Publications

Anna Gambin

Number of publications: 129

2024

• Stanisław Giziński, Grzegorz Preibisch, Piotr Kucharski, Michał Tyrolski, Michał Rembalski, Piotr Grzegorczyk, Anna Gambin , Enhancing Antigenic Peptide Discovery: Improved MHC-I Binding Prediction and Methodology, Methods, 2024, p. 1-29. See in PBN
• Dariusz Gołowicz, Krzysztof Kazimierczuk, Anna Gambin , Barbara Domżał, Ewa Klaudia Nawrocka, Michał Aleksander Ciach, Błażej Miasojedow , Magnetstein: An Open-Source Tool for Quantitative NMR Mixture Analysis Robust to Low Resolution, Distorted Lineshapes, and Peak Shifts, Analytical Chemistry, 96 (1) 2024, p. 188-196. See in PBN
• Piotr Prostko , Piotr Radziński , Michał Ciach, Youzhong Liu, Michał Startek , Frederik Lermyte, Thomas De Vijlder, Anna Gambin , Simon Appeltans, Dirk Valkenborg, MIND4OLIGOS: Determining the Monoisotopic Mass of Oligonucleotides Observed in High-Resolution Mass Spectrometry, Analytical Chemistry, 96 (23) 2024, p. 9343-9352. See in PBN

2023

• Grzegorz Skoraczyński, Mateusz Kitlas, Błażej Miasojedow , Anna Gambin , Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning, Journal of Cheminformatics, 15 (1) 2023, p. 1-9. See in PBN
• Nimisha Ghosh, Indrajit Saha, Anna Gambin , Interactome-Based Machine Learning Predicts Potential Therapeutics for COVID-19, ACS Omega, 8 (15) 2023, p. 13840-13854. See in PBN
• Joanna Mańdziuk, Magdalena Okarska-Napierała, Weronika Woźniak, Ada Hryniewicka, Piotr Radziński , Anna Gambin , Edyta Podsiadły, Urszula Demkow, Ernest Kuchar, Monte Carlo Regression for Evaluating Children’s Role in the Pandemic Spread on the Example of Delta COVID-19 Wave, Pediatric Infectious Disease Journal, 42 (12) 2023, p. 1086-1092. See in PBN
• Barbara Poszewiecka, Krzysztof Gogolewski , Justyna A. Karolak, Paweł Stankiewicz, Anna Gambin , PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fusion going from 48 to 46 chromosomes in hominin evolution, GENOME BIOLOGY, 24 (1) 2023. See in PBN
• Stanisław Giziński, Grzegorz Preibisch, Piotr Kucharski, Michał Tyrolski, Michał Rembalski, Piotr Grzegorczyk, Anna Gambin , Towards antigenic peptide discovery with better MHC-I binding prediction and improved benchmark methodology, International Conference on Learning Representations, Kigali, Rwanda, 1 May 2023 - 5 May 2023. See in PBN
• Michał Ciach, Grzegorz Bokota, Aneta Manda-Handzlik, Weronika Kuźmicka, Urszula Demkow, Anna Gambin , Trapalyzer: a computer program for quantitative analyses in fluorescent live-imaging studies of neutrophil extracellular trap formation, Frontiers in Immunology, 14 2023, p. 1-12. See in PBN

2022

• Grzegorz Skoraczyński, Anna Gambin , Błażej Miasojedow , Alignstein: Optimal transport for improved LC-MS retention time alignment, GigaScience, 11 2022. See in PBN
• Krzysztof Gogolewski , Błażej Miasojedow , Małgorzata Sadkowska-Todys, Małgorzata Stępień, Urszula Demkow, Agnieszka Lech, Ewa Szczurek , Daniel Rabczenko, Magdalena Rosińska, Anna Gambin , Data-driven case fatality rate estimation for the primary lineage of SARS-CoV-2 in Poland, Methods, 203 2022, p. 584-593. See in PBN
• Piotr Radziński , Dirk Valkenborg, Michał Startek , Anna Gambin , Envemind: Accurate Monoisotopic Mass Determination Based On Isotopic Envelope, JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 33 (11) 2022, p. 2063-2069. See in PBN
• Kaustav Sengupta , Anna Gambin , Subhadip Basu, Dariusz Plewczyński, MultiNet: A Diffusion-Based Approach to Assign Directionality in Protein Interactions Using a Consensus of Eight Protein Interaction Datasets, International Conference on Frontiers in Computing and Systems, Shillong, India, 29 September 2021 - 1 October 2021. See in PBN
• Johannes Bracher, Daniel Wolffram, Jannik Deuschel, Konstantin Görgen, Jakob L. Ketterer, Alexander Ullrich, Sam Abbott, Maria V. Barbarossa, Dimitris Bertsimas, Sangeeta Bhatia, Marcin Bodych, Nikos I. Bosse, Jan Pablo Burgard, Lauren Castro, Geoffrey Fairchild, Jochen Fiedler, Jan Fuhrmann, Sebastian Funk, Anna Gambin , Krzysztof Gogolewski , Stefan Heyder, Thomas Hotz, Yuri Kheifetz, Holger Kirsten, Tyll Krueger, Ekaterina Krymova, Neele Leithäuser, Michael L. Li, Jan H. Meinke, Błażej Miasojedow , Isaac J. Michaud, Jan Mohring, Pierre Nouvellet, Jedrzej M. Nowosielski, Tomasz Ozanski, Maciej Radwan, Franciszek Rakowski, Markus Scholz, Saksham Soni, Ajitesh Srivastava, Tilmann Gneiting, Melanie Schienle, National and subnational short-term forecasting of COVID-19 in Germany and Poland during early 2021, Communications Medicine, 2 2022, p. 136:1-17. See in PBN
• Barbara Poszewiecka, Krzysztof Gogolewski , Paweł Stankiewicz, Anna Gambin , Revised time estimation of the ancestral human chromosome 2 fusion, BMC Genomics, 23 (S6) 2022, p. 1-15. See in PBN
• Barbara Poszewiecka, Victor Murcia Pienkowski, Karol Nowosad, Jérôme D Robin, Krzysztof Gogolewski , Anna Gambin , TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure, Nucleic Acids Research, 50 (W1) 2022, p. W744-W752. See in PBN

2021

• Johannes Bracher, Daniel Wolffram, Jannik Deuschel, Konstantin Görgen, Jakob Ketterer, Alexander Ullrich, Sam Abbott, Maria Vittoria Barbarossa, Dimitris Bertsimas, Sangeeta Bhatia, MARCIN BODYCH, Nikos I. Bosse, Jan Pablo Burgard, Lauren Castro, Geoffrey Fairchild, Jan Fuhrmann, Sebastian Funk, Krzysztof Gogolewski , Quanquan Gu, Stefan Heyder, Thomas Hotz, Yuri Kheifetz, Holger Kirsten, Ekaterina Krymova, Michael Lingzhi Li, Jan H. Meinke, Isaac J. Michaud, Karol Niedzielewski, Tomasz Ożański, Franciszek Rakowski, Markus Scholz, Saksham Soni, Ajitesh Srivastava, Jakub Zieliński, Difan Zou, Tilmann Gneiting, Melanie Schienle, Hamza Tazi Bouardi, Omar Skali Lami, Łukasz Górski , Magdalena Gruziel-Słomka, Artur Kaczorek, Antoni Moszyński, Jedrzej Nowosielski, Maciej Radwan, Marcin Semeniuk, Rafał Bartczuk, Jan Kisielewski, Przemysław Biecek , VIKTOR BEZBORODOV, Dave A. Osthus, Anna Gambin , Błażej Miasojedow , Ewa Szczurek , Daniel Rabczenko, Magdalena Rosińska, Barbara Pabjan, EWARYST RAFAJŁOWICZ, EWA SKUBALSKA-RAFAJŁOWICZ, WOJCIECH RAFAJŁOWICZ, Agata Migalska, Antoine Flahault, Elisa Manetti, Christine Choirat, Benjamín Béjar Haro, Gavin Lee, Guillaume Obozinski, Tao Sun, Dorina Thanou, Pan Xu, Jinghui Chen, Lingxiao Wang, Weitong Zhang, Viktor K. Prasanna, Frost Tianjian Xu, MAREK BAWIEC, TYLL KRÜGER, A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave, Nature Communications, vol. 12 (art. 5173) 2021, p. 1-16. See in PBN
• Ewa Olchowik-Grabarek, Michał Aleksander Ciach, Krzysztof Gogolewski , Natalia Dobros, Paulina Ciechowicz, Hélène Freichels, Anna Gambin , Katerina Makarova, Katarzyna Zawada, Joanna Sajkowska-Kozielewicz, Harvest time affects antioxidant capacity, total polyphenol and flavonoid content of Polish St John’s wort’s (Hypericum perforatum L.) flowers, Scientific Reports, 11 (1) 2021, p. 1-12. See in PBN

2020

• Victor Murcia Pienkowski, Marzena Kucharczyk, Barbara Poszewiecka, Katarzyna Pachota, Marlena Młynek, Piotr Stawiński, Katarzyna Wojciechowska, Agata Cieślikowska, Dorota Wicher, Agnieszka Stembalska, Anna Gambin , Karolina Matuszewska, Anna Materna-Kiryluk, Krystyna Chrzanowska, Małgorzata Krajewska-Walasek, Rafał Płoski, Monika Lejman, Małgorzata Rydzanicz, Agnieszka Pollak, Joanna Kosińska, Breakpoint Mapping of Symptomatic Balanced Translocations Links the EPHA6, KLF13 and UBR3 Genes to Novel Disease Phenotype, Journal of Clinical Medicine, 9 (5) 2020, p. 1-12. See in PBN
• Marcin Kostecki, Krzysztof Gogolewski , Anna Gambin , Low Entropy Sub-Networks Prevent the Integration of Metabolomic and Transcriptomic Data, Entropy, 22 (11) 2020, p. 1238. See in PBN
• Michał Aleksander Ciach, Grzegorz Skoraczyński, Szymon Majewski, Dirk Valkenborg, Michał Startek , Anna Gambin , Błażej Miasojedow , Masserstein: Linear regression of mass spectra by optimal transport, Rapid Communications in Mass Spectrometry, 2020. See in PBN

2019

• Anna Gambin , Bartosz Grzybowski, Wojciech Jaworski, Michal Kazmierowski, TOMASZ KLUCZNIK, BARBARA MIKULAK-KLUCZNIK, Krzysztof Piecuch, Jan Rydzewski, Sara Szymkuć, Automatic mapping of atoms across both simple and complex chemical reactions, Nature Communications, 10 (1) 2019, p. 1434:1-11. See in PBN
• Grzegorz Dudziuk, Anna Gambin , Mikołaj Jakub Rybiński, Zuzanna Szymańska, Weronika Wronowska, Biologically sound formal model of Hsp70 heat induction, Journal of Theoretical Biology, 478 2019, p. 74-101. See in PBN
• Neo Christopher Chung , Błażej Miasojedow , Michał Startek , Anna Gambin , Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data, BMC Bioinformatics, 20 (S15) 2019, p. 1-11. See in PBN
• Aleksandra I Jarmolinska, Anna Gambin , Joanna Sułkowska, Knot_pull—python package for biopolymer smoothing and knot detection, Bioinformatics, 2019. See in PBN
• Victor Murcia Pieńkowski, Marzena Kucharczyk, Marlena Młynek, Krzysztof Szczałuba, Małgorzata Rydzanicz, Barbara Poszewiecka, Agata Skórka, Maciej Sykulski, ANNA BIERNACKA, Agnieszka Koppolu, Renata Posmyk, Anna Walczak, Joanna Kosińska, Paweł Krajewski, Jennifer Castańeda, Ewa Obersztyn, Elżbieta Jurkiewicz, Robert Śmigiel, Anna Gambin , Krystyna Chrzanowska, Małgorzata Krajewska-Walasek, Rafał Płoski, Mapping of breakpoints in balanced chromosomal translocations by shallow whole-genome sequencing points to EFNA5, BAHD1 and PPP2R5E as novel candidates for genes causing human Mendelian disorders, Journal of Medical Genetics, 56 (2) 2019, p. 104-112. See in PBN
• Mateusz Krzysztof Łącki, Frederik Lermyte, Błażej Miasojedow , Michał Startek , Frank Sobott, Dirk Valkenborg, Anna Gambin , masstodon: A tool for assigning peaks and modeling electron transfer reactions in top-down mass spectrometry, Analytical Chemistry, 91 (3) 2019, p. 1801-1807. See in PBN
• Frederik Lermyte, Piotr Dittwald, Jürgen Claesen, Geert Baggerman, Frank Sobott, Peter B. O’Connor, Kris Laukens, Jef Hooyberghs, Anna Gambin , Dirk Valkenborg, MIND: A Double-Linear Model To Accurately Determine Monoisotopic Precursor Mass in High-Resolution Top-Down Proteomics, Analytical Chemistry, 91 (15) 2019, p. 10310-10319. See in PBN
• Krzysztof Gogolewski , Maciej Sykulski, Anna Gambin , Neo Christopher Chung , Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell RNA Sequencing Data, Journal of Computational Biology, 26 (8) 2019, p. 782-793. See in PBN

2018

• Anna Gambin , Monika Heiner, Advances in Biological processes and Petri nets (BioPPN) Preface, Fundamenta Informaticae, 160 (1-2) 2018, p. v-vii. See in PBN
• M. A. Ciach, Mateusz Łącki, Błażej Miasojedow , F. Lermyte, D. Valkenborg, F. Sobott, Anna Gambin , Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry, Journal of Computational Biology, 25 (3) 2018, p. 282-301. See in PBN
• Justyna Karolak, Anna Gambin , Paweł Stankiewicz, LINE- and Alu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV., Human Mutation, 39 (12) 2018, p. 1916-1925. See in PBN
• Krzysztof Gogolewski , Marcin Kostecki, Anna Gambin , Renal cell carcinoma classification: a case study of pitfalls associated with metabolic landscape analysis, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madryt, Spain, 2 December 2018 - 5 December 2018. See in PBN
• Anna Gambin , Tomasz Gambin, Barbara Poszewiecka, Paweł Stankiewicz, TADeus-a tool for clinical interpretation of structural variants modifying chromatin organization, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madryt, Spain, 2 December 2018 - 5 December 2018. See in PBN
• Anna Gambin , Sławomir Lasota , Michał Lula, Mikołaj Rybiński, Tav4SB: grid environment for analysis of kinetic models of biological systems, 2018. See in PBN
• Michał Aleksander Ciach, Anna Gambin , Szymon Majewski, Błażej Miasojedow , Wanda Niemyska , Michał Startek , The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution, 18th Workshop on Algorithms in Bioinformatics, Helsinki, Finland, 20 August 2018 - 22 August 2018. See in PBN

2017

• Krzysztof Gogolewski , Weronika Wronowska, Agnieszka Lech, Bogdan Lesyng, Anna Gambin , Inferring Molecular Processes Heterogeneity from Transcriptional Data, BioMed Research International, 2017 2017, p. 6961786:1-14. See in PBN
• Michał Startek , Jakub Nogły, Dariusz Grzebelus, Anna Gambin , Agnieszka Gromadka, Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool, BMC Bioinformatics, 18 (suppl. 12) 2017, p. 57-66. See in PBN
• Mateusz K Łącki, Michał Startek , Dirk Valkenborg, Anna Gambin , IsoSpec: Hyperfast Fine Structure Calculator, Analytical Chemistry, 89 (6) 2017, p. 3272–3277. See in PBN
• Ludwik Wiktor Bielczyński, Mateusz Łącki, Iris Hoefnagels, Anna Gambin , Roberta Croce, Leaf and plant age affects photosynthetic performance and photoprotective capacity, Plant Physiology, 175 (4) 2017, p. 1634–1648. See in PBN
• Piotr Dittwald, Błażej Miasojedow , Sara Szymkuć, Ewa Gajewska, Bartosz Grzybowski, Anna Gambin , Grzegorz Skoraczyński, Predicting the outcomes of organic reactions via machine learning: are current descriptors sufficient?, Scientific Reports, 7 (1) 2017, p. 3582:1-3582:9. See in PBN

2016

• Anna Gambin , M. K. ??cki, F. Lermyte, F. Sobott, D. Valkenborg, Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin, JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 1 (28) 2016, p. 69-76. See in PBN
• K. A. Baggerly, J. Bondaruk, W. Choi, B. Czerniak, V. Dadhania, C. Dinney, E. Fuentes-Mattei, Anna Gambin , C. C. Guo, A. M. Kamat, T. Majewski, D. McConkey, A. Siefker-Radtke, M. Sykulski, Y. Wang, J. N. Weinstein, W. Wronowska, L. Zhang, S. Zhang, Gene Expression Profile of the Clinically Aggressive Micropapillary Variant of Bladder Cancer, European Urology, 2016. See in PBN
• Woonyoung Choi, Vipulkumar Dadhania, Colin Dinney, Anna Gambin , Charles Guo, Tadeusz Majewski, David McConkey, Maciej Sykulski, Weronika Wronowska, Miao Zhang, Immunohistochemical Profiles of Molecular Subtypes of Bladder Cancer, 2016. See in PBN
• Anna Gambin , Brandi L. Carofino, Avinash V. Dharmadhikari, Mary E. Dickinson, Krzysztof Gogolewski, Misty Hill, Monica J. Justice, Vladimir V. Kalinichenko, Tadeusz Majewski, Russell S. Ray, Pawel Stankiewicz, Jenny J. Sun, Przemyslaw Szafranski, Vladimir Ustiyan, Lethal lung hypoplasia and vascular defects in mice with conditional Foxf1 overexpression, Biology Open, 11 (5) 2016, p. 1595-1606. See in PBN
• Jolanta Bondaruk, Vipulkumar Dadhania, Colin Dinney, Anna Gambin , Charles C Guo, Ashish Kamat, Tadeusz Majewski, Maciej Sykulski, Weronika Wronowska, Li Zhang, Molecular Characterization of Clinically Aggressive Micropapillary Bladder Cancer, 2016. See in PBN

2015

• Agata Charzynska, Anna Gambin , Karol Nienałtowski, Weronika Wronowska, Computational modeling of sphingolipid metabolism, BMC Systems Biology, 2015. See in PBN
• Ian M. Campbell, Anna Gambin , Tomasz Gambin, Patricia Hixson, Chad A. Shaw, Paweł Stankiewicz, Michał Startek , Przemyslaw Szafranski, Genome-wide analyses of LINE–LINE-mediated nonallelic homologous recombination, Nucleic Acids Research, 2015. See in PBN
• Agata Charzyńska, Anna Gambin , Improvement of the k-nn Entropy Estimator with Applications in Systems Biology, Entropy, 2015. See in PBN
• Anna Gambin , Dariusz Grzebelus, Michał Startek , Krzysztof Stawujak, MuTAnT: a family of Mutator-like transposable elements targeting TA microsatellites in Medicago truncatula, Genetica, 2015. See in PBN
• Anna Gambin , Piotr Dittwald, J. Claesen, A. L. Rockwood, D. Valkenborg, On the Fine Isotopic Distribution and Limits to Resolution in Mass Spectrometry, JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 26 (10) 2015, p. 1732-1745. See in PBN
• Geert Baggerman, Anna Gambin , Frederik Lermyte, Frank Sobott, Dirk Valkenborg, Mateusz Krzysztof Łącki, Understanding reaction pathways in top-down ETD by dissecting isotope distributions: A mammoth task, International Journal of Mass Spectrometry, 2015. See in PBN

2014

• Joanna Bernaciak, Anna Kutkowska-Kaźmierczak, Marta Kędzior, Lech Korniszewski, Magdalena Bartnik-Głaska, Natalia Bezniakow, C. A. Shaw, Katarzyna Derwińska, Maciej Sykulski, Kamila Ziemkiewicz, Beata Nowakowska, Anna Gambin , Ewa Obersztyn, Paweł Stankiewicz, Jakub Klapecki, Tadeusz Mazurczak, Ewa Bocian, Barbara Wiśniowiecka-Kowalnik, Joanna Bernaciak, Marta Kędzior, Krzysztof Szczałuba, Application of array comparative genomic hybridization in 256 patients with developmental delay or intellectual disability, Journal of Applied Genetics, 2014. See in PBN
• J. Belmont, M. Bray, H. M. Brown, A. V. Dharmadhikari, Anna Gambin , M. J. Justice, T. V. Kalin, V. V. Kalinichenko, C. Langston, T. Majewski, M. A. Mohammad, X. Ren, P. Sen, Paweł Stankiewicz, P. Szafranski, S. Thevananther, S. Welty, J. Zabielska, Comparative analyses of lung transcriptomes in patients with alveolar capillary dysplasia with misalignment of pulmonary veins and in foxf1 heterozygous knockout mice, PLoS ONE, 2014. See in PBN
• Anna Gambin , Piotr Dittwald, C. R. Beck, I. M. Campbell, Tomasz Gambin, P. Hixson, A. Patel, J. A. Rosenfeld, C. A. Shaw, A. Shuvarikov, P. Stankiewicz, Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination, BMC BIOLOGY, 12 2014, p. 74. See in PBN
• Anna Gambin , J. Andrieux, K. Becker, F. Boidein, W. Cao, S. Cheung, B. Delobel, A. V. Dharmadhikari, B. Duban-Bedu, P. Fang, Tomasz Gambin, J. K. George-Abraham, Krzysztof Gogolewski , S. Golla, E. Holinski-Feder, W. Jin, F. J. Probst, P. Stankiewicz, P. Szafranski, Molecular and clinical analyses of 16q24.1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite, BMC Medical Genetics, 15 (1) 2014, p. 128. See in PBN
• Anna Gambin , A. Charzyńska, T. Jetka, Michał Komorowski, M. P. Stumpf, StochDecomp--Matlab package for noise decomposition in stochastic biochemical systems, Bioinformatics, 30 (1) 2014, p. 137-138. See in PBN
• Anna Gambin , Piotr Dittwald, R. M. Caprioli, G. A. Harris, K. Laukens, V. T. Nghia, D. Valkenborg, R. Van de Plas, Towards automated discrimination of lipids versus peptides from full scan mass spectra, EuPA Open Proteomics, 4 2014, p. 87-100. See in PBN

2013

• Tomasz Burzykowski, Jurgen Claesen, Piotr Dittwald, Anna Gambin , Dirk Valkenborg, BRAIN: A Universal Tool for High-Throughput Calculations of the Isotopic Distribution for Mass Spectrometry, Analytical Chemistry, 2013. See in PBN
• Anna Gambin , Przemyslaw Szafranski, Paweł Stankiewicz, Michał Startek , Marta Smyk, Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter, Chromosome Research, 2013. See in PBN
• Agata Charzyńska, Aleksandra Ellert-Miklaszewska, Anna Gambin , Mikołaj Rybiński, Computational models of the JAK1/2-STAT1 signaling., 2013. See in PBN
• Anna Gambin , S.W. Cheung, A.C. Chinault, C. Coarfa, Tomasz Gambin, M.A. Goodell, R.A. Harris, M. Jeong, S. H. Kang, J. Li, J.R. Lupski, A. Milosavlevic, A. Patel, C. Shaw, L.D. White, Confounding by Repetitive Elements and CpG Islands Does Not Explain the Association between Hypomethylation and Genomic Instability, PLoS Genetics, 9 (2) 2013, p. 1-3. See in PBN
• Anna Gambin , Tomasz Gambin, Paweł Stankiewicz, Maciej Sykulski, Functional performance of aCGH design for clinical cytogenetics, Computers in Biology and Medicine, 2013. See in PBN
• Pierre Capy, Anna Gambin , Dariusz Grzebelus, Arnaud Le Rouzic, Michał Startek , Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations, Theoretical Population Biology, 90 (Complete) 2013, p. 145-151. See in PBN
• Anna Gambin , Piotr Dittwald, Claudia Carvalho, Tomasz Gambin, Claudia Gonzaga-Jauregui, James Lupski, Paweł Stankiewicz, Inverted Low-Copy Repeats and Genome Instability, Human Mutation, 34 (1) 2013, p. 210-220. See in PBN
• Anna Gambin , Sławomir Lasota , Mikołaj Jakub Rybiński, Zuzanna Szymańska, Modelling the efficacy of hyperthermia treatment, Journal of the Royal Society Interface, 10 (88) 2013, p. 1-10. See in PBN
• Anna Gambin , Piotr Dittwald, S. Agadi, S. Amato, C. A. Bacino, A. L. Beaudet, W. Bi, A. Breman, S. W. Cheung, M. Y. Divon, L. E. Elton, D. Francis, Tomasz Gambin, S. H. Kang, S. R. Lalani, J. Li, J. R. Lupski, A. Milosavljevic, A. Patel, L. X. Rodriguez Rojas, J. A. Rosenfeld, C. P. Schaaf, D. A. Scott, C. A. Shaw, Paweł Stankiewicz, A. K. Stevens, P. Szafranski, W. Torres-Martinez, NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits, Genome Research, 23 (9) 2013, p. 1395-1409. See in PBN
• Anna Gambin , Jarosław Paszek , Michał Startek , Tomasz Gambin, Dariusz Grzebelus, Krzysztof Walczak, TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats, Evolutionary Bioinformatics, 9 2013, p. 17-27. See in PBN

2012

• Anna Gambin , Anna Marciniak-Czochra, Damian Niwiński , Alan Turing and Systems Biology, ERCIM News, 2012. See in PBN
• Magdalena Bartnik-Głaska, Elżbieta Szczepanik, Katarzyna Derwińska, Barbara Wiśniowiecka-Kowalnik, Tomasz Gambin, Maciej Sykulski, Kamila Ziemkiewicz, Marta Kędzior, Monika Gos, Dorota Hoffman-Zacharska, Tomasz Mazurczak, Anetta Jeziorek, Dorota Antczak-Marach, Mariola Rudzka-Dybała, Hanna Mazurkiewicz, Alicja Goszczańska-Ciuchta, Zofia Zalewska-Miszkurka, Iwona Terczyńska, Małgorzata Sobierajewicz, Chad A Shaw, Anna Gambin , Hanna Mierzewska, Tadeusz Mazurczak, Ewa Obersztyn, Ewa Bocian, Paweł Stankiewicz, 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) 2012, p. 760-771. See in PBN
• Tomasz Gambin, Magdalena Bartnik-Głaska, Maciej Sykulski, Katarzyna Derwińska, Chad Shaw, Anna Gambin , Ewa Obersztyn, Monika Kastory-Bronowska, Paweł Stankiewicz, Tadeusz Mazurczak, Ewa Bocian, Dorota Szumbarska, Ewa Ziemka, Wanda Dymczak-Domini, Barbara Wiśniowiecka-Kowalnik, Krzysztof Szczałuba, Application of custom-designed oligonucleotide array CGH in 145 patients with autistic spectrum disorders, European Journal of Human Genetics, 2012. See in PBN
• Anna Gambin , Magdalena Bartnik-Głaska, Ewa Bocian, Katarzyna Derwińska, Anna Kutkowska-Kaźmierczak, Tadeusz Mazurczak, Ewa Obersztyn, Paweł Stankiewicz, Barbara Wiśniowiecka-Kowalnik, Tomasz Gambin, M. Jagła, Wanda Kawalec, Jacek j. Pietrzyk, A. Rudziński, Maciej Sykulski, L. Ziółkowska, Assessment of the role of copy-number variants in 150 patients with congenital heart defects, Medycyna wieku rozwojowego, 16 (3) 2012, p. 175-182. See in PBN
• A. Bułak, Anna Gambin , G. Kucherov, Sławomir Lasota, L. Noé, Michał Startek , Maciej Sykulski, Efficient alternatives to PSI-BLAST, Bulletin of the Polish Academy of Sciences: Technical Sciences, 2012. See in PBN
• S.W. Cheung, A.C. Chinault, C. Coarfa, Anna Gambin , T. Gambin, M.A. Goodell, R.A. Harris, M. Jeong, S. H. Kang, J. Li, R.A. Lupski, A. Milosavljevic, A. Patel, C. Shaw, L. D. White, Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome, PLoS Genetics, 2012. See in PBN
• Piotr Dittwald, Anna Gambin , Jakub Karczmarski, Jerzy Ostrowski, Inferring serum proteolytic activity from LC-MS/MS data, BMC Bioinformatics, 2012. See in PBN
• Anna Gambin , Mikołaj Rybiński, Model-based selection of the robust JAK-STAT activation mechanism, Journal of Theoretical Biology, 2012. See in PBN
• Agata Charzyńska, Anna Gambin , Anna Nałęcz, Mikołaj Jakub Rybiński, Sensitivity analysis of mathematical models of signaling pathways, Biotechnologia, 2012. See in PBN
• A. Charzynska, Anna Gambin , A. Nalecz, M. Rybinski, Sensitivity analysis of mathematical models of signalling pathways, Biotechnologia, 2012. See in PBN
• Paweł Banasik, Anna Gambin , Sławomir Lasota , Michał Lula, Mikołaj Rybiński, Tav4SB: integrating tools for analysis of kinetic models of biological systems, BMC Systems Biology, 6 2012, p. 25:1-11. See in PBN
• Anna Gambin , Anna Marciniak-Czochra, Watching the Daisies Grow: from Biology to Biomathematics and Bioinformatics, 2012. See in PBN

2011

• Anna Gambin , Tomasz Gambin, Paweł Stankiewicz, A stable density approach to probe selection for a custom aCGH design, Biotechnologia, 2011. See in PBN
• Magdalena Bartnik, Katarzyna Derwińska, Anna Gambin , Tomasz Gambin, Maciej Sykulski, Efficient multiple samples aCGH analysis for rare CNVs detection, 2011. See in PBN
• Piotr Dittwald, Anna Gambin , Jakub Karczmarski, Jerzy Ostrowski, Inferring serum proteolytic activity from LC, 2011. See in PBN
• Anna Gambin , Michał Kistowski, Optimization algorithm for de novo analysis of tandem mass spectrometry data, Biotechnologia, 2011. See in PBN
• Anna Gambin , Tomasz Gambin, Paweł Stankiewicz, Maciej Sykulski, Robustness of exon CGH array designs, 2011. See in PBN
• Anna Gambin , Gregory Kucherov, Sławomir Lasota , Laurent Noe, Michał Startek , Maciej Sykulski, Subset seed extension to protein BLAST, Proc. Int. Conf. on Bioinformatics Models, Methods and Algorithms Bioinformatics'11, 2011. See in PBN

2010

• Anna Gambin , Bogusław Kluge, Modeling Proteolysis from Mass Spectrometry Proteomic Data, Fundamenta Informaticae, 2010. See in PBN
• Anna Gambin , Damian Niwiński , Paweł Urzyczyn , Preface, Fundamenta Informaticae, 2010. See in PBN

2009

• Anna Gambin , Janusz Dutkowski, Michał Dadlez, Ewa Szczurek , Magdalena Bakun, Classification of peptide mass fingerprint data by novel no-regret boosting method, Computers in Biology and Medicine, 2009. See in PBN
• Anna Gambin , Bogusław Kluge, Wojciech Niemiro , Modeling Exopeptidase Activity from LC-MS Data, Journal of Computational Biology, 2009. See in PBN
• Eugenia Furletova, Anna Gambin , Gregory Kucherov, Sławomir Lasota , Laurent Noé, Mikhail A. Roytberg, Ewa Szczurek , On Subset Seeds for Protein Alignment, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2009. See in PBN
• Anna Gambin , Barbara Golis, Mirosława Gładysz, Tomasz Gambin, Alicja Macko-Podgórni, Roksana Rakoczy, Dariusz Grzebelus, Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula, Gene, 2009. See in PBN
• Anna Gambin , Jakub Karczmarski, Bogusław Kluge, Jerzy Ostrowski, Marta Łuksza, Two-Stage Model-Based Clustering for Liquid Chromatography Mass Spectrometry Data Analysis, Statistical Applications in Genetics and Molecular Biology, 2009. See in PBN

2008

• Anna Gambin , Piotr Krzyżanowski, Piotr Pokarowski , Aggregation Algorithms for Perturbed Markov Chains with Applications to Networks Modeling, SIAM Journal of Scientific Computing, 2008. See in PBN
• Eugenia Furletova, Anna Gambin , Gregory Kucherov, Sławomir Lasota , Laurent Noé, Mikhail A. Roytberg, Ewa Szczurek , Efficient Seeding Techniques for Protein Similarity Search, 2008. See in PBN

2007

• Bogusław Kluge, Jakub Karczmarski, Jerzy Ostrowski, Krzysztof Kowalczyk, Anna Gambin , Jarosław Poznański, Michał Dadlez, Janusz Dutkowski, Jerzy Tiuryn , Magdalena Bakun, Automated reduction and interpretation of multidimensional mass spectra for analysis of complex peptide mixtures, International Journal of Mass Spectrometry, 2007. See in PBN
• Anna Gambin , P. Wojtalewicz, CTX-BLAST - context sensitive version of protein BLAST, Bioinformatics, 2007. See in PBN
• Anna Gambin , Mikołaj Rybiński, Details of the JAK-STAT Signaling Pathway Model, Acta Biochimica Polonica, 2007. See in PBN
• Anna Gambin , Tomasz Gambin, Dariusz Grzebelus, Gregory Kucherov, Sławomir Lasota , Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula, BMC Genomics, 2007. See in PBN
• Ł. Bolikowski, Anna Gambin , New Metrics for Phylogenies, Fundamenta Informaticae, 2007. See in PBN
• Anna Gambin , Ewa Szczurek , No-regret boosting, Lecture Notes in Computer Science, 2007. See in PBN
• Janusz Dutkowski, Anna Gambin , On consensus biomarker selection, BMC Bioinformatics, 2007. See in PBN

2006

• Anna Gambin , Jerzy Tiuryn , Jerzy Tyszkiewicz , Alignment with context dependent scoring function, Journal of Computational Biology, 2006. See in PBN
• Anna Gambin , Sławomir Lasota , Michal Rutkowski, Analyzing stationary states of gene regulatory network using Petri nets, In Silico Biology, 2006. See in PBN
• Norbert Dojer , Anna Gambin , A. Mizera, Jerzy Tiuryn , Bartosz Wilczyński , Applying Dynamic Bayesian Networks to Perturbed Gene Expression Data, BMC Bioinformatics, 2006. See in PBN
• K. Bożek, Anna Gambin , Jerzy Tiuryn , Bartosz Wilczynski, Automated modeling of genetic control in Arabidopsis thaliana, Journal of Fruit and Ornamental Plant Research, 2006. See in PBN
• Katarzyna Bozek, Anna Gambin , Jerzy Tiuryn , Bartosz Wilczyński , Automated modelling of genetic control in Arabidopsis thaliana, Journal of Fruit and Ornamental Plant Research, 2006. See in PBN
• Janusz Dutkowski, J. Ostrowski, Anna Gambin , M. Dadlez, J. Poznanski, Bogusław Kluge, Jakub Karczmarski, K. Kowalczyk, Jerzy Tiuryn , Magdalena Bakun, Automated reduction and interpretation of multidimensional mass spectra for analysis of complex peptide mixtures, International Journal of Mass Spectrometry, 2006. See in PBN
• Anna Gambin , Jakub Karczmarski, Bogusław Kluge, Jerzy Ostrowski, Marta Łuksza, Efficient Model-Based Clustering for LC-MS Data, Lecture Notes in Computer Science, 2006. See in PBN

2005

• Anna Gambin , Damian Wójtowicz, Almost FPRAS for Lattice Models of Protein Folding (Extended Abstract), Lecture Notes in Computer Science, 2005. See in PBN
• Anna Gambin , Rafał Otto, Contextual multiple sequence alignment, JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY, 2005. See in PBN
• Anna Gambin , Piotr Slonimski, Hierarchical clustering based upon contextual alignment of proteins: a different way to approach phylogeny, Comptes Rendus - Biologies, 2005. See in PBN
• Jerzy Tyszkiewicz , Sławomir Lasota , Jan Van den Bussche, Anna Gambin , Natalia Kwaśnikowska, Jan Hidders, Jacek Sroka , Well Constructed Workflows in Bioinformatics, Workshop on Database Issues in Biological Databases (DBiBD 2005), 2005. See in PBN

2004

• Anna Gambin , Piotr Slonimski, Hierarchical clustering based upon contextual alignment of proteins: a different way to approach phylogeny, 2004. See in PBN
• Anna Gambin , Bronisław Kluge, Statistical Significance of Contextual Alignment, 2004. See in PBN

2003

• Anna Gambin , Damian Wójtowicz, Almost FPRAS for Lattice Models of Protein Folding, 2003. See in PBN
• Anna Gambin , Rafał Otto, Contextual Multiple Sequence Alignment (Context helps in aligning orphan genes, 2003. See in PBN

2002

• Anna Gambin , Sławomir Lasota , Radosław Szklarczyk, Jerzy Tiuryn , Jerzy Tyszkiewicz , Contextual Alignment of Biological Sequences, Bioinformatics, 2002. See in PBN
• Anna Gambin , Jerzy Tyszkiewicz , Substitution tables for contextual alignment, 2002. See in PBN

2001

• Anna Gambin , Piotr Pokarowski , A Combinatorial Aggregation Algorithm for Stationary Distribution of a Large Markov Chain (Extended Abstract), Lecture Notes in Computer Science, Fundamentals of Computation Theory, 2001. See in PBN
• Anna Gambin , Piotr Pokarowski , A new combinatorial algorithm for large Markov chains., 2001. See in PBN

1999

• Anna Gambin , On Approximation of the Number of Bases of Exchange Preserving Matroids, Lecture Notes in Computer Science, Mathematical Foundation in Computer Science, 1999. See in PBN
• Anna Gambin , Adam Malinowski, Randomized Gossiping by Packets in Faulty Networks, Lecture Notes in Computer Science, SOFSEM 1999: Conference on Current Trends in Theory and Practice of Computer Science, 1999. See in PBN

1998

• Anna Gambin , Adam Malinowski, Randomized Meldable Priority Queues, Lecture Notes in Computer Science, SOFSEM '98: Theory and Practice of Informatics, 25th Conference on Current Trends in Theory and Practice of Informatics, 1998. See in PBN

1996

• Anna Gambin , Sławomir Lasota , On the Semantics of Multistage Interconnection Networks, Lecture Notes in Computer Science, SOFSEM '96: Theory and Practice of Informatics, 23rd Seminar on Current Trends in Theory and Practice of Informatics, 1996. See in PBN
• Bogdan Chlebus, Anna Gambin , Piotr Indyk, Shared-Memory Simulation on a FaultyMemory DMM, Lecture Notes in Computer Science, International Colloquium on Automata, Languages and Programming, 1996. See in PBN

1994

• Bogdan Chlebus, Anna Gambin , Piotr Indyk, PRAM Computations Resilient to Memory Faults, Lecture Notes in Computer Science, European Symposium on Algorithms, 1994. See in PBN

Others

• Anna Gambin , Krzysztof Gogolewski , PCA-like Methods for the Integration of Single Cell RNA-seq Data with Metabolic Networks, 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), , p. 1-1. See in PBN
• Neo Christopher Chung, Anna Gambin , Krzysztof Gogolewski , Maciej Sykulski, Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell RNA-seq Data. See in PBN