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T. Przytycka , PhD
NCBI, NLM, NIH
Computational Biology Branch
Building 38A 8S812
Bethesda, MD 20894
Tel: 301-402 1723
Fax: 301-480-9241
Email: przytyck@ncbi.nlm.nih.gov
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Research
Interests:
- Biological networks and
Systems Biology
- Protein and genome
evolution.
- Application of discrete
algorithms and graph theory to molecular and systems biology
- Protein structure and
protein folding.
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Open
Postdoctoral Positions
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Note for prospective
post-doctoral fellows
Group Members:
Jie Zheng
Yang Huang
Damian Wojtowicz
Former Group Members:
Elena
Zotenko (2004-7) (next position – Max Planck Institute)
Raja Jothi (2004-7) (next position -
LMI/NHBI)
Katia Guimaraes (2005-7) (next
position - UFPE, Brazil)
Publications
(all)
Publications
in PubMed
Publication
in DBLP server (Computer Science)
Book
chapters
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Current
and Recent Research Projects and Collaborations
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Protein and domain interactions
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Analysis of overlapping Protein Complexes
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Predicting domain-domain interactions from PPI network
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MORPH- predicting protein interactions by
searching tree automorphism space
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RCDP – predicting domain-domain interaction
from co-evolution principle
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Separating co-speciation from
functional co-evolution in interacting domains
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DOMINE – a data base of protein
domain interactions
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Discovering functional linkages
Evolution of Protein Sequence and Proteins
Sequence Analysis
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Graph theoretical insight into evolution of
multidomain proteins
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COCO-CL-hierarchical clustering of Homology
Relation
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Study of selective pressure
acting on conserved ortholog groups
Structural Biology
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Structure Comparison by Projection Methods
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Predicting beta-sheet topology
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Protein folding simulations
Phylogenetics
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Evolutionary trees and graph motifs
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Support for the Coelomata hypothesis from intron
pattern conservation
New Projects /Projects under development
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Crosstalk between EGF, IGF and IG signaling
pathways
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Recombination Hot Spots in Human Population
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Optimization of codon usage
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Evolution of Spliceosomal small nuclear RNA genes
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Participation in Scientific
Program Committees (recent)
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- IEEE 21th International
Conference on Advanced Information Networking and Applications,
Niagara Falls, Canada,
May 21-23, 2007(PC).
- SIAM Meeting on
Discrete Mathematics: Minisymposium in Computational Biology, June 2006, Victoria, Canada,
(invited organizer).
- DIMACS
Workshop on Sequence, Structure and Systems Approach to Predict Protein
Function, Rutgers, May 2006,
(co-organizer)
- 2nd
International Workshop on Bioinformatics Research and Applications,
University of Reading,
UK,
May 2006, (PC)
- The First
Annual RECOMB Satellite
Workshop on Systems Biology
San Diego,
December 2005, (PC and OC)
- CompBioNets
2005 Algorithms and Computational Methods for Biochemical and
Evolutionary Biology; Lyon,
December 2005, (PC)
- DIMACS
Workshop on Biomolecular Networks: Topological Properties and
Evolution Rutgers, May 2005
(co-organizer)
- DIMACS
Workshop on Protein Domains: Identification, Classification and
Evolution Rutgers, February 2003
(co-organizer)
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Recent Invited Conference Talks
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- 39th
Symposium on the Interface: Systems Biology Philadelphia, May, 2007.
- First
Bertinoro Systems Biology Meeting, Bertinoro, Italy,
May 2007
- SIAM Meeting on
Discrete Mathematics Minisymposium in Computational Biology, June 2006, Victoria, Canada. Graph
Theoretical Approach to Predicting Dynamics of Protein Association
- 2nd
International Workshop on Bioinformatics title:
Chordal Graphs in Computational
Biology - New Insights and Application Research and
Applications 2006 (keynote talk)
- Fifth
Virtual Conference on Genomics and Bioinformatics, October 2005. Genomics meets Graph Theory.
- Biological
Networks: Interaction with Genome and Developmental Evolution Bertinoro, May 2005. Network motifs and evolution of hard
to gain and hard to lose character traits.
- BCB
2004 Second Bertinoro Computational Biology Meeting: Evolutionary
neighborhood graphs are unlikely to be scale free.
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Recent Contributed Conference
Presentations
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- WABI 2007 Bringing folding pathways into strand pairing prediction (joint
work with Jieun Jeong and Piotr Berman)
- RECOMB 2006 An important
connection between network motifs and parsimony models.
- RECOMB Satellite Workshop on Systems
Biology 2005 Decomposition of Overlapping
Protein Complexes: A Graph Theoretical Method for Analyzing Static and
Dynamic Protein Associations (joint work with Elena Zotenko, Katia
Guimaraes and Raja Jothi)
- ISMB 2005 Predicting Protein-Protein Interaction by Searching Evolutionary
Tree Automorphism Space.(Joint work with Raja Jothi and Maricel Kann presented by Raja
Jothi)
- RECOMB 2005 Graph Theoretical Insights into Dollo Parsimony and Evolution of
Multidomain Proteins.(Joint work with Nan Song, George Davis and Dannie Durand)
- ISMB 2004 Divergent Evolutionary Drift Contradicts Power Law (Joint work with Yi-Kuo Yu).
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Selected
non-conference invited talks
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- November
2007, University of Illinois, Chicago
- May
2007, University
of Calgary
- June
2006 Simon
Fraser University
- May
2006 Warsaw
University
- February
2006 George
Mason University
- December
2006, Princeton
- November
2006, New York
Academy of
Science
- September
2006, MIT
- April
2006 George
Washington University.
- March
2005 Colloquium, Penn
State University.
- Dec.
2005 Colloquium, Department of Mathematics, University of Maryland.
- Dec
2001 JHU Biophysical Evening Series
- Oct
2001 Polish Academy of Science, Physics, Warsaw
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