Zielinski, Rafal, Przytycki, Pawel F, Zheng, Jie, Zhang, David, Przytycka, Teresa M, Capala, Jacek
Abstract Background Cellular response to external stimuli requires propagation of corresponding signals through molecular signaling pathways. However, signaling pathways are not isolated information...
Phenotypic variation meets systems biology (2009)
Abstract A report of the 18th Annual Growth Factor and Signal Transduction Symposium, Ames, USA, 11-14 June 2009.
Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum (2009)
Huang, Yang, Wuchty, Stefan, Ferdig, Michael T., Przytycka, Teresa M.
Motivation: Analysis of expression quantitative trait loci (eQTL) significantly contributes to the determination of gene regulation programs. However, the discovery and analysis of associations of...
Huang, Yang, Koonin, Eugene V., Lipman, David J., Przytycka, Teresa M.
In a wide range of genomes, it was observed that the usage of synonymous codons is biased toward specific codons and codon patterns. Factors that are implicated in the selection for codon usage...
Differences in evolutionary pressure acting within highly conserved ortholog groups (2008)
Przytycka, Teresa M, Jothi, Raja, Aravind, L, Lipman, David J
Abstract Background In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence...
BIOINFORMATICS ORIGINAL PAPER (2008)
Genome Analysis, Raja Jothi, Elena Zotenko, Asba Tasneem, Teresa M. Przytycka
doi:10.1093/bioinformatics/btl009 COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
Interrogating domain-domain interactions with parsimony based approaches (2008)
Guimarães, Katia S, Przytycka, Teresa M
Abstract Background The identification and characterization of interacting domain pairs is an important step towards understanding protein interactions. In the last few years, several methods to...
DOMINE: a database of protein domain interactions (2008)
Raghavachari, Balaji, Tasneem, Asba, Przytycka, Teresa M., Jothi, Raja
DOMINE is a database of known and predicted protein domain interactions compiled from a variety of sources. The database contains domain–domain interactions observed in PDB entries, and those that...
Ming-yang Kao, Tak-wah Lam, Teresa M. Przytycka, Hing-fung Ting
This paper presents two sets of techniques for comparing unrooted evolutionary trees, namely, label compression and four-way dynamic programming. The technique of four-way dynamic programming...
Martin Farach, Teresa M. Przytycka, Mikkel Thorup
We consider the problem of computing the Maximum Agreement Subtree (MAST) of a set of leaf labeled trees. We give an algorithm which computes the MAST of k trees on n species where some tree has...
Raymond Greenlaw, Teresa M. Przytycka
This paper places the optimal tree ranking problem in NC. A ranking is a labeling of the nodes with natural numbers such that if nodes u and v have the same label then there exists another node with...
Zheng, Jie, Rogozin, Igor B., Koonin, Eugene V., Przytycka, Teresa M.
Many intron positions are conserved in varying subsets of eukaryotic genomes and, consequently, comprise a potentially informative class of phylogenetic characters. Roy and Gilbert developed a method...
Structural footprinting in protein structure comparison: the impact of structural fragments (2007)
Zotenko, Elena, Islamaj Dogan, Rezarta, Wilbur, W John, O'Leary, Dianne P, Przytycka, Teresa M
Abstract Background One approach for speeding-up protein structure comparison is the projection approach , where a protein structure is mapped to a high-dimensional vector and structural similarity...
Jothi, Raja, Przytycka, Teresa M, Aravind, L
Abstract Background A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with similar profiles...
Bmc Bioinformatics, Raja Jothi, Teresa M Przytycka, L Aravind
Research article Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
State of the art: refinement of multiple sequence alignments (2006)
Chakrabarti, Saikat, Lanczycki, Christopher J, Panchenko, Anna R, Przytycka, Teresa M, Thiessen, Paul A, Bryant, Stephen H
Abstract Background Accurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have...
Predicting domain-domain interactions using a parsimony approach (2006)
Guimarães, Katia S, Jothi, Raja, Zotenko, Elena, Przytycka, Teresa M
Abstract We propose a novel approach to predict domain-domain interactions from a protein-protein interaction network. In our method we apply a parsimony-driven explanation of the network, where the...
Zotenko, Elena, O'Leary, Dianne P, Przytycka, Teresa M
Abstract Background Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein...
Zotenko, Elena, Guimarães, Katia S, Jothi, Raja, Przytycka, Teresa M
Abstract Background Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while...
Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res (2006)
Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant
core regions
Decomposition of overlapping protein complexes: A graph (2006)
Elena Zotenko, Katia S Guimarães, Raja Jothi, Teresa M Przytycka, Teresa M Przytycka
theoretical method for analyzing static and dynamic protein associations
Research article State of the art: refinement of multiple sequence alignments (2006)
Bmc Bioinformatics, Saikat Chakrabarti, Christopher J Lanczycki, Anna R Panchenko, Teresa M Przytycka, Paul A Thiessen, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Refining multiple sequence alignments with conserved core regions (2006)
Chakrabarti, Saikat, Lanczycki, Christopher J., Panchenko, Anna R., Przytycka, Teresa M., Thiessen, Paul A., Bryant, Stephen H.
Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their...
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations (2006)
Jothi, Raja, Zotenko, Elena, Tasneem, Asba, Przytycka, Teresa M.
Motivation: Determining orthology relations among genes across multiple genomes is an important problem in the post-genomic era. Identifying orthologous genes can not only help predict functional...
Predicting protein-protein interaction by searching evolutionary tree automorphism space (2005)
Jothi, Raja, Kann, Maricel G., Przytycka, Teresa M.
Motivation: Uncovering the protein–protein interaction network is a fundamental step in the quest to understand the molecular machinery of a cell. This motivates the search for efficient...
Jørgen Bang-Jensen, Mohammed El Haddad, Yannis Manoussakis, Teresa M. Przytycka
We give an O(log 4 n)-time O(n 2 )-processor CRCW PRAM algorithm to find a hamiltonian cycle in a strong semicomplete bipartite digraph, B, provided that a factor of B (i.e. a collection of vertex...
Parallel Maximum Independent Set In Convex Bipartite Graphs (1996)
Artur Czumaj, Instytut Informatyki, Uniwersytet Warszawski, Teresa M. Przytycka
A bipartite graph G = (V; W;E) is called convex if the vertices in W can be ordered in such a way that the elements of W adjacent to any vertex v 2 V form an interval (i.e. a sequence consecutively...
Constructing Huffman Trees in parallel (1995)
Lawrence L. Larmore, Teresa M. Przytycka
We present a parallel algorithm for the Huffman Coding problem. We reduce the Huffman Coding problem to the Concave Least Weight Subsequence problem and give a parallel algorithm that solves the...
On the Agreement of Many Trees (1995)
Martin Farach, Teresa M. Przytycka, Mikkel Thorup
We consider the problem of computing the Maximum Agreement Subtree (MAST) of a set of rooted leaf labeled trees. We give an algorithm which computes the MAST of k trees on n leaves where some tree...
On the Agreement of Many Trees (1995)
Martin Farach, Teresa M. Przytycka, Mikkel Thorup
We consider the problem of computing the Maximum Agreement Subtree (MAST) of a set of leaf labeled trees. We give an algorithm which computes the MAST of k trees on n species where some tree has...
The Maximum Agreement Subtree Problem for Binary Trees (1995)
Martin Farach, Teresa M. Przytycka, Mikkel Thorup
We consider the problem of computing the Maximum Agreement Subtree (a maximum common topological restriction) of two binary labeled trees. We show that the problem can be solved in O(n log 3 n) using...
Surface Triangulations Without Short Noncontractible Cycles (1993)
ABSTRACT. We discuss three methods of constructing surface triangulations that do not have short noncontractible cycles (equivalently, that have high representativity). The three methods are: the...
Parallel Construction Of Optimal Alphabetic Trees (1993)
Lawrence L. Larmore, Teresa M. Przytycka, Wojciech Rytter
A parallel algorithm is given which constructs an optimal alphabetic tree in O(log 3 n) time with n 2 log n processors. The construction is basically a parallelization of the Garsia-Wachs version [5]...
A Simple Construction of High Representativity Triangulations (1993)
Teresa M. Przytycka, Józef H. Przytycki, J'ozef H. Przytycki
. We show a construction of high representativity triangulations of compact surfaces, equivalently, triangulations without short non-contractible cycles, and give a polynomial time algorithm to carry...
Subexponentially Computable Truncations of Jones-type Polynomials (1993)
Teresa M. Przytycka, Josef H. Przytycki
. We show that an essential part of the new (Jones-type) polynomial link invariants can be computed in subexponential time. This is in a sharp contrast to the result of Jaeger, Vertigan and Welsh...
Refining multiple sequence alignments with conserved core regions
Chakrabarti, Saikat, Lanczycki, Christopher J., Panchenko, Anna R., Przytycka, Teresa M., Thiessen, Paul A., Bryant, Stephen H.
Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their...
State of the art: refinement of multiple sequence alignments
Chakrabarti, Saikat, Lanczycki, Christopher J, Panchenko, Anna R, Przytycka, Teresa M, Thiessen, Paul A, Bryant, Stephen H
Refining multiple sequence alignments with conserved core regions
Chakrabarti, Saikat, Lanczycki, Christopher J., Panchenko, Anna R., Przytycka, Teresa M., Thiessen, Paul A., Bryant, Stephen H.
Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their...
State of the art: refinement of multiple sequence alignments
Chakrabarti, Saikat, Lanczycki, Christopher J, Panchenko, Anna R, Przytycka, Teresa M, Thiessen, Paul A, Bryant, Stephen H
Predicting domain-domain interactions using a parsimony approach
Guimarães, Katia S, Jothi, Raja, Zotenko, Elena, Przytycka, Teresa M
A new parsimony approach for the prediction of domain-domain interactions is presented and demonstrated to provide improvement in prediction coverage and accuracy.
Structural footprinting in protein structure comparison: the impact of structural fragments
Zotenko, Elena, Islamaj Dogan, Rezarta, Wilbur, W John, O'Leary, Dianne P, Przytycka, Teresa M
DOMINE: a database of protein domain interactions
Raghavachari, Balaji, Tasneem, Asba, Przytycka, Teresa M., Jothi, Raja
DOMINE is a database of known and predicted protein domain interactions compiled from a variety of sources. The database contains domain–domain interactions observed in PDB entries, and those that...
Differences in evolutionary pressure acting within highly conserved ortholog groups
Przytycka, Teresa M, Jothi, Raja, Aravind, L, Lipman, David J
Zotenko, Elena, Mestre, Julian, O'Leary, Dianne P., Przytycka, Teresa M.
The centrality-lethality rule, which notes that high-degree nodes in a protein interaction network tend to correspond to proteins that are essential, suggests that the topological prominence of a...
Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum
Huang, Yang, Wuchty, Stefan, Ferdig, Michael T., Przytycka, Teresa M.
Motivation: Analysis of expression quantitative trait loci (eQTL) significantly contributes to the determination of gene regulation programs. However, the discovery and analysis of associations of...
Jothi, Raja, Balaji, S, Wuster, Arthur, Grochow, Joshua A, Gsponer, Jörg, Przytycka, Teresa M, ...
Although several studies have provided important insights into the general principles of biological networks, the link between network organization and the genome-scale dynamics of the underlying...
Huang, Yang, Koonin, Eugene V., Lipman, David J., Przytycka, Teresa M.
In a wide range of genomes, it was observed that the usage of synonymous codons is biased toward specific codons and codon patterns. Factors that are implicated in the selection for codon usage...