Computational Biology Group at the Faculty of Mathematics,
Informatics and Mechanics, University of Warsaw

Our peer reviewed publications:

2014

  • P. Dittwald, V.T. Nghia, G.A. Harris, R.M. Caprioli, R. Van de Plas, K. Laukens, A. Gambin, D. Valkenborg, 2014,
    Towards automated discrimination of lipids versus peptides from full scan mass spectra, EuPA Open Proteom., 4:87-100.
  • I.M. Campbell, T. Gambin, P. Dittwald, C.R. Beck, A. Shuvarikov, P. Hixson, A. Patel, A. Gambin, C.A. Shaw, J.A. Rosenfeld, P. Stankiewicz, 2014,
    Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination, BMC Biol., 12:74.
  • P. Dittwald, D. Valkenborg, 2014,
    BRAIN 2.0: time and memory complexity improvements in the algorithm for calculating the isotope distribution, J Am Soc Mass Spectrom., 25(4):588-94.
  • A. V. Dharmadhikari, T. Gambin, P. Szafranski, W. Cao, F. J. Probst, W. Jin, P. Fang, K. Gogolewski, A. Gambin, J. K. George-Abraham, S. Golla, F. Boidein, B. Duban-Bedu, B. Delobel, J. Andrieux, K. Becker, E. Holinski-Feder, S. Cheung i P. Stankiewicz, 2014,
    Molecular and clinical analyses of 16q24.1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite, BMC Medical Genetics, 15(1):128.
  • Ryszard Rudnicki, Jerzy Tiuryn, 2014, Size Distribution of gene familes in a genome, Mathematical Models and Methods in Applied Sciences Vol. 24, No. 4, 697–717.
  • Paweł Górecki, Olivier Eulenstein, 2014, DrML: probabilistic modeling of gene duplications, Journal of Computational Biology, 21(1): 89-98.
  • T. Jetka, A. Charzynska, A. Gambin, M.P. Stumpf, M. Komorowski, 2014, StochDecomp--Matlab package for noise decomposition in stochastic biochemical systems, Bioinformatics, 30(1):137-138.
  • Pawel Bednarz, Bartek Wilczynski, 2014, Supervised learning method for predicting chromatin boundary associated insulator elements, Journal of Bioinformatics and Computational Biology 12, no. 06

2013

  • M. Bartnik, B. Nowakowska, K. Derwińska, B. Wiśniowiecka-Kowalnik, M. Kędzior, J. Bernaciak, K. Ziemkiewicz, T. Gambin, M. Sykulski, N. Bezniakow, L. Korniszewski, A. Kutkowska-Kaźmierczak, J. Klapecki, K. Szczałuba, C.A. Shaw, T. Mazurczak, A. Gambin, E. Obersztyn, E. Bocian, P. Stankiewicz, 2013, Application of array comparative genomic hybridization in 256 patients with developmental delay or intellectual disability, Journal of Applied Genetics, 2013 Dec 3. [Epub ahead of print].
  • M. Smyk, P. Szafranski, M. Startek, A. Gambin, P. Stankiewicz, 2013, Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter, Chromosome Research, 21(8):781-8.
  • Michał Startek, Arnoud Le Rouzic, Pierre Capy, Dariusz Grzebelus, Anna Gambin, 2013, Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations, Theoretical Population Biology, 90:145-51.
  • Maciej Sykulski, Tomasz Gambin, Magdalena Bartnik, Katarzyna Derwińska, Barbara Wiśniowiecka-Kowalnik, Paweł Stankiewicz, Anna Gambin, 2013, Multiple samples aCGH analysis for rare CNVs detection, Journal of Clinical Bioinformatics, 3(1):12.
  • Tomasz Gambin, Paweł Stankiewicz, Maciej Sykulski, Anna Gambin, 2013, Functional performance of aCGH design for clinical cytogenetics, Computers in Biology and Medicine, 43(6):775-85.
  • R.A. Harris, C. Shaw, J. Li, S.W. Cheung, C. Coarfa, M. Jeong, M.A. Goodell, L.D. White, A. Patel, S.H. Kang, A.C. Chinault, T. Gambin, A. Gambin, J.R. Lupski, A. Milosavljevic, 2013, Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability, PLoS Genetetics, 9(2):e1003333.
  • B. Wiśniowiecka-Kowalnik, M. Kastory-Bronowska, M. Bartnik, K. Derwińska, W. Dymczak-Domini, D. Szumbarska, E. Ziemka, K. Szczałuba, M. Sykulski, T. Gambin, A. Gambin, C.A. Shaw, T. Mazurczak, E. Obersztyn, E. Bocian, P. Stankiewicz, 2013, Application of custom-designed oligonucleotide array CGH in 145 patients with autistic spectrum disorders, European Journal of Human Genetics, 21(6):620-5.
  • Jun Yang, Abhishek Mitra, Norbert Dojer, Shuhua Fu, Maga Rowicka and Allan R. Brasier, 2013, A probabilistic approach to learn chromatin architecture and accurate inference of the NF-κB/RelA regulatory network using ChIP-Seq, Nucleic Acid Research 41(15): 7240-7259 .
  • Norbert Dojer, Paweł Bednarz, Agnieszka Podsiadło and Bartek Wilczyński, 2013, BNFinder2: Faster Bayesian network learning and Bayesian classification, Bioinformatics 29(16): 2068–2070 .
  • Piotr Jaroszyński and Norbert Dojer, 2013, Efficient and error-tolerant sequencing read mapping, Proceedings of IWBBIO 2013: 353-364 .
  • Michal Modzelewski and Norbert Dojer, 2013, MSARC: Multiple Sequence Alignment by Residue Clustering, Proceedings of WABI 2013: 259-272 , LNBI 8126.
  • Han Hu, Piotr Dittwald, Joseph Zaia, Dirk Valkenborg, 2013, Comment on "Computation of Isotopic Peak Center-Mass Distribution by Fourier Transform", Anal Chem. 85(24):12189-92 .
  • Wen-Chien Chang, Paweł Górecki, Oliver Eulenstein, Exact solutions for species tree inference from discordant gene trees, Journal of Bioinformatics and Computational Biology, 2013, 11(5):1342005 , doi:10.1142/S0219720013420055
  • Anna Gambin, Agata Charzyńska, Aleksandra Ellert-Miklaszewska, Mikołaj Rybiński, 2013, Computational models of JAK1/2-STAT1 signaling, JAKSTAT. 2013 Jul 1;2(3):e24672
  • Mikołaj Rybiński, Zuzanna Szymańska, Sławomir Lasota, Anna Gambin, 2013, Modelling the efficacy of hyperthermia treatment, J R Soc Interface. 2013 Aug 28;10(88):20130527, doi: 10.1098/rsif.2013.0527
  • Janusz Dutkowski, Jerzy Tiuryn, 2013, A Probabilistic Model of Neutral and Selective Dynamics of Protein Network Evolution, Journal of Computational Biology 20 (9):631–642, doi: 10.1089/cmb.2012.0295.
  • Aleksander Jankowski, Ewa Szczurek, Ralf Jauch, Jerzy Tiuryn, Shyam Prabhakar, 2013, Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers, Genome Research, 23 (8): 1307-1318, doi:10.1101/gr.154922.113.
  • Paweł Górecki, Oliver Eulenstein, 2013, Algorithms for Unrooted Gene Trees with Polytomies, ISBRA.
  • Wen-Chieh Chang, Andre Wehe, Paweł Górecki, Oliver Eulenstein, 2013, Exact Solutions for Classical Gene Tree Parsimony Problems, BICoB.
  • Paweł Górecki, Oliver Eulenstein, Jerzy Tiuryn, 2013, Unrooted Tree Reconciliation: A Unified Approach, IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(2), pp.522-536, doi:10.1109/TCBB.2013.22
  • P. Dittwald, T. Gambin, P. Szafranski, J. Li, S. Amato, M.Y. Divon, L.X. Rodríguez Rojas, L.E. Elton, D.A. Scott, C.P. Schaaf, W. Torres-Martinez, A.K. Stevens, J.A. Rosenfeld, S. Agadi, D. Francis, S.H. Kang, A. Breman, S.R. Lalani, C.A. Bacino, W. Bi, A. Milosavljevic, A.L. Beaudet, A. Patel, C.A. Shaw, J.R. Lupski, A. Gambin, S.W. Cheung, P. Stankiewicz, 2013, NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits, Genome Research, 23(9):1395-409. doi: 10.1101/gr.152454.112.
  • Janusz M. Bujnicki, Jerzy Tiuryn, 2013, Bioinformatics and computational biology in Poland, PLoS Comput Biol. 2013 May;9(5):e1003048. doi: 10.1371/journal.pcbi.1003048.
  • Nicola Crosetto, Abhishek Mitra, Maria Joao Silva, Magda Bienko, Norbert Dojer, Qi Wang, Elif Karaca, Roberto Chiarle, Magdalena Skrzypczak, Krzysztof Ginalski, Philippe Pasero, Maga Rowicka, Ivan Dikic, 2013, Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing , Nature Methods 10: 361–365.
  • Piotr Dittwald, Jürgen Claesen, Tomasz Burzykowski, Dirk Valkenborg, Anna Gambin, 2013, BRAIN: A Universal Tool for High-Throughput Calculations of the Isotopic Distribution for Mass Spectrometry , Analytical Chemistry 85(4): 1991-1994.
  • Piotr Dittwald, Tomasz Gambin, Claudia Gonzaga-Jauregui, Claudia M. Carvalho, James R. Lupski, Paweł Stankiewicz, Anna Gambin, 2013, Inverted low-copy repeats and genome instability-a genome-wide analysis, Human Mutation, 34(1):210-20. doi: 10.1002/humu.22217
  • P. Szafranski, A.V. Dharmadhikari, E. Brosens, P. Gurha, K.E. Kolodziejska, O. Zhishuo, P. Dittwald, T. Majewski, K.N. Mohan, B. Chen, R.E. Person, D. Tibboel, A. de Klein, J. Pinner, M. Chopra, G. Malcolm, G. Peters, S. Arbuckle, S.F. 3rd Guiang, V.A. Hustead, J. Jessurun, R. Hirsch, D.P. Witte, I. Maystadt, N. Sebire, R. Fisher, C. Langston, P. Sen, P. Stankiewicz, 2013, Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder, Genome Research, 23(1):23-33. doi: 10.1101/gr.141887.112.

2012

  • M. Bartnik, E. Szczepanik, K. Derwińska, B. Wiśniowiecka-Kowalnik, T. Gambin, M. Sykulski, K. Ziemkiewicz, M. Kędzior, M. Gos, D. Hoffman-Zacharska, T. Mazurczak, A. Jeziorek, D. Antczak-Marach, M. Rudzka-Dybała, H. Mazurkiewicz, A. Goszczańska-Ciuchta, Z. Zalewska-Miszkurka, I. Terczyńska, M. Sobierajewicz, C.A. Shaw, A. Gambin, H. Mierzewska, T. Mazurczak, E. Obersztyn, E. Bocian, P. Stankiewicz, 2012, Application of array comparative genomic hybridization in 102 patients with epilepsy and additional neurodevelopmental disorders, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 159B(7):760-71.
  • K. Derwińska, M. Bartnik, B. Wiśniowiecka-Kowalnik, M. Jagła, A. Rudziński, J.J. Pietrzyk, W. Kawalec, L. Ziółkowska, A. Kutkowska-Kaźmierczak, T. Gambin, M. Sykulski, C.A. Shaw, A. Gambin, T. Mazurczak, E. Obersztyn, E. Bocian, P. Stankiewicz, 2012, Assessment of the role of copy-number variants in 150 patients with congenital heart defects, Medycyna Wieku Rozwojowego, 16(3):175-82..
  • Michal Wozniak, Jerzy Tiuryn, Limsoon Wong, 2012, An approach to identifying drug resistance associated mutations in bacterial strains, BMC Genomics. 13 Suppl 7:S23. doi: 10.1186/1471-2164-13-S7-S23 .
  • B. Wilczynski, YH.Liu, ZX.Yeo, EEM Furlong, Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state PLoS Computational Biology, 2012, featured in Nat. Rev. Genetics
  • Agata Charzyńska, Anna Nałęcz, Mikołaj Rybiński and Anna Gambin, 2012, Sensitivity analysis of mathematical models of signaling pathways, BioTechnologia, 93(3):291-308.
  • Paweł Górecki and Oliver Eulenstein Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms, LNCS, COCOON 2012, Vol. 7434, 531-542
  • Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. Martínez, Robert Otillar, Joseph W. Spatafora, Jagjit S. Yadav, Andrea Aerts, Isabelle Benoit, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Ronald P. de Vries, Patricia Ferreira, Keisha Findley, Brian Foster, Jill Gaskell, Dylan Glotzer, Paweł Górecki, et al. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes, Science, 29 June 2012: Vol. 336 no. 6089 pp. 1715-1719 DOI: 10.1126/science.1221748
  • Paweł Górecki and Oliver Eulenstein, Algorithms: Simultaneous Error-Correction and Rooting for Gene Tree Reconciliation and the Gene Duplication Problem, BMC Bioinformatics 13(Suppl 10):S14, 2012
  • Paweł Górecki, J. Gordon Burleigh and Oliver Eulenstein GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches, (ISBRA 2012), LNCS 7292, 115-126, 2012
  • Paweł Górecki and Oliver Eulenstein, A Robinson-Foulds measure to compare unrooted trees with rooted trees (ISBRA 2012), LNCS 7292, 102-114, 2012
  • Paweł Górecki and Jerzy Tiuryn, Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model, LNCS 7230, 83-105, 2012
  • Mikołaj Rybiński and Anna Gambin, 2012, Model-based selection of the robust JAK-STAT activation mechanism, Journal of Theoretical Biology, 309, pp. 34–46.
  • M. Rybiński, M. Lula, P. Banasik, S. Lasota, A. Gambin, 2012,
    Tav4SB: integrating tools for analysis of kinetic models of biological systems,
    BMC Systems Biology, 6(1), p.25.
  • S. Bonn, RP. Zinzen, C. Girardot, EH. Gustafson, A. Perez-Gonzalez, N. Delhomme, Y. Ghavi-Helm, B. Wilczyński, A. Riddell, EEM. Furlong
    Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
    Nature Genetics, Volume 44, Number 2, pages 148–156, 2012, doi:10.1038/ng.1064
  • Piotr Dittwald, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin,
    Inferring serum proteolytic activity from LC-MS/MS data.
    BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S7.
  • Jürgen Claesen, Piotr Dittwald, Tomasz Burzykowski, Dirk Valkenborg, An efficient method to calculate the aggregated isotopic distribution and exact center-masses. Journal of the American Society for Mass Spectrometry, 2012 Apr;23(4):753-63.

2011

  • Maciej Sykulski, Tomasz Gambin, Magdalena Bartnik, Katarzyna Derwińska, Barbara Wiśniowiecka-Kowalnik, Paweł Stankiewicz, and Anna Gambin,
    Efficient multiple samples aCGH analysis for rare CNVs detection,
    accepted to 2011 IEEE International Conference on Bioinformatics & Biomedicine (BIBM)
  • Michal Wozniak, Limsoon Wong, Jerzy Tiuryn
    CAMBer: an approach to support comparative analysis of multiple bacterial strains,
    2011; 12(Suppl 2):S6, BMC Genomics
  • Piotr Dittwald, Anna Gambin, Jakub Karczmarski and Jerzy Ostrowski
    Inferring serum proteolytic activity from LC-MS/MS data,
    Proc. IEEE 1st International Conference on Computational Advances in Bio and medical Sciences (ICCABS), pp. 81-86, 2011.
  • Anna Gambin, Tomasz Gambin, Paweł Stankiewicz and Maciej Sykulski,
    Robustness of exon CGH array designs,
    Proc. Int Conf. on Bioinformatics Models, Methods and Algorithms Bioinformatics'11., pp. 173-182, 2011.
  • Anna Gambin, Gregory Kucherov, Sławomir Lasota, Laurent Noe, Michał Startek and Maciej Sykulski,
    Subset seed extension to protein BLAST,
    Proc. Int. Conf. on Bioinformatics Models, Methods and Algorithms Bioinformatics'11., pp. 149 - 158, 2011.
  • Michał Kistowski, Anna Gambin,
    Optimization algorithm for de novo analysis of tandem mass spectrometry data,
    accepted to Journal of Biotechnology, Computational Biology and Bionanotechnology
  • Tomasz Gambin, Paweł Stankiewicz, Anna Gambin,
    Stable density approach to probe selection for custom aCGH design, accepted to Journal of Biotechnology,
    Computational Biology and Bionanotechnology
  • Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemysław Biecek, Jerzy Tiuryn and Martin Vingron
    Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data,
    BMC Bioinformatics 2011, 12:249
  • Iwona Gisterek, Ewelina Lata, Agnieszka Halon, Rafal Matkowski, Jolanta Szelachowska, Przemyslaw Biecek, Jan Kornafel
    Prognostic role of c-met expression in breast cancer patients,
    Reports of Practical Oncology & Radiotherapy Volume 16, Issue 5, September-October 2011, Pages 173-177
  • Norbert Dojer, Przemyslaw Biecek and Jerzy Tiuryn
    Bi-Billboard: Symmetrization and Careful Choice of Informant Species Results in Higher Accuracy of Regulatory Element Prediction,
    Journal of Computational Biology. June 2011, 18(6): 809-819. doi:10.1089/cmb.2010.0299.
  • Maciej Jończyk, Alicja Sobkowiak, Paweł Siedlecki, Przemysław Biecek, Joanna Trzcinska-Danielewicz, Jerzy Tiuryn, Jan Fronk, Paweł Sowiński
    Rhythmic Diel Pattern of Gene Expression in Juvenile Maize Leaf,
    2011 PLoS ONE 6(8): e23628. doi: 10.1371/journal.pone.0023628.
  • Wojciech Kustrzycki, Joanna Rymaszewska, Katarzyna Malcher, Joanna Szczepanska-Gieracha, Przemyslaw Biecek
    Risk factors of depressive and anxiety symptoms 8 years after coronary artery bypass grafting,
    2011 European Journal of Cardio-Thoracic Surgery
  • M. Rybiński, M. Lula, S. Lasota, A. Gambin
    Tav4SB: grid environment for analysis of kinetic models of biological systems,
    ISBRA 2011 Short Abstracts, 2011, pp. 92-95.
  • Paweł Górecki and Oliver Eulenstein
    A linear time algorithm for error-corrected reconciliation of unrooted gene trees,
    2011, LNCS 6674 (ISBRA 2011), pg.148-159
  • Paweł Górecki, Gordon J. Burleigh and Oliver Eulenstein
    Maximum likelihood models and algorithms for gene tree evolution with duplications and losses,
    BMC Bioinformatics 2011, 12(Suppl. 1):S15

2010

2009

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
  • Rybinski, M. and Gambin, A.
    Details of the JAK-STAT Signalling Pathway Model
    Acta Biochimica Polonica, Vol. 54, supplement 3, 2007, pp. 63-64.

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.