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ORCIDThomas E. Ferrin
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2010 – 2019
- 2017
[j20]Gemma L. Holliday
, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt:
Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database J. Biol. Databases Curation 2017: bax006 (2017)- [j19]Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt:
Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database J. Biol. Databases Curation 2017: bax045 (2017) - [j18]Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow:
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput. Biol. 13(2) (2017) - 2016
- [j17]Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt, Jacquelyn S. Fetrow:
DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinform. 17: 458:1-458:13 (2016) - 2015
- [j16]John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin:
cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinform. 31(1): 134-136 (2015) - [j15]Jonathan E. Chen, Conrad C. Huang, Thomas E. Ferrin:
RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Bioinform. 31(9): 1484-1486 (2015) - [i3]John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin:
CyAnimator: Simple Animations of Cytoscape Networks. F1000Research 4: 482 (2015) - 2014
- [j14]Eyal Akiva, Shoshana D. Brown, Daniel E. Almonacid, Alan E. Barber II, Ashley F. Custer, Michael A. Hicks, Conrad C. Huang, Florian Lauck, Susan T. Mashiyama, Elaine C. Meng, David Mischel, John H. Morris, Sunil Ojha, Alexandra M. Schnoes, Doug Stryke, Jeffrey M. Yunes, Thomas E. Ferrin, Gemma L. Holliday, Patricia C. Babbitt:
The Structure-Function Linkage Database. Nucleic Acids Res. 42(Database-Issue): 521-530 (2014) - [j13]Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin:
Enhancing UCSF Chimera through web services. Nucleic Acids Res. 42(Webserver-Issue): 478-484 (2014) - [i2]John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico:
enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Research 3: 147 (2014) - [i1]John H. Morris, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Thomas E. Ferrin:
setsApp: Set operations for Cytoscape Nodes and Edges. F1000Research 3: 149 (2014) - 2011
- [j12]Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin:
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinform. 27(3): 326-333 (2011) - [j11]John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin:
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinform. 12: 436 (2011) - [j10]Ursula Pieper, 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, Mallur S. Madhusudhan, Kimmen Sjölander, Thomas E. Ferrin, Stephen K. Burley, Andrej Sali:
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39(Database-Issue): 465-474 (2011)
2000 – 2009
- 2007
- [j9]John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin:
structureViz: linking Cytoscape and UCSF Chimera. Bioinform. 23(17): 2345-2347 (2007) - 2006
- [j8]Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, Conrad C. Huang, Thomas E. Ferrin:
Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinform. 7: 339 (2006) - [j7]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, Janet Rossant, Patricia Ruiz, William C. Skarnes, Philippe Soriano, William L. Stanford, Doug Stryke, Harald von Melchner, Wolfgang Wurst, Ken-ichi Yamamura, Stephen G. Young, Patricia C. Babbitt, Thomas E. Ferrin:
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 34(Database-Issue): 642-648 (2006) - 2005
- [c7]Thomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris:
Enhancing Data Sharing in Collaborative Research Projects with DASH. Pacific Symposium on Biocomputing 2005 - [c6]Scott C.-H. Pegg, Shoshana D. Brown, Sunil Ojha, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt:
Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies. Pacific Symposium on Biocomputing 2005 - 2004
- [j6]Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin:
UCSF Chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25(13): 1605-1612 (2004) - [j5]Ursula Pieper, Narayanan Eswar, Hannes Braberg, Mallur S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Martí-Renom, András Fiser, Ben M. Webb, Daniel M. Greenblatt, Conrad C. Huang, Thomas E. Ferrin, Andrej Sali:
MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 32(Database-Issue): 217-222 (2004) - 2003
- [j4]Andrew I. Jewett, Conrad C. Huang, Thomas E. Ferrin:
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinform. 19(5): 625-634 (2003) - [j3]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, William C. Skarnes, Patricia C. Babbitt, Thomas E. Ferrin:
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res. 31(1): 278-281 (2003) - [j2]Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt:
The Structure Superposition Database. Nucleic Acids Res. 31(1): 505-510 (2003) - [c5]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:
SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project. Pacific Symposium on Biocomputing 2003: 535-547 - 2001
- [c4]David E. Konerding, Conrad C. Huang, Thomas E. Ferrin:
Chimera: Affordable Desktop Molecular Modeling on Linux Workstations. Annual Linux Showcase & Conference 2001 - [c3]Thomas E. Ferrin, Bruce A. Foster, Richard Hughey:
High Performance Computing for Computational Biology - Session Introduction. Pacific Symposium on Biocomputing 2001: 238-239
1990 – 1999
- 1999
- [c2]Thomas E. Ferrin, Eileen T. Kraemer:
Molecules to Maps: Tools for Visualization & Interaction - Session Introduction. Pacific Symposium on Biocomputing 1999: 338-340 - 1998
- [j1]Eileen T. Kraemer, Thomas E. Ferrin:
Molecules to maps: tools for visualization and interaction in support of computational biology. Bioinform. 14(9): 764-771 (1998) - 1992
- [c1]Thomas E. Ferrin, Conrad C. Huang, Gregory S. Couch, Eric F. Pettersen, Robert Langridge:
The MidasPlus molecular modeling system. CHI 1992: 521-522
Coauthor Index
aka: John H. Morris
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