Mining MEDLINE: Abstracts, Sentences, or Phrases? - Jing Ding; Daniel Berleant; Dan Nettleton; Eve Syrkin Wurtele (Pacific Symposium on Biocomputing, 2002)

Creating Metabolic Network Models using Text Mining and Expert Knowledge. - Julie A. Dickerson; Daniel Berleant; Z. Cox; W. Qi; Eve Syrkin Wurtele (Computational Biology and Genome Informatics, 2003)

Using the biological taxonomy to access biological literature with PathBinderH. - Jing Ding; Karthikeyan Viswanathan; Daniel Berleant; Laron M. Hughes; Eve Syrkin Wurtele; Daniel A. Ashlock; Julie A. Dickerson; Andy W. Fulmer; Patrick S. Schnable (Bioinform., 2005)

Integration of metabolic networks and gene expression in virtual reality. - Yuting Yang; Levent Engin; Eve Syrkin Wurtele; Carolina Cruz-Neira; Julie A. Dickerson (Bioinform., 2005)

Modeling gene expression networks using fuzzy logic. - Pan Du; Jian Gong; Eve Syrkin Wurtele; Julie A. Dickerson (IEEE Trans. Syst. Man Cybern. Part B, 2005)

Hierarchical visualization of metabolic networks using virtual reality. - Yuting Yang; Eve Syrkin Wurtele; Carolina Cruz-Neira; Julie A. Dickerson (VRCIA, 2006)

PubMed Assistant: a biologist-friendly interface for enhanced PubMed search. - Jing Ding; Laron M. Hughes; Daniel Berleant; Andy W. Fulmer; Eve Syrkin Wurtele (Bioinform., 2006)

Identifying differentially expressed genes in unreplicated multiple-treatment microarray timecourse experiments. - Rhonda DeCook; Dan Nettleton; Carol Foster; Eve Syrkin Wurtele (Comput. Stat. Data Anal., 2006)

A tool for comprehensive analysis of protein interaction networks. - Tian Xia; Jie Li; Eve Syrkin Wurtele; Xun Gu (BIOCOMP, 2007)

Reaction Centric Layout for Metabolic Networks. - Muhieddine El Kaissi; Ming Jia; Dirk Reiners; Julie A. Dickerson; Eve Syrkin Wurtele (ISVC (2), 2009)

Visualization of Gene Regulatory Networks. - Muhieddine El Kaissi; Ming Jia; Dirk Reiners; Julie A. Dickerson; Eve Syrkin Wurtele (ISVC (2), 2009)

PathBinder - text empirics and automatic extraction of biomolecular interactions. - Lifeng Zhang; Daniel Berleant; Jing Ding; Tuan Cao; Eve Syrkin Wurtele (BMC Bioinform., 2009)

Visualizing Multivariate Hierarchic Data Using Enhanced Radial Space-Filling Layout. - Ming Jia; Ling Li 009; Erin Boggess; Eve Syrkin Wurtele; Julie A. Dickerson (ISVC (1), 2010)

MetNetGE: interactive views of biological networks and ontologies. - Ming Jia; Suh-Yeon Choi; Dirk Reiners; Eve Syrkin Wurtele; Julie A. Dickerson (BMC Bioinform., 2010)

Meta!Blast computer game: a pipeline from science to 3D art to education. - William Schneller; P. J. Campbell; Diane Bassham; Eve Syrkin Wurtele (ERVR, 2012)

MetNet Online: a novel integrated resource for plant systems biology. - Yves Sucaet; Yi Wang; Jie Li; Eve Syrkin Wurtele (BMC Bioinform., 2012)

BirdsEyeView (BEV): graphical overviews of experimental data. - Lifeng Zhang; Daniel Berleant; Yi Wang; Ling Li 009; Diane J. Cook; Eve Syrkin Wurtele (BMC Bioinform., 2012)

Comprehensive analysis of correlation coefficients estimated from pooling heterogeneous microarray data. - Márcia M. Almeida-de-Macedo; Nick Ransom; Yaping Feng; Jonathan Hurst; Eve Syrkin Wurtele (BMC Bioinform., 2013)

Automatic extraction of biomolecular interactions: an empirical approach. - Lifeng Zhang; Daniel Berleant; Jing Ding; Eve Syrkin Wurtele (BMC Bioinform., 2013)

phylostratr: a framework for phylostratigraphy. - Zebulun Arendsee; Jing Li; Urminder Singh; Arun S. Seetharam; Karin S. Dorman; Eve Syrkin Wurtele (Bioinform., 2019)

fagin: synteny-based phylostratigraphy and finer classification of young genes. - Zebulun Arendsee; Jing Li; Urminder Singh; Priyanka Bhandary; Arun S. Seetharam; Eve Syrkin Wurtele (BMC Bioinform., 2019)

orfipy: a fast and flexible tool for extracting ORFs. - Urminder Singh; Eve Syrkin Wurtele (Bioinform., 2021)

rmonad: pipelines you can compute on. - Zebulun Arendsee; Jennifer Chang; Eve Syrkin Wurtele (R J., 2022)