Professor
Chris Bystroff
Current
Position: Assistant Professor of Biology, Rensselaer
Polytechnic Institute.
Research
interests: Prof. Bystroff's research addresses the protein
folding problem, specifically the nature of the folding
pathway. Algorithms for protein structure prediction are
seen as models for the physical folding process. >>More
Future
research: Understanding folding pathways may lead to
an understanding of why some proteins misfold to form amyloid
and others require molecular chapaerones for folding. Late
folding intermediate states might identify highly antigenic
sites on the protein surface. Alignments of three-dimensional
structures without regard to permutations in the sequence
order can be used to develop a new type of hidden Markov
model, which may be able to detect very remote homologous
relationships between sequences.
Involvement
in teaching and student education: Prof. Bystroff teaches
courses in Sequence Analysis, Molecular Modeling, and X-ray
Crystallography
Education:
Prof. Bystroff received his B.A. at Carleton College
in 1983, and Ph.D. at University of California at San Diego
in 1988.
Dr. Ye Ding
Current
Position: Research Scientist at Bioinformatics lab
of the Wadsworth Center.
Research
interests: Dr. Ding's research is focused on novel
statistical algorithms for RNA secondary structure prediction
and rational design of RNA-targeting nucleic acids for
gene down-regulation. >>
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Future
research: Dr. Ding's future research directions include:
1) prediction of target sites for microRNAs (natural regulatory
antisense RNAs);
2) application of RNA-targeting nucleic acids design to
infectious pathogens;
3) statistical algorithms for RNA pseudoknot prediction;
4) statistical prediction of common structures of homologous
RNA sequences;
5) development of statistical models for the prediction
of small regulatory RNAs in eukaryotic genomes;
6) rational
design tools for molecular beacons and developement of
a module Sprobe for Sfold.
Education:
Dr. Ye Ding received his Ph.D. in Statistics from Carnegie
Mellon University in 1990.
Professor Mark Embrechts
Current
Position: Assistant Professor of Chemistry, RPI
Research
interests: Prof. Embrecht's areas of interest relate
to data mining, soft computing, computational intelligence,
and neural networks. He is a member of IEEE, ANS and is
past Chapter President of the American Nuclear Society
Education:
Professor Embrechts received his Ph.D. from Virginia
Polytechnic Institute in 1981
Professor
Shekhar Garde
Current
Position: Assistant Professor of Chemistry, Rensselaer
Polytechnic Institute.
Research
interests: molecular thermodynamics and simulations
of biological systems, statistical mechanics of liquids
and polymers, and solvation phenomena -- especially in
aqueous solutions (water structure, hydrophobic interactions).
Professor Grarde focuses on understanding and modeling
the role of water structure in inducing interactions between
various hydrophobic, polar, and ionic molecules which ultimately
leads to many important self-assembly processes in water.
Education:
Professor Garde received his Ph.D. from University
of Delaware in 1997.
Dr.
Lee Ann McCue
Current
Position: Research Scientist, Bioinformatics Lab, Wadsworth
Center.
Research
interests: The research of Dr. McCue focuses on transcription
regulation in prokaryotes, using bioinformatics and comparative
genomics approaches to study regulatory networks at the
whole-genome scale. Her research involves identifying the
cis-acting regulatory signals in prokaryotic promoters and
working to understand how trans-acting transcription factors
specifically recognize and interact with their cognate sites.
Current projects include: 1) the de novo prediction of cis-regulatory
sites on the genome scale for Escherichia coli K12, Synechocystis
PCC6803, Shewanella oneidensis, Yersinia pestis, and Pseudomonas
aeruginosa by comparative genomics; >>
More
Education:
Dr. McCue received her Ph.D. in Microbiology from The
Ohio State University in 1994.
Professor Lee Newberg
Current
Position: Joint appointment as a Research Scientist
in the Bioinformatics Laboratory, Wadsworth Center and
as a Research Associate Professor in the Rensselaer Computer
Science Department.
Research
interests: Algorithmic, statistical, and mathematical
combinatorics approaches to computational molecular biology.
In particular, using multiple species and phylogenetic
relationships, to enhance algorithms for locating transcription
factor binding sites; relevant to the regulation of gene
expression.
Short
biography: Prof. Lee Newberg worked in computational
biology as an undergraduate with Eric Lander (Whitehead
Institute, MIT) and as a graduate student with Richard
Karp (University of California, Berkeley) producing several
useful algorithms and mathematical results suitable for
publication. >>
More
Education:
Prof. Lee Newberg received his B.S. degrees in Mathematics
and Physics from MIT in 1986 and his Ph.D. degree in Computer
Science from The University of California at Berkeley in
1993.
Professor
John Salerno
Current
Position:Professor of Biology, Rensselaer Polytechnic
Institute.
Research
interests: Structure, Function and Control of Nitric
Oxide Synthases; P450 superfamily enzymes Structure and
Function in small heat shock protein superfamily Bioinformatics,
structural modeling, protein design and directed evolution.
Courses:
Bioinformatics II: Molecular Modeling (Spring 2003)
Education:
Professor Salerno received his Bachelor degree in Physics
from the Massachusetts Institute of Technology in 1972
and his Ph.D. in Biophysics from the University of Pennsylvania,
School of Medicine in 1977.
Professor Mark Wentland
Current
Position: Professor of Chemistry, Rensselaer Polytechnic
Institute.
Research
interests: In collaboration with Dr. Jean M. Bidlack
and coworkers at the University of Rochester and with funding
from the National Institute on Drug Abuse, the main goal
of Professor Wentland's research is to design and synthesize
potential medications to treat cocaine and heroin abuse
in humans.>>
More
Short
biography: Mark Wentland began his 33 year career in
drug design and discovery in 1970 when he joined the medicinal
chemistry department at Sterling Winthrop Inc. Prior to
this he was at Rice University where he earned his Ph.D.
in synthetic organic chemistry under the direction of the
late Professor Robert V. Stevens. During his 24 years at
Sterling Winthrop, he held various positions of scientific
and administrative responsibility... >>
more
Courses:
Drug
Discovery (CHEM-4330, 6330) and Medicinal Chemistry
(CHEM-4300, 6300). >>
short description
Education:
Professor Wentland received his Ph.D. degree in chemistry
from Rice University, Houston, TX, in 1970.
Professor Mohammed J. Zaki
Current
Position: Assistant Professor of Computer Science,
Rensselaer Polytechnic Institute.
Research
interests: the design of efficient, scalable, and
parallel algorithms for various data mining techniques.
Professor Zaki is specially interested in developing novel
data mining techniques for bioinformatics. >>
More
Future
research: to address other important problems in bioinformatics,
namely, multiple sequence alignment via sequence mining
techniques, gene mapping ... >>
more
Courses:
Bioinformatics:
Algorithms and Systems (Spring 2003)
Education:
Professor Zaki received his Ph.D. degree in computer science
from the University of Rochester in 1998.
Prof. Zuker
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