Carnegie Mellon University

The Merck Computational Biology and Chemistry Program

Student Participants

Merck Graduate Fellows
2004 Merck Summer Scholars
2003 Merck Summer Scholars	Fall 2003/Spring 2004 Undergraduate Grant Recipients
2002 Merck Summer Scholars	Fall 2002/Spring 2003 Undergraduate Grant Recipients
2001 Merck Summer Scholars	Fall 2001/Spring 2002 Undergraduate Grant Recipients
2000 Merck Summer Scholars	Fall 2000/Spring 2001 Undergraduate Grant Recipients
1999 Merck Summer Scholars	Fall 1999/Spring 2000 Undergraduate Grant Recipients
	Spring 1999 Undergraduate Grant Recipients

Merck Graduate Fellows

*Fellow*	*Ph.D. Department/Program*	*Research Advisor(s)*	*Project*	*Graduation Date*	*Postdoctoral Position*
Xiang Chen	Biological Sciences/Computational and Statistical Learning	Dr. Robert F. Murphy	Subcellular Location Trees and Protein Location Systematics
Yanhua Hu	Biological Sciences	Dr. Robert F. Murphy	Protein Location Dynamics
Arun Krishnaswamy	Biological Sciences	Drs. Christopher Langmead and Gordon Rule	Protein and nucleic acid chemical shift prediction
Angela Liu	Chemistry	Dr. David Yaron	Modeling the PhotoPhysics of Disordered Organic and Biological Molecules
Kathleen Pushkar	Mechanical Engineering	Drs. Philip LeDuc and Russell Schwartz	Understanding Biological Structure Through Dimensionally-Constrained Modeling
Stefan Niculescu	Computer Science	Dr. Tom M. Mitchell	Machine learning approaches to functional Magnetic Resonance Image data
Yanjun Qi	Language Technologies Institute	Drs. Ziv Bar-Joseph and Judith Klein-Seetharaman	Inferring protein-protein interactions and pathways from high throughput biological data
Narayanan Raghupathy	Biological Sciences	Dr. Dannie Durand	Conservation of gene clusters in vertebrates
Nan Song	Biological Sciences	Dr. Dannie Durand	Evolution and function of multi-domain proteins
Tiequan Zhang	Biological Sciences	Dr. Russell Schwartz	Discrete Event Simulation of Self-Assembly Kinetics
Aimee Tomlinson	Chemistry	Dr. David Yaron	Modeling the Photophysics of Biological Dye Assemblies	August 2004	Eckerd College
Kai Huang	Biological Sciences/Computational and Statistical Learning	Dr. Robert F. Murphy	Data Mining Approaches for Interpreting Protein Subcellular Location Patterns in Fluorescence Microscope Images	May 2004	Credit Suisse First Boston
Bjarni V. Halldórsson	Algorithms, Combinatorics and Optimization	Drs. Ramamoorthi Ravi and Jonathan Minden	Protein Identification by Epitope Recognition	May 2001	Celera Genomics

Fall 2003/Spring 2004 Merck Undergraduate Research Grant Recipients

*Recipient*	*Class Year, Major*	*Research Advisor(s)*	*Project*
Leonard Apeltsin	Junior, Computer Science and Biological Sciences	Dr. Russell Schwartz	Cellular Automata Simulation of Actin Assembly
Sue Yi Chew	Junior, Computer Science	Dr. Russell Schwartz	Optimising the event queue in discrete-event simulation of self-assembly systems
Andrew Hsieh	Sophomore, Computational Biology	Drs. William Cohen & Robert F. Murphy	Subcellular Location Image Finder
Michael Kong	Senior, Computational Biology	Dr. Russell Schwartz	Cellular Automata Simulation of Macromolecular Assembly
Jonathan Lustgarten	Senior, Computational Biology	Dr. Russell Schwartz	Simulating Protein Sorting in the Golgi
Rori Rohlfs	Senior, Computer Science	Dr. Russell Schwartz	Discrete-Event Simulation of Self-Assembly

Summer 2003 Merck Summer Scholars

*Scholar*	*Class Year, Major*	*College/University*	*Research Advisor(s)*	*SURP web page*
Julianna Conde-Adorno	Senior, Computer Science	Universidad Metropolitano	Dr. Robert Murphy	SURP link
Kuok Chiang Kim	Junior, Electrical and Computer Engineering & Biomedical Engineering	Carnegie Mellon University	Dr. Russell Schwartz	SURP link
Daniel Kleinbaum	Junior, Biological Sciences	Carnegie Mellon University	Drs. William Brown and Gordon Rule	SURP link
Yenixsa Rivera Sierra	Senior, Computer Science	Universidad Metropolitano	Dr. Russell Schwartz	SURP link
Ruben Valas	Junior, Computer Science	Carnegie Mellon University	Drs. Michael Erdmann and Gordon Rule	SURP link
Ling Wang	Senior, Biological Sciences	Carnegie Mellon University	Dr. Nathan Urban	SURP link

Fall 2002/Spring 2003 Merck Undergraduate Research Grant Recipients

*Recipient*	*Class Year, Major*	*Research Advisor(s)*	*Project*
Andrew Hsieh	Freshman, Mellon College of Science	Drs. William Cohen and Robert F. Murphy	Information extraction from image and text in on-line journal articles
Matthew Joffe	Senior, Mathematical Sciences	Drs. Robert F. Murphy and William Cohen	Figure segmentation for interpretation of microscope images in on-line journal articles
Michael Kong	Junior, Computational Biology	Dr. Russell Schwartz	Cellular Automata Simulation of Macromolecular Assembly
Rori Rohlfs	Junior, Computer Science and Biological Sciences	Dr. Russell Schwartz	Discrete-Event Simulation of Self-Assembly Systems
Julia Wang	Sophomore, Computational Biology	Dr. Russell Schwartz	Analyzing Human Genome Polymorphism and Haplotype Structure

Summer 2002 Merck Summer Scholars

*Scholar*	*Class Year, Major*	*College/University*	*Research Advisor(s)*	*SURP web page*
Craig Gallek	Senior, Chemistry	Carnegie Mellon University	Dr. David Yaron	SURP link
Neil Halelamien	Senior, Computer Science	Carnegie Mellon University	Dr. Nathan Urban	SURP link
Richard Wang	Senior, Computer Science	Carnegie Mellon University	Drs. Tom Mitchell and Robert Murphy	SURP link
Oliver Wojtyna	Senior, Chemistry	Carnegie Mellon University	Dr. David Yaron	SURP link

Fall 2001/Spring 2002 Merck Undergraduate Research Grant Recipients

*Recipient*	*Class Year, Major*	*Research Advisor(s)*	*Project*
Len Matsuyama	Senior, Information Systems/Computer Science	Dr. M. Dannie Durand	New methods for detecting gene homology
Aaron Rising	Sophomore, Biological Sciences	Dr. Robert F. Murphy	A Supervised Learning Approach to Interpreting Fluorescence Microscope Images in Online Journals

Summer 2001 Merck Summer Scholars

*Scholar*	*Class Year, Major*	*College/University*	*Research Advisor(s)*	*SURP web page*
Jennifer Airone	Senior, Chemical Engineering/Biomedical & Health Engineering	Carnegie Mellon University	Dr. Frederick Lanni	SURP link
Courtney Davis	Junior, Mathematics	Trinity University	Dr. Eric Ahrens	SURP link
Craig Gallek	Senior, Chemistry	Carnegie Mellon University	Dr. David Yaron	SURP link
Matthew Kofke	Senior, Chemistry	Carnegie Mellon University	Dr. David Yaron	SURP link
Gregory Porreca	Senior, Biology/Computer Science	The College of New Jersey	Dr. Robert Murphy	SURP link

Fall 2000/Spring 2001 Merck Undergraduate Research Grant Recipients

*Recipient*	*Class Year, Major*	*Research Advisor(s)*	*Project*
Syed Hussain	Junior, Physics	Dr. Phil Campbell	Computational Model of Collagen Type I Protein
Jennifer Lin	Junior, Biological Sciences/Computational Biology track	Dr. Robert F. Murphy	Typical Image Selection and Image Database Implementation
Anushka Nethisinghe	Junior, Computer Science/Biology minor	Dr. Raul Valdes-Perez	Data Mining Yeast Gene Expression Data
Aaron Rising	Freshman, Biological Sciences	Dr. Robert F. Murphy	Automated interpretation of 3D confocal microscope images

Summer 2000 Merck Summer Scholars

*Scholar*	*Class Year, Major*	*Research Advisor(s)*	*Project*	*SURP web page*
Danny Lam	Junior, Chemistry/Computational Chemistry track	Dr. David Yaron	Computer Simulation of Soliton Effects on Conjugated Polymers	SURP link
Jennifer Lin	Junior, Biological Sciences/Computational Biology track	Dr. Robert F. Murphy	Alternative Methods of Typical Image Selection and Image Database Development	SURP link
Anushka Nethisinghe	Senior, Computer Science	Dr. Raul Valdes-Perez	Analysis of Gene Expression Data	SURP link

Fall 1999/Spring 2000 Merck Undergraduate Research Grant Recipients

*Recipient*	*Class Year, Major*	*Research Advisor(s)*	*Project*
Brandon Franklin	Freshman, Biological Sciences/Computer Science	Dr. Robert F. Murphy	Extracting Protein Localization Images from On-line Journals
Kiarri Kershaw	Junior, Biological Sciences/Computer Science	Dr. Robert F. Murphy	Building a Knowledge Base of Protein Subcellular Location
Christopher Mason	Junior, Biological Sciences/Computer Science	Drs. Michael Erdmann and Gordon Rule	Computational Methods for Detection of Homology with NMR

Summer 1999 Merck Summer Scholars

*Scholar*	*Class Year, Major*	*Research Advisor(s)*	*Project*	*SURP web page*	*Link to Powerpoint presentation*
Ryle Goodrich	Senior, Biological Sciences/Computational Biology option	Dr. David Hackney	Brownian Dynamics Modeling of Kinesin and Microtubules	SURP link
Kiarri Kershaw	Junior, Biological Sciences/Computational Biology track	Drs. Mark Craven and Robert F. Murphy	Creation of a knowledge base for protein localization	SURP link
Christopher Mason	Senior, Biological Sciences/Computer Science	Drs. Michael Erdmann and Gordon Rule	Methods for homology based structure determination by NMR	SURP link	Slide Show
Matt Vieta	Senior, Mathematics	Dr. Frederick Lanni	Computing vector fields from image-derived deformation data	SURP link
Daniel Vogel	Sophomore, Chemistry/Computer Science minor	Dr. David Yaron	Parallel Processing Issues in Computational Chemistry	SURP link

Spring 1999 Merck Undergraduate Research Grant Recipients

*Recipient*	*Class Year, Major*	*Research Advisor(s)*	*Project*
Toby Goldstein	Junior, Computer Science	Drs. Mark Craven and Robert F. Murphy	Creation of a knowledge base for protein localization
Kiarri Kershaw	Freshman, Biological Sciences/Computational Biology option	Drs. Mark Craven and Robert F. Murphy	Creation of a knowledge base for protein localization
Matt Vieta	Junior, Mathematics	Dr. Frederick Lanni	Computing vector fields from image-derived deformation data

Please send inquiries to murphy@cmu.edu or

Dr. Robert F. Murphy
Director, Merck Computational Biology and Chemistry Program
Carnegie Mellon University
4400 Fifth Avenue/Box 52
Pittsburgh, PA 15213