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Submissions from 2016

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Programmable DNA Nanosystem for Molecular Interrogation, Davita Mathur and Eric R. Henderson

Submissions from 2015

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Nourishment level affects caste-related gene expression in Polistes wasps, Ali J. Berens, James H. Hunt, and Amy L. Toth

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Transcriptional profiling of overwintering gene expression in the small carpenter bee, Ceratina calcarata, Dusty R. Durant, Ali J. Berens, Amy L. Toth, and Sandra Rehan

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Computational prediction of protein interfaces: A review of data driven methods, Li C. Xue, Drena Dobbs, Alexandre M.J.J. Bonvin, and Vasant Honavar

Submissions from 2014

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Code-Assisted Discovery of TAL Effector Targets in Bacterial Leaf Streak of Rice Reveals Contrast with Bacterial Blight and a Novel Susceptibility Gene, Raul A. Cernadas, Erin L. Doyle, David O. Niño-Liu, Katherine E. wilkins, Timothy J. Bancroft, Li Wang, Clarice L. Schmidt, Rico Caldo, Bing Yang, Frank F. White, Roger P. Wise, and Adam J. Bogdanove

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Cytonuclear Evolution of Rubisco in Four Allopolyploid Lineages, Lei Gong, Mischa Olson, and Jonathan F. Wendel

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Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems, Ruolin Liu, Ann E. Loraine, and Julie Dickerson

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At the brink of eusociality: transcriptomic correlates of worker behaviour in a small carpenter bee, Sandra Rehan, Ali J. Berens, and Amy L. Toth

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Transcriptomic Analysis of Carboxylic Acid Challenge in Escherichia coli: Beyond Membrane Damage, Liam A. Royce, Erin E. Boggess, Yao Fu, Ping Liu, Jacqueline V. Shanks, Julie A. Dickerson, and Laura R. Jarboe

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Shared genes related to aggression, rather than chemical communication, are associated with reproductive dominance in paper wasps (Polistes metricus), Amy L. Toth, John F. Tooker, Srihari Radhakrishnan, Robert Minard, Michael T. Henshaw, and Christina M. Grozinger

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Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding, Chijioke N. Umunnakwe, Hyelee Loyd, Kinsey Cornick, Jerald R. Chavez, Drena Dobbs, and Susan Carpenter

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RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins, Rasna R. Walia, Li C. Xue, Katherine E. Wilkins, Yasser El-Manzalawy, Drena L. Dobbs, and Vasant G. Honavar

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A computational platform to maintain and migrate manual functional annotations for BioCyc databases, Jesse R. Walsh, Taner Z. Sen, and Julie Dickerson

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Flor Revisited (Again): eQTL and Mutational Analysis of NB-LRR Mediated Immunity to Powdery Mildew in Barley, Roger P. Wise, Priyanka Surana, Gregory S. Fuerst, Ruo Xu, Divya Mistry, Julie A. Dickerson, and Dan Nettleton Dr.

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DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction, Li C. Xue, Rafael A. Jordan, Yasser EL-Manzalawy, Drena Dobbs, and Vasant Honavar

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Elastic network models capture the motions apparent within ensembles of RNA structures, Michael T. Zimmermann and Robert L. Jernigan

Submissions from 2013

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Fingerloop activates cargo delivery and unloading during cotranslational protein targeting, Aileen R. Ariosa, Stacy S. Duncan, Oshu Saraogi, Xiaodong Lu, April Brown, Gregory J. Phillips, and Shu-Ou Shan

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A global approach to analysis and interpretation of metabolic data for plant natural product discovery, Manhoi Hur, Alexis Ann Campbell, Márcia M. Almeida de Macedo, Ling Li, Nick Ransom, Adarsh Jose, Matthew C. Crispin, Basil J. Nikolau, and Eve S. Wurtele

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Complex DNA Nanostructures from Oligonucleotide Ensembles, Divita Mathur and Eric R. Henderson

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Computational Tools for Investigating RNA-Protein Interaction Partners, Usha K. Muppirala, Benjamin A. Lewis, and Drena L. Dobbs

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Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements, Jianbo Zhang, Tao Zuo, and Thomas A. Peterson

Submissions from 2012

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Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics—database and tools update, Preeti Bais, Stephanie M. Moon-Quanbeck, Basil J. Nikolau, and Julie A. Dickerson

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PLEXdb: gene expression resources for plants and plant pathogens, Sudhansu Dash, John L. Van Hemert, Lu Hong, Roger P. Wise, and Julie A. Dickerson

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A massive human co-expression-network and its medical applications, Yaping Feng, Jonathan Hurst, Marcia Almeida-De-Macedo, Xi Chen, Ling Li, Nick Ransom, and Eve S. Wurtele

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Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences, Jérôme` Grimplet, John L. Van Hemert, Pablo Carbonell-Bejerano, José Díaz-Riquelme, Julie A. Dickerson, Anne Fennell, Mario Pezzotti, and José M. Martínez-Zapater

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Predicting protein-protein interface residues using local surface structural similarity, Rafael R. Jordan, Yasser El-Manzalawy, Drena Dobbs, and Vasant Honavar

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Differential accumulation of host mRNAs on polyribosomes during obligate pathogen-plant interactions, Jackson R. Moeller, Matthew J. Moscou, Timothy J. Bancroft, Ronald W. Skadsen, Roger P. Wise, and Steven A. Whitham

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Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”, Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip M. Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barkan, Iris Lange, B. Markus Lange, Insuk Lee, Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, and Basil J. Nikolau

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ParsEval: parallel comparison and analysis of gene structure annotations, Daniel S. Standage and Volker P. Brendel

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Phytohormone signaling pathway analysis method for comparing hormone responses in plant-pest interactions, Matthew Edward Studham and Gustavo C. Macintosh

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MetNet Online: a novel integrated resource for plant systems biology, Yves Sucaet, Yi Wang, and Eve Syrkin Wurtele

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Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art, Rasna R. Walia, Cornelia Caragea, Benjamin A. Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, and Vasant Honavar

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Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis, Tian Xia, Jiansong Tong, Shailendra S. Rathore, Xun Gu, and Julie A. Dickerson

Submissions from 2011

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Predicting MHC-II binding affinity using multiple instance regression, Yasser EL-Manzalawy, Drena Dobbs, and Vasant Honavar

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PRIDB: a protein–RNA interface database, Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant Honavar, and Drena Dobbs

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Predicting RNA-Protein Interactions Using Only Sequence Information, Usha Muppirala, Vasant G. Honavar, and Drena Dobbs

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ZFNGenome: A comprehensive resource for locating zinc finger nuclease target sites in model organisms, Deepak Reyon, Jessica R. Kirkpatrick, Jeffry D. Sander, Feng Zhang, Daniel F. Voytas, J Keith Joung, Drena Dobbs, and Clark R. Coffman

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Selection-Free Zinc-Finger Nuclease Engineering by Context-Dependent Assembly (CoDA), Jeffry D. Sander, Elizabeth J. Dahlborg, Matthew J. Goodwin, Lindsay Cade, Feng Zhang, Daniel Cifuentes, Shaun J. Curtin, Jessica S. Blackburn, Stacey Thibodeau-Beganny, Yiping Qi, Christopher J. Pierick, Ellen Hoffman, Morgan L. Maeder, Cyd Khayter, Deepak Reyon, Drena Dobbs, David M. Langenau, Robert M. Stupar, Antonio J. Giraldez, Daniel F. Voytas, Randall T. Peterson, Jing-Ruey J. Yeh, and J. Keith Joung

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HomPPI: a class of sequence homology based protein-protein interface prediction methods, Li C. Xue, Drena Dobbs, and Vasant Honavar

Submissions from 2010

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The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps, Carson M. Andorf, Carolyn J. Lawrence, Lisa C. Harper, Mary L. Schaeffer, Darwin A. Campbell, and Taner Z. Sen

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DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data, Stacy Duncan, Ruchita Sirkanungo, Leslie Miller, and Gregory J. Phillips

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ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool, Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, and Drena Dobbs

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Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences, Jeffry D. Sander, Deepak Reyon, Morgan L. Maeder, Jonathan E. Foley, Stacey Thibodeau-Beganny, Xiaohong Li, Maureen R. Regan, Elizabeth J. Dahlborg, Matthew J. Goodwin, Fengli Fu, Daniel F. Voytas, J Keith Joung, and Drena Dobbs

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A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences, Tonia S. Schwartz, Hongseok Tae, Youngik Yang, Keithanne Mockaitis, John L. Van Hemert, Stephen R. Proulx, Jeong-Hyeon Choi, and Anne M. Bronikowski

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Choosing a genome browser for a Model Organism Database: surveying the Maize community, Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, and Carolyn J. Lawrence

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MetNetAPI: A flexible method to access and manipulate biological network data from MetNet, Yves Sucaet and Eve Syrkin Wurtele

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Struct-NB: Predicting Protein-RNA Binding Sites Using Structural Features, Fadi Towfic, Cornelia Caragea, David C. Gemperline, Drena Dobbs, and Vasant Honavar

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Detection of gene orthology from gene co-expression and protein interaction networks, Fadi George Towfic, Susan R. VanderPlas, Casey A. Oiver, Oliver Couture, Christopher K. Tuggle, M. Heather West Greenlee, and Vasant Honavar

Submissions from 2009

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Initiation and Early Development of Fiber in Wild and Cultivated Cotton, Kara M. Butterworth, Dean C. Adams, Harry T. Horner, and Jonathan F. Wendel

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Development and implementation of high-throughput SNP genotyping in barley, Timothy J. Close, Prasanna R. Bhat, Stefano Lonardi, Yonghui Wu, Nils Rostoks, Luke Ramsay, Arnis Druka, Nils Stein, Jan T. Svensson, Steve Wanamaker, Serdar Bozdag, Mikeal L. Roose, Matthew J. Moscou, Shiaoman Chao, Rajeev K. Varshney, Péter Szűcs, Kazuhiro Sato, Patrick M. Hayes, David E. Matthews, Andris Kleinhofs, Gary J. Muehlbauer, Joseph DeYoung, David F. Marshall, Kavitha Madishetty, Raymond D. Fenton, Pascal Condamine, Andreas Graner, and Robbie Waugh

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VitisNet: “Omics” Integration through Grapevine Molecular Networks, Jérôme Grimplet, Grant R. Cramer, Julie Dickerson, Kathy Mathiason, John L. Van Hemert, and Anne Y. Fennell

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Structural Model of the Rev Regulatory Protein from Equine Infectious Anemia Virus, Yungok Ihm, Wendy O. Sparks, Jae-Hyung Lee, Haibo Cao, Susan Carpenter, Cai-Zhuang Wang, Kai-Ming Ho, and Drena Dobbs

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Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize, Brent A. Kronmiller and Roger P. Wise

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Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, and Patrick S. Schnable

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Arabidopsis gene co-expression network and its functional modules, Linyong Mao, John L. Van Hemert, Sudhansu Dash, and Julie A. Dickerson

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Blufensin1 Negatively Impacts Basal Defense in Response to Barley Powdery Mildew, Yan Meng, Matthew J. Moscou, and Roger P. Wise

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An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins, Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, and Drena L. Dobbs

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MaizeGDB becomes ‘sequence-centric, Taner Z. Sen, Carson M. Andorf, Mary L. Schaeffer, Lisa C. Harper, Michael E. Sparks, Jon Duvick, Volker P. Brendel, Ethalinda Cannon, Darwin A. Campbell, and Carolyn J. Lawrence

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Proline isomerization preorganizes the Itk SH2 domain for binding the Itk SH3 domain, Andrew J. Severin, Raji E. Joseph, Scott E. Boyken, D. Bruce Fulton, and Amy H. Andreotti

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Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content, Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng-Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Daniel S. Nettleton, and Patrick S. Schnable

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PRTAD: A Database for Protein Residue Torsion Angle Distributions, Xiaoyong Sun, Di Wu, Robert L. Jernigan, and Zhijun Wu

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High-throughput linkage analysis of Mutator insertion sites in maize, Gibum Yi, Diane Luth, Timothy D. Goodman, Carolyn J. Lawrence, and Philip W. Becraft

Submissions from 2008

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PlantGDB: a resource for comparative plant genomics, Jon Duvick, Ann Fu, Usha Muppirala, Mukul Sabharwal, Matthew D. Wilkerson, Carolyn J. Lawrence, Carol Lushbough, and Volker Brendel

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On Evaluating MHC-II Binding Peptide Prediction Methods, Yasser EL-Manzalawy, Drena Dobbs, and Vasant Honavar

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Predicting linear B-cell epitopes using string kernels, Yasser EL-Manzalawy, Drena Dobbs, and Vasant Honavar

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Analysis of the EIAV Rev-Responsive Element (RRE) Reveals a Conserved RNA Motif Required for High Affinity Rev Binding in Both HIV-1 and EIAV, Jae-Hyung Lee, Gloria Culver, Susan Carpenter, and Drena Dobbs

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Rapid “Open-Source” Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification, Morgan L. Maeder, Stacey Thibodeau-Beganny, Anna Osiak, David A. Wright, Reshma M. Anthony, Magdalena Eichtinger, Tao Jiang, Jonathan E. Foley, Ronnie J. Winfrey, Jeffrey A. Townsend, Erica Unger-Wallace, Jeffry D. Sander, Felix Müller-Lerch, Fengli Fu, Joseph Pearlberg, Carl Göbel, Justin P. Dassie, Shondra M. Pruett-Miller, Matthew H. Porteus, Dennis C. Sgroi, A. John Iafrate, Drena Dobbs, Paul B. McCray Jr., Toni Cathomen, Daniel F. Voytas, and J. Keith Joung

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OmicsViz: Cytoscape plug-in for visualizing omics data across species, Tian Xia and Julie A. Dickerson

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Characterization of Protein–Protein Interfaces, Changhui Yan, Feihong Wu, Robert L. Jernigan, Drena Dobbs, and Vasant Honavar

Submissions from 2007

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Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach, Carson Andorf, Drena Dobbs, and Vasant Honavar

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Glycosylation site prediction using ensembles of Support Vector Machine classifiers, Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, and Vasant Honavar

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Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool, Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, and Drena Dobbs

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RNABindR: a server for analyzing and predicting RNA-binding sites in proteins, Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant Honavar, and Drena Dobbs

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Transcript Profiling in Host–Pathogen Interactions, Roger P. Wise, Matthew J. Moscou, Adam J. Bogdanove, and Steven A. Whitham

Submissions from 2006

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Evolution of Alternative Splicing after Gene Duplication, Zhixi Su, Jianmin Wang, Xiaoqiu Huang, and Xun Gu

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Prediction of RNA binding sites in proteins from amino acid sequence, Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Vasant Honavar, and Drena Dobbs

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Predicting DNA-binding sites of proteins from amino acid sequence, Changhui Yan, Michael Terribilini, Feihong Wu, Robert L. Jernigan, Drena Dobbs, and Vasant Honavar

Submissions from 2005

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Using the biological taxonomy to access biological literature with PathBinderH, J. Ding, Karthik Viswanathan, Daniel Berleant, L. Hughes, Eve S. Wurtele, Daniel Ashlock, Julie A. Dickerson, A. Fulmer, and Patrick S. Schnable

Submissions from 2004

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Predicting binding sites of hydrolase-inhibitor complexes by combining several methods, Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan, Changhui Yan, Vasant Honovar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, and Drena Dobbs

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Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach, Changhui Yan, Vasant Honavar, and Drena Dobbs

Submissions from 1999

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CAP3: A DNA Sequence Assembly Program, Xiaoqiu Huang and Anup Madan

Submissions from 1996

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Methods for Comparing a DNA Sequence with a Protein Sequence, Xiaoqiu Huang and Jinghui Zhang