Curriculum Vitae

Reece Hart, Ph.D.

1 Sussex Street, San Francisco, CA 94131

Home: 415-452-9916 • Work: 650-225-6133

E-mail: reece@harts.net • Web: http://harts.net/reece/

(CV online at http://harts.net/reece/cv.pdf)

Objective

I seek apply my broad expertise in computational biology to understanding significant and unmet questions in human disease. The ideal position will enable wide-ranging interactions between computational and experimental biologists in an dynamic, collaborative, and focused environment.

Career Summary

• Computational biologist with graduate degrees in biophysics (PhD) and computer science (MS).

• Seven-year scientist at Genentech with deep knowledge of computational biology and high-performance computing; broad exposure to many other scientific computing applications.

• Four-year manager of Research computing architecture and operations at Genentech (concurrent with scientific role); extensive relationships at all levels in Research and throughout Genentech.

• Responsible for $8M Research-IT budget, including the approval of all IT-related purchases.

Education and Employment

Publications, Presentations, Patents, Software

Full list available online at http://harts.net/reece/pubs/.

Papers

Unison: An Integrated Platform for Computational Biology Discovery

Hart RK, Mukhyala K.

Pac Symp Biocomput. (2009). PDF

Functional characterization of the Bcl-2 gene family in the zebrafish.

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 PDF

Computational identification and Experimental Validation of Novel Zebrafish Bcl2 Family Members

Mukhyala K, Kratz E, Ashkenazi A, Hart RK

unpublished manuscript (2005). PDF supplementary data

Systematic and Fully Automatic Discovery of Protein Sequence Patterns

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

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.

Exploring the Similarities Between Potential Smoothing and Simulated Annealing.

Hart RK, Pappu RV, and Ponder JW
J. Comput. Chem. 21(7):531-52 (2000). Abstract PDF

Analysis and Application of Potential Energy Smoothing for Global Optimization

Pappu RV, Hart RK, and Ponder JW
J. Phys. Chem. B 102:9725-9742 (1998). Abstract PDF

Patent

Methods and Compositions Relating to ZPA Polypeptides

Avi Ashkenazi, Reece Hart, Erika Kratz, Kiran Mukhyala

Filed May 4, 2006

Provides new model systems for investigating apoptosis in vivo and in vitro, and provides methods for identifying agents that modulate apoptosis.

Presentations and Posters

Mining for Novel TNF Ligands using Unison, an Open Source Database for Target Discovery

poster at ISMB, 2005; Detroit, MI PDF

Introduction to and Applications of Unison, an Open Source Database for Target Discovery

poster at Automated Function Prediction 2005; Detroit, MI PDF

Structuring Structural Biology with PostgreSQL

presentation at OSCON (O'Reilly OpenSource Conference) 2004; Portland, OR PDF

Software

Unison Protein Database

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/

TINKER - Software Tools for Molecular Design

Co-contributor of potential smoothing and Ewald summation methods to Jay Ponder's TINKER package

http://dasher.wustl.edu/tinker/

Honors and Awards

• Genentech Joint Appointment in Protein Engineering (2002-current)

• Carl and Gerty Cori Graduate Student Fellowship (1995-1996)

• National Library of Medicine grant (LM07049; 1991-1994)

• NIH Training Grant (1994-1998)

Research Interests

• Remote homology detection and protein structure prediction

• Genome sequence/structure variation and disease implications

• Oncology target discovery

• Data integration

Academic Activities and Service

• Editorial services to Nature Genetics,Biocomputing, Bioinformatics, IEEE Computational Biology, IBM Systems Journal, and others

• Current or past memberships: International Society for Computational Biology, AAAS, Protein Society, Biophysical Society

• NIH/NIAID Grant Review RFP-AI2008-010 (Genomic Sequencing Centers for Infectious Diseases)

Personal Information and Activities

• United States Citizen

• Born Nov 22, 1968

• Married to Hanna, with three children, Madeline, Margot, and Graham

• Weekly parent teacher in daughters' preschool

• Hobbies: ultimate frisbee, remote controlled planes, aviation (instrument-rated pilot with 500 hours), volleyball, Go (a strategy board game)

References

References will be provided upon request.

Informal recommendations may be available through http://www.linkedin.com/in/reece .

Major Activities at Genentech

Scientific Activities

• Unison data integration tool and applications (2002-)

  Designed and developed Unison, a database of precomputed predictions on a comprehensive database of sequences. Unison is the source for internal protein annotations at Genentech and enabled most of my group's mining efforts (below). The tool and non-proprietary data are freely available (http://unison-db.org/).

• Zebrafish Bcl-2 remote homolog mining (2006-2007)

  Directed and contributed to the building of Hidden Markov Models and use of our Unison mining platform (below) to identify five novel proapoptotic Bcl-2 family members in Zebrafish. Four of these candidates were shown experimentally to strongly induce apoptosis.

• E3 ligase mining (2006)

  Implemented a computational test of a complex hypothesis regarding E3 ligases involved in apoptotic signaling.

• NOD protein modeling (2005)

  Directed the modeling of polymorphisms in NOD2 that led to hypotheses of the mechanistic consequences of these SNPs.

• Immunoreceptor Tyrosine Activating/Inhibitory/Switch Motif (ITxM) mining (2003-2004)

  We used our Unison mining platform to continually search for ITxM family proteins. One novel candidate was found and subsequently reported by another group.

• Helical cytokine mining (2002-2003)

  Directed our structure prediction effort to identify distant homologs of long- and short-chain helical cytokines. No new candidates were identified.

• Death Domain mining (2002-2003)

  Directed and contributed to the use of structure prediction to identify death domain-containing proteins from human and pathogenic sequences and gene predictions.

• Tumor Necrosis Factor (TNF) ligand mining (2001-2003)

  Led an extensive effort to computationally identify ligands for TNF receptors that had no known cognate ligand. A small number of candidates were identified in human and pathogenic sequences, but Genentech opted to not pursue non-human TNF ligands.

Computer Operations & Informatics

In my role as the manager of Research Computing Architecture and Operations, I was involved in all aspects of strategic planning, architecture, budgeting, project management, and operational issues related to our environment. Examples of my experience are below.

• Advocated for and oversaw the consolidation of independent computing facilities, leading to greatly improved consistency and efficiency for users and streamlined operations for IT staff.

• Developed the technical requirements for centralized Research storage and designed the file system hierarchy in our storage environment.

• Provided critical leadership for the stabilization of several problematic services and one major disk corruption incident that resulted from a vendor bug.

• Indirectly oversaw the activities of ~20 IT personnel.

• Streamlined software contract processes.

• Managed Research's IT budget ($8M).

• Was primary liaison between enterprise IT and Research scientific staff.