 DOI: 10.7490/F1000Research.1112919.1  0.708
2015 Birol I, Chu J, Mohamadi H, Jackman SD, Raghavan K, Vandervalk BP, Raymond A, Warren RL. Spaced Seed Data Structures for De Novo Assembly. International Journal of Genomics. 2015: 196591. PMID 26539459 DOI: 10.1155/2015/196591  0.701
2015 Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I. Konnector v2.0: pseudo-long reads from paired-end sequencing data. Bmc Medical Genomics. 8: S1. PMID 26399504 DOI: 10.1186/1755-8794-8-S3-S1  0.646
2015 Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I. Sealer: a scalable gap-closing application for finishing draft genomes. Bmc Bioinformatics. 16: 230. PMID 26209068 DOI: 10.1186/S12859-015-0663-4  0.73
2015 Jackman SD, Bohlmann J, Birol İ. UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation. Plos One. 10: e0128026. PMID 26020645 DOI: 10.1371/Journal.Pone.0128026  0.674
2015 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, et al. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. The Plant Journal : For Cell and Molecular Biology. 83: 189-212. PMID 26017574 DOI: 10.1111/Tpj.12886  0.694
2015 Mohamadi H, Vandervalk BP, Raymond A, Jackman SD, Chu J, Breshears CP, Birol I. DIDA: Distributed Indexing Dispatched Alignment. Plos One. 10: e0126409. PMID 25923767 DOI: 10.1371/Journal.Pone.0126409  0.645
2015 Chikhi R, Limasset A, Jackman S, Simpson JT, Medvedev P. On the representation of de Bruijn graphs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 336-52. PMID 25629448 DOI: 10.1089/Cmb.2014.0160  0.327
2015 Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, Karsan A. Kleat: cleavage site analysis of transcriptomes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 347-58. PMID 25592595  0.529
2015 Jackman S, Raghavan K, Vandervalk B, Paulino D, Chu J, Mohamadi H, Raymond A, Warren R, Birol I. Scaling ABySS to longer reads using spaced k -mers and Bloom filters F1000research. 6. DOI: 10.7490/F1000Research.1097878.1  0.51
2015 Jackman SD, Bohlmann J, Birol I. UniqTag: Content-derived unique and stable identifiers for gene annotation Plos One. 10. DOI: 10.1371/journal.pone.0128026  0.506
2015 Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I. Sealer: A scalable gap-closing application for finishing draft genomes Bmc Bioinformatics. 16. DOI: 10.1186/s12859-015-0663-4  0.646
2014 Chu J, Sadeghi S, Raymond A, Jackman SD, Nip KM, Mar R, Mohamadi H, Butterfield YS, Robertson AG, Birol I. BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters. Bioinformatics (Oxford, England). 30: 3402-4. PMID 25143290 DOI: 10.1093/Bioinformatics/Btu558  0.562
2014 Jackman S, Vandervalk B, Raymond A, Mohamadi H, Yang C, Attali D, Chu J, Warren R, Birol I. ABySS-Konnector: connect paired-end reads by navigating a Bloom filter de Bruijn graph F1000research. 5. DOI: 10.7490/F1000Research.1096524.1  0.519
2014 Birol I, Mohamadi H, Raymond A, Raghavan K, Chu J, Vandervalk BP, Jackman SD, Warren RL. Spaced seed data structures Proceedings - 2014 Ieee International Conference On Bioinformatics and Biomedicine, Ieee Bibm 2014. 15-22. DOI: 10.1109/BIBM.2014.6999305  0.435
2014 Vandervalk BP, Jackman SD, Raymond A, Mohamadi H, Yang C, Attali DA, Chu J, Warren RL, Birol I. Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph Proceedings - 2014 Ieee International Conference On Bioinformatics and Biomedicine, Ieee Bibm 2014. 51-58. DOI: 10.1109/BIBM.2014.6999126  0.469
2013 Lenassi M, Gostinčar C, Jackman S, Turk M, Sadowski I, Nislow C, Jones S, Birol I, Cimerman NG, Plemenitaš A. Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by De Novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii Plos One. 8. PMID 23977017 DOI: 10.1371/Journal.Pone.0071328  0.67
2013 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, et al. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. Bmc Genomics. 14: 550. PMID 23941359 DOI: 10.1186/1471-2164-14-550  0.573
2013 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, ... ... Jackman SD, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10  0.72
2013 Haridas S, Wang Y, Lim L, Massoumi Alamouti S, Jackman S, Docking R, Robertson G, Birol I, Bohlmann J, Breuil C. The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera. Bmc Genomics. 14: 373. PMID 23725015 DOI: 10.1186/1471-2164-14-373  0.668
2013 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, et al. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics (Oxford, England). 29: 1492-7. PMID 23698863 DOI: 10.1093/Bioinformatics/Btt178  0.731
2013 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, et al. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biology. 14: R27. PMID 23537049 DOI: 10.1186/Gb-2013-14-3-R27  0.687
2013 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, ... ... Jackman SD, et al. The genetic landscape of high-risk neuroblastoma. Nature Genetics. 45: 279-84. PMID 23334666 DOI: 10.1038/Ng.2529  0.564
2012 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, ... ... Jackman SD, et al. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 488: 49-56. PMID 22832581 DOI: 10.1038/Nature11327  0.537
2012 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, et al. Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. The Journal of Pathology. 226: 7-16. PMID 22072542 DOI: 10.1002/Path.2995  0.525
2011 Chu Y, Gao P, Zhao P, He Y, Liao N, Jackman S, Zhao Y, Birol I, Duan X, Lu Z. Genome sequence of mycoplasma capricolum subsp. capripneumoniae strain M1601 Journal of Bacteriology. 193: 6098-6099. PMID 21994928 DOI: 10.1128/Jb.05980-11  0.607
2011 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, ... ... Jackman SD, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111  0.534
2011 Chan QWT, Cornman RS, Birol I, Liao NY, Chan SK, Docking TR, Jackman SD, Taylor GA, Jones SJM, de Graaf DC, Evans JD, Foster LJ. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees Bmc Genomics. 12. PMID 21923906 DOI: 10.1186/1471-2164-12-450  0.686
2011 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, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma Nature. 476: 298-303. PMID 21796119 DOI: 10.1038/Nature10351  0.542
2010 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, et al. De novo assembly and analysis of RNA-seq data. Nature Methods. 7: 909-12. PMID 20935650 DOI: 10.1038/Nmeth.1517  0.596
2010 Jackman SD, Birol I. Assembling genomes using short-read sequencing technology Genome Biology. 11. PMID 20128932 DOI: 10.1186/Gb-2010-11-1-202  0.687
2010 Morin RD, Mendez-Lago M, Mungall AJ, Johnson NA, Goya R, Severson T, Mungall K, An J, Yakovenko O, Jackman S, Krzywinski M, Griffith M, Chan S, Tam A, Smailus D, et al. Identification of Genes Frequently Mutated In FL and DLBCL with Transcriptome, Genome and Exome Sequencing Blood. 116: 804-804. DOI: 10.1182/Blood.V116.21.804.804  0.564
2009 Nielsen CB, Jackman SD, Birol I, Jones SJM. ABySS-explorer: Visualizing genome sequence assemblies Ieee Transactions On Visualization and Computer Graphics. 15: 881-888. PMID 19834150 DOI: 10.1109/Tvcg.2009.116  0.681
2009 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 SJM. De novo transcriptome assembly with ABySS Bioinformatics. 25: 2872-2877. PMID 19528083 DOI: 10.1093/Bioinformatics/Btp367  0.691
2009 Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. ABySS: A parallel assembler for short read sequence data Genome Research. 19: 1117-1123. PMID 19251739 DOI: 10.1101/Gr.089532.108  0.716
2009 Mungall AJ, Chu A, Chiu R, Corbett R, Field MA, Jackman SD, Mungall KL, Wong K, Boyle M, Carlsen R, Chan SY, Coope RJN, Hirst CA, Hirst M, Johnson N, et al. Base-Pair Resolution of Somatic and Germline-Derived Genome Rearrangement Breakpoints in Follicular Lymphoma. Blood. 114: 439-439. DOI: 10.1182/Blood.V114.22.439.439  0.702
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