Publications, Presentations, Patents, Software
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Full list available online at http://harts.net/reece/pubs/.
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Papers
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Storage and Data
Management for Life Sciences Research
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Hart
RK
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invited
review for Drug
Discov. Today
(in preparation)
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Unison: An Integrated
Platform for Computational Biology Discovery
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Hart RK, Mukhyala K.
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Pac Symp Biocomput.
(2009).
PDF
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Functional characterization of the Bcl-2 gene family in the
zebrafish.
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Kratz E, Eimon PM, Mukhyala K, Stern H, Zha J, Strasser A, Hart R,
Ashkenazi A.
Cell Death Differ. 13(10):1631-40 (2006).
PubMed
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Computational identification and Experimental Validation of Novel
Zebrafish Bcl2 Family Members
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Mukhyala K, Kratz E, Ashkenazi A, Hart RK
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unpublished manuscript (2005). PDF
supplementary
data
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Systematic and Fully Automatic Discovery of Protein Sequence
Patterns
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Hart RK, Stolovitzky G, Royyuru AK, and Califano A
J Comput
Biol. 7(3-4):585-600 (2000). PubMed
PDF
WWW -
Automatic Discovery of PROSITE Motifs
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Hart RK, Stolovitzky G, Royyuru AK, and Califano A
Proceedings
of the RECOMB 2000 Conference, Tokyo, Japan (2000). -
Note: The J Comput Biol paper above subsumes most of these results.
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Exploring the Similarities Between Potential Smoothing and Simulated
Annealing.
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Hart RK, Pappu RV, and Ponder JW
J. Comput. Chem.
21(7):531-52 (2000). Abstract
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Potential Function Smoothing with Application to Molecular Docking
(Ph.D. Thesis)
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Thesis in Molecular Biophysics (1998). Abstract
PDF
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Analysis and Application of Potential Energy Smoothing for Global
Optimization
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Pappu RV, Hart RK, and Ponder JW
J. Phys. Chem. B
102:9725-9742 (1998). Abstract
PDF -
An Object-Oriented System for the Analysis of Automated DNA
Sequencing Data
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Thesis in Computer Science (1994) PDF
WWW
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Isolation, localization, and physical mapping of a highly
polymorphic locus on human chromosome 11q13.
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Eubanks JH, Selleri L, Hart R, Rosette C, Evans GA
Genomics
11(3):720-9 (1991 Nov) PubMed
Patent
- Methods and Compositions Relating to ZPA
Polypeptides
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Avi Ashkenazi, Reece Hart, Erika Kratz, Kiran Mukhyala
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Filed May 4, 2006
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Provides new model systems for investigating apoptosis in vivo
and in vitro, and provides methods for identifying agents that
modulate apoptosis.
Presentations and Posters
- A Tour of Research Computing at Genentech
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Invited presentation, Bio-IT World Expo, Boston, April 2009. PDF
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Unison: Enabling easy, rapid, and
comprehensive proteomic mining
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UCSF / San Francisco PostgreSQL Users' Group, March 2009. PDF
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Integrating Public and Private Data: Lessons Learned with Unison
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invited presentation, Molecular Medicine Tri-Conference, San
Francisco, February 2009. PDF
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Unison: An Integrated
Platform for Computational Biology Discovery
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Pacific Symposium on Biocomputing, Hawaii, January 2009. PDF
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Mining for Novel TNF Ligands using Unison, an Open Source Database
for Target Discovery
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poster at ISMB, 2005; Detroit, MI PDF
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Introduction to and Applications of Unison, an Open Source Database
for Target Discovery
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poster at Automated Function Prediction 2005; Detroit, MI PDF
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Structuring Structural Biology with PostgreSQL
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presentation at OSCON (O'Reilly OpenSource Conference) 2004;
Portland, OR PDF
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Mining for protein sequences with Unison
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poster at Gordon Research Conferences, Queen's College, England.
(2003)
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Systematic and Automated Discovery of Patterns in PROSITE Families
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Hart RK, Califano A, Stolovitzky G, Kumar AR
presentation at
RECOMB 2000, April 7-11; Tokyo,Japan
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SPLASH: Completely Automatic Discovery of PROSITE motifs
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Hart RK, Califano A, Stolovitzky G, Kumar AR
poster presentation
at the Proteins Gordon Research Conference, Holderness, New
Hampshire (1999)
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A Detailed Analysis of Potential Smoothing, Analogies with Simulated
Annealing, and Applications to Molecular Docking
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Invited presentation to the American Chemical Society, Computational
Chemistry Subsection
1998 October 28, St. Louis
Software
- Unison Protein Database
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Unison is an open source project that provides an easily-updated
infrastructure for protein sequence analysis, feature-based mining,
and other common tasks. (2003)
http://unison-db.org/
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Prospect Interface
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Perl module for manipulating protein threading results
Available
via http://sourceforge.net/projects/prospect-if
and CPAN. (2002)
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autoseq - Automated DNA Sequence Analysis
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C++ classes for the manipulation of automated sequencing data and
the implementation of a Bayesian peak identification model
autoseq
home page -
TINKER - Software Tools for Molecular Design
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Co-contributor of potential smoothing and Ewald summation methods to
Jay Ponder's TINKER package
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http://dasher.wustl.edu/tinker/