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)

SIGNAL-Sequence Information and GeNomic AnaLysis. - Jonathan D. Wren; David A. Mittelman; Harold R. Garner (Comput. Methods Programs Biomed., 2002)

Letter to the Editor. - Lisa M. Schilling; Jonathan D. Wren; Robert P. Dellavalle (Bioinform., 2004)

404 not found: the stability and persistence of URLs published in MEDLINE. - Jonathan D. Wren (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)

Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. - Jonathan D. Wren; Harold R. Garner (Bioinform., 2004)

Extending the mutual information measure to rank inferred literature relationships. - Jonathan D. Wren (BMC Bioinform., 2004)

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)

Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set. - Jonathan D. Wren; David K. Johnson 001; Le Gruenwald (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)

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 007; Leming M. Shi; Helen Duhart; Syed F. Ali; William Slikker Jr. (BMC Bioinform., 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)

Theory and reality for software patents: good in concept, not so good in practice. - Jonathan D. Wren (Bioinform., 2006)

A scalable machine-learning approach to recognize chemical names within large text databases. - Jonathan D. Wren (BMC Bioinform., 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)

Using fuzzy set theory and scale-free network properties to relate MEDLINE terms. - Jonathan D. Wren (Soft Comput., 2006)

Evolving research trends in bioinformatics. - Carolina Perez-Iratxeta; Miguel A. Andrade-Navarro; Jonathan D. Wren (Briefings 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)

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)

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)

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)

URL decay in MEDLINE - a 4-year follow-up study. - Jonathan D. Wren (Bioinform., 2008)

Databases, data tombs and dust in the wind. - Jonathan D. Wren; Alex Bateman (Bioinform., 2008)

Large-scale directional relationship extraction and resolution. - Cory B. Giles; Jonathan D. Wren (BMC Bioinform., 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)

A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. - Jonathan D. Wren (Bioinform., 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)

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)

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)

Question answering systems in biology and medicine - the time is now. - Jonathan D. Wren (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)

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. - Mikhail G. Dozmorov; Jonathan D. Wren (BMC Bioinform., 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)

GenomeRunner: automating genome exploration. - Mikhail G. Dozmorov; Lukas R. Cara; Cory B. Giles; Jonathan D. Wren (Bioinform., 2012)

Bioimage informatics: a new category in Bioinformatics. - Hanchuan Peng; Alex Bateman; Alfonso Valencia; Jonathan D. Wren (Bioinform., 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)

Systematic classification of non-coding RNAs by epigenomic similarity. - Mikhail G. Dozmorov; Cory B. Giles; Kristi A. Koelsch; Jonathan D. Wren (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)

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)

Trends in the production of scientific data analysis resources. - Jason Hennessey; Constantin Georgescu; Jonathan D. Wren (BMC Bioinform., 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)

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., 2015)

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)

Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades. - Jonathan D. Wren (Bioinform., 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)

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)

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)

Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values. - Constantin Georgescu; Jonathan D. Wren (Bioinform., 2018)

Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention. - Jonathan D. Wren; Alfonso Valencia; Janet Kelso (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)

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)

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)

Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers. - Ruichu Cai; Xuexin Chen; Yuan Fang 001; Min Wu 008; Yuexing Hao; 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)

Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach. - Siqi Liang 002; Haiyuan Yu; Jonathan D. Wren (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; et al. (Bioinform., 2020)

Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. - Jonathan D. Wren; Yongsheng Bai; Zhaohui S. Qin; Da Yan 001; Ramin Homayouni (BMC Bioinform., 2020)

Detecting anomalous referencing patterns in PubMed papers suggestive of author-centric reference list manipulation. - Jonathan D. Wren; Constantin Georgescu (Scientometrics, 2022)

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)