Anna Gambin

Anna Gambin

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Anna Gambin

Publications by authors named "Anna Gambin"

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Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data.

BMC Bioinformatics 2019 Dec 24;20(Suppl 15):644. Epub 2019 Dec 24.

Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, Warsaw, 02-097, Poland.

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http://dx.doi.org/10.1186/s12859-019-3118-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6929325PMC
December 2019

Biologically sound formal model of Hsp70 heat induction.

J Theor Biol 2019 Oct 8;478:74-101. Epub 2019 Jun 8.

Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, ul. Banacha 2, Warsaw 02-097, Poland; Department of Biosystems, Science and Engineering, ETH Zurich, Basel, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2019.05.022DOI Listing
October 2019

Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell RNA Sequencing Data.

J Comput Biol 2019 Aug 1;26(8):782-793. Epub 2019 May 1.

1Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland.

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http://dx.doi.org/10.1089/cmb.2018.0255DOI Listing
August 2019

MIND: A Double-Linear Model To Accurately Determine Monoisotopic Precursor Mass in High-Resolution Top-Down Proteomics.

Anal Chem 2019 Aug 23;91(15):10310-10319. Epub 2019 Jul 23.

UA-VITO Center for Proteomics , University of Antwerp , 2000 Antwerp , Belgium.

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http://dx.doi.org/10.1021/acs.analchem.9b02682DOI Listing
August 2019

Knot_pull-python package for biopolymer smoothing and knot detection.

Bioinformatics 2019 Aug 16. Epub 2019 Aug 16.

Centre of New Technologies.

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http://dx.doi.org/10.1093/bioinformatics/btz644DOI Listing
August 2019

Automatic mapping of atoms across both simple and complex chemical reactions.

Nat Commun 2019 03 29;10(1):1434. Epub 2019 Mar 29.

Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, Warsaw, 02-224, Poland.

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http://dx.doi.org/10.1038/s41467-019-09440-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441094PMC
March 2019

masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry.

Anal Chem 2019 Feb 28;91(3):1801-1807. Epub 2019 Jan 28.

Department of Mathematics, Informatics, and Mechanics , University of Warsaw , Warsaw 02-097 , Poland.

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http://pubs.acs.org/doi/10.1021/acs.analchem.8b01479
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http://dx.doi.org/10.1021/acs.analchem.8b01479DOI Listing
February 2019

Inferring Molecular Processes Heterogeneity from Transcriptional Data.

Biomed Res Int 2017 6;2017:6961786. Epub 2017 Dec 6.

Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.

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http://dx.doi.org/10.1155/2017/6961786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736944PMC
August 2018

Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry.

J Comput Biol 2018 03 25;25(3):282-301. Epub 2017 Sep 25.

1 Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw , Warsaw, Poland .

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http://dx.doi.org/10.1089/cmb.2017.0156DOI Listing
March 2018

Leaf and Plant Age Affects Photosynthetic Performance and Photoprotective Capacity.

Plant Physiol 2017 Dec 10;175(4):1634-1648. Epub 2017 Oct 10.

Biophysics of Photosynthesis/Energy, Faculty of Sciences, Department of Physics and Astronomy, VU Amsterdam, 1081 HV Amsterdam, The Netherlands.

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http://www.plantphysiol.org/lookup/doi/10.1104/pp.17.00904
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http://dx.doi.org/10.1104/pp.17.00904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717728PMC
December 2017

Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool.

BMC Bioinformatics 2017 Oct 16;18(Suppl 12):422. Epub 2017 Oct 16.

Institute of Informatics, University of Warsaw, Banacha 2, Warsaw, 02097, Poland.

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http://dx.doi.org/10.1186/s12859-017-1824-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657132PMC
October 2017

IsoSpec: Hyperfast Fine Structure Calculator.

Anal Chem 2017 03 8;89(6):3272-3277. Epub 2017 Mar 8.

Department of Mathematics, Informatics, and Mechanics, University of Warsaw , 02-097 Warsaw, Poland.

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http://dx.doi.org/10.1021/acs.analchem.6b01459DOI Listing
March 2017

Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin.

J Am Soc Mass Spectrom 2017 01 5;28(1):69-76. Epub 2016 Aug 5.

Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium.

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http://dx.doi.org/10.1007/s13361-016-1444-7DOI Listing
January 2017

Analyzing stationary States of gene regulatory network using petri nets.

Stud Health Technol Inform 2011 ;162:143-59

Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warszawa, Poland.

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April 2016

On the Fine Isotopic Distribution and Limits to Resolution in Mass Spectrometry.

J Am Soc Mass Spectrom 2015 Oct 12;26(10):1732-45. Epub 2015 Aug 12.

Institute of Informatics, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1007/s13361-015-1180-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565875PMC
October 2015

MuTAnT: a family of Mutator-like transposable elements targeting TA microsatellites in Medicago truncatula.

Genetica 2015 Aug 17;143(4):433-40. Epub 2015 May 17.

Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425, Kraków, Poland.

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http://link.springer.com/10.1007/s10709-015-9842-5
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http://dx.doi.org/10.1007/s10709-015-9842-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486113PMC
August 2015

Computational modeling of sphingolipid metabolism.

BMC Syst Biol 2015 Aug 15;9:47. Epub 2015 Aug 15.

Institute of Informatics, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1186/s12918-015-0176-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537549PMC
August 2015

Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination.

Nucleic Acids Res 2015 Feb 22;43(4):2188-98. Epub 2015 Jan 22.

Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego street, 02-106 Warsaw, Poland

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http://dx.doi.org/10.1093/nar/gku1394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344489PMC
February 2015

Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination.

BMC Biol 2014 Sep 23;12:74. Epub 2014 Sep 23.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12915-014-0074-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4195946PMC
September 2014

Towards automated discrimination of lipids versus peptides from full scan mass spectra.

EuPA Open Proteom 2014 Sep;4:87-100

Applied Bio & molecular Systems, VITO, Mol, Belgium ; Center for Proteomics, Antwerp, Belgium ; Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.

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http://dx.doi.org/10.1016/j.euprot.2014.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234154PMC
September 2014

StochDecomp--Matlab package for noise decomposition in stochastic biochemical systems.

Bioinformatics 2014 Jan 4;30(1):137-8. Epub 2013 Nov 4.

Institute of Fundamental Technological Research, Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland, Faculty of Mathematics Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland and Division of Molecular Biosciences, Imperial College London, London, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btt631DOI Listing
January 2014

Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations.

Theor Popul Biol 2013 Dec 12;90:145-51. Epub 2013 Aug 12.

College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Poland.

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https://linkinghub.elsevier.com/retrieve/pii/S00405809130006
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http://dx.doi.org/10.1016/j.tpb.2013.07.004DOI Listing
December 2013

Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter.

Chromosome Res 2013 Dec 20;21(8):781-8. Epub 2013 Nov 20.

Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.

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http://dx.doi.org/10.1007/s10577-013-9386-4DOI Listing
December 2013

Modelling the efficacy of hyperthermia treatment.

J R Soc Interface 2013 Nov 28;10(88):20130527. Epub 2013 Aug 28.

Institute of Informatics, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1098/rsif.2013.0527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785818PMC
November 2013

Functional performance of aCGH design for clinical cytogenetics.

Comput Biol Med 2013 Jul 16;43(6):775-85. Epub 2013 Mar 16.

Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.

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http://dx.doi.org/10.1016/j.compbiomed.2013.02.008DOI Listing
July 2013

Computational models of the JAK1/2-STAT1 signaling.

JAKSTAT 2013 Jul 15;2(3):e24672. Epub 2013 Apr 15.

Institute of Informatics; University of Warsaw; Warsaw, Poland ; Mossakowski Medical Research Centre; Polish Academy of Sciences; Warsaw, Poland.

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http://dx.doi.org/10.4161/jkst.24672DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772111PMC
July 2013

Multiple samples aCGH analysis for rare CNVs detection.

J Clin Bioinforma 2013 Jun 11;3(1):12. Epub 2013 Jun 11.

Institute of Informatics, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1186/2043-9113-3-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691624PMC
June 2013

Inverted low-copy repeats and genome instability--a genome-wide analysis.

Hum Mutat 2013 Jan 11;34(1):210-20. Epub 2012 Oct 11.

Institute of Informatics, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1002/humu.22217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738003PMC
January 2013

Model-based selection of the robust JAK-STAT activation mechanism.

J Theor Biol 2012 Sep 5;309:34-46. Epub 2012 Jun 5.

Institute of Informatics, University of Warsaw, ul. Banacha 2, Warsaw, Poland.

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http://dx.doi.org/10.1016/j.jtbi.2012.04.031DOI Listing
September 2012

Tav4SB: integrating tools for analysis of kinetic models of biological systems.

BMC Syst Biol 2012 Apr 5;6:25. Epub 2012 Apr 5.

Institute of Informatics, University of Warsaw, ul, Banacha 2, 02-097, Warsaw, Poland.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-6-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495710PMC
April 2012

Inferring serum proteolytic activity from LC-MS/MS data.

BMC Bioinformatics 2012 Apr 12;13 Suppl 5:S7. Epub 2012 Apr 12.

Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.

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http://dx.doi.org/10.1186/1471-2105-13-S5-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358667PMC
April 2012

Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula.

Gene 2009 Dec 17;448(2):214-20. Epub 2009 Jun 17.

Department of Genetics, Plant Breeding and Seed Science, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland.

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http://dx.doi.org/10.1016/j.gene.2009.06.004DOI Listing
December 2009

On subset seeds for protein alignment.

IEEE/ACM Trans Comput Biol Bioinform 2009 Jul-Sep;6(3):483-94

Institute of Mathematical Problems in Biology, Pushchino, Moscow Region 142290, Russia.

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http://dx.doi.org/10.1109/TCBB.2009.4DOI Listing
November 2009

Classification of peptide mass fingerprint data by novel no-regret boosting method.

Comput Biol Med 2009 May 21;39(5):460-73. Epub 2009 Apr 21.

Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland.

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http://dx.doi.org/10.1016/j.compbiomed.2009.03.006DOI Listing
May 2009

Alignment with context dependent scoring function.

J Comput Biol 2006 Jan-Feb;13(1):81-101

Institute of Informatics, Warsaw University, 02-097 Warszawa, Poland.

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http://dx.doi.org/10.1089/cmb.2006.13.81DOI Listing
February 2009

Modeling exopeptidase activity from LC-MS data.

J Comput Biol 2009 Feb;16(2):395-406

Institute of Informatics, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1089/cmb.2008.22TTDOI Listing
February 2009

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula.

BMC Genomics 2007 Nov 9;8:409. Epub 2007 Nov 9.

Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, Al, 29 Listopada 54, 31-425 Krakow, Poland.

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http://dx.doi.org/10.1186/1471-2164-8-409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2213677PMC
November 2007

CTX-BLAST: context sensitive version of protein BLAST.

Bioinformatics 2007 Jul 25;23(13):1686-8. Epub 2007 Apr 25.

Institute of Informatics, Warsaw University, Banacha 2, 02-097, Warsaw, Poland.

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https://academic.oup.com/bioinformatics/article/23/13/1686/2
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http://dx.doi.org/10.1093/bioinformatics/btm136DOI Listing
July 2007

On consensus biomarker selection.

BMC Bioinformatics 2007 May 24;8 Suppl 5:S5. Epub 2007 May 24.

Institute of Informatics, Warsaw University, Banacha 2 02-097 Warsaw, Poland.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1471-2105-8-S5-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892093PMC
May 2007

Analyzing stationary states of gene regulatory network using petri nets.

In Silico Biol 2006 ;6(1-2):93-109

Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warszawa, Poland.

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November 2006

Applying dynamic Bayesian networks to perturbed gene expression data.

BMC Bioinformatics 2006 May 8;7:249. Epub 2006 May 8.

Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warszawa, Poland.

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http://dx.doi.org/10.1186/1471-2105-7-249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513402PMC
May 2006

Contextual alignment of biological sequences (Extended abstract).

Bioinformatics 2002 ;18 Suppl 2:S116-27

Institute of Informatics, Warsaw University, Poland.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_2.s116DOI Listing
September 2005

Contextual multiple sequence alignment.

J Biomed Biotechnol 2005 Jun;2005(2):124-31

Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland.

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http://www.hindawi.com/journals/bmri/2005/945084/abs/
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http://dx.doi.org/10.1155/JBB.2005.124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1184041PMC
June 2005

Hierarchical clustering based upon contextual alignment of proteins: a different way to approach phylogeny.

C R Biol 2005 Jan;328(1):11-22

Institute of Informatics, Warsaw University, Warsaw, Poland.

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http://dx.doi.org/10.1016/j.crvi.2004.11.001DOI Listing
January 2005