Jonathan D. Wren

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 17

Top Topics

Computational Biology

Top Venues

Frontiers Artif. Intell.

Publications

Michal J. Winnicki, Chase A. Brown, Hunter Porter, Cory B. Giles, Jonathan D. Wren
BioVDB: biological vector database for high-throughput gene expression meta-analysis. Frontiers Artif. Intell. 7 (2024)
Jonathan D. Wren, Constantin Georgescu
Detecting anomalous referencing patterns in PubMed papers suggestive of author-centric reference list manipulation. Scientometrics 127 (10) (2022)
Ruichu Cai, Xuexin Chen, Yuan Fang, Min Wu, Yuexing Hao, Jonathan D. Wren
Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers. Bioinform. 36 (16) (2020)
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
ccNetViz: a WebGL-based JavaScript library for visualization of large networks. Bioinform. 36 (16) (2020)
Jonathan D. Wren, Yongsheng Bai, Zhaohui S. Qin, Da Yan, Ramin Homayouni
Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. (4) (2020)
Enio Gjerga, Panuwat Trairatphisan, Attila Gábor, Hermann Koch, Céline Chevalier, Franceco Ceccarelli, Aurélien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez, Jonathan D. Wren
Converting networks to predictive logic models from perturbation signalling data with CellNOpt. Bioinform. 36 (16) (2020)
Siqi Liang, Haiyuan Yu, Jonathan D. Wren
Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach. Bioinform. 36 (16) (2020)
Jonathan D. Wren, Alfonso Valencia, Janet Kelso
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention. Bioinform. 35 (18) (2019)
Nicholas Kinney, Kyle Titus-Glover, Jonathan D. Wren, Robin T. Varghese, Pawel Michalak, Han Liao, Ramu Anandakrishnan, Arichanah Pulenthiran, Lin Kang, Harold R. Garner
CAGm: a repository of germline microsatellite variations in the 1000 genomes project. Nucleic Acids Res. 47 (Database-Issue) (2019)
Jonathan D. Wren, Robert J. Doerksen, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar
Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. BMC Bioinform. (2) (2019)
Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren
MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations. BMC Bioinform. (2) (2019)
Constantin Georgescu, Jonathan D. Wren
Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values. Bioinform. 34 (10) (2018)
Cory B. Giles, Chase A. Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz, Jonathan D. Wren
ALE: automated label extraction from GEO metadata. BMC Bioinform. 18 (14) (2017)
Jonathan D. Wren, Mikhail G. Dozmorov, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar
Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 18 (14) (2017)
Jonathan D. Wren, Inimary T. Toby, Huxiao Hong, Bindu Nanduri, Rakesh Kaundal, Mikhail G. Dozmorov, Shraddha Thakkar
Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 17 (S-13) (2016)
Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren
GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets. Bioinform. 32 (15) (2016)
Jonathan D. Wren
Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades. Bioinform. 32 (17) (2016)
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
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. BMC Bioinform. 16 (S13) (2015)
Jason Hennessey, Constantin Georgescu, Jonathan D. Wren
Trends in the production of scientific data analysis resources. BMC Bioinform. 15 (S-11) (2014)
Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Andy D. Perkins, Chaoyang Zhang, Peter Hoyt, Rakesh Kaundal
Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 15 (S-11) (2014)
Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Andy D. Perkins, Edward J. Perkins, Doris M. Kupfer, Gordon K. Springer
Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 14 (S-14) (2013)
Cory B. Giles, Reshmi Girijadevi, Mikhail G. Dozmorov, Jonathan D. Wren
mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis. BMC Bioinform. 14 (S-14) (2013)
Mikhail G. Dozmorov, Cory B. Giles, Kristi A. Koelsch, Jonathan D. Wren
Systematic classification of non-coding RNAs by epigenomic similarity. BMC Bioinform. 14 (S-14) (2013)
Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren
: automating genome exploration. Bioinform. 28 (3) (2012)
Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Susan Bridges, Doris M. Kupfer
Proceedings of the 2012 MidSouth computational biology and bioinformatics society (MCBIOS) conference. BMC Bioinform. 13 (S-15) (2012)
Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren
. Bioinform. 28 (8) (2012)
Mikhail G. Dozmorov, Cory B. Giles, Jonathan D. Wren
Predicting gene ontology from a global meta-analysis of 1-color microarray experiments. BMC Bioinform. 12 (S-10) (2011)
Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Stephen Winters-Hilt, Mikhail G. Dozmorov, Ulisses M. Braga-Neto
Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 12 (S-10) (2011)
Mikhail G. Dozmorov, Jonathan D. Wren
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. BMC Bioinform. 12 (S-10) (2011)
Jonathan D. Wren
Question answering systems in biology and medicine - the time is now. Bioinform. 27 (14) (2011)
Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Daniel Berleant
Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 11 (S-6) (2010)
Mounir Errami, Zhaohui Sun, Angela C. George, Tara C. Long, Michael A. Skinner, Jonathan D. Wren, Harold R. Garner
Identifying duplicate content using statistically improbable phrases. Bioinform. 26 (11) (2010)
Jonathan D. Wren, Yuriy Gusev, Raphael D. Isokpehi, Daniel Berleant, Ulisses M. Braga-Neto, Dawn Wilkins, Susan Bridges
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 10 (S-11) (2009)
Jonathan D. Wren
A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. Bioinform. 25 (13) (2009)
Jonathan D. Wren, Alex Bateman
Databases, data tombs and dust in the wind. Bioinform. 24 (19) (2008)
Cory B. Giles, Jonathan D. Wren
Large-scale directional relationship extraction and resolution. BMC Bioinform. 9 (S-9) (2008)
Jonathan D. Wren, Dawn Wilkins, James C. Fuscoe, Susan Bridges, Stephen Winters-Hilt, Yuriy Gusev
Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 9 (S-9) (2008)
Mounir Errami, Justin M. Hicks, Wayne G. Fisher, David Trusty, Jonathan D. Wren, Tara C. Long, Harold R. Garner
Déjà vu - A study of duplicate citations in Medline. Bioinform. 24 (2) (2008)
Jonathan D. Wren
URL decay in MEDLINE - a 4-year follow-up study. Bioinform. 24 (11) (2008)
Mounir Errami, Jonathan D. Wren, Justin M. Hicks, Harold R. Garner
eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Carolina Perez-Iratxeta, Miguel A. Andrade-Navarro, Jonathan D. Wren
Evolving research trends in bioinformatics. Briefings Bioinform. 8 (2) (2007)
Mark F. Burkart, Jonathan D. Wren, Jason I. Herschkowitz, Charles M. Perou, Harold R. Garner
Clustering microarray-derived gene lists through implicit literature relationships. Bioinform. 23 (15) (2007)
Dawn Wilkins, Yuriy Gusev, Raja Loganantharaj, Susan Bridges, Stephen Winters-Hilt, Jonathan D. Wren
Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. BMC Bioinform. 8 (S-7) (2007)
Jonathan D. Wren
Using fuzzy set theory and scale-free network properties to relate MEDLINE terms. Soft Comput. 10 (4) (2006)
Jonathan D. Wren
A scalable machine-learning approach to recognize chemical names within large text databases. BMC Bioinform. 7 (S-2) (2006)
Jonathan D. Wren
Theory and reality for software patents: good in concept, not so good in practice. Bioinform. 22 (13) (2006)
Jonathan D. Wren, Yuriy Gusev, Andrey A. Ptitsyn, Stephen Winters-Hilt
Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. BMC Bioinform. 7 (S-2) (2006)
Jonathan D. Wren, William Slikker Jr.
Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. BMC Bioinform. 6 (S-2) (2005)
Zengjun Xu, Tucker A. Patterson, Jonathan D. Wren, Tao Han, Leming M. Shi, Helen Duhart, Syed F. Ali, William Slikker Jr.
-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools. BMC Bioinform. 6 (S-2) (2005)
Jonathan D. Wren, William H. Hildebrand, Sreedevi Chandrasekaran, Ulrich Melcher
Markov model recognition and classification of DNA/protein sequences within large text databases. Bioinform. 21 (21) (2005)
Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman
Biomedical term mapping databases. Nucleic Acids Res. 33 (Database-Issue) (2005)
Jonathan D. Wren, David Johnson, Le Gruenwald
Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set. BMC Bioinform. 6 (S-2) (2005)
Jonathan D. Wren
404 not found: the stability and persistence of URLs published in MEDLINE. Bioinform. 20 (5) (2004)
Lisa M. Schilling, Jonathan D. Wren, Robert P. Dellavalle
Letter to the Editor. Bioinform. 20 (17) (2004)
Jonathan D. Wren
Extending the mutual information measure to rank inferred literature relationships. BMC Bioinform. 5 (2004)
Jonathan D. Wren, Harold R. Garner
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinform. 20 (2) (2004)
Jonathan D. Wren, Raffi Bekeredjian, Jelena A. Stewart, Ralph V. Shohet, Harold R. Garner
Knowledge discovery by automated identification and ranking of implicit relationships. Bioinform. 20 (3) (2004)
Jonathan D. Wren, David A. Mittelman, Harold R. Garner
SIGNAL-Sequence Information and GeNomic AnaLysis. Comput. Methods Programs Biomed. 68 (2) (2002)
Amit V. Kulkarni, Noelle Sevilir Williams, Yun Lian, Jonathan D. Wren, David Mittelman, Alexander Pertsemlidis, Harold R. Garner
ARROGANT: an application to manipulate large gene collections. Bioinform. 18 (11) (2002)