Jonathan D. Wren

59 papers Journal 59
YearRankTypeTitle / Venue / Authors
2024 J jnl
BioVDB: biological vector database for high-throughput gene expression meta-analysis.
Frontiers Artif. Intell.
Michal J. Winnicki, Chase A. Brown, Hunter Porter, Cory B. Giles, Jonathan D. Wren
2022 J jnl
Detecting anomalous referencing patterns in PubMed papers suggestive of author-centric reference list manipulation.
Scientometrics
Jonathan D. Wren, Constantin Georgescu
2020 J jnl
Converting networks to predictive logic models from perturbation signalling data with CellNOpt.
Bioinform.
Enio Gjerga, Panuwat Trairatphisan, Attila Gábor, Hermann Koch, Céline Chevalier, Franceco Ceccarelli, Aurélien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez, Jonathan D. Wren
2020 J jnl
Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers.
Bioinform.
Ruichu Cai, Xuexin Chen, Yuan Fang, Min Wu, Yuexing Hao, Jonathan D. Wren
2020 J jnl
Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Yongsheng Bai, Zhaohui S. Qin, Da Yan, Ramin Homayouni
2020 J jnl
Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach.
Bioinform.
Siqi Liang, Haiyuan Yu, Jonathan D. Wren
2020 J jnl
ccNetViz: a WebGL-based JavaScript library for visualization of large networks.
Bioinform.
Ales Saska, David Tichy, Robert Moore, Achilles Rasquinha, Caner Akdas, Xiaodong Zhao, Renato Fabbri, Ana Jelicic, Gaurav Grover, Himanshu Jotwani, Mohamed Shadab, Resa M. K. Helikar, Tomás Helikar, Jonathan D. Wren
2019 J jnl
CAGm: a repository of germline microsatellite variations in the 1000 genomes project.
Nucleic Acids Res.
Nicholas Kinney, Kyle Titus-Glover, Jonathan D. Wren, Robin T. Varghese, Pawel Michalak, Han Liao, Ramu Anandakrishnan, Arichanah Pulenthiran, Lin Kang, Harold R. Garner
2019 J jnl
MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.
BMC Bioinform.
Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren
2019 J jnl
Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference.
BMC Bioinform.
Jonathan D. Wren, Robert J. Doerksen, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar
2019 J jnl
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention.
Bioinform.
Jonathan D. Wren, Alfonso Valencia, Janet Kelso
2018 J jnl
Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values.
Bioinform.
Constantin Georgescu, Jonathan D. Wren
2017 J jnl
ALE: automated label extraction from GEO metadata.
BMC Bioinform.
Cory B. Giles, Chase A. Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz, Jonathan D. Wren
2017 J jnl
Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Mikhail G. Dozmorov, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar
2016 J jnl
Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades.
Bioinform.
Jonathan D. Wren
2016 J jnl
GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets.
Bioinform.
Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren
2016 J jnl
Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Inimary T. Toby, Huxiao Hong, Bindu Nanduri, Rakesh Kaundal, Mikhail G. Dozmorov, Shraddha Thakkar
2015 J jnl
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data.
BMC Bioinform.
Mikhail G. Dozmorov, Indra Adrianto, Cory B. Giles, Edmund R. Glass, Stuart B. Glenn, Courtney Montgomery, Kathy L. Sivils, Lorin E. Olson, Tomoaki Iwayama, Willard M. Freeman, Christopher J. Lessard, Jonathan D. Wren
2014 J jnl
Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Andy D. Perkins, Chaoyang Zhang, Peter Hoyt, Rakesh Kaundal
2014 J jnl
Trends in the production of scientific data analysis resources.
BMC Bioinform.
Jason Hennessey, Constantin Georgescu, Jonathan D. Wren
2013 J jnl
Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Andy D. Perkins, Edward J. Perkins, Doris M. Kupfer, Gordon K. Springer
2013 J jnl
Systematic classification of non-coding RNAs by epigenomic similarity.
BMC Bioinform.
Mikhail G. Dozmorov, Cory B. Giles, Kristi A. Koelsch, Jonathan D. Wren
2013 J jnl
mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis.
BMC Bioinform.
Cory B. Giles, Reshmi Girijadevi, Mikhail G. Dozmorov, Jonathan D. Wren
2012 J jnl
Bioimage informatics: a new category in
Bioinform.
Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren
2012 J jnl
Genome
Bioinform.
Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren
2012 J jnl
Proceedings of the 2012 MidSouth computational biology and bioinformatics society (MCBIOS) conference.
BMC Bioinform.
Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Susan Bridges, Doris M. Kupfer
2011 J jnl
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses.
BMC Bioinform.
Mikhail G. Dozmorov, Jonathan D. Wren
2011 J jnl
Predicting gene ontology from a global meta-analysis of 1-color microarray experiments.
BMC Bioinform.
Mikhail G. Dozmorov, Cory B. Giles, Jonathan D. Wren
2011 J jnl
Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Stephen Winters-Hilt, Mikhail G. Dozmorov, Ulisses M. Braga-Neto
2011 J jnl
Question answering systems in biology and medicine - the time is now.
Bioinform.
Jonathan D. Wren
2010 J jnl
Identifying duplicate content using statistically improbable phrases.
Bioinform.
Mounir Errami, Zhaohui Sun, Angela C. George, Tara C. Long, Michael A. Skinner, Jonathan D. Wren, Harold R. Garner
2010 J jnl
Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Daniel Berleant
2009 J jnl
A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide.
Bioinform.
Jonathan D. Wren
2009 J jnl
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Yuriy Gusev, Raphael D. Isokpehi, Daniel Berleant, Ulisses M. Braga-Neto, Dawn Wilkins, Susan Bridges
2008 J jnl
Databases, data tombs and dust in the wind.
Bioinform.
Jonathan D. Wren, Alex Bateman
2008 J jnl
Déjà vu - A study of duplicate citations in Medline.
Bioinform.
Mounir Errami, Justin M. Hicks, Wayne G. Fisher, David Trusty, Jonathan D. Wren, Tara C. Long, Harold R. Garner
2008 J jnl
Large-scale directional relationship extraction and resolution.
BMC Bioinform.
Cory B. Giles, Jonathan D. Wren
2008 J jnl
Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Dawn Wilkins, James C. Fuscoe, Susan Bridges, Stephen Winters-Hilt, Yuriy Gusev
2008 J jnl
URL decay in MEDLINE - a 4-year follow-up study.
Bioinform.
Jonathan D. Wren
2007 J jnl
Clustering microarray-derived gene lists through implicit literature relationships.
Bioinform.
Mark F. Burkart, Jonathan D. Wren, Jason I. Herschkowitz, Charles M. Perou, Harold R. Garner
2007 J jnl
Evolving research trends in bioinformatics.
Briefings Bioinform.
Carolina Perez-Iratxeta, Miguel A. Andrade-Navarro, Jonathan D. Wren
2007 J jnl
Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.
BMC Bioinform.
Dawn Wilkins, Yuriy Gusev, Raja Loganantharaj, Susan Bridges, Stephen Winters-Hilt, Jonathan D. Wren
2007 J jnl
eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications.
Nucleic Acids Res.
Mounir Errami, Jonathan D. Wren, Justin M. Hicks, Harold R. Garner
2006 J jnl
A scalable machine-learning approach to recognize chemical names within large text databases.
BMC Bioinform.
Jonathan D. Wren
2006 J jnl
Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.
BMC Bioinform.
Jonathan D. Wren, Yuriy Gusev, Andrey A. Ptitsyn, Stephen Winters-Hilt
2006 J jnl
Theory and reality for software patents: good in concept, not so good in practice.
Bioinform.
Jonathan D. Wren
2006 J jnl
Using fuzzy set theory and scale-free network properties to relate MEDLINE terms.
Soft Comput.
Jonathan D. Wren
2005 J jnl
A microarray study of MPP
BMC Bioinform.
Zengjun Xu, Tucker A. Patterson, Jonathan D. Wren, Tao Han, Leming M. Shi, Helen Duhart, Syed F. Ali, William Slikker Jr.
2005 J jnl
Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set.
BMC Bioinform.
Jonathan D. Wren, David K. Johnson, Le Gruenwald
2005 J jnl
Biomedical term mapping databases.
Nucleic Acids Res.
Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman
2005 J jnl
Markov model recognition and classification of DNA/protein sequences within large text databases.
Bioinform.
Jonathan D. Wren, William H. Hildebrand, Sreedevi Chandrasekaran, Ulrich Melcher
2005 J jnl
Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.
BMC Bioinform.
Jonathan D. Wren, William Slikker Jr.
2004 J jnl
404 not found: the stability and persistence of URLs published in MEDLINE.
Bioinform.
Jonathan D. Wren
2004 J jnl
Extending the mutual information measure to rank inferred literature relationships.
BMC Bioinform.
Jonathan D. Wren
2004 J jnl
Knowledge discovery by automated identification and ranking of implicit relationships.
Bioinform.
Jonathan D. Wren, Raffi Bekeredjian, Jelena A. Stewart, Ralph V. Shohet, Harold R. Garner
2004 J jnl
Letter to the Editor.
Bioinform.
Lisa M. Schilling, Jonathan D. Wren, Robert P. Dellavalle
2004 J jnl
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network.
Bioinform.
Jonathan D. Wren, Harold R. Garner
2002 J jnl
ARROGANT: an application to manipulate large gene collections.
Bioinform.
Amit V. Kulkarni, Noelle Sevilir Williams, Yun Lian, Jonathan D. Wren, David Mittelman, Alexander Pertsemlidis, Harold R. Garner
2002 J jnl
SIGNAL-Sequence Information and GeNomic AnaLysis.
Comput. Methods Programs Biomed.
Jonathan D. Wren, David A. Mittelman, Harold R. Garner