The MidasPlus molecular modeling system. - Thomas E. Ferrin; Conrad C. Huang; Gregory S. Couch; Eric F. Pettersen; Robert Langridge (CHI, 1992)

Molecules to maps: tools for visualization and interaction in support of computational biology. - Eileen T. Kraemer; Thomas E. Ferrin (Bioinform., 1998)

Molecules to Maps: Tools for Visualization & Interaction - Session Introduction. - Thomas E. Ferrin; Eileen T. Kraemer (Pacific Symposium on Biocomputing, 1999)

Chimera: Affordable Desktop Molecular Modeling on Linux Workstations. - David E. Konerding; Conrad C. Huang; Thomas E. Ferrin (Annual Linux Showcase & Conference, 2001)

High Performance Computing for Computational Biology - Session Introduction. - Thomas E. Ferrin; Bruce A. Foster; Richard Hughey (Pacific Symposium on Biocomputing, 2001)

SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project. - Doug Stryke; Conrad C. Huang; Michiko Kawamoto; Susan J. Johns; Elaine J. Carlson; Joseph A. Deyoung; Maya K. Leabman; Ira Herskowitz; Kathleen M. Giacomini; Thomas E. Ferrin (Pacific Symposium on Biocomputing, 2003)

MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. - Andrew I. Jewett; Conrad C. Huang; Thomas E. Ferrin (Bioinform., 2003)

The Structure Superposition Database. - Ranyee A. Chiang; Elaine C. Meng; Conrad C. Huang; Thomas E. Ferrin; Patricia C. Babbitt (Nucleic Acids Res., 2003)

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. - Doug Stryke; Michiko Kawamoto; Conrad C. Huang; Susan J. Johns; Leslie A. King; Courtney A. Harper; Elaine C. Meng; Roy E. Lee; Alice Yee; Larry L'Italien; Pao-Tien Chuang; Stephen G. Young; et al. (Nucleic Acids Res., 2003)

UCSF Chimera - A visualization system for exploratory research and analysis. - Eric F. Pettersen; Thomas D. Goddard; Conrad C. Huang; Gregory S. Couch; Daniel M. Greenblatt; Elaine C. Meng; Thomas E. Ferrin (J. Comput. Chem., 2004)

MODBASE, a database of annotated comparative protein structure models, and associated resources. - Ursula Pieper 001; Narayanan Eswar; Hannes Braberg; Mallur S. Madhusudhan; Fred P. Davis; Ashley C. Stuart; Nebojsa Mirkovic; Andrea Rossi 005; Marc A. Martí-Renom; András Fiser; Ben M. Webb; Daniel M. Greenblatt; et al. (Nucleic Acids Res., 2004)

Enhancing Data Sharing in Collaborative Research Projects with DASH. - Thomas E. Ferrin; Conrad C. Huang; Daniel M. Greenblatt; Doug Stryke; Kathleen M. Giacomini; John H. Morris (Pacific Symposium on Biocomputing, 2005)

Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies. - Scott C.-H. Pegg; Shoshana D. Brown; Sunil Ojha; Conrad C. Huang; Thomas E. Ferrin; Patricia C. Babbitt (Pacific Symposium on Biocomputing, 2005)

Tools for integrated sequence-structure analysis with UCSF Chimera. - Elaine C. Meng; Eric F. Pettersen; Gregory S. Couch; Conrad C. Huang; Thomas E. Ferrin (BMC Bioinform., 2006)

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. - Alex S. Nord; Patricia J. Chang; Bruce R. Conklin; Antony V. Cox; Courtney A. Harper; Geoffrey G. Hicks; Conrad C. Huang; Susan J. Johns; Michiko Kawamoto; Songyan Liu; Elaine C. Meng; John H. Morris; et al. (Nucleic Acids Res., 2006)

structureViz: linking Cytoscape and UCSF Chimera. - John H. Morris; Conrad C. Huang; Patricia C. Babbitt; Thomas E. Ferrin (Bioinform., 2007)

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. - Leonard Apeltsin; John H. Morris; Patricia C. Babbitt; Thomas E. Ferrin (Bioinform., 2011)

clusterMaker: a multi-algorithm clustering plugin for Cytoscape. - John H. Morris; Leonard Apeltsin; Aaron M. Newman; Jan Baumbach; Tobias Wittkop; Gang Su; Gary D. Bader; Thomas E. Ferrin (BMC Bioinform., 2011)

ModBase, a database of annotated comparative protein structure models, and associated resources. - Ursula Pieper 001; Benjamin M. Webb; David T. Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C. Meng; Eric F. Pettersen; Conrad C. Huang; Ruchira S. Datta; Parthasarathy Sampathkumar; et al. (Nucleic Acids Res., 2011)

enhancedGraphics: a Cytoscape app for enhanced node graphics. - John H. Morris; Allan Kuchinsky; Thomas E. Ferrin; Alexander R. Pico (F1000Research, 2014)

setsApp: Set operations for Cytoscape Nodes and Edges. - John H. Morris; Allan Wu; Nadezhda T. Doncheva; Mario Albrecht; Thomas E. Ferrin (F1000Research, 2014)

The Structure-Function Linkage Database. - Eyal Akiva; Shoshana D. Brown; Daniel E. Almonacid; Alan E. Barber II; Ashley F. Custer; Michael A. Hicks 002; Conrad C. Huang; Florian Lauck; Susan T. Mashiyama; Elaine C. Meng; David Mischel; John H. Morris; et al. (Nucleic Acids Res., 2014)

Enhancing UCSF Chimera through web services. - Conrad C. Huang; Elaine C. Meng; John H. Morris; Eric F. Pettersen; Thomas E. Ferrin (Nucleic Acids Res., 2014)

RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. - Jonathan E. Chen; Conrad C. Huang; Thomas E. Ferrin (Bioinform., 2015)

cddApp: a Cytoscape app for accessing the NCBI conserved domain database. - John H. Morris; Allan Wu; Roxanne A. Yamashita; Aron Marchler-Bauer; Thomas E. Ferrin (Bioinform., 2015)

CyAnimator: Simple Animations of Cytoscape Networks. - John H. Morris; Vijay Dhameliya; Steven Federowicz; Alexander R. Pico; Thomas E. Ferrin (F1000Research, 2015)

DASP3: identification of protein sequences belonging to functionally relevant groups. - Janelle B. Leuthaeuser; John H. Morris; Angela F. Harper; Thomas E. Ferrin; Patricia C. Babbitt; Jacquelyn S. Fetrow (BMC Bioinform., 2016)

Biocuration in the structure-function linkage database: the anatomy of a superfamily. - Gemma L. Holliday; Shoshana D. Brown; Eyal Akiva; David Mischel; Michael A. Hicks 002; John H. Morris; Conrad C. Huang; Elaine C. Meng; Scott C.-H. Pegg; Thomas E. Ferrin; Patricia C. Babbitt (Database J. Biol. Databases Curation, 2017)

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. - Angela F. Harper; Janelle B. Leuthaeuser; Patricia C. Babbitt; John H. Morris; Thomas E. Ferrin; Leslie B. Poole; Jacquelyn S. Fetrow (PLoS Comput. Biol., 2017)