Steven J. M. Jones

Publication Activity (10 Years)

Years Active: 2002-2023
Publications (10 Years): 16

Top Topics

Knowledge Discovery

Survival Analysis

Top Venues

Nucleic Acids Res.

Publications

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
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Res. 51 (D1) (2023)
Xuanjin Cheng, Yongxing Liu, Jiahe Wang, Yujie Chen, Andrew Gordon Robertson, Xuekui Zhang, Steven J. M. Jones, Stefan Taubert
cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines. Briefings Bioinform. 23 (3) (2022)
Nawar Malhis, Matthew Jacobson, Steven J. M. Jones, Jörg Gsponer
LIST-S2: taxonomy based sorting of deleterious missense mutations across species. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Yiping Wang, David Farnell, Hossein Farahani, Mitchell Nursey, Basile Tessier-Cloutier, Steven J. M. Jones, David G. Huntsman, C. Blake Gilks, Ali Bashashati
Classification of Epithelial Ovarian Carcinoma Whole-Slide Pathology Images Using Deep Transfer Learning. CoRR (2020)
Clarice S. Groeneveld, Vinicius S. Chagas, Steven J. M. Jones, A. Gordon Robertson, Bruce A. J. Ponder, Kerstin B. Meyer, Mauro A. A. Castro
RTNsurvival: an R/Bioconductor package for regulatory network survival analysis. Bioinform. 35 (21) (2019)
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
MAVIS: merging, annotation, validation, and illustration of structural variants. Bioinform. 35 (3) (2019)
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
RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons. Bioinform. 35 (24) (2019)
Shaun D. Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O'Huiginn, Lance Bailey, Inanç Birol, Steven J. M. Jones
ORCA: a comprehensive bioinformatics container environment for education and research. Bioinform. 35 (21) (2019)
René L. Warren, Lauren Coombe, Hamid Mohamadi, Jessica Zhang, Barry Jaquish, Nathalie Isabel, Steven J. M. Jones, Jean Bousquet, Jörg Bohlmann, Inanç Birol
ntEdit: scalable genome sequence polishing. Bioinform. 35 (21) (2019)
Jake Lever, Sitanshu Gakkhar, Michael Gottlieb, Tahereh Rashnavadi, Santina Lin, Celia Siu, Maia Smith, Martin R. Jones, Martin Krzywinski, Steven J. M. Jones
A collaborative filtering-based approach to biomedical knowledge discovery. Bioinform. 34 (4) (2018)
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
Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinform. 19 (1) (2018)
Oleksandr Yakovenko, Steven J. M. Jones
Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations. J. Comput. Aided Mol. Des. 32 (1) (2018)
Robert Lesurf, Kelsy C. Cotto, Grace Wang, Malachi Griffith, Katayoon Kasaian, Steven J. M. Jones, Stephen B. Montgomery, Obi L. Griffith
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 44 (Database-Issue) (2016)
Hamid Younesy, Cydney B. Nielsen, Matthew C. Lorincz, Steven J. M. Jones, Mohammad M. Karimi, Torsten Möller
ChAsE: chromatin analysis and exploration tool. Bioinform. 32 (21) (2016)
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
Integrative analysis of 111 reference human epigenomes Open. Nat. 518 (7539) (2015)
Hamid Younesy, Torsten Möller, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones
VisRseq: R-based visual framework for analysis of sequencing data. BMC Bioinform. 16 (S11) (2015)
Hamid Younesy, Torsten Möller, Alireza Heravi Moussavi, Jeffrey B. Cheng, Joseph F. Costello, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones
ALEA: a toolbox for allele-specific epigenomics analysis. Bioinform. 30 (8) (2014)
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
) genome from whole-genome shotgun sequencing data. Bioinform. 29 (12) (2013)
Alireza Hadj Khodabakhshi, Anthony P. Fejes, Inanç Birol, Steven J. M. Jones
Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline. BMC Bioinform. 14 (2013)
Hamid Younesy, Cydney B. Nielsen, Torsten Möller, Olivia Alder, Rebecca Cullum, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones
An Interactive Analysis and Exploration Tool for Epigenomic Data. Comput. Graph. Forum 32 (3) (2013)
Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra
Hive plots - rational approach to visualizing networks. Briefings Bioinform. 13 (5) (2012)
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
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinform. 28 (14) (2012)
Byron J. Gao, Obi L. Griffith, Martin Ester, Hui Xiong, Qiang Zhao, Steven J. M. Jones
On the Deep Order-Preserving Submatrix Problem: A Best Effort Approach. IEEE Trans. Knowl. Data Eng. 24 (2) (2012)
Yvonne Y. Li, Jianghong An, Steven J. M. Jones
A Computational Approach to Finding Novel Targets for Existing Drugs. PLoS Comput. Biol. 7 (9) (2011)
Anthony P. Fejes, Alireza Hadj Khodabakhshi, Inanç Birol, Steven J. M. Jones
Human variation database: an open-source database template for genomic discovery. Bioinform. 27 (8) (2011)
R. T. F. Wong, Stephane Flibotte, Richard Corbett, Parvaneh Saeedi, Steven J. M. Jones, Marco A. Marra, Jacqueline E. Schein, Inanç Birol
LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. IEEE Trans Autom. Sci. Eng. 7 (3) (2010)
Nawar Malhis, Steven J. M. Jones
High quality SNP calling using Illumina data at shallow coverage. Bioinform. 26 (8) (2010)
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
Genomic analysis of a rare human tumor. BMC Bioinform. 11 (S-4) (2010)
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
transcriptome assembly with ABySS. Bioinform. 25 (21) (2009)
Obi L. Griffith, Byron J. Gao, Mikhail Bilenky, Yuliya Prichyna, Martin Ester, Steven J. M. Jones
KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis CoRR (2009)
Nawar Malhis, Yaron S. N. Butterfield, Martin Ester, Steven J. M. Jones
Slider - maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinform. 25 (1) (2009)
Cydney B. Nielsen, Shaun D. Jackman, Inanç Birol, Steven J. M. Jones
ABySS-Explorer: Visualizing Genome Sequence Assemblies. IEEE Trans. Vis. Comput. Graph. 15 (6) (2009)
Anthony P. Fejes, Gordon Robertson, Mikhail Bilenky, Richard Varhol, Matthew N. Bainbridge, Steven J. M. Jones
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinform. 24 (15) (2008)
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
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36 (Database-Issue) (2008)
Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, Gordon Robertson, Steven J. M. Jones
THOR: targeted high-throughput ortholog reconstructor. Bioinform. 23 (19) (2007)
René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt
Assembling millions of short DNA sequences using SSAKE. Bioinform. 23 (4) (2007)
Stephen B. Montgomery, Obi L. Griffith, Johanna M. Schuetz, Angela Brooks-Wilson, Steven J. M. Jones
A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms. PLoS Comput. Biol. 3 (6) (2007)
Babu Sundaram, Barbara M. Chapman, Bernard Li, Mark Mayo, Asim S. Siddiqui, Steven J. M. Jones
Sun Grid Engine Package for OSCAR - A Google Summer Of Code 2005 Project. HPCS (2006)
Byron J. Gao, Obi L. Griffith, Martin Ester, Steven J. M. Jones
Discovering significant OPSM subspace clusters in massive gene expression data. KDD (2006)
Stephen B. Montgomery, Obi L. Griffith, Monica C. Sleumer, Casey M. Bergman, Misha Bilenky, Erin Pleasance, Y. Prychyna, X. Zhang, Steven J. M. Jones
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinform. 22 (5) (2006)
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
cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res. 34 (Database-Issue) (2006)
Peter Ruzanov, Steven J. M. Jones
An interactive tool for visualization of relationships between gene expression profiles. BMC Bioinform. 7 (2006)
Yvonne Y. Li, Steven J. M. Jones, Artem Cherkasov
Selective Targeting of Indel-inferred Differences in Spatial Structures of Homologous Proteins. J. Bioinform. Comput. Biol. 4 (2) (2006)
Jörg Sander, Raymond T. Ng, Monica C. Sleumer, Man Saint Yuen, Steven J. M. Jones
A methodology for analyzing SAGE libraries for cancer profiling. ACM Trans. Inf. Syst. 23 (1) (2005)
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
cis-Regulatory Element Prediction in Mammalian Genomes. CSB Workshops (2005)
Artem Cherkasov, Zheng Shi, Yvonne Y. Li, Steven J. M. Jones, Magid Fallahi, Geoffrey L. Hammond
'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. 45 (6) (2005)
Chris D. Bajdik, Byron Kuo, Shawn Rusaw, Steven J. M. Jones, Angela Brooks-Wilson
CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes. BMC Bioinform. 6 (2005)
Artem Cherkasov, Steven J. M. Jones
An approach to large scale identification of non-obvious structural similarities between proteins. BMC Bioinform. 5 (2004)
Artem Cherkasov, Shannan J. Ho Sui, Robert C. Brunham, Steven J. M. Jones
Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics. BMC Bioinform. 5 (2004)
Artem Cherkasov, Steven J. M. Jones
Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinform. 5 (2004)
Scott D. Zuyderduyn, Steven J. M. Jones
A knowledge discovery object model API for Java. BMC Bioinform. 4 (2003)
S. R. Ness, W. Terpstra, Martin Krzywinski, Marco A. Marra, Steven J. M. Jones
Assembly of fingerprint contigs: parallelized FPC. Bioinform. 18 (3) (2002)
Sheldon J. McKay, Steven J. M. Jones
AcePrimer: automation of PCR primer design based on gene structure. Bioinform. 18 (11) (2002)