Affiliation

My papers:

Journals

  • Dittwald, P., Claesen, J., Burzykowski, T., Valkenborg, D., Gambin A. BRAIN: A Universal Tool for High-Throughput Calculations of the Isotopic Distribution for Mass Spectrometry. Analytical Chemistry 85(4): 1991-1994, 2013.

  • C. Carvalho, P. Dittwald, T. Gambin, C. Gonzaga-Jauregui, J. Lupski, P. Stankiewicz, Gambin, A. Inverted Low-Copy Repeats and Genome Instability. Human Mutation 34(1): 210-220, 2013.

  • Startek, M., Paszek, J., Gambin, T., Walczak, K., Grzebelus, D., Gambin, A. TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats, Evolutionary Bioinformatics vol. 9:17-27, 2013.

  • Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin, A., Lupski JR, Milosavljevic A. Confounding by Repetitive Elements and CpG Islands Does Not Explain the Association between Hypomethylation and Genomic Instability, PLoS Genetics 9(2), 2013.

  • Rybinski, M., Lasota, S., Lula, M., Banasik, P., Gambin, A. Tav4SB: integrating tools for analysis of kinetic models of biological systems. BMC Systems Biology 6(1), s. 25, 2012.

  • Rybinski, M., Gambin, A. Model-based selection of the robust JAK-STAT activation mechanism. Journal of Theoretical Biology 309:. 34-46, 2012.

  • Anna Gambin, Anna Marciniak-Czochra, Damian Niwinżski, Alan Turing and Systems Biology. ERCIM News 2012(91), 2012.

  • Anna Gambin, Anna Marciniak-Czochra, (red.), Special Alan Turing Issue: Watching the Daisies Grow: from Biology to Biomathematics and Bioinformatics., Preface. Fundamenta Informaticae 118(4), 2012.

  • Charzynska, A., Nalecz, A., Rybinski, M., Gambin, A. Sensitivity analysis of mathematical models of signaling pathways, Journal of Biotechnology, Computational Biology and Bionanotechnology, 93(3):291-308, 2012.

  • Dittwald, P., Karczmarski, J., Ostrowski, J., Gambin, A. Inferring serum pro- teolytic activity from LC-MS/MS data. BMC Bioinformatics 13(5), s. S7, 2012.

  • Startek, M., Lasota, S., Sykulski, M., Bulak, A., Noe,L., Kucherov, G., Gambin, A. Efficient alternatives to PSI-BLAST. Bulletin of the Polish Academy of Sciences: Technical Sciences, 60(3):495-505, 2012.

  • Li, J. et. al. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genetics 8(5), 2012.

  • Derwinska, K, et al. Assessment of the role of copy-number variants in 150 patients with congenital heart defects. Developmental Period Medicine 16(3):175-82, 2012.

  • Bartnik M, et. al Application of array comparative genomic hybridization in 102 patients with epilepsy and additional neurodevelopmental disorders. Americal Journal on Medical Genetics B Neuropsychiatric Genetics 159B(6), 2012.

  • Wisniowiecka-Kowalnik, B., et al. Application of custom-designed oligonucleotide array CGH in 145 patients with autistic spectrum disorders. European Journal of Human Genetics 1, 2012.

  • Anna Gambin, Michał Kistowski Optimization algorithm for de novo analysis of tandem mass spectrometry data. Journal of Biotechnology, Computational Biology and Bionanotechnology, vol. 92(3), pp. 296-300, 2011

  • Tomasz Gambin, Paweł Stankiewicz, Anna Gambin, A stable density approach to probe selection for a custom aCGH design, Journal of Biotechnology, Computational Biology and Bionanotechnology, vol. 92(3), pp. 283-295 , 2011

  • Anna Gambin, Boguslaw Kluge Modeling Proteolysis from Mass Spectrometry Proteomic Data. Fundam. Inform. 103(1-4): 89-104, 2010.

  • Anna Gambin, Damian Niwinski, Pawel Urzyczyn (Editors) From mathematical beauty to the truth of nature. Fundam. Inform. 103(1-4): 89-104, 2010.

  • Grzebelus, D., Gładysz, M., Macko-Podgórni, A., Gambin, T., Golis, B., Rakoczy, R., Gambin, A. Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula. Gene. 2009 Dec 15;448(2):214-20.

  • 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. 39(5):460-73, 2009.

  • Kluge, B., Niemiro, W., Gambin, A. Modeling exopeptidase activity from LC-MS data, Journal of Computational Biology, 16(2): 395-406, 2009.

  • Furletova, E., Gambin, A., Kucherov, G.,. Lasota, S., Noe, L., Roytberg, M., Szczurek, E. On subset seeds for protein alignment. IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):483-94.

  • Łuksza, M., Kluge, B., Ostrowski, J., Karczmarski, J., Gambin, A. Two-stage Model-Based Clustering for Liquid Chromatography Mass Spectrometry Data Analysis, Statistical Applications in Genetics and Molecular Biology, Berkeley Press, 8(1):Article 15, 2009.

  • Gambin, A., Krzyżanowski, P. and Pokarowski, P. Aggregation Algorithms for Perturbed Markov Chains with Applications to Networks Modeling, SIAM Journal on Scientific Computing, vol. 31 (1):45-73, 2008.

  • Grzebelus, D., Lasota, S., Gambin, T., Kucherov, G., Gambin, A. Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula, BMC Genomics 2007, 8:409.

  • Gambin, A., Wojtalewicz, P. CTX-BLAST - context sensitive version of protein BLAST, Bioinformatics. 2007; 23(13):1686-8.

  • Dutkowski, J., Gambin, A. On Consensus Biomarker Selection, BMC Bioinformatics. 2007 May 24;8 Suppl 5:S5.

  • Bolikowski, Ł., Anna Gambin, A 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, 2007, 260:20-30.

  • Dojer, N., Gambin, A., Mizera, A., Wilczyński, B., Tiuryn, J. Applying Dynamic Bayesian Networks to Perturbed Gene Expression Data, BMC Bioinformatics, 2006, 7:249

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

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

  • 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.

  • Gambin, A., Otto, R. Contextual Multiple Alignment (Context helps in aligning orphan genes), Journal of Biomedicine and Biotechnology, 2005(2):124-31.

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

  • Dietzfelbinger, M., Gambin, A., Lasota, S. On Different Models for Packet Flow in Multistage Interconnection Networks, Fundamenta Informaticae 46(4):287-314, 2001.

Reviewed conference proceedings

  • Piotr Dittwald, Anna Gambin, Jakub Karczmarski i Jerzy Ostrowski, Inferring serum proteolytic activity from LC-MS data. Proc. IEEE 1st International Conference on Computational Advances in Bio and medical Sciences (ICCABS), s. 81-86, 2011.

  • Anna Gambin, Tomasz Gambin, Paweł Stankiewicz i Maciej Sykulski, Robustness of exon CGH array designs. Proc. Int Conf. on Bioinformatics Models, Methods and Algorithms Bioinformatics'11., s. 173-182, 2011.

  • Anna Gambin, Gregory Kucherov, Sławomir Lasota, Laurent Noe, Michał Startek i Maciej Sykulski, Subset seed extension to protein BLAST. Proc. Int. Conf. on Bioinformatics Models, Methods and Algorithms Bioinformatics'11., s. 149 - 158, 2011.

  • Maciej Sykulski, Tomasz Gambin, Magdalena Bartnik, Katarzyna Derwińska, Barbara Wi¶niowiecka-Kowalnik, Paweł Stankiewicz, and Anna Gambin, Efficient multiple samples aCGH analysis for rare CNVs detection IEEE International Conference Bioinformatics and Biomedicine, s. 406-409, 2011.

  • Anna Gambin, Sławomir Lasota, Michał Lula i Mikołaj Rybiński, Tav4SB: grid environment for analysis of kinetic models of biological systems. International Symposium on Bioinformatics Research and Applications (ISBRA), s. 92-95, 2011.

  • 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.

  • Gambin, A., Szczurek, E. No-regret boosting International Conference on Adaptive and Natural Computing Algorithms (ICANNGA 2007),  LNCS 4431:422-431.

  • Gambin, A., Łuksza, M., Kluge, B., Ostrowski, J., Karczmarski, J. Efficient Model-Based Clustering for LC-MS Data Proc. WABI 2006 Workshop on Algorithms in Bioinformatics, LNBI 4175:32-44.

  • Gambin, A., Wojtowicz, D. Almost FPRAS for Lattice Models of Protein Folding (Extended Abstract), WEA 2005: 4th International Workshop on Efficient and Experimental Algorithms, LNCS Springer-Verlag, pp. 34-44.

  • 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)

  • 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.

  • Gambin, A., Pokarowski, P. A combinatorial aggregation algorithm for stationary distribution of a large Markov chain. R. Freivalds (Ed.): Fundamentals of Computation Theory 13th International Symposium, FCT 2001, Riga, Latvia, Springer LNCS 2138, p. 384-388.

  • Gambin, A., Pokarowski, P. A new combinatorial algorithm for large Markov chains. Proc. Computer Algebra in Scientific Computing, CASC'01, V.G. Ghanza, E.W. Mayr, E.V. Vorozthsov (eds.), Springer, Berlin 2001, pp. 195-212.

  • Gambin, A. On Approximation of the Number of Bases of Exchange Preserving Matroids. Proc. Mathematical Foundations of Computer Science MFCS'99, Springer LNCS 1672, pp 332-342.

  • Gambin, A., Malinowski, A. Randomized Gossiping by Packets in Faulty Networks. Proc. 26th Seminar on Current Trends in Theory and Practice of Informatics SOFSEM '99, Springer LNCS 1725, pp 387-394.

  • Gambin, A., Malinowski, A. Randomized Meldable Priority Queues. Proc. 25th Seminar on Current Trends in Theory and Practice of Informatics SOFSEM '98, Springer LNCS 1521, pp. 344-350, 1998.

  • Chlebus, B.S, Gambin, A., Indyk, P. Shared-Memory Simulation on a Faulty-Memory DMM. Proc. 23-rd ICALP, Paderborn, Germany 1996, Springer LNCS 1099, pp. 586-697.

  • Gambin, A., Lasota, S. On the Semantics of Multistage Interconnnection Networks. Proc. 23rd Seminar on Current Trends in Theory and Practice of Informatics SOFSEM '96, LNCS 1175, pp. 359-368, 1996.

  • Chlebus, B.S, Gambin, A., Indyk, P. PRAM Computations Resilient to Memory Faults. Proc. 2nd ESA, Utrecht, The Netherlands, 1994, Springer LNCS 855, pp. 401-412.

  • Gambin, A., Indyk, P. Finding Minimum DNF Formula on the Boltzmann Machine Proc. 21st Seminar on Current Trends in Theory and Practice of Informatics SOFSEM '94

Conference posters

  • Piotr Dittwald, Dirk Valkenborg, Raf Van de Plas, Anna Gambin Discriminant analysis of lipids versus peptides towards automated mass spectral peak annotation 60th ASMS Conference on Mass Spectrometry and Allied Topics Vancouver, BC, Canada.

  • P. Dittwald, T. Gambin, P. Szafranski, J. Li, R.S. Amato, M. Divon, K. Maliszewski, E.E. Dolgado Bohorquez, L. Elton, D. Scott, S.-H.L. Kang, A.M. Breman, S.R. Lalani, C. Bacino, W. Bi, A. Milosavljevic, J.R. Lupski, A.L. Beaudet, C.A. Shaw, A. Patel, A. Gambin, S.W. Cheung, P. Stankiewicz Genome-wide analyses of recurrent genomic rearrangements - identification of three novel genomic disorders. 62nd American Society of Human Genetics Annual Meeting in San Francisco, California,

  • M. Rybiński, S. Lasota, Z. Szymanska A. Gambin, Modelling the efficacy of hiperthermia treatment, International Conference on Systems Biology (ICSB) 2012, Toronto.

  • SYKULSKI MACIEJ, MATTHEW HURLES, GAMBIN ANNA, LUPSKI JAMES R, STANKIEWICZ PAWEL, GAMBIN TOMASZ GENOME-WIDE IDENTIFICATION OF GENE REGULATORY ELEMENTS FOR THE DESIGN OF CLINICAL CHROMOSOMAL MICROARRAY Genomic Disorders, 2012, The Genomics of Rare Diseases, Wellcome Trust Conference Centre, Hinxton.

  • P. Banasik, A. Gambin, M. Rybiński, A. Gambin, Taverna services for sysstems biology, Computational Methods in Systems Biology (CMSB) 2008, Edinburgh.

  • J. Li, P. Stankiewicz, S. Wai Cheung, A. Patel, S-H. Kang, C. Shaw, A. C. Chinault, L. White, T. Gambin, A. Gambin, J. R. Lupski, A. Milosavljevic, Array CGH design based on a novel genome-wide analysis of LCRs yield insights into genomic disease, population genetics, and human genome evolution. Genomic Disorders, 2008, Studying the Genome to Understand Human Development and Disease, Wellcome Trust Conference Centre, Hinxton.

  • M. Rybiński, A. Gambin, Details of the JAK-STAT Signalling Pathway Model, Poster at 5th International Conference: Inhibitors of Protein Kinases 2007, Warsaw. Acta Biochimica Polonica Vol. 54, Supplement 3, 2007, pp. 63-64.

  • M. Rybiński, A. Gambin, Inferring Receptor Activation Mechanism Details in the JAK-STAT Signalling Pathway Model, Poster at Computational Methods in Systems Biology (CSMB) 2007, Edinburgh.

  • Całkiewicz J., Gambin A., Wróbel B. Ewolucja elementów transpozonowych, szczególnie z rodziny Tc1/mariner, w całkowicie zsekwencjonowanych genomach ryb. II Polski Kongres Genetyki, Warszawa 2007.

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

  • J. Dutkowski and A. Gambin Biomarker selection method based on rank aggregation, Currents in Computational Molecular Biology, RECOMB 2006, Venice

  • 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.

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

  • A. Gambin, D. Wojtowicz 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.

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

  • A. Gambin, J. Tyszkiewicz Substitution matrices for contextual alignment, JOBIM Journees Ouvertes Biologie Informatique Mathematique, St Malo, France, June 2002.

Technical reports

  • Bolikowski,Ł, Gambin, A. New metrics for phylogenies Technical report 282, Institute of Informatics, Warsaw University, 2006. [ gzipped postscript ]

  • Dojer, N., Gambin, A., Mizera, A., Wilczyński, B., Tiuryn, J. Applying Dynamic Bayesian Networks to Perturbed Gene Expression Data Technical report 279, Institute of Informatics, Warsaw University, 2004. [ gzipped postscript ]

  • Dietzfelbinger, M., Gambin, A., Lasota, S. On Different Models for Packet Flow in Multistage Interconnection Networks. Technical report 97-11(248), Institute of Informatics, Warsaw University, 1997. [ gzipped postscript ]

  • Gambin, A. Combinatorial Methods in Approximation Algorithms for Markov Chains with Large State Space (PhD thesis). Technical report 99-05(260), Institute of Informatics, Warsaw University, 1999. [ gzipped postscript ]