Computational Biology Branch

 Teresa M. Przytycka Publications

J -journal; B – book/ book chapter/edited book C - peer reviewed conference proceedings

2009
82.	J.	Zheng J, Zhang D, Przytycki PF, Zielinski R, Capala J., Przytycka TM*. SimBoolNet - A Cytoscape Plugin for Dynamic Simulation of Signaling Networks. Bioinformatics, accepted.	PubMed
81.	J.	Huang Y, Koonin EV, Lipman DJ, Przytycka TM. Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage. Nucleic Acids Res. 2009 Sep 10.	PubMed
80.	J	Zielinski R, Przytycki PF, Zheng J, Zhang D, Przytycka TM*, Capala J. The crosstalk between EGF, IGF, and Insulin cell signaling pathways--computational and experimental analysis, BMC, Systems Biology (*corresponding author)	PubMed
79.	J	Teresa M. Przytycka Phenotypic variations meets systems biology, Genome Biology. 2009;10(8):313. Epub 2009 Aug 3.	PubMed
78.	J	Raja Jothi, S. Balaji, Arthur Wuster, Joshua A Grochow, Jörg Gsponer, Teresa M. Przytycka, L. Aravind and M. Madan Babu. Dissecting the dynamics of yeast transcription factors. Nature, Molecular Systems Biology, ;5:294. Epub 2009.	PubMed
77.	J,C	Yang Huang, Stefan Wuchty, Michael T. Ferdig, Teresa M. Przytycka^.Graph theoretical approach to study eQTL: A case study of Plasmodium falciparum. Bioinformatics; Jun 15;25(12):i15-20 ISMB 2009.	PubMed
76	B	Yang Huang, Teresa M. Przytycka, Jie Zheng. Discovery of regulatory mechanisms from gene expression variation by eQTL analysis. Biological Data Mining to be published (2009) by Chapman & Hall/CRC Press	pdf
75.	J	Maricel G. Kann, Benjamin A. Shoemaker, Anna R. Panchenko and Teresa M. Przytycka. Correlated evolution of interacting proteins: looking behind the mirrortree. Journal of Molecular Biology, 2009.	PubMed
74.	B	Katia S. Guimarães, Anna Panchenko, Teresa M. Przytycka (Ed): Advances in Bioinformatics and Computational Biology, 4th Brazilian Symposium on Bioinformatics, BSB 2009, Porto Alegre, Brazil, July 29-31, 2009. Proceedings Springer 2009
2008
73.	C	Raja Jothi, S. Balaji, Arthur Wuster, Joshua A Grochow, Jörg Gsponer, Teresa M. Przytycka, L. Aravind and M. Madan Babu. Global analysis of regulatory proteins within a hierarchical framework reveals distinct static and dynamic attribute. RECOMB Systems Biology and Regulatory Genomics 2008.
72.	J	Jieun Jeong, Piotr Berman, and Teresa M.Przytycka Improving strand pairing prediction through exploring folding cooperativity. IEEE Transactions on Computational Biology, 2008, Oct-Dec;5(4):484-91.	PubMed
71.	J	Elena Zotenko, Julian Mestre, Dianne P. O’Leary , and Teresa M. Przytycka Why do hubs in the yeast protein interaction network tend to be essential: Re-examining the connection between the network topology and essentiality, PLOS Computational Biology 2008.	PubMed
70.	J	Teresa M. Przytycka, Raja Jothi, L. Aravind, David J. Lipman, Differences in evolutionary pressure acting within highly conserved ortholog groups, BMC Bioinformatics; 2008 Jul 17;8(1):208. PMID: 18637201	PubMed
69.	J	Guimaraes KS., and Przytycka TM, Interrogating domain-domain interactions with parsimony based approaches, BMC Bioinformatics, Mar 26;9:171 2008	PubMed
68.	J	Raghavachari B, Tasneem A, Przytycka TM, Jothi R. DOMINE: a database of protein domain interactions. Nucleic Acids Res. (2008).	PubMed
67.	B	Teresa M. Przytycka. Agreement of three or more trees (1995; Farach, Przytycka, Thorup). Encyclopedia of Algorithms; ISBN: 978-0-387-30770-1 Kao, Ming Yang (Ed.) Springer. 2008	pdf book_info
66.	B	Katia Guimares and Teresa M. Przytycka, Protein interaction network based prediction of domain-domain and domain-peptide interactions in Protein-protein interactions and networks: identification, analysis and prediction Anna Panchenko and Teresa Przytycka (Eds) Springer, 2008.	pdf book_info
65.	B	Teresa M. Przytycka and Elena Zotenko, Graph theoretical approaches to delineate dynamics of biological processes. Bioinformatics Algorithms: Techniques and Application; Wiley Book Series on Bioinformatics, 2008 Ion Mandoiu and Alexander Zelikovsky (Eds)	pdf book_info
64.	B	Raja Jothi and Teresa M. Przytycka. Computational approaches to predict protein-protein and domain-domain interactions. in Bioinformatics Algorithms: Techniques and Application; Wiley Book Series on Bioinformatics, 2008, Editors Ion Mandoiu and Alexander Zelikovsky(Eds)	pdf book_info
2007
63.	C	Pawel Przytycki, Rafal Zielinski, Teresa M. Przytycka and Jacek Capala. The crosstalk between EGF, IGF, and Insulin Cell Signaling Pathways- computational and experimental analysis. Proceedings of RECOMB Systems Biology 2007
62.	J	Zheng J, Rogozin IB, Koonin EV, Przytycka TM Support for the Coelomata Clade of Animals From a Rigorous Analysis of the Pattern of Intron Conservation. Mol Biol Evol. 2007 PMID: 17893400	PubMed
61.	J	Elena Zotenko, Rozerta Islamah Dogan, John W. Wilbur, Dianne P O'Leary, Teresa M Przytycka. Structureal footprinting in protein structure comparission: The impact of structural fragments, BMC Structural Biol. 2007 7(1):53	PubMed
60.	C	Jie Zheng, Igor Rogozin, Eugene Koonin and Teresa M. Przytycka. A rigorous analysis of the pattern of intron conservation supports the Coelomata clade of animals. RECOMB Comparative Genomics 2007. LNCS 4751 p.177-92.
59.	J	Raja Jothi, Teresa M Przytycka and L Aravind. Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment BMC Bioinformatics. 2007 May 23;8(1):173	PubMed
58.	C	Jieun Jeong, Piotr Berman, and Teresa M. Przytycka, Bringing folding pathways into strand pairing prediction; The Workshop on Algorithms in Bioinformatics WABI 2007. LNCS 4645 p.38-49.	pdf
57.	J	Teresa M. Przytycka. Stability of characters and construction of phylogenetic trees. (2007) Journal of Computational Biology 14(5):539-49.	PubMed
56.	J	Maricel G. Kann, Raja Jothi, Praveen F. Cherukuri, and Teresa M. Przytycka Predicting Protein Domain Interactions From Coevolution of Conserved Regions PROTEINS: Structure, Function, and Bioinformatics 67: 811-820,2007	PubMed
2006
55.	J	Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH State of the art: refinement of multiple sequence alignments. BMC Bioinformatics. 2006 Nov 14;7:499.	PubMed
54.	J	Katia Guimares, Raja Jothi, Elena Zotenko, and Teresa Przytycka, Predicting Domain-Domain Interactions Using a Parsimony Approach Genome Biology 7:R104	PubMed
53.	J	Raja Jothi, Praveen F. Cherukuri, Asba Tasneem and Teresa M. Przytycka. Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions Journal of Molecular Biology, 2006 Sep 29;362(4):861-75.	PubMed
52.	J	Elena Zotenko, Dianne P O'Leary, Teresa M Przytycka Secondary structure spatial conformation footprint: A novel method for fast protein structure comparison. BMC Struct Biol. 2006 Jun 8;6(1):12	PubMed
51.	C	Teresa M. Przytycka. Chordal Graphs in Computational Biology - New Insights and Applications. International Conference on Computational Science (2), IWBRA 2006 Lecture Notes In Computer Science vol. 3992, pp 620-621
50.	J	Elena Zotenko, Katia S. Guimaraes, Raja Jothi, Teresa M. Przytycka Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations Algorithms for Molecular Biology, 2006 1:7 (26 April 2006)	PubMed
49.	J	Saikat Chakrabarti, Christopher Lanczycki, Anna Panchenko, Teresa M. Przytycka, Paul Thiessen, Stephen Bryant Refining multiple sequence alignment with conserved core regions. Nucleic Acid Research, 2006 May 17;34(9):2598-606.	PubMed
48.	J	Jieun Jeong, Piotr Berman, Teresa M. Przytycka. Fold classification based on secondary structure --- how much is gained by including loop topology? BMC Structural Biology 2006, 6:3	PubMed
47.	J	Raja Jothi, Elena Zotenko, Asba Tasneem and Teresa M. Przytycka. COCO-CL Hierarchical Clustering of Homology Relations Based on Evolutionary Correlations. Bioinformatics, 2006	PubMed
46	J	Teresa M. Przytycka, George Davis, Nan Song, Dannie Durand. Graph Theoretical Insights into Dollo Parsimony and Evolution of Multidomain Protein. Journal of Computational Biology 2006, Mar;13(2):351-63.	PubMed
45.	C	Teresa M. Przytycka. An important connection between network motifs and parsimony models. RECOMB 2006 Lecture Notes in Computational Biology, 2006. pp 321-335	pdf
2005
44.	C	Elena Zotenko, Katia S. Guimaraes, Raja Jothi, Teresa M. Przytycka Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations. RECOMB2005 Satellite Meeting on Systems Biology. Lecture Notes in Computational Biology Vol 4023 p 23-38.	pdf
43.	J/C	Jothi R., Kann M., Przytycka T. Predicting Protein-Protein Interaction by Searching Evolutionary Tree Automorphism Space. Bioinformatics Jun 1;21 Suppl 1:i241-i250 (2005) (ISMB 2005 special issue)	PubMed
42.	C	Przytycka, T. , Davis G., Song N., Durand, D. Graph Theoretical Insights into Multidomain Protein Evolution. RECOMB 2005 Lecture Notes in Computational Biology 3500, (2005) 311-325.
2004
41.	J	Przytycka, T, Yi-Kuo Yu (authors alphabetized). Critical Assessment of Fitting Biological Data using Scale Free Framework. Computational Chemistry and Biology 28 (2004), 257-264. Preliminary version presented at ISMB 2004 as a short paper.	PubMed
40.	J	Teresa M. Przytycka. Significance of conformational biases in Monte Carlo simulations of protein folding: lessons from the Metropolis-Hastings approach. ROTEINS: Structure, Function and Bioinformatics 57, (2004), 338-344.	PubMed
2003 and before
39.	B	Teresa M. Przytycka. Hidden Markov Models.Teresa M. Przytycka. Nature Encyclopedia of the Human Genome Nature Publishing Group, June 2003 (2003), ISBN 0-333-80386-8.	pdf book_info
38.	J	Przytycka T., Srinivasan R., Rose G.D. Recursive Domains in Proteins. Protein Science 11, (2002) 409-417.	PubMed
37.	J	Cole, M. Farach, R. Hariharan, T. Przytycka, M. Thorup (authors alphabetized). An O(n log n) Algorithm for the Maximum Agreement Subtree Problem. SIAM Journal on Computing 30(5) (2000) 1385-1404.
36	J	Przytycka,T. Aurora R., Rose G.D. A protein Taxonomy Based on Secondary Structure. Nature Structural Biology Vol 6, No 7, (1999) 672-682.	PubMed
35.	C	Rao S.Kosaraju, Teresa Przytycka, and Rayan Borgstorm.(first two authors alphabetized).On an Optimal Split Tree Problem. Lecture Notes in Computer Science, WADS 1999, pp.157-168.
34.	J	Teresa M. Przytycka. Transforming Rooted Agreement into Unrooted Agreement. Journal of Computational Biology (1998) Vol 5, No 2. 333 – 348.	PubMed
33.	J	T.Przytycka, L.L.Larmore. Optimal alphabetic tree problem revisited. Journal of Algorithms. 28 (1998), No. 1, 1--20.
32	J	Lisa Higham, Teresa M. Przytycka (authors alphabetized).Asymptotically Optimal Election on Weighted Rings SIAM J. Comput. (1998) 28(2): 720-732.
31.	J	Jorgen Bang-Jensen, Mohamed El Haddad, Yannis Manoussakis, and Teresa M.Przytycka (authors alphabetized). Hamiltonian cycle and Hamiltonian problems in semi-complete bipartite digraphs. Algorithmica 1, 1997, pp. 67--87.
30.	J	T.Przytycka J.Przytycki (authors alphabetized). Simple Construction of High Representativity Triangulation. Discrete Mathematics. 173, 1997, 209-228.
29.	C	Ming-Yang Kao, Tak Wah Lam, Teresa Przytycka, Wing Kin Sung and Hing Fung Ting. (authors alphabetized) Efficient Algorithms for Comparing Evolutionary Trees Symposium on Theoretical Computer Science (STOC’1997), ACM press 1997, pp 54-65.
28	B	Teresa M. Przytycka, Sparse Dynamic Programming for Maximum Agreement Subtree Problem in Mathematical Hierarchies in Biology DIMACS series in Discrete Mathematics and Theoretical Computer Science , Amer. Math. Society, Providence, 1997. B. Mirkin, F.R. McMorris, F.S. Roberts, and A.Rzhetsky (Eds.)
27.	J	L.Larmore, T.Przytycka (authors alphabetized). A parallel algorithm for almost optimal alphabetic trees. Journal on Parallel and Distributed Computing, 35 (1996) pp. 49--56.
26.	J	M.Paterson, T.Przytycka (authors alphabetized). On complexity of the string folding problem. Discrete Applied Mathematics. Vol 71, No 1-3, pp. 217 - 230, 1996.
25.	C	T.Przytycka, L.Higham Optimal Cost Sensitive MST algorithm. Proceedings of 5th Scandinavian Workshop on Algorithm Theory (SWAT) Lecture Notes in Computer Science, p. 246-258. 1996.
24.	C	M.Paterson, T.Przytycka (authors alphabetized). On complexity of the string folding problem Proceedings of 23st International Colloquium on Automata, Languages and Programming, ICALP'96, LNCS, Springer-Verlag 1996, pp 658-669.
23.	J	A.Czumaj, K.Diks, T.Przytycka, (authors alphabetized) Parallel Maximum Independent Set in Convex Bipartite Graphs Information Processing Letters. 59 (1996) pp.289--294.
22.	J	D.G.Kirkpatrick, T.Przytycka Parallel construction of binary trees with almost optimal weighted path length Algorithmica (1996) 15: 172-192.
21.	J	M.Farach, T.Przytycka, M.Thorup (authors alphabetized). On the Agreement of Many Trees. Information Processing Letters 55, (1995) pp. 297--301.
20.	J	L.Larmore, T.M.Przytycka (authors alphabetized). Constructing Huffman Trees in Parallel SIAM Journal on Computing, Vol 24, No 6,(1995) pp. 1163--1169.
19.	C	M.Farach, T.Przytycka, M.Thorup (authors alphabetized) Computing the Agreement of Trees with Bounded Degrees. Proceedings of 3rd European Symposium on Algorithms, ESA 1995 LNCS, 381-393 (1995)
18	J	L.L.Larmore, T.Przytycka (authors alphabetized). A Fast Algorithm for Optimum Height Limited Alphabetic Binary Trees. SIAM Journal on Computing, 23, (1994) pp. 1283--1312.
17.	J	L.Higham, T.Przytycka (authors alphabetized). A Simple, Efficient Algorithm for Maximum Finding on Rings. Information Processing Letters 58 (1994) pp.319 --324.
16	J	Ch.Levcopoulos, T.Przytycka (authors alphabetized). Trade-offs in parallel computation of Huffman trees and Concave Least Subsequence. Parallel Processing Letters 4. 7-43. 1994.
15	C	T.Przytycka, L.L.Larmore. Optimal alphabetic tree problem revisited. Proceedings of 21st International Colloquium on Automata, Languages and Programming, ICALP'94, LNCS 820, Springer-Verlag, 1994, pp 251--262.
14	C	L.Higham, T.Przytycka (authors alphabetized), Asymptotically Optimal Election on Weighted Rings. Proceedings of 4th Scandinavian Workshop on Algorithm Theory, SWAT’94 LNCS 824, Springer-Verlag, (1994) pp 207--218.
13.	C	L.Higham, T.M.Przytycka. (authors alphabetized) A Simple, Efficient Algorithm for Maximum Finding on Rings. WDA’93. Lecture Notes in Computer Science 725, Springer Verlag, (1993) pp 245--260
12.	C	L.L.Larmore, T.M.Przytycka, and W.Rytter (authors alphabetized). Parallel construction of optimal alphabetic Trees. Proceedings 5th Symposium on Parallel Algorithms and Architectures, SPAA’93. LNCS, Springer-Verlag (1993), pp. 214--244.
11.	J	S.Bellantoni, I.Ben-Arrago Hartman, T.Przytycka, S.Whitesides (authors alphabetized). Grid intersection graphs and boxicity. Discrete Math. 114 (1993) pp. 41 -49.
10.	J	Pilar de la Torre, R.Greenlaw, T. Przytycka (authors alphabetized). Super critical tree numbering and optimal tree ranking is NC. Parallel Processing Letters (1992), pp. 31--42.
9.	C	L.L.Larmore, T.Przytycka (authors alphabetized). Parallel construction of trees with optimal weighted path length Proceedings of 3nd Annual Symposium on Parallel Algorithms and Architectures, SPAA’91 (1991) pp. 71--80.
8.	J	T.Przytycka, J.H.Przytycki (authors alphabetized). Embeddings of graphs without short noncontractible Cycles. Contemporary Mathematics 147, Graph Structure Theory, (1991) pp. 303--341.
7.	J	T.Przytycka, J.H.Przytycki. (authors alphabetized) Subexponentially computable truncations of link invariants. Contemporary Mathematics 147, Graph Structure Theory, (1991) pp. 63--108.
6.	J	T.Przytycka, D.Corneil. Parallel algorithms for parity graphs, Journal of Algorithms 12 (1991) pp. 96--109.
5.	J	D.G.Kirkpatrick, T.Przytycka (authors alphabetized). Parallel recognition of cographs and cotree construction. Discrete Applied Mathematics, 29 (1990) 79-96.
4.	C	D.G.Kirkpatrick, T. Przytycka (authors alphabetized). An optimal parallel minimax tree algorithm. Proceedings 2nd IEEE Symposium on Parallel and Distributed Processing,. (1990) pp. 293--300.
3.	J	T.Przytycka, J.H.Przytycki (authors alphabetized) On lower bounds for short noncontractible cycles in embedded graphs. SIAM Journal on Discrete Math. Vol. 3, No. 2(1990) pp. 281--293.
2.	J	K.Abrahamson, N.Dadoun, D.G.Kirkpatrick, T.Przytycka (authors alphabetized). A simple parallel tree contraction algorithm. Journal of Algorithms 10, (1989) pp. 287--302.
1.	C	K.Abrahamson, N.Dadoun, D.G.Kirkpatrick, T.Przytycka (authors alphabetized). A simple parallel tree contraction algorithm. Journal of Fifth Allerton Conference on Communication, Control and Computing, pages 624--633, September 1987.