|
2008
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|
68.
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J.
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Guimaraes
KS., and Przytycka TM, Interrogating
domain-domain interactions with parsimony based approaches, BMC Bioinformatics, 2008
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|
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67.
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J
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Raghavachari
B, Tasneem A,
Przytycka TM, Jothi R.
DOMINE:
a database of protein domain interactions. Nucleic Acids Res. (2008).
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PubMed
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|
66.
|
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. to appear
2008
|
pdf
book_info
|
|
65.
|
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, to appear 2008.
|
pdf
book_info
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|
64.
|
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)
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pdf
book_info
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|
63.
|
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
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|
2007
|
|
62.
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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 
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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
BMC 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
|
|
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
|
|
2002 and
before
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|
38.
|
J
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Przytycka
T., Srinivasan R., Rose G.D. Recursive
Domains in Proteins. Protein
Science 11, (2002) 409-417.
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PubMed
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|
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
|
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