Jonathan D. Wren

According to our database, Jonathan D. Wren authored at least 59 papers between 2002 and 2024.

Collaborative distances:

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

2024

BioVDB: biological vector database for high-throughput gene expression meta-analysis.

Michal J. Winnicki, Chase A. Brown, Hunter Porter, Cory B. Giles, Jonathan D. Wren

Frontiers Artif. Intell., 2024

2022

Detecting anomalous referencing patterns in PubMed papers suggestive of author-centric reference list manipulation.

Jonathan D. Wren, Constantin Georgescu

Scientometrics, 2022

2020

Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Yongsheng Bai, Zhaohui S. Qin, Da Yan, Ramin Homayouni

BMC Bioinform., 2020

ccNetViz: a WebGL-based JavaScript library for visualization of large networks.

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

Bioinform., 2020

Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach.

Siqi Liang, Haiyuan Yu, Jonathan D. Wren

Bioinform., 2020

Converting networks to predictive logic models from perturbation signalling data with CellNOpt.

Enio Gjerga, Panuwat Trairatphisan, Attila Gábor, Hermann Koch, Céline Chevalier, Franceco Ceccarelli, Aurélien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez, Jonathan D. Wren

Bioinform., 2020

Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers.

Ruichu Cai, Xuexin Chen, Yuan Fang, Min Wu, Yuexing Hao, Jonathan D. Wren

Bioinform., 2020

2019

CAGm: a repository of germline microsatellite variations in the 1000 genomes project.

Nicholas Kinney, Kyle Titus-Glover, Jonathan D. Wren, Robin T. Varghese, Pawel Michalak, Han Liao, Ramu Anandakrishnan, Arichanah Pulenthiran, Lin Kang, Harold R. Garner

Nucleic Acids Res., 2019

Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference.

Jonathan D. Wren, Robert J. Doerksen, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar

BMC Bioinform., 2019

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.

Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren

BMC Bioinform., 2019

Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention.

Jonathan D. Wren, Alfonso Valencia, Janet Kelso

Bioinform., 2019

2018

Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values.

Constantin Georgescu, Jonathan D. Wren

Bioinform., 2018

2017

Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Mikhail G. Dozmorov, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar

BMC Bioinform., 2017

ALE: automated label extraction from GEO metadata.

Cory B. Giles, Chase A. Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz, Jonathan D. Wren

BMC Bioinform., 2017

2016

Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Inimary T. Toby, Huxiao Hong, Bindu Nanduri, Rakesh Kaundal, Mikhail G. Dozmorov, Shraddha Thakkar

BMC Bioinform., 2016

Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades.

Jonathan D. Wren

Bioinform., 2016

GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets.

Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren

Bioinform., 2016

2015

Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data.

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

BMC Bioinform., December, 2015

2014

Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Andy D. Perkins, Chaoyang Zhang, Peter Hoyt, Rakesh Kaundal

BMC Bioinform., 2014

Trends in the production of scientific data analysis resources.

Jason Hennessey, Constantin Georgescu, Jonathan D. Wren

BMC Bioinform., 2014

2013

Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Andy D. Perkins, Edward J. Perkins, Doris M. Kupfer, Gordon K. Springer

BMC Bioinform., 2013

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis.

Cory B. Giles, Reshmi Girijadevi, Mikhail G. Dozmorov, Jonathan D. Wren

BMC Bioinform., 2013

Systematic classification of non-coding RNAs by epigenomic similarity.

Mikhail G. Dozmorov, Cory B. Giles, Kristi A. Koelsch, Jonathan D. Wren

BMC Bioinform., 2013

2012

Proceedings of the 2012 MidSouth computational biology and bioinformatics society (MCBIOS) conference.

Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Susan Bridges, Doris M. Kupfer

BMC Bioinform., 2012

Bioimage informatics: a new category in <i>Bioinformatics</i>.

Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren

Bioinform., 2012

Genome<i>Runner</i>: automating genome exploration.

Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren

Bioinform., 2012

2011

Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Stephen Winters-Hilt, Mikhail G. Dozmorov, Ulisses M. Braga-Neto

BMC Bioinform., 2011

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses.

Mikhail G. Dozmorov, Jonathan D. Wren

BMC Bioinform., 2011

Predicting gene ontology from a global meta-analysis of 1-color microarray experiments.

Mikhail G. Dozmorov, Cory B. Giles, Jonathan D. Wren

BMC Bioinform., 2011

Question answering systems in biology and medicine - the time is now.

Jonathan D. Wren

Bioinform., 2011

2010

Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Daniel Berleant

BMC Bioinform., 2010

Identifying duplicate content using statistically improbable phrases.

Mounir Errami, Zhaohui Sun, Angela C. George, Tara C. Long, Michael A. Skinner, Jonathan D. Wren, Harold R. Garner

Bioinform., 2010

2009

Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Yuriy Gusev, Raphael D. Isokpehi, Daniel Berleant, Ulisses M. Braga-Neto, Dawn Wilkins, Susan Bridges

BMC Bioinform., 2009

A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide.

Jonathan D. Wren

Bioinform., 2009

2008

Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Jonathan D. Wren, Dawn Wilkins, James C. Fuscoe, Susan Bridges, Stephen Winters-Hilt, Yuriy Gusev

BMC Bioinform., 2008

Large-scale directional relationship extraction and resolution.

Cory B. Giles, Jonathan D. Wren

BMC Bioinform., 2008

Databases, data tombs and dust in the wind.

Jonathan D. Wren, Alex Bateman

Bioinform., 2008

URL decay in MEDLINE - a 4-year follow-up study.

Jonathan D. Wren

Bioinform., 2008

Déjà vu - A study of duplicate citations in Medline.

Mounir Errami, Justin M. Hicks, Wayne G. Fisher, David Trusty, Jonathan D. Wren, Tara C. Long, Harold R. Garner

Bioinform., 2008

2007

eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications.

Mounir Errami, Jonathan D. Wren, Justin M. Hicks, Harold R. Garner

Nucleic Acids Res., 2007

Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.

Dawn Wilkins, Yuriy Gusev, Raja Loganantharaj, Susan Bridges, Stephen Winters-Hilt, Jonathan D. Wren

BMC Bioinform., 2007

Clustering microarray-derived gene lists through implicit literature relationships.

Mark F. Burkart, Jonathan D. Wren, Jason I. Herschkowitz, Charles M. Perou, Harold R. Garner

Bioinform., 2007

Evolving research trends in bioinformatics.

Carolina Perez-Iratxeta, Miguel A. Andrade-Navarro, Jonathan D. Wren

Briefings Bioinform., 2007

2006

Using fuzzy set theory and scale-free network properties to relate MEDLINE terms.

Jonathan D. Wren

Soft Comput., 2006

Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.

Jonathan D. Wren, Yuriy Gusev, Andrey A. Ptitsyn, Stephen Winters-Hilt

BMC Bioinform., 2006

A scalable machine-learning approach to recognize chemical names within large text databases.

Jonathan D. Wren

BMC Bioinform., 2006

Theory and reality for software patents: good in concept, not so good in practice.

Jonathan D. Wren

Bioinform., 2006

2005

Biomedical term mapping databases.

Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman

Nucleic Acids Res., 2005

A microarray study of MPP⁺-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools.

Zengjun Xu, Tucker A. Patterson, Jonathan D. Wren, Tao Han, Leming M. Shi, Helen Duhart, Syed F. Ali, William Slikker Jr.

BMC Bioinform., 2005

Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.

Jonathan D. Wren, William Slikker Jr.

BMC Bioinform., 2005

Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set.

Jonathan D. Wren, David K. Johnson, Le Gruenwald

BMC Bioinform., 2005

Markov model recognition and classification of DNA/protein sequences within large text databases.

Jonathan D. Wren, William H. Hildebrand, Sreedevi Chandrasekaran, Ulrich Melcher

Bioinform., 2005

2004

Extending the mutual information measure to rank inferred literature relationships.

Jonathan D. Wren

BMC Bioinform., 2004

Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network.

Jonathan D. Wren, Harold R. Garner

Bioinform., 2004

Knowledge discovery by automated identification and ranking of implicit relationships.

Jonathan D. Wren, Raffi Bekeredjian, Jelena A. Stewart, Ralph V. Shohet, Harold R. Garner

Bioinform., 2004

404 not found: the stability and persistence of URLs published in MEDLINE.

Jonathan D. Wren

Bioinform., 2004

Letter to the Editor.

Lisa M. Schilling, Jonathan D. Wren, Robert P. Dellavalle

Bioinform., 2004

2002

SIGNAL-Sequence Information and GeNomic AnaLysis.

Jonathan D. Wren, David A. Mittelman, Harold R. Garner

Comput. Methods Programs Biomed., 2002

ARROGANT: an application to manipulate large gene collections.

Amit V. Kulkarni, Noelle Sevilir Williams, Yun Lian, Jonathan D. Wren, David Mittelman, Alexander Pertsemlidis, Harold R. Garner

Bioinform., 2002