Steven J. M. Jones

According to our database, Steven J. M. Jones authored at least 55 papers between 2001 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of two.

2023

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, Sarah Ridd, Nicholas C. Spies, Veronica Andric, Andreea Chiorean, Damian Tobias Rieke, Kaitlin A. Clark, Caralyn Reisle, Ajay C. Venigalla, Mark Evans, Payal Jani, Hideaki Takahashi, Avila Suda, Peter Horák, Deborah i Ritter, Xin Zhou, Benjamin J. Ainscough, Sean Delong, Chimene Kesserwan, Mario Lamping, Haolin Shen, Alex Marr, My Hoang, Kartik Singhal, Mariam Khanfar, Brian V. Li, Wan-Hsin Lin, Panieh Terraf, Laura B. Corson, Yasser Salama, Katie M. Campbell, Kirsten M. Farncombe, Jianling Ji, Xiaonan Zhao, Xinjie Xu, Rashmi Kanagal-Shamanna, Ian King, Kelsy C. Cotto, Zachary L. Skidmore, Jason R. Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y. Patel, Rachel H. Giles, Raymond H. Kim, Lynn M. Schriml, Elaine R. Mardis, Steven J. M. Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H. Wagner, Malachi Griffith, Obi L. Griffith

Nucleic Acids Res., January, 2023

2022

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

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

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

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

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, Steven J. M. Jones

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

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

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

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

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

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

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

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

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., December, 2015

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, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis

Nat., 2015

2014

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

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

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

Assembling the 20 Gb white spruce (<i>Picea glauca</i>) 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, Richard A. Moore, Yongjun Zhao, Andrew J. Mungall, Barry Jaquish, Alvin Yanchuk, Carol Ritland, Brian Boyle, Jean Bousquet, Kermit Ritland, John MacKay, Jörg Bohlmann, Steven J. M. Jones

Bioinform., 2013

2012

On the Deep Order-Preserving Submatrix Problem: A Best Effort Approach.

Byron J. Gao, Obi L. Griffith, Martin Ester, Hui Xiong, Qiang Zhao, Steven J. M. Jones

IEEE Trans. Knowl. Data Eng., 2012

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.

Ken Chen, 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, Li Ding

Bioinform., 2012

Hive plots - rational approach to visualizing networks.

Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra

Briefings Bioinform., 2012

2011

A Computational Approach to Finding Novel Targets for Existing Drugs.

Yvonne Y. Li, Jianghong An, Steven J. M. Jones

PLoS Comput. Biol., 2011

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

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

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, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D. Morin, Trevor J. Pugh, Tesa Severson, Sohrab P. Shah, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A. Moore, David G. Huntsman, Inanç Birol, Martin Hirst, Robert A. Holt, Marco A. Marra

BMC Bioinform., 2010

High quality SNP calling using Illumina data at shallow coverage.

Nawar Malhis, Steven J. M. Jones

Bioinform., 2010

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

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

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

<i>De novo</i> transcriptome assembly with ABySS.

Inanç Birol, Shaun D. Jackman, Cydney B. Nielsen, Jenny Q. Qian, Richard Varhol, Greg Stazyk, Ryan D. Morin, Yongjun Zhao, Martin Hirst, Jacqueline E. Schein, Douglas E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, Steven J. M. Jones

Bioinform., 2009

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, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter J. De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth W. Wasserman, Ross C. Hardison, Casey M. Bergman, Steven J. M. Jones

Nucleic Acids Res., 2008

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

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

Assembling millions of short DNA sequences using SSAKE.

René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt

Bioinform., 2007

THOR: targeted high-throughput ortholog reconstructor.

Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, Gordon Robertson, Steven J. M. Jones

Bioinform., 2007

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, Monica C. Sleumer, W. Pan, Erin Pleasance, M. Chuang, H. Hao, Yvonne Y. Li, Neil Robertson, C. Fjell, Bernard Li, Stephen B. Montgomery, Tamara Astakhova, Jianjun Zhou, Jörg Sander, Asim S. Siddiqui, Steven J. M. Jones

Nucleic Acids Res., 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

An interactive tool for visualization of relationships between gene expression profiles.

Peter Ruzanov, Steven J. M. Jones

BMC Bioinform., 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

Discovering significant OPSM subspace clusters in massive gene expression data.

Byron J. Gao, Obi L. Griffith, Martin Ester, Steven J. M. Jones

Proceedings of the Twelfth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2006

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

Proceedings of the 20th Annual International Symposium on High Performance Computing Systems and Applications (HPCS 2006), 2006

2005

A methodology for analyzing SAGE libraries for cancer profiling.

Jörg Sander, Raymond T. Ng, Monica C. Sleumer, Man Saint Yuen, Steven J. M. Jones

ACM Trans. Inf. Syst., 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

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

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, Monica C. Sleumer, Kevin Teague, Richard Varhol, Maggie Zhang, Steven J. M. Jones

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

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

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.

Artem Cherkasov, Steven J. M. Jones

BMC Bioinform., 2004

2003

A knowledge discovery object model API for Java.

Scott D. Zuyderduyn, Steven J. M. Jones

BMC Bioinform., 2003

IslandPath: aiding detection of genomic islands in prokaryotes.

William W. L. Hsiao, Ivan Wan, Steven J. M. Jones, Fiona S. L. Brinkman

Bioinform., 2003

2002

Assembly of fingerprint contigs: parallelized FPC.

S. R. Ness, W. Terpstra, Martin Krzywinski, Marco A. Marra, Steven J. M. Jones

Bioinform., 2002

AcePrimer: automation of PCR primer design based on gene structure.

Sheldon J. McKay, Steven J. M. Jones

Bioinform., 2002

2001

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