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Steven J. M. Jones
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2020 – today
- 2023
- [j50]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): 1230-1241 (2023) - 2022
- [j49]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) - 2020
- [j48]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): W154-W161 (2020) - [i2]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 abs/2005.10957 (2020)
2010 – 2019
- 2019
- [j47]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): 515-517 (2019) - [j46]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): 4430-4432 (2019) - [j45]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): 4448-4450 (2019) - [j44]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): 4488-4489 (2019) - [j43]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): 5357-5358 (2019) - 2018
- [j42]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): 652-659 (2018) - [j41]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): 393:1-393:10 (2018) - [j40]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): 299-311 (2018) - 2016
- [j39]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): 3324-3326 (2016) - [j38]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): 126-132 (2016) - 2015
- [j37]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): S2 (2015) - [j36]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): 317-330 (2015) - 2014
- [j35]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): 1172-1174 (2014) - 2013
- [j34]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:
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinform. 29(12): 1492-1497 (2013) - [j33]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: 167 (2013) - [j32]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): 91-100 (2013) - 2012
- [j31]Martin Krzywinski, Inanç Birol, Steven J. M. Jones, Marco A. Marra:
Hive plots - rational approach to visualizing networks. Briefings Bioinform. 13(5): 627-644 (2012) - [j30]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): 1923-1924 (2012) - [j29]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): 309-325 (2012) - 2011
- [j28]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): 1155-1156 (2011) - [j27]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) - 2010
- [j26]Nawar Malhis, Steven J. M. Jones:
High quality SNP calling using Illumina data at shallow coverage. Bioinform. 26(8): 1029-1035 (2010) - [j25]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): O3 (2010) - [j24]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): 706-708 (2010)
2000 – 2009
- 2009
- [j23]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): 6-13 (2009) - [j22]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:
De novo transcriptome assembly with ABySS. Bioinform. 25(21): 2872-2877 (2009) - [j21]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): 881-888 (2009) - [i1]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 abs/0904.1931 (2009) - 2008
- [j20]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): 1729-1730 (2008) - [j19]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): 107-113 (2008) - 2007
- [j18]René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt:
Assembling millions of short DNA sequences using SSAKE. Bioinform. 23(4): 500-501 (2007) - [j17]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): 2622-2624 (2007) - [j16]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) - 2006
- [j15]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): 637-640 (2006) - [j14]Peter Ruzanov, Steven J. M. Jones:
An interactive tool for visualization of relationships between gene expression profiles. BMC Bioinform. 7: 193 (2006) - [j13]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): 403-414 (2006) - [j12]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): 68-73 (2006) - [c3]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: 41 - [c2]Byron J. Gao, Obi L. Griffith, Martin Ester, Steven J. M. Jones:
Discovering significant OPSM subspace clusters in massive gene expression data. KDD 2006: 922-928 - 2005
- [j11]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: 78 (2005) - [j10]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): 1842-1853 (2005) - [j9]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): 35-60 (2005) - [c1]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: 203-206 - 2004
- [j8]Artem Cherkasov, Steven J. M. Jones:
Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinform. 5: 37 (2004) - [j7]Artem Cherkasov, Steven J. M. Jones:
An approach to large scale identification of non-obvious structural similarities between proteins. BMC Bioinform. 5: 61 (2004) - [j6]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: 101 (2004) - 2003
- [j5]William W. L. Hsiao, Ivan Wan, Steven J. M. Jones, Fiona S. L. Brinkman:
IslandPath: aiding detection of genomic islands in prokaryotes. Bioinform. 19(3): 418-420 (2003) - [j4]Scott D. Zuyderduyn, Steven J. M. Jones:
A knowledge discovery object model API for Java. BMC Bioinform. 4: 51 (2003) - 2002
- [j3]S. R. Ness, W. Terpstra, Martin Krzywinski, Marco A. Marra, Steven J. M. Jones:
Assembly of fingerprint contigs: parallelized FPC. Bioinform. 18(3): 484-485 (2002) - [j2]Sheldon J. McKay, Steven J. M. Jones:
AcePrimer: automation of PCR primer design based on gene structure. Bioinform. 18(11): 1538-1539 (2002) - 2001
- [j1]Fiona S. L. Brinkman, Ivan Wan, Robert E. W. Hancock, Ann M. Rose, Steven J. M. Jones:
PhyloBLAST: facilitating phylogenetic analysis of BLAST results. Bioinform. 17(4): 385-387 (2001)
Coauthor Index
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