Steven J. M. Jones

55 papers A* 1Journal 52Unranked 2
YearRankTypeTitle / Venue / Authors
2024 J jnl
Enhancing clinical genomic accuracy with panelGC: a novel metric and tool for quantifying and monitoring GC biases in hybridization capture panel sequencing.
Briefings Bioinform.
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, Sean Young, Richard A. Moore, Karen L. Mungall, Stephen Yip, Steven J. M. Jones
2023 J jnl
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.
Nucleic Acids Res.
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
2022 J jnl
cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines.
Briefings Bioinform.
Xuanjin Cheng, Yongxing Liu, Jiahe Wang, Yujie Chen, Andrew Gordon Robertson, Xuekui Zhang, Steven J. M. Jones, Stefan Taubert
2020 J jnl
Classification of Epithelial Ovarian Carcinoma Whole-Slide Pathology Images Using Deep Transfer Learning.
CoRR
Yiping Wang, David Farnell, Hossein Farahani, Mitchell Nursey, Basile Tessier-Cloutier, Steven J. M. Jones, David G. Huntsman, C. Blake Gilks, Ali Bashashati
2020 J jnl
LIST-S2: taxonomy based sorting of deleterious missense mutations across species.
Nucleic Acids Res.
Nawar Malhis, Matthew Jacobson, Steven J. M. Jones, Jörg Gsponer
2019 J jnl
MAVIS: merging, annotation, validation, and illustration of structural variants.
Bioinform.
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
2019 J jnl
ORCA: a comprehensive bioinformatics container environment for education and research.
Bioinform.
Shaun D. Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O'Huiginn, Lance Bailey, Inanç Birol, Steven J. M. Jones
2019 J jnl
RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons.
Bioinform.
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
2019 J jnl
RTNsurvival: an R/Bioconductor package for regulatory network survival analysis.
Bioinform.
Clarice S. Groeneveld, Vinicius S. Chagas, Steven J. M. Jones, A. Gordon Robertson, Bruce A. J. Ponder, Kerstin B. Meyer, Mauro A. A. Castro
2019 J jnl
ntEdit: scalable genome sequence polishing.
Bioinform.
René L. Warren, Lauren Coombe, Hamid Mohamadi, Jessica Zhang, Barry Jaquish, Nathalie Isabel, Steven J. M. Jones, Jean Bousquet, Jörg Bohlmann, Inanç Birol
2018 J jnl
A collaborative filtering-based approach to biomedical knowledge discovery.
Bioinform.
Jake Lever, Sitanshu Gakkhar, Michael Gottlieb, Tahereh Rashnavadi, Santina Lin, Celia Siu, Maia Smith, Martin R. Jones, Martin Krzywinski, Steven J. M. Jones
2018 J jnl
Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations.
J. Comput. Aided Mol. Des.
Oleksandr Yakovenko, Steven J. M. Jones
2018 J jnl
Tigmint: correcting assembly errors using linked reads from large molecules.
BMC Bioinform.
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
2016 J jnl
ChAsE: chromatin analysis and exploration tool.
Bioinform.
Hamid Younesy, Cydney B. Nielsen, Matthew C. Lorincz, Steven J. M. Jones, Mohammad M. Karimi, Torsten Möller
2016 J jnl
ORegAnno 3.0: a community-driven resource for curated regulatory annotation.
Nucleic Acids Res.
Robert Lesurf, Kelsy C. Cotto, Grace Wang, Malachi Griffith, Katayoon Kasaian, Steven J. M. Jones, Stephen B. Montgomery, Obi L. Griffith
2015 J jnl
Integrative analysis of 111 reference human epigenomes Open.
Nat.
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
2015 J jnl
VisRseq: R-based visual framework for analysis of sequencing data.
BMC Bioinform.
Hamid Younesy, Torsten Möller, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones
2014 J jnl
ALEA: a toolbox for allele-specific epigenomics analysis.
Bioinform.
Hamid Younesy, Torsten Möller, Alireza Heravi Moussavi, Jeffrey B. Cheng, Joseph F. Costello, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones
2013 J jnl
An Interactive Analysis and Exploration Tool for Epigenomic Data.
Comput. Graph. Forum
Hamid Younesy, Cydney B. Nielsen, Torsten Möller, Olivia Alder, Rebecca Cullum, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones
2013 J jnl
Assembling the 20 Gb white spruce (
Bioinform.
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
2013 J jnl
Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline.
BMC Bioinform.
Alireza Hadj Khodabakhshi, Anthony P. Fejes, Inanç Birol, Steven J. M. Jones
2012 J jnl
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.
Bioinform.
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
2012 J jnl
Hive plots - rational approach to visualizing networks.
Briefings Bioinform.
Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra
2012 J jnl
On the Deep Order-Preserving Submatrix Problem: A Best Effort Approach.
IEEE Trans. Knowl. Data Eng.
Byron J. Gao, Obi L. Griffith, Martin Ester, Hui Xiong, Qiang Zhao, Steven J. M. Jones
2011 J jnl
A Computational Approach to Finding Novel Targets for Existing Drugs.
PLoS Comput. Biol.
Yvonne Y. Li, Jianghong An, Steven J. M. Jones
2011 J jnl
Human variation database: an open-source database template for genomic discovery.
Bioinform.
Anthony P. Fejes, Alireza Hadj Khodabakhshi, Inanç Birol, Steven J. M. Jones
2010 J jnl
Genomic analysis of a rare human tumor.
BMC Bioinform.
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
2010 J jnl
High quality SNP calling using Illumina data at shallow coverage.
Bioinform.
Nawar Malhis, Steven J. M. Jones
2010 J jnl
LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images.
IEEE Trans Autom. Sci. Eng.
R. T. F. Wong, Stephane Flibotte, Richard Corbett, Parvaneh Saeedi, Steven J. M. Jones, Marco A. Marra, Jacqueline E. Schein, Inanç Birol
2009 J jnl
ABySS-Explorer: Visualizing Genome Sequence Assemblies.
IEEE Trans. Vis. Comput. Graph.
Cydney B. Nielsen, Shaun D. Jackman, Inanç Birol, Steven J. M. Jones
2009 J jnl
KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis
CoRR
Obi L. Griffith, Byron J. Gao, Mikhail Bilenky, Yuliya Prichyna, Martin Ester, Steven J. M. Jones
2009 J jnl
Slider - maximum use of probability information for alignment of short sequence reads and SNP detection.
Bioinform.
Nawar Malhis, Yaron S. N. Butterfield, Martin Ester, Steven J. M. Jones
2008 J jnl
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology.
Bioinform.
Anthony P. Fejes, Gordon Robertson, Mikhail Bilenky, Richard Varhol, Matthew N. Bainbridge, Steven J. M. Jones
2008 J jnl
ORegAnno: an open-access community-driven resource for regulatory annotation.
Nucleic Acids Res.
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
2007 J jnl
A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms.
PLoS Comput. Biol.
Stephen B. Montgomery, Obi L. Griffith, Johanna M. Schuetz, Angela Brooks-Wilson, Steven J. M. Jones
2007 J jnl
Assembling millions of short DNA sequences using SSAKE.
Bioinform.
René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt
2007 J jnl
THOR: targeted high-throughput ortholog reconstructor.
Bioinform.
Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, Gordon Robertson, Steven J. M. Jones
2006 J jnl
An interactive tool for visualization of relationships between gene expression profiles.
BMC Bioinform.
Peter Ruzanov, Steven J. M. Jones
2006 A* conf
Discovering significant OPSM subspace clusters in massive gene expression data.
KDD
Byron J. Gao, Obi L. Griffith, Martin Ester, Steven J. M. Jones
2006 J jnl
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
Bioinform.
Stephen B. Montgomery, Obi L. Griffith, Monica C. Sleumer, Casey M. Bergman, Misha Bilenky, Erin Pleasance, Y. Prychyna, X. Zhang, Steven J. M. Jones
2006 J jnl
Selective Targeting of Indel-inferred Differences in Spatial Structures of Homologous Proteins.
J. Bioinform. Comput. Biol.
Yvonne Y. Li, Steven J. M. Jones, Artem Cherkasov
2006 — conf
Sun Grid Engine Package for OSCAR - A Google Summer Of Code 2005 Project.
HPCS
Babu Sundaram, Barbara M. Chapman, Bernard Li, Mark Mayo, Asim S. Siddiqui, Steven J. M. Jones
2006 J jnl
cisRED: a database system for genome-scale computational discovery of regulatory elements.
Nucleic Acids Res.
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
2005 J jnl
'Inductive' Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand.
J. Chem. Inf. Model.
Artem Cherkasov, Zheng Shi, Yvonne Y. Li, Steven J. M. Jones, Magid Fallahi, Geoffrey L. Hammond
2005 J jnl
A methodology for analyzing SAGE libraries for cancer profiling.
ACM Trans. Inf. Syst.
Jörg Sander, Raymond T. Ng, Monica C. Sleumer, Man Saint Yuen, Steven J. M. Jones
2005 J jnl
CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.
BMC Bioinform.
Chris D. Bajdik, Byron Kuo, Shawn Rusaw, Steven J. M. Jones, Angela Brooks-Wilson
2005 — conf
cis-Regulatory Element Prediction in Mammalian Genomes.
CSB Workshops
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
2004 J jnl
An approach to large scale identification of non-obvious structural similarities between proteins.
BMC Bioinform.
Artem Cherkasov, Steven J. M. Jones
2004 J jnl
Structural characterization of genomes by large scale sequence-structure threading.
BMC Bioinform.
Artem Cherkasov, Steven J. M. Jones
2004 J jnl
Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics.
BMC Bioinform.
Artem Cherkasov, Shannan J. Ho Sui, Robert C. Brunham, Steven J. M. Jones
2003 J jnl
A knowledge discovery object model API for Java.
BMC Bioinform.
Scott D. Zuyderduyn, Steven J. M. Jones
2003 J jnl
IslandPath: aiding detection of genomic islands in prokaryotes.
Bioinform.
William W. L. Hsiao, Ivan Wan, Steven J. M. Jones, Fiona S. L. Brinkman
2002 J jnl
AcePrimer: automation of PCR primer design based on gene structure.
Bioinform.
Sheldon J. McKay, Steven J. M. Jones
2002 J jnl
Assembly of fingerprint contigs: parallelized FPC.
Bioinform.
Steven R. Ness, W. Terpstra, Martin Krzywinski, Marco A. Marra, Steven J. M. Jones
2001 J jnl
PhyloBLAST: facilitating phylogenetic analysis of BLAST results.
Bioinform.
Fiona S. L. Brinkman, Ivan Wan, Robert E. W. Hancock, Ann M. Rose, Steven J. M. Jones