Our publications:

Peer reviewed (journals and conference proceedings):

2009

E. Szczurek, I. Gat-Viks, J. Tiuryn, M. Vingron,
Elucidating Regulatory Mechanisms Downstream of a Signaling Pathway Using Informative Experiments,
Molecular Systems Biology, 5 287. Epub 2009 Jul 7
Łuksza M, Kluge B, Ostrowski J, Karczmarski J, Gambin A.,
Two-stage model-based clustering for liquid chromatography mass spectrometry data analysis,
Stat Appl Genet Mol Biol. 2009 Jan;8(1):Article 15. Epub 2009 Feb 12. PMID: 19222382
Gambin A, Szczurek E, Dutkowski J, Bakun M, Dadlez M.,
Classification of peptide mass fingerprint data by novel no-regret boosting method,
Comput Biol Med. 2009 May;39(5):460-73. Epub 2009 Apr 21. PMID: 19386298
Roytberg M, Gambin A, Noé L, Lasota S, Furletova E, Szczurek E, Kucherov G.,
On subset seeds for protein alignment,
IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):483-94, PMID: 19644175
Wilczyński B, Furlong EE.,
Challenges for modeling global gene regulatory networks during development: Insights from Drosophila,
Developmental Biology 2009 Oct 27
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczyński B, de Hoon MJ.,
Biopython: freely available Python tools for computational molecular biology and bioinformatics,
Bioinformatics. 2009 Jun 1;25(11):1422-3. Epub 2009 Mar 20.
Wilczyński B, Dojer N, Patelak M, Tiuryn J.,
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs,
BMC Bioinformatics. 2009 Mar 10;10:82, suplement.
Bogusław Kluge, Anna Gambin, Wojciech Niemiro,
Modeling Exopeptidase Activity from LC-MS Data,
Journal of Computational Biology. February 2009, 16(2): 395-406.
Bartek Wilczyński, Norbert Dojer
BNFinder: Exact and efficient method for learning Bayesian networks,
Bioinformatics. 2009 25(2):286-7

2008

Gambin, A., Krzyżanowski, P. and Pokarowski, P.,
Aggregation Algorithms for Perturbed Markov Chains with Applications to Networks Modeling,
SIAM Journal on Scientific Computing,2008, Volume 31, Issue 1, pp. 45-73
Roytberg, M., Gambin, A., Noe, L., Lasota, S., Furletova, E., Szczurek, E., Kucherov, G.,
Efficient seeding techniques for protein similarity search,
Proc. of the 2nd International Conference BIRD 2008, Communications in Computer and Information Science, vol.13, pp.466-478, Springer Verlag.
Przemysław Biecek, Stanisław Cebrat,
Why Y chromosome is shorter and women live longer?,
European Physical Journal B, 2008, Volume 65, number 1, p. 149-153, Populations and Evolution.
Małgorzata Bogdan, Florian Frommlet, Przemysław Biecek, Riyan Cheng, Jayanta K. Ghosh, R.W. Doerge,
Extending the Modified Bayesian Information Criterion (mBIC) to dense markers and multiple interval mapping,
Biometrics, 2008, 64.
Marta Zawierta, Wojciech Waga, Dorota Mackiewicz, Przemysław Biecek, Stanisław Cebrat,
Phase Transition in Sexual Reproduction and Biological Evolution,
International Journal of Modern Physics,2008,19(6), 917 - 926.
Pawel Mackiewicz, Przemyslaw Biecek, Dorota Mackiewicz, Joanna Kiraga, Krystian Baczkowski, Maciej Sobczynski, Stanislaw Cebrat,
Optimisation of Asymmetric Mutational Pressure and Selection Pressure Around the Universal Genetic Code,
Lecture Notes in Computer Science, 2008, 3, p. 100-109.
Katarzyna Bońkowska, Przemysław Biecek, Agnieszka Łaszkiewicz, Stanisław Cebrat,
Relationship between the selection pressure and the rate of mutation accumulation,
Banach Center Publ.,2008, 80, 223-228.

2007

Dariusz Grzebelus, Slawomir Lasota, Tomasz Gambin, Gregory Kucherov, Anna Gambin
Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago Truncatula
BMC Genomics 2007, 8:409
Bartek Wilczyński
A Stochastic Extension of R.Thomas Regulatory Network Modelling
In post-proceedings of Stochastic models in biological sciences, Warsaw, 2006, Banach Center Publications 80, 271-276, 2008.
Gambin, A., Wojtalewicz, P.
CTX-BLAST - context sensitive version of protein BLAST
Bioinformatics. 2007; 23(13):1686-8
Bartek Wilczynski, Jerzy Tiuryn
Reconstruction of Mammalian Cell Cycle Regulatory Network from Microarray Data using Stochastic Logical Networks
in proceedings of Computational Methods in Systems Biology 2007 (Lecture Notes in Bioinformatics 4695 pp. 121-135, ed. Calder and Gilmore)
Janusz Dutkowski, Jerzy Tiuryn
Identification of functional modules from conserved ancestral protein-protein interactions
Bioinformatics 2007 23: i149-i158, proceedings of ISMB/ECCB 2007.
Janusz Dutkowski, Anna Gambin
On consensus biomarker selection
BMC Bioinformatics,2007, 8(Suppl 5):S5 doi:10.1186/1471-2105-8-S5-S5
Damian Wójtowicz, Jerzy Tiuryn,
Evolution of gene families based on gene duplication, loss, accumulated change, and innovation,
Journal of Computational Biology 14/4, pages 479--495, 2007.
Michał Drabikowski, Szymon Nowakowski and Jerzy Tiuryn
Library of Local Descriptors Models the Core of Proteins Accurately
Proteins, 2007 Nov 15;69(3):499-510.
Jerzy Tiuryn, Damian Wójtowicz, Ryszard Rudnicki,
A Discrete Model of Evolution of Small Paralog Families,
Mathematical Models and Methods in Applied Sciences 17(6), pages 933--956, 2007.
Anna Gambin, Ewa Szczurek
No-regret boosting
International Conference on Adaptive and Natural Computing Algorithms (ICANNGA 2007), Lecture Notes in Computer Science, Springer, 4431:422-431
Paweł Górecki, Jerzy Tiuryn
URec: a system for unrooted reconciliation
Bioinformatics (Application Notes) (in press)
Łukasz Bolikowski, Anna Gambin
New metrics for phylogenies,
Fundamenta Informaticae, 2007, 78(2):199-216
Gambin, A., Dutkowski, J., Jakub Karczmarski, J., Kluge, B., Kowalczyk, K., Ostrowski, J., Poznański, J., Tiuryn, J., Bakun, M., Dadlez, M.
Automated reduction and interpretation of multidimensional mass spectra for analysis of complex peptide mixtures,
International Journal of Mass Spectrometry Vol. 260, Issue 1, 15 January 2007, pp. 20-30

2006

Ryszard Rudnicki, Jerzy Tiuryn, Damian Wójtowicz
A model for the evolution of paralog families in genomes
Journal of Mathematical Biology 53(5), pp. 759-770

B. Wilczyński, TR. Hvidsten, A.Kryshtafovych, J. Tiuryn, J. Komorowski, K. Fidelis
Using local gene expression similarities to discover regulatory binding site modules
BMC Bioinformatics 2006, 7:505 DOI: 10.1186/1471-2105-7-505

Gambin A, Lasota S, Rutkowski M.
Analyzing stationary states of gene regulatory network using Petri nets
In Silico Biol. 2006 Feb 19;6(1-2):0010

Szymon Nowakowski and Jerzy Tiuryn,
A New Approach to the Assessment of the Quality of Predictions of Transcription Factor Binding Sites,
Journal of Biomedical Informatics, 40(2) p. 139-149, 2007 (e-published 2006) doi:10.1016/j.jbi.2006.07.001

Paweł Górecki and Jerzy Tiuryn,
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science, Vol. 359, 2006, pp. 378-399. doi:10.1016/j.tcs.2006.05.019

Norbert Dojer, Anna Gambin, Andrzej Mizera, Bartek Wilczyński, Jerzy Tiuryn
Applying Dynamic Bayesian Networks to Perturbed Gene Expression Data
BMC Bioinformatics, 2006, 7:249

Anna Gambin, Katarzyna Bożek, Bartek Wilczyński, Jerzy Tiuryn
Automated modeling of genetic control in Arabidopsis thaliana,
Journal of Fruit and ornamental plant research, Vol. XIV, Supp. 1, pp. 163-171, 2006.

Gambin, A., Tiuryn J., Tyszkiewicz, J.
Alignment with context dependent scoring function
Journal of Computational Biology, 2006 Jan-Feb;13(1):81-101. full version supplement

Gambin, A., Łuksza, M., Kluge, Ostrowski, J., Karczmarski, J.
Efficient Model-Based Clustering for LC-MS Data
In proc. WABI 2006, LNBI 4175, pp.32--43.

Damian Wójtowicz, Jerzy Tiuryn
On genome evolution with accumulated change and innovation,
Proceedings of RECOMB Comparative Genomics Satellite Workshop, 2006, Lecture Notes in Computer Science, Springer 4205, pages 40--50.

Bartek Wilczyński and Jerzy Tiuryn
Regulatory Network Reconstruction using Stochastic Logical Networks
in proceedings of Computational Methods in Systems Biology, 2006, (Lecture Notes in Bioinformatics, 4210, pp.142-154, ed. C. Priami, Springer)

Norbert Dojer
Learning Bayesian Networks Does Not Have to Be NP-Hard
Proceedings of Mathematical Foundations of Computer Science, 2006, Lecture Notes in Computer Science, Springer 4162, pp. 305-314 doi:10.1007/11821069_27

Damian Wójtowicz, Jerzy Tiuryn
On genome evolution with innovation
Proceedings of Mathematical Foundations of Computer Science 2006, Lecture Notes in Computer Science, Springer 4162, pages 801--811

Paweł Górecki and Jerzy Tiuryn
Inferring phylogeny from whole genomes,
European Conference on Computational Biology 2006, (ECCB 2006)

Szymon Nowakowski, Krzysztof Fidelis, Jerzy Tiuryn
Introducing Dependencies into Alignment Analysis and Its Use for Local Structure Prediction in Proteins,
editor R. Wyrzykowski, Proceedings of the Sixth International Conference on Parallel Processing and Applied Mathematics (PPAM'05), Lecture Notes in Computer Science, Springer 3911, Springer, 1106-1113 (2006)

2005

Gambin, A., Otto, R.
Contextual Multiple Alignment (Context helps in aligning orphan genes),
J Biomed Biotechnol. 2005; 2005(2): 124-131.

Gambin, A., Slonimski, P.
Hierarchical clustering based upon contextual alignment of proteins: a different way to approach phylogeny,
C.R. Biologie Acad. Science Paris 328:11-22, 2005.

T.R. Hvidsten, B. Wilczyński, A. Kryshtafovych, J. Tiuryn, J. Komorowski and K. Fidelis
Discovering regulatory binding site modules using rule-based learning,
Genome Research 2005 15: 856-866.

Gambin, A., Wojtowicz, D.
Almost FPRAS for Lattice Models of Protein Folding (Extended Abstract),
WEA 2005: 4th International Workshop on Efficient and Experimental Algorithms, Lecture Notes in Computer Science, Springer, vol. 3503, 2005, pp.534-544, Springer-Verlag.

2004

Jerzy Tiuryn, Ryszard Rudnicki, Damian Wójtowicz
A Case Study of Genome Evolution: From Continuous to Discrete Time Model,
Mathematical Foundations of Computer Science 2004, 29th International Symposium, MFCS 2004, Prague, Czech Republic, August 22-27, 2004, Proceedings, pp. 1-24.

Paweł Górecki and Jerzy Tiuryn,
On the structure of reconciliations
2005, Lecture Notes in Computer Science, Springer, vol. 3388, pg. 42-54, Comparative Genomics: RECOMB 2004 International Workshop, RCG 2004, Bertinoro, Italy, October 16-19, 2004

Paweł Górecki,
Reconciliation problems for duplication, loss and horizontal gene transfer,
Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), March 27-31, 2004, San Diego, California, USA

2003

Paweł Górecki,
Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model,
Proceedings of the European Conference on Computational Biology, (ECCB 2003), Sept. 27-30, 2003, Paris, France

B.Wilczyński, T.R. Hvidsten, A. Kryshtafovych, L. Stubbs, J. Komorowski, K. Fidelis.
A rule-based framework for gene regulation pathways discovery,
2nd IEEE Computer Society Bioinformatics Conference (CSB 2003): Stanford, 11-14. August, 2003, IEEE Computer Society, pp. 435-436. (short paper)

2002

Gambin, A., Lasota, S., Szklarczyk, R., Tiuryn, J., Tyszkiewicz, J.
Contextual Alignment of Biological Sequences.
Bioinformatics, 18:116-127, 2002.

Other (reports, posters, etc.):

2009

M. Rybiński, A. Gambin,
Model selection of the JAK–STAT pathway activation mechanism,
Acta Biochimica Polonica, tom 56, suplement, 2009, str. 58

2008

M. Rybiński, P. Banasik, A. Gambin,
Taverna services for systems biology,
Poster at 6th Conference on Computational Methods in Systems Biology (CMSB) 2008, Rostock, Germany.

2007

M. Rybinski, A. Gambin
Details of the JAK-STAT Signalling Pathway Model
Acta Biochimica Polonica, tom 54, suplement 3, 2007, str. 63-64.

M. Rybinski, A. Gambin
Inferring Receptor Activation Mechanism Details in the JAK-STAT Signalling Pathway Model
Poster at 5th Conference on Computational Methods in Systems Biology (CSMB) 2007, Edinburgh, UK.

Bartek Wilczynski, Jerzy Tiuryn
Reconstruction of Mammalian Cell Cycle Regulatory Network from Microarray Data using Stochastic Logical Networks
Poster at RECOMB 2007 in San Diego and ISMB/ECCB 2007 in Vienna

2006

Ł. Bolikowski, A. Gambin
New metrics for phylogenies
TR IIUW No. 282.

Gambin, A. and Szczurek, E.
Novel boosting technique applied to mass spectrometry data,
Poster at RECOMB 2006, Venice, full version submitted.

Janusz Dutkowski and Anna Gambin
Biomarker selection method based on rank aggregation
Poster at RECOMB 2006, Venice

Bartek Wilczyński and Jerzy Tiuryn
Regulatory network reconstruction with generalized boolean networks
Poster at RECOMB 2006, Venice

2005

Norbert Dojer, Anna Gambin, Bartek Wilczyński, Jerzy Tiuryn
Applying Dynamic Bayesian Networks to Perturbed Gene Expression Data
Technical report, 2005

Paweł Górecki and Jerzy Tiuryn,
Reconciling gene and species evolution in the presence of horizontal gene transfer,
ECCB 2005, Madrid (poster session)

D.Wójtowicz, J.Tiuryn, R.Rudnicki
A Simple Probabilistic Model of Evolution of Paralog Families in Genomes,
poster, The 3rd RECOMB Satellite Workshop on Comparative Genomics, September 18-10, 2005, Trinity College Dublin

A. Gambin, J.Hidders, N. Kwasnikowska,S. Lasota, J. Sroka, J. Tyszkiewicz, J. Van den Bussche
NRC as a formal model for expressing bioinformatics workflows
Intelligent Systems for Molecular Biology (ISMB), Chicago, 2005.

Gambin, A., Hidders, J., Kwasnikowska, N., Lasota, S., Sroka, J., Tyszkiewicz,J., Van den Bussche, J.
Well Constructed Workflows in Bioinformatics,
Proc. Workshop on Database Issues in Biological Databases (DBiBD 2005)

2004

Michał Drabikowski, Jerzy Tiuryn
Complexity analysis of finding optimal assignments' problem in local descriptor- based approach to protein structure prediction
Technical report, 2004

D. Wójtowicz, J.Tiuryn
A Markovian model of genome evolution: distribution of paralogs,
poster, RECOMB 2004, San Diego.

A. Gambin, B. Kluge
Statistical significance of contextual alignment,
Intelligent Systems for Molecular Biology (ISMB),Glasgow, UK, August 2004.

B. Wilczyński, T.R. Hvidsten, A. Kryshtafovych, J. Komorowski and K. Fidelis
An iterative approach to gene regulation pathways discovery - Poster Paper
Pacific Symposium on Biocomputing 2004, Hawaii, USA.

2003

Paweł Górecki,
Maximum likelihood estimation for duplication-loss model
Currents in Computational Molecular Biology 2003, RECOMB, Berlin (poster session)

A. Gambin, D. Wójtowicz
Almost FPRAS for Lattice Models of Protein Folding,
Currents in Computational Molecular Biology, RECOMB 03, Berlin, Germany, 2003.

A. Gambin, R. Otto
Contextual Multiple Sequence Alignment (Context Helps in Aligning Orphan Genes),
Currents in Computational Molecular Biology, RECOMB 03, Berlin, Germany, 2003

B. Wilczyński, A. Szczepek, J. Tiuryn
Selecting optimum oligos for microarray probes in the probabilistic melting model,
in Currents in Computational Molecular Biology - RECOMB 2003, edited by R. Spang, P. Beziat and M. Vingron, April 10-13, 2003, Berlin, Germany.

B. Wilczyński, T.R. Hvidsten, A. Kryshtafovych, L. Stubbs , J. Komorowski and K. Fidelis
Identifying Gene Regulation Mechanisms based on Local Gene Expression Similarities using Rule Based Classifiers,
in Currents in Computational Molecular Biology - RECOMB 2003, edited by R. Spang, P. Beziat and M. Vingron, April 10-13, 2003, Berlin, Germany.

2002

Gambin, A. Tyszkiewicz, J.
Substitution tables for contextual alignment.
Proc. Journees Ouvertes Biologie Informatique Mathematique JOBIM 2002, San Malo, France.
Poster version in Currents in Computational Molecular Biology RECOMB 2002, pp. 61-62.

A. Gambin, J. Tiuryn, J, Tyszkiewicz
Contextual Alignment of Biological Sequences
Currents in Computational Molecular Biology, RECOMB 02,Washington, USA, 2002.