PhyloBLAST: facilitating phylogenetic analysis of BLAST results. - Fiona S. L. Brinkman; Ivan Wan; Robert E. W. Hancock; Ann M. Rose; Steven J. M. Jones (Bioinform., 2001)

AcePrimer: automation of PCR primer design based on gene structure. - Sheldon J. McKay; Steven J. M. Jones (Bioinform., 2002)

Assembly of fingerprint contigs: parallelized FPC. - Steven R. Ness; W. Terpstra; Martin Krzywinski; Marco A. Marra; Steven J. M. Jones (Bioinform., 2002)

IslandPath: aiding detection of genomic islands in prokaryotes. - William W. L. Hsiao; Ivan Wan; Steven J. M. Jones; Fiona S. L. Brinkman (Bioinform., 2003)

A knowledge discovery object model API for Java. - Scott D. Zuyderduyn; Steven J. M. Jones (BMC Bioinform., 2003)

Structural characterization of genomes by large scale sequence-structure threading. - Artem Cherkasov; Steven J. M. Jones (BMC Bioinform., 2004)

An approach to large scale identification of non-obvious structural similarities between proteins. - Artem Cherkasov; Steven J. M. Jones (BMC Bioinform., 2004)

Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics. - Artem Cherkasov; Shannan J. Ho Sui; Robert C. Brunham; Steven J. M. Jones (BMC Bioinform., 2004)

cis-Regulatory Element Prediction in Mammalian Genomes. - Asim S. Siddiqui; Gordon Robertson; Misha Bilenky; Tamara Astakhova; Obi L. Griffith; Maik Hassel; Keven Lin; Stephen B. Montgomery; Mehrdad Oveisi; Erin Pleasance; Neil Robertson 004; Monica C. Sleumer; et al. (CSB Workshops, 2005)

CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes. - Chris D. Bajdik; Byron Kuo; Shawn Rusaw; Steven J. M. Jones; Angela Brooks-Wilson (BMC Bioinform., 2005)

'Inductive' Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand. - Artem Cherkasov; Zheng Shi; Yvonne Y. Li; Steven J. M. Jones; Magid Fallahi; Geoffrey L. Hammond (J. Chem. Inf. Model., 2005)

A methodology for analyzing SAGE libraries for cancer profiling. - Jörg Sander 001; Raymond T. Ng; Monica C. Sleumer; Man Saint Yuen; Steven J. M. Jones (ACM Trans. Inf. Syst., 2005)

Sun Grid Engine Package for OSCAR - A Google Summer Of Code 2005 Project. - Babu Sundaram; Barbara M. Chapman; Bernard Li; Mark Mayo; Asim S. Siddiqui; Steven J. M. Jones (HPCS, 2006)

Discovering significant OPSM subspace clusters in massive gene expression data. - Byron J. Gao; Obi L. Griffith; Martin Ester; Steven J. M. Jones (KDD, 2006)

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. - Stephen B. Montgomery; Obi L. Griffith; Monica C. Sleumer; Casey M. Bergman; Misha Bilenky; Erin Pleasance; Y. Prychyna; X. Zhang; Steven J. M. Jones (Bioinform., 2006)

An interactive tool for visualization of relationships between gene expression profiles. - Peter Ruzanov; Steven J. M. Jones (BMC Bioinform., 2006)

Selective Targeting of Indel-inferred Differences in Spatial Structures of Homologous Proteins. - Yvonne Y. Li; Steven J. M. Jones; Artem Cherkasov (J. Bioinform. Comput. Biol., 2006)

cisRED: a database system for genome-scale computational discovery of regulatory elements. - Gordon Robertson; Misha Bilenky; Keven Lin; An He; W. Yuen; M. Dagpinar; Richard Varhol; Kevin Teague; Obi L. Griffith; X. Zhang; Y. Pan; Maik Hassel; et al. (Nucleic Acids Res., 2006)

THOR: targeted high-throughput ortholog reconstructor. - Matthew N. Bainbridge; René L. Warren; An He; Mikhail Bilenky; Gordon Robertson; Steven J. M. Jones (Bioinform., 2007)

Assembling millions of short DNA sequences using SSAKE. - René L. Warren; Granger G. Sutton; Steven J. M. Jones; Robert A. Holt (Bioinform., 2007)

A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms. - Stephen B. Montgomery; Obi L. Griffith; Johanna M. Schuetz; Angela Brooks-Wilson; Steven J. M. Jones (PLoS Comput. Biol., 2007)

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. - Anthony P. Fejes; Gordon Robertson; Mikhail Bilenky; Richard Varhol; Matthew N. Bainbridge; Steven J. M. Jones (Bioinform., 2008)

ORegAnno: an open-access community-driven resource for regulatory annotation. - Obi L. Griffith; Stephen B. Montgomery; Bridget Bernier; Bryan Chu; Katayoon Kasaian; Stein Aerts; Shaun Mahony; Monica C. Sleumer; Mikhail Bilenky; Maximilian Haeussler; Malachi Griffith; Steven M. Gallo; et al. (Nucleic Acids Res., 2008)

De novo transcriptome assembly with ABySS. - Inanç Birol; Shaun D. Jackman; Cydney B. Nielsen; Jenny Q. Qian; Richard Varhol; Greg Stazyk; Ryan D. Morin; Yongjun Zhao 002; Martin Hirst; Jacqueline E. Schein; Douglas E. Horsman; Joseph M. Connors; et al. (Bioinform., 2009)

Slider - maximum use of probability information for alignment of short sequence reads and SNP detection. - Nawar Malhis; Yaron S. N. Butterfield; Martin Ester; Steven J. M. Jones (Bioinform., 2009)

KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis - Obi L. Griffith; Byron J. Gao; Mikhail Bilenky; Yuliya Prichyna; Martin Ester; Steven J. M. Jones (CoRR, 2009)

ABySS-Explorer: Visualizing Genome Sequence Assemblies. - Cydney B. Nielsen; Shaun D. Jackman; Inanç Birol; Steven J. M. Jones (IEEE Trans. Vis. Comput. Graph., 2009)

High quality SNP calling using Illumina data at shallow coverage. - Nawar Malhis; Steven J. M. Jones (Bioinform., 2010)

Genomic analysis of a rare human tumor. - Steven J. M. Jones; Janessa Laskin; Yvonne Y. Li; Obi L. Griffith; Jianghong An; Mikhail Bilenky; Yaron S. N. Butterfield; Timothee Cezard; Eric Chuah; Richard Corbett; Anthony P. Fejes; Malachi Griffith; et al. (BMC Bioinform., 2010)

LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. - R. T. F. Wong; Stephane Flibotte; Richard Corbett; Parvaneh Saeedi; Steven J. M. Jones; Marco A. Marra; Jacqueline E. Schein; Inanç Birol (IEEE Trans Autom. Sci. Eng., 2010)

Human variation database: an open-source database template for genomic discovery. - Anthony P. Fejes; Alireza Hadj Khodabakhshi; Inanç Birol; Steven J. M. Jones (Bioinform., 2011)

A Computational Approach to Finding Novel Targets for Existing Drugs. - Yvonne Y. Li; Jianghong An; Steven J. M. Jones (PLoS Comput. Biol., 2011)

Hive plots - rational approach to visualizing networks. - Martin Krzywinski; Inanç Birol; Steven J. M. Jones; Marco A. Marra (Briefings Bioinform., 2012)

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. - Ken Chen 001; John W. Wallis; Cyriac Kandoth; Joelle M. Kalicki-Veizer; Karen L. Mungall; Andrew J. Mungall; Steven J. M. Jones; Marco A. Marra; Timothy J. Ley; Elaine R. Mardis; Richard K. Wilson; John N. Weinstein; et al. (Bioinform., 2012)

On the Deep Order-Preserving Submatrix Problem: A Best Effort Approach. - Byron J. Gao; Obi L. Griffith; Martin Ester; Hui Xiong 001; Qiang Zhao; Steven J. M. Jones (IEEE Trans. Knowl. Data Eng., 2012)

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. - Inanç Birol; Anthony Raymond; Shaun D. Jackman; Stephen Pleasance; Robin Coope; Greg A. Taylor; Macaire Man Saint Yuen; Christopher I. Keeling; Dana Brand; Benjamin P. Vandervalk; Heather Kirk; Pawan Pandoh; et al. (Bioinform., 2013)

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline. - Alireza Hadj Khodabakhshi; Anthony P. Fejes; Inanç Birol; Steven J. M. Jones (BMC Bioinform., 2013)

An Interactive Analysis and Exploration Tool for Epigenomic Data. - Hamid Younesy; Cydney B. Nielsen; Torsten Möller; Olivia Alder; Rebecca Cullum; Matthew C. Lorincz; Mohammad M. Karimi; Steven J. M. Jones (Comput. Graph. Forum, 2013)

ALEA: a toolbox for allele-specific epigenomics analysis. - Hamid Younesy; Torsten Möller; Alireza Heravi Moussavi; Jeffrey B. Cheng; Joseph F. Costello; Matthew C. Lorincz; Mohammad M. Karimi; Steven J. M. Jones (Bioinform., 2014)

Integrative analysis of 111 reference human epigenomes Open. - Roadmap Epigenomics Consortium; Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi Moussavi; Pouya Kheradpour; ZhiZhuo Zhang; Jianrong Wang; Michael J. Ziller; Viren Amin; et al. (Nat., 2015)

VisRseq: R-based visual framework for analysis of sequencing data. - Hamid Younesy; Torsten Möller; Matthew C. Lorincz; Mohammad M. Karimi; Steven J. M. Jones (BMC Bioinform., 2015)

ChAsE: chromatin analysis and exploration tool. - Hamid Younesy; Cydney B. Nielsen; Matthew C. Lorincz; Steven J. M. Jones; Mohammad M. Karimi; Torsten Möller (Bioinform., 2016)

ORegAnno 3.0: a community-driven resource for curated regulatory annotation. - Robert Lesurf; Kelsy C. Cotto; Grace Wang; Malachi Griffith; Katayoon Kasaian; Steven J. M. Jones; Stephen B. Montgomery; Obi L. Griffith (Nucleic Acids Res., 2016)

A collaborative filtering-based approach to biomedical knowledge discovery. - Jake Lever; Sitanshu Gakkhar; Michael Gottlieb; Tahereh Rashnavadi; Santina Lin; Celia Siu; Maia Smith; Martin R. Jones; Martin Krzywinski; Steven J. M. Jones (Bioinform., 2018)

Tigmint: correcting assembly errors using linked reads from large molecules. - Shaun D. Jackman; Lauren Coombe; Justin Chu; René L. Warren; Benjamin P. Vandervalk; Sarah Yeo; Zhuyi Xue; Hamid Mohamadi; Jörg Bohlmann; Steven J. M. Jones; Inanç Birol (BMC Bioinform., 2018)

Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations. - Oleksandr Yakovenko; Steven J. M. Jones (J. Comput. Aided Mol. Des., 2018)

RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons. - Vinicius S. Chagas; Clarice S. Groeneveld; Kelin G. Oliveira; Sheyla Trefflich; Rodrigo C. de Almeida; Bruce A. J. Ponder; Kerstin B. Meyer; Steven J. M. Jones; A. Gordon Robertson; Mauro A. A. Castro (Bioinform., 2019)

RTNsurvival: an R/Bioconductor package for regulatory network survival analysis. - Clarice S. Groeneveld; Vinicius S. Chagas; Steven J. M. Jones; A. Gordon Robertson; Bruce A. J. Ponder; Kerstin B. Meyer; Mauro A. A. Castro (Bioinform., 2019)

ORCA: a comprehensive bioinformatics container environment for education and research. - Shaun D. Jackman; Tatyana Mozgacheva; Susie Chen; Brendan O'Huiginn; Lance Bailey; Inanç Birol; Steven J. M. Jones (Bioinform., 2019)

MAVIS: merging, annotation, validation, and illustration of structural variants. - Caralyn Reisle; Karen L. Mungall; Caleb Choo; Daniel Paulino; Dustin W. Bleile; Amir Muhammadzadeh; Andrew J. Mungall; Richard A. Moore; Inna Shlafman; Robin Coope; Stephen Pleasance; Yussanne Ma; et al. (Bioinform., 2019)

ntEdit: scalable genome sequence polishing. - René L. Warren; Lauren Coombe; Hamid Mohamadi; Jessica Zhang; Barry Jaquish; Nathalie Isabel; Steven J. M. Jones; Jean Bousquet; Jörg Bohlmann; Inanç Birol (Bioinform., 2019)

Classification of Epithelial Ovarian Carcinoma Whole-Slide Pathology Images Using Deep Transfer Learning. - Yiping Wang; David Farnell; Hossein Farahani; Mitchell Nursey; Basile Tessier-Cloutier; Steven J. M. Jones; David G. Huntsman; C. Blake Gilks; Ali Bashashati (CoRR, 2020)

LIST-S2: taxonomy based sorting of deleterious missense mutations across species. - Nawar Malhis; Matthew Jacobson; Steven J. M. Jones; Jörg Gsponer (Nucleic Acids Res., 2020)

cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines. - Xuanjin Cheng; Yongxing Liu; Jiahe Wang; Yujie Chen; Andrew Gordon Robertson; Xuekui Zhang; Steven J. M. Jones; Stefan Taubert (Briefings Bioinform., 2022)

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. - Kilannin Krysiak; Arpad M. Danos; Jason Saliba; Joshua F. McMichael; Adam C. Coffman; Susanna Kiwala; Erica K. Barnell; Lana Sheta; Cameron J. Grisdale; Lynzey Kujan; Shahil Pema; Jake Lever; et al. (Nucleic Acids Res., 2023)

Enhancing clinical genomic accuracy with panelGC: a novel metric and tool for quantifying and monitoring GC biases in hybridization capture panel sequencing. - Xuanjin Cheng; Murathan T. Goktas; Laura M. Williamson; Martin Krzywinski; David T. Mulder; Lucas Swanson; Jill Slind; Jelena Sihvonen; Cynthia R. Chow; Amy Carr; Ian Bosdet; Tracy Tucker; et al. (Briefings Bioinform., 2024)