Our publications:

Peer reviewed (journals and conference proceedings):

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

2005

  • Gambin, A., Otto, R.
    Contextual Multiple Alignment (Context helps in aligning orphan genes),
         J Biomed Biotechnol. 2005; 2005(2): 124-131. pdf
  • 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. pdf
  • 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. pdf
  • Gambin, A., Wojtowicz, D.
    Almost FPRAS for Lattice Models of Protein Folding (Extended Abstract), pdf
    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 pdf
    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, pdf
    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)     pdf

2002

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

Other (reports, posters, etc.):

2007

  • M. Rybinski, A. Gambin
    Details of the JAK-STAT Signalling Pathway Model, Poster at 5th International Conference: Inhibitors of Protein Kinases
    Kinases 2007, Warsaw. Acta Biochimica Polonica Vol. 54, Supplement 3, 2007, pp. 63-64.
  • M. Rybinski, A. Gambin
    Inferring Receptor Activation Mechanism Details in the JAK-STAT Signalling Pathway Model
    Poster at Computational Methods in Systems Biology (CSMB) 2007, Edinburgh.
  • 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

  • Bolikowski, Ł. Gambin, A.
    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     pdf
  • Paweł Górecki and Jerzy Tiuryn,
    Reconciling gene and species evolution in the presence of horizontal gene transfer,
    ECCB 2005, Madrid (poster session)     pdf
  • 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     pdf
  • 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.