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2020 – today
- 2024
[j59]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)- 2022
- [j58]Jonathan D. Wren
, Constantin Georgescu:
Detecting anomalous referencing patterns in PubMed papers suggestive of author-centric reference list manipulation. Scientometrics 127(10): 5753-5771 (2022) - 2020
- [j57]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): 4458-4465 (2020) - [j56]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): 4490-4497 (2020) - [j55]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): 4523-4524 (2020) - [j54]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): 4527-4529 (2020) - [j53]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. 21-S(4): 254 (2020)
2010 – 2019
- 2019
- [j52]Jonathan D. Wren, Alfonso Valencia, Janet Kelso:
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention. Bioinform. 35(18): 3217-3218 (2019) - [j51]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. 20-S(2): 59-71 (2019) - [j50]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. 20-S(2): 95:1-95:5 (2019) - [j49]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): D39-D45 (2019) - 2018
- [j48]Constantin Georgescu, Jonathan D. Wren:
Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values. Bioinform. 34(10): 1758-1766 (2018) - 2017
- [j47]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): 7-16 (2017) - [j46]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): 498:1-498:5 (2017) - 2016
- [j45]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): 2256-2263 (2016) - [j44]Jonathan D. Wren:
Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades. Bioinform. 32(17): 2686-2691 (2016) - [j43]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): 356 (2016) - 2015
- [j42]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): S10 (2015) - 2014
- [j41]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): I1 (2014) - [j40]Jason Hennessey, Constantin Georgescu, Jonathan D. Wren:
Trends in the production of scientific data analysis resources. BMC Bioinform. 15(S-11): S7 (2014) - 2013
- [j39]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): S1 (2013) - [j38]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): S17 (2013) - [j37]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): S2 (2013) - 2012
- [j36]Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren:
GenomeRunner: automating genome exploration. Bioinform. 28(3): 419-420 (2012) - [j35]Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren:
Bioimage informatics: a new category in Bioinformatics. Bioinform. 28(8): 1057 (2012) - [j34]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): S1 (2012) - 2011
- [j33]Jonathan D. Wren:
Question answering systems in biology and medicine - the time is now. Bioinform. 27(14): 2025-2026 (2011) - [j32]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): S1 (2011) - [j31]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): S14 (2011) - [j30]Mikhail G. Dozmorov, Jonathan D. Wren:
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. BMC Bioinform. 12(S-10): S2 (2011) - 2010
- [j29]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): 1453-1457 (2010) - [j28]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): S1 (2010)
2000 – 2009
- 2009
- [j27]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): 1694-1701 (2009) - [j26]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): 1 (2009) - 2008
- [j25]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): 243-249 (2008) - [j24]Jonathan D. Wren:
URL decay in MEDLINE - a 4-year follow-up study. Bioinform. 24(11): 1381-1385 (2008) - [j23]Jonathan D. Wren, Alex Bateman:
Databases, data tombs and dust in the wind. Bioinform. 24(19): 2127-2128 (2008) - [j22]Cory B. Giles, Jonathan D. Wren:
Large-scale directional relationship extraction and resolution. BMC Bioinform. 9(S-9) (2008) - [j21]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) - 2007
- [j20]Carolina Perez-Iratxeta, Miguel A. Andrade-Navarro, Jonathan D. Wren:
Evolving research trends in bioinformatics. Briefings Bioinform. 8(2): 88-95 (2007) - [j19]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): 1995-2003 (2007) - [j18]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) - [j17]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): 12-15 (2007) - 2006
- [j16]Jonathan D. Wren:
Theory and reality for software patents: good in concept, not so good in practice. Bioinform. 22(13): 1543-1545 (2006) - [j15]Jonathan D. Wren:
A scalable machine-learning approach to recognize chemical names within large text databases. BMC Bioinform. 7(S-2) (2006) - [j14]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) - [j13]Jonathan D. Wren:
Using fuzzy set theory and scale-free network properties to relate MEDLINE terms. Soft Comput. 10(4): 374-381 (2006) - 2005
- [j12]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): 4046-4053 (2005) - [j11]Jonathan D. Wren, David K. Johnson, Le Gruenwald:
Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set. BMC Bioinform. 6(S-2) (2005) - [j10]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) - [j9]Zengjun Xu, Tucker A. Patterson, Jonathan D. Wren, Tao Han, Leming M. Shi, Helen Duhart, Syed F. Ali, William Slikker Jr.:
A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools. BMC Bioinform. 6(S-2) (2005) - [j8]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): 289-293 (2005) - 2004
- [j7]Jonathan D. Wren, Harold R. Garner:
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinform. 20(2): 191-198 (2004) - [j6]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): 389-398 (2004) - [j5]Jonathan D. Wren:
404 not found: the stability and persistence of URLs published in MEDLINE. Bioinform. 20(5): 668-672 (2004) - [j4]Lisa M. Schilling, Jonathan D. Wren, Robert P. Dellavalle:
Letter to the Editor. Bioinform. 20(17): 2903 (2004) - [j3]Jonathan D. Wren:
Extending the mutual information measure to rank inferred literature relationships. BMC Bioinform. 5: 145 (2004) - 2002
- [j2]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): 1410-1417 (2002) - [j1]Jonathan D. Wren, David A. Mittelman, Harold R. Garner:
SIGNAL-Sequence Information and GeNomic AnaLysis. Comput. Methods Programs Biomed. 68(2): 177-181 (2002)
Coauthor Index
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