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1

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

Jothi, Raja, Balaji, S, Wuster, Arthur, Grochow, Joshua A, Gsponer, Jörg, Przytycka, Teresa M, Aravind, L, Babu, M Madan

Journal:

Molecular Systems Biology

Year:

2009

Language:

english

File:

PDF, 2.58 MB

english, 2009

2

Chapter 5: Network Biology Approach to Complex Diseases

Cho, Dong-Yeon, Kim, Yoo-Ah, Przytycka, Teresa M., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 394 KB

english, 2012

3

MONET: Multi-omic module discovery by omic selection

Rappoport, Nimrod, Safra, Roy, Shamir, Ron, Przytycka, Teresa M.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 4.05 MB

2020

4

The Optimal Alphabetic Tree Problem Revisited

Lawrence L Larmore, Teresa M Przytycka

Journal:

Journal of Algorithms

Year:

1998

Language:

english

File:

PDF, 202 KB

english, 1998

5

A Parallel Algorithm for Optimum Height-Limited Alphabetic Binary Trees

Lawrence L. Larmore, Teresa M. Przytycka

Journal:

Journal of Parallel and Distributed Computing

Year:

1996

Language:

english

File:

PDF, 317 KB

english, 1996

6

On the agreement of many trees

Martin Farach, Teresa M Przytycka, Mikkel Thorup

Journal:

Information Processing Letters

Year:

1995

Language:

english

File:

PDF, 431 KB

english, 1995

7

A simple, efficient algorithm for maximum finding on rings

Lisa Higham, Teresa Przytycka

Journal:

Information Processing Letters

Year:

1996

Language:

english

File:

PDF, 560 KB

english, 1996

8

Scale-free networks versus evolutionary drift

Teresa M. Przytycka, Yi-Kuo Yu

Journal:

Computational Biology and Chemistry

Year:

2004

Language:

english

File:

PDF, 217 KB

english, 2004

9

A simple construction of high representativity triangulations

Teresa M. Przytycka, Józef H. Przytycki

Journal:

Discrete Mathematics

Year:

1997

Language:

english

File:

PDF, 962 KB

english, 1997

10

On the complexity of string folding

Mike Paterson, Teresa Przytycka

Journal:

Discrete Applied Mathematics

Year:

1996

Language:

english

File:

PDF, 1001 KB

english, 1996

11

Fold classification based on secondary structure – how much is gained by including loop topology?

Jieun Jeong, Piotr Berman, Teresa Przytycka

Journal:

BMC Structural Biology

Year:

2006

Language:

english

File:

PDF, 594 KB

english, 2006

12

Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification

Elena Zotenko, Dianne P O'Leary, Teresa M Przytycka

Journal:

BMC Structural Biology

Year:

2006

Language:

english

File:

PDF, 1.18 MB

english, 2006

13

Structural footprinting in protein structure comparison: the impact of structural fragments

Elena Zotenko, Rezarta Islamaj Dogan, W John Wilbur, Dianne P O'Leary, Teresa M Przytycka

Journal:

BMC Structural Biology

Year:

2007

Language:

english

File:

PDF, 2.54 MB

english, 2007

14

Network integration meets network dynamics

Teresa M Przytycka, Yoo-Ah Kim

Journal:

Year:

2010

Language:

english

File:

PDF, 392 KB

english, 2010

15

Systems-biology dissection of eukaryotic cell growth

Teresa M Przytycka, Justen Andrews

Journal:

Year:

2010

Language:

english

File:

PDF, 2.53 MB

english, 2010

16

Significance of conformational biases in Monte Carlo simulations of protein folding: Lessons from Metropolis–Hastings approach

Teresa Przytycka

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 277 KB

english, 2004

17

Predicting protein domain interactions from coevolution of conserved regions

Maricel G. Kann, Raja Jothi, Praveen F. Cherukuri, Teresa M. Przytycka

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 506 KB

english, 2007

18

Parallel maximum independent set in convex bipartite graphs

Artur Czumaj, Krzysztof Diks, Teresa M. Przytycka

Journal:

Information Processing Letters

Year:

1996

Language:

english

File:

PDF, 606 KB

english, 1996

19

10.1038/10728

Rose, George D., Przytycka, Teresa, Aurora, Rajeev

Journal:

Natural Structural Biology

Year:

1999

Language:

english

File:

PDF, 2.02 MB

english, 1999

20

Recursive domains in proteins

Teresa Przytycka, Rajgopal Srinivasan, George D. Rose

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 879 KB

english, 2002

21

Crystal Structures of the Outer Membrane Domain of Intimin and Invasin from Enterohemorrhagic E. coli and Enteropathogenic Y. pseudotuberculosis

James W. Fairman, Nathalie Dautin, Damian Wojtowicz, Wei Liu, Nicholas Noinaj, Travis J. Barnard, Eshwar Udho, Teresa M. Przytycka, Vadim Cherezov, Susan K. Buchanan

Journal:

Year:

2012

Language:

english

File:

PDF, 1.56 MB

english, 2012

22

State of the art: refinement of multiple sequence alignments

Saikat Chakrabarti, Christopher J Lanczycki, Anna R Panchenko, Teresa M Przytycka, Paul A Thiessen, Stephen H Bryant

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 146 KB

english, 2010

23

State of the art: refinement of multiple sequence alignments

Saikat Chakrabarti, Christopher J Lanczycki, Anna R Panchenko, Teresa M Przytycka, Paul A Thiessen, Stephen H Bryant

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 577 KB

english, 2006

24

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

Raja Jothi, Teresa M Przytycka, L Aravind

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 2.97 MB

english, 2007

25

Interrogating domain-domain interactions with parsimony based approaches

Katia S Guimarães, Teresa M Przytycka

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.17 MB

english, 2008

26

Differences in evolutionary pressure acting within highly conserved ortholog groups

Teresa M Przytycka, Raja Jothi, L Aravind, David J Lipman

Journal:

BMC Evolutionary Biology

Year:

2008

Language:

english

File:

PDF, 622 KB

english, 2008

27

Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots

Wu, Min, Kwoh, Chee-Keong, Przytycka, Teresa M, Li, Jing, Zheng, Jie

Journal:

Proteome Science

Year:

2012

Language:

english

File:

PDF, 967 KB

english, 2012

28

The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis

Rafal Zielinski, Pawel F Przytycki, Jie Zheng, David Zhang, Teresa M Przytycka, Jacek Capala

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 1.76 MB

english, 2009

29

Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain–Domain Interactions Mediating Protein–Protein Interactions

Raja Jothi, Praveen F. Cherukuri, Asba Tasneem, Teresa M. Przytycka

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.24 MB

english, 2006

30

Correlated Evolution of Interacting Proteins: Looking Behind the Mirrortree

Maricel G. Kann, Benjamin A. Shoemaker, Anna R. Panchenko, Teresa M. Przytycka

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.04 MB

english, 2009

31

A Fast Algorithm For Optimum Height-Limited Alphabetic Binary Trees

Larmore, Lawrence L., Przytycka, Teresa M.

Journal:

SIAM Journal on Computing

Year:

1994

Language:

english

File:

PDF, 3.31 MB

english, 1994

32

Asymptotically Optimal Election on Weighted Rings

Higham, Lisa, Przytycka, Teresa

Journal:

SIAM Journal on Computing

Year:

1998

Language:

english

File:

PDF, 302 KB

english, 1998

33

An O ( n log n ) Algorithm for the Maximum Agreement Subtree Problem for Binary Trees

Cole, Richard, Farach-Colton, Martin, Hariharan, Ramesh, Przytycka, Teresa, Thorup, Mikkel

Journal:

SIAM Journal on Computing

Year:

2000

Language:

english

File:

PDF, 238 KB

english, 2000

34

Constructing Huffman Trees in Parallel

Larmore, Lawrence L., Przytycka, Teresa M.

Journal:

SIAM Journal on Computing

Year:

1995

Language:

english

File:

PDF, 858 KB

english, 1995

35

Mediation ofDrosophilaautosomal dosage effects and compensation by network interactions

John H Malone, Dong-Yeon Cho, Nicolas R Mattiuzzo, Carlo G Artieri, Lichun Jiang, Ryan K Dale, Harold E Smith, Jennifer McDaniel, Sarah Munro, Marc Salit, Justen Andrews, Teresa M Przytycka, Brian Oli

Journal:

Year:

2012

Language:

english

File:

PDF, 2.97 MB

english, 2012

36

Transcription-dependent dynamic supercoiling is a short-range genomic force

Kouzine, Fedor, Gupta, Ashutosh, Baranello, Laura, Wojtowicz, Damian, Ben-Aissa, Khadija, Liu, Juhong, Przytycka, Teresa M, Levens, David

Journal:

Nature Structural and Molecular Biology

Year:

2013

Language:

english

File:

PDF, 914 KB

english, 2013

37

[Lecture Notes in Computer Science] Advances in Bioinformatics and Computational Biology Volume 5676 || Comparing Methods for Multilabel Classification of Proteins Using Machine Learning Techniques

Guimarães, Katia S., Panchenko, Anna, Przytycka, Teresa M.

Year:

2009

Language:

english

File:

PDF, 228 KB

english, 2009

38

Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome

Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero, Teresa M Przytycka

Journal:

Year:

2010

Language:

english

File:

PDF, 1.07 MB

english, 2010

39

Phenotypic variation meets systems biology

Teresa M Przytycka

Journal:

Year:

2009

Language:

english

File:

PDF, 171 KB

english, 2009

40

Predicting domain-domain interactions using a parsimony approach

Katia S Guimarães, Raja Jothi, Elena Zotenko, Teresa M Przytycka

Journal:

Year:

2006

Language:

english

File:

PDF, 534 KB

english, 2006

41

A Gene-Specific Method for Predicting Hemophilia-Causing Point Mutations

Hamasaki-Katagiri, Nobuko, Salari, Raheleh, Wu, Andrew, Qi, Yini, Schiller, Tal, Filiberto, Amanda C., Schisterman, Enrique F., Komar, Anton A., Przytycka, Teresa M., Kimchi-Sarfaty, Chava

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 448 KB

english, 2013

42

[Lecture Notes in Computer Science] Algorithms in Bioinformatics Volume 6833 || Algorithm for Identification of Piecewise Smooth Hybrid Systems: Application to Eukaryotic Cell Cycle Regulation

Przytycka, Teresa M., Sagot, Marie-France

Year:

2011

Language:

english

File:

PDF, 419 KB

english, 2011

43

[Computational Biology] Protein-protein Interactions and Networks Volume 9 || Experimental Methods for Protein Interaction Identification and Characterization

Panchenko, Anna, Przytycka, Teresa

Year:

2008

Language:

english

File:

PDF, 1.26 MB

english, 2008

44

[Computational Biology] Protein-protein Interactions and Networks Volume 9 || Handling Diverse Protein Interaction Data: Integration, Storage and Retrieval

Panchenko, Anna, Przytycka, Teresa

Year:

2008

Language:

english

File:

PDF, 509 KB

english, 2008

45

[Computational Biology] Protein-protein Interactions and Networks Volume 9 || Protein Interaction Network Based Prediction of Domain-Domain and Domain-Peptide Interactions

Panchenko, Anna, Przytycka, Teresa

Year:

2008

Language:

english

File:

PDF, 390 KB

english, 2008

46

[Computational Biology] Protein-protein Interactions and Networks Volume 9 || Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints

Panchenko, Anna, Przytycka, Teresa

Year:

2008

Language:

english

File:

PDF, 698 KB

english, 2008

47

[Computational Biology] Protein-protein Interactions and Networks Volume 9 || Computational Methods to Predict Protein Interaction Partners

Panchenko, Anna, Przytycka, Teresa

Year:

2008

Language:

english

File:

PDF, 361 KB

english, 2008

48

[Computational Biology] Protein-protein Interactions and Networks Volume 9 || Principles of Protein Recognition and Properties of Protein-protein Interfaces

Panchenko, Anna, Przytycka, Teresa

Year:

2008

Language:

english

File:

PDF, 463 KB

english, 2008

49

[Lecture Notes in Computer Science] Algorithms in Bioinformatics Volume 6833 || Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph

Przytycka, Teresa M., Sagot, Marie-France

Year:

2011

Language:

english

File:

PDF, 236 KB

english, 2011

50

LDsplit: screening forcis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms

Yang, Peng, Wu, Min, Guo, Jing, Kwoh, Chee, Przytycka, Teresa M, Zheng, Jie

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 665 KB

english, 2014