SJ
Shaun D. Jackman
SoftwareGenome, PlantABySSAlgorithmsbioinformaticsGene Expression ProfilinggenomeGenomegenome assemblyGenome, Bacterial
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
43 papers in the corpus · 2009–2022The western redcedar genome reveals low genetic diversity in a self-compatible conifer.36109148 · Shalev, Tal J, Gamal El-Dien, Omnia, Yuen, Macaire M S et al.2022 · 37 citationsGenome research. 2022;32(10):1952-1964
Author Correction: A robust benchmark for detection of germline large deletions and insertions.32699374 · Zook, Justin M, Hansen, Nancy F, Olson, Nathan D et al.2020 · 4 citationsNature biotechnology. 2020;38(11):1357
Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure.32449750 · Jackman, Shaun D, Coombe, Lauren, Warren, René L et al.2021 · 138 citationsGenome biology and evolution. 2020;12(7):1174-1179
A robust benchmark for detection of germline large deletions and insertions.32541955 · Zook, Justin M, Hansen, Nancy F, Olson, Nathan D et al.2020 · 399 citationsNature biotechnology. 2020;38(11):1347-1355
ORCA: a comprehensive bioinformatics container environment for education and research.31004474 · Jackman, Shaun D, Mozgacheva, Tatyana, Chen, Susie et al.2020 · 13 citationsBioinformatics (Oxford, England). 2019;35(21):4448-4450
The Genome of the Steller Sea Lion (Eumetopias jubatus).31248052 · Kwan, Harwood H, Culibrk, Luka, Taylor, Gregory A et al.2020 · 5 citationsGenes. 2019;10(7)
Complete Chloroplast Genome Sequence of an Engelmann Spruce (Picea engelmannii, Genotype Se404-851) from Western Canada.31196920 · Lin, Diana, Coombe, Lauren, Jackman, Shaun D et al.2024 · 4 citationsMicrobiology resource announcements. 2019;8(24)
A robust benchmark for germline structural variant detection10.1101/664623v3 · Zook, J. M., Hansen, N. F., Olson, N. D. et al.2019 · 60 citationsbioRxiv
Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada.31171622 · Lin, Diana, Coombe, Lauren, Jackman, Shaun D et al.2020 · 9 citationsMicrobiology resource announcements. 2019;8(23)
The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.30513700 · Taylor, Gregory A, Kirk, Heather, Coombe, Lauren et al.2020 · 39 citationsGenes. 2018;9(12)
Tigmint: correcting assembly errors using linked reads from large molecules.30367597 · Jackman, Shaun D, Coombe, Lauren, Chu, Justin et al.2018 · 128 citationsBMC bioinformatics. 2018;19(1):393
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.29925315 · Coombe, Lauren, Zhang, Jessica, Vandervalk, Benjamin P et al.2019 · 105 citationsBMC bioinformatics. 2018;19(1):234
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.28232478 · Jackman, Shaun D, Vandervalk, Benjamin P, Mohamadi, Hamid et al.2018 · 681 citationsGenome research. 2017;27(5):768-777
Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.27632164 · Coombe, Lauren, Warren, René L, Jackman, Shaun D et al.2017 · 36 citationsPloS one. 2016;11(9):e0163059
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.26645680 · Jackman, Shaun D, Warren, René L, Gibb, Ewan A et al.2016 · 54 citationsGenome biology and evolution. 2015;8(1):29-41
Sealer: a scalable gap-closing application for finishing draft genomes.26209068 · Paulino, Daniel, Warren, René L, Vandervalk, Benjamin P et al.2016 · 132 citationsBMC bioinformatics. 2015;16:230
Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.26017574 · Warren, René L, Keeling, Christopher I, Yuen, Macaire Man Saint et al.2016 · 198 citationsThe Plant journal : for cell and molecular biology. 2015;83(2):189-212
UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation.26020645 · Jackman, Shaun D, Bohlmann, Joerg, Birol, İnanç2016 · 0 citationsPloS one. 2015;10(5):e0128026
DIDA: Distributed Indexing Dispatched Alignment.25923767 · Mohamadi, Hamid, Vandervalk, Benjamin P, Raymond, Anthony et al.2016 · 13 citationsPloS one. 2015;10(4):e0126409
On the representation of de Bruijn graphs.25629448 · Chikhi, Rayan, Limasset, Antoine, Jackman, Shaun et al.2016 · 76 citationsJournal of computational biology : a journal of computational molecular cell biology. 2015;22(5):336-52
Kleat: cleavage site analysis of transcriptomes.25592595 · Birol, Inanç, Raymond, Anthony, Chiu, Readman et al.2016 · 24 citationsPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2015:347-58
Konnector v2.0: pseudo-long reads from paired-end sequencing data.26399504 · Vandervalk, Benjamin P, Yang, Chen, Xue, Zhuyi et al.2016 · 20 citationsBMC medical genomics. 2015;8 Suppl 3:S1
Spaced Seed Data Structures for De Novo Assembly.26539459 · Birol, Inanç, Chu, Justin, Mohamadi, Hamid et al.2015 · 9 citationsInternational journal of genomics. 2015;2015:196591
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.25143290 · Chu, Justin, Sadeghi, Sara, Raymond, Anthony et al.2015 · 123 citationsBioinformatics (Oxford, England). 2014;30(23):3402-4
On the representation of de Bruijn graphs1401.5383v4 · Rayan Chikhi, Antoine Limasset, Shaun Jackman et al.2014 · 100 citationsarXiv
Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii.23977017 · Lenassi, Metka, Gostinčar, Cene, Jackman, Shaun et al.2014 · 105 citationsPloS one. 2013;8(8):e71328
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.23941359 · Swanson, Lucas, Robertson, Gordon, Mungall, Karen L et al.2013 · 15 citationsBMC genomics. 2013;14:550
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera.23725015 · Haridas, Sajeet, Wang, Ye, Lim, Lynette et al.2013 · 79 citationsBMC genomics. 2013;14:373
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.23698863 · Birol, Inanc, Raymond, Anthony, Jackman, Shaun D et al.2013 · 368 citationsBioinformatics (Oxford, England). 2013;29(12):1492-7
Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest.23537049 · Keeling, Christopher I, Yuen, Macaire M S, Liao, Nancy Y et al.2015 · 296 citationsGenome biology. 2013;14(3):R27
The genetic landscape of high-risk neuroblastoma.23334666 · Pugh, Trevor J, Morozova, Olena, Attiyeh, Edward F et al.2013 · 1,196 citationsNature genetics. 2013;45(3):279-84
Subgroup-specific structural variation across 1,000 medulloblastoma genomes.22832581 · Northcott, Paul A, Shih, David J H, Peacock, John et al.2012 · 898 citationsNature. 2012;488(7409):49-56
Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers.22072542 · Yip, Stephen, Butterfield, Yaron S, Morozova, Olena et al.2012 · 308 citationsThe Journal of pathology. 2012;226(1):7-16
Genome sequence of Mycoplasma capricolum subsp. capripneumoniae strain M1601.21994928 · Chu, Yuefeng, Gao, Pengchen, Zhao, Ping et al.2011 · 26 citationsJournal of bacteriology. 2011;193(21):6098-9
Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees.21923906 · Chan, Queenie W T, Cornman, R Scott, Birol, Inanc et al.2012 · 43 citationsBMC genomics. 2011;12:450
Assemblathon 1: a competitive assessment of de novo short read assembly methods.21926179 · Earl, Dent, Bradnam, Keith, St John, John et al.2012 · 507 citationsGenome research. 2011;21(12):2224-41
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.21796119 · Morin, Ryan D, Mendez-Lago, Maria, Mungall, Andrew J et al.2011 · 1,611 citationsNature. 2011;476(7360):298-303
De novo assembly and analysis of RNA-seq data.20935650 · Robertson, Gordon, Schein, Jacqueline, Chiu, Readman et al.2010 · 998 citationsNature methods. 2010;7(11):909-12
Assembling genomes using short-read sequencing technology.20128932 · Jackman, Shaun D, Birol, Inanç2010 · 31 citationsGenome biology. 2010;11(1):202
ABySS-Explorer: visualizing genome sequence assemblies.19834150 · Nielsen, Cydney B, Jackman, Shaun D, Birol, Inanç et al.2010 · 62 citationsIEEE transactions on visualization and computer graphics. 2009;15(6):881-8
De novo transcriptome assembly with ABySS.19528083 · Birol, Inanç, Jackman, Shaun D, Nielsen, Cydney B et al.2010 · 400 citationsBioinformatics (Oxford, England). 2009;25(21):2872-7
ABySS: a parallel assembler for short read sequence data.19251739 · Simpson, Jared T, Wong, Kim, Jackman, Shaun D et al.2009 · 3,613 citationsGenome research. 2009;19(6):1117-23
Career total: at least 82 works. 43 are in this corpus.
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