Publications by authors named "Valentina Boeva"

37Publications

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution.

Cell Rep 2020 02;30(6):1767-1779.e6

INSERM U900, 75005 Paris, France; Mines ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France; Institut Curie, PSL Research University, 75005 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.01.049DOI Listing
February 2020

CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells.

Genome Biol 2020 01 16;21(1):13. Epub 2020 Jan 16.

Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1186/s13059-019-1904-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966897PMC
January 2020

Meta-mining of copy number profiles of high-risk neuroblastoma tumors.

Sci Data 2018 10 30;5:180240. Epub 2018 Oct 30.

Center for Medical Genetics, Ghent University, Ghent, Belgium.

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http://dx.doi.org/10.1038/sdata.2018.240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207068PMC
October 2018

Calling Chromosome Alterations, DNA Methylation Statuses, and Mutations in Tumors by Simple Targeted Next-Generation Sequencing: A Solution for Transferring Integrated Pangenomic Studies into Routine Practice?

J Mol Diagn 2017 09;19(5):776-787

Institut Cochin, INSERMU1016, Centre National de la Recherche Scientifique UMR_8104, Paris, France; Department of Endocrinology, Reference Center for Rare Adrenal Diseases, Reference Center for Rare Adrenal Cancer Network COMETE, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15251578173026
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http://dx.doi.org/10.1016/j.jmoldx.2017.06.005DOI Listing
September 2017

Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes.

Genome Res 2017 02 13;27(2):259-268. Epub 2016 Dec 13.

Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France.

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http://dx.doi.org/10.1101/gr.203679.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5287231PMC
February 2017

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 10 10;7:13205. Epub 2016 Oct 10.

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http://dx.doi.org/10.1038/ncomms13205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062501PMC
October 2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 08 23;7:12460. Epub 2016 Aug 23.

Sage Bionetworks, Seattle, Washington 98115, USA.

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http://dx.doi.org/10.1038/ncomms12460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996969PMC
August 2016

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells.

Authors:
Valentina Boeva

Front Genet 2016 23;7:24. Epub 2016 Feb 23.

Centre de Recherche, Institut CurieParis, France; INSERM, U900Paris, France; Mines ParisTechFontainebleau, France; PSL Research UniversityParis, France; Department of Development, Reproduction and Cancer, Institut CochinParis, France; INSERM, U1016Paris, France; Centre National de la Recherche Scientifique UMR 8104Paris, France; Université Paris Descartes UMR-S1016Paris, France.

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http://dx.doi.org/10.3389/fgene.2016.00024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763482PMC
March 2016

SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability.

Bioinformatics 2016 04 6;32(7):984-92. Epub 2016 Jan 6.

Institut Curie, Centre De Recherche, Paris Inserm, Department of Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, U900, Paris, France Mines ParisTech, Centre for Computational Biology, Fontainebleau, France PSL Research University, Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btv751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896370PMC
April 2016

Changes in correlation between promoter methylation and gene expression in cancer.

BMC Genomics 2015 Oct 28;16:873. Epub 2015 Oct 28.

UMR932, Immunity and Cancer Team, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France.

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http://dx.doi.org/10.1186/s12864-015-1994-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4625954PMC
October 2015

RNF: a general framework to evaluate NGS read mappers.

Bioinformatics 2016 Jan 9;32(1):136-9. Epub 2015 Sep 9.

LIGM/CNRS, Université Paris-Est, 77454 Marne-la-Vallée, France.

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http://dx.doi.org/10.1093/bioinformatics/btv524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681991PMC
January 2016

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.

Bioinformatics 2014 Dec 12;30(24):3443-50. Epub 2014 Jul 12.

Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/btu436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253825PMC
December 2014

SegAnnDB: interactive Web-based genomic segmentation.

Bioinformatics 2014 Jun 3;30(11):1539-46. Epub 2014 Feb 3.

Department of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, FranceDepartment of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, FranceDepartment of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, France.

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http://dx.doi.org/10.1093/bioinformatics/btu072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029035PMC
June 2014

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.

Bioinformatics 2013 Dec 9;29(23):2979-86. Epub 2013 Sep 9.

Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia, Institut Curie, 75248 Paris Cedex 05, France, INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Mines ParisTech, Fontainebleau 77300, France and UMR 144 CNRS, Subcellular Structure and Cellular Dynamics.

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http://dx.doi.org/10.1093/bioinformatics/btt524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834794PMC
December 2013

Nebula--a web-server for advanced ChIP-seq data analysis.

Bioinformatics 2012 Oct 24;28(19):2517-9. Epub 2012 Jul 24.

Institut Curie, Paris 75248, France.

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http://dx.doi.org/10.1093/bioinformatics/bts463DOI Listing
October 2012

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.

Algorithms Mol Biol 2007 Oct 10;2:13. Epub 2007 Oct 10.

Institute of Genetics and Selection of Industrial Microorganisms, GosNIIGenetika, 117545 Moscow, Russia.

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http://dx.doi.org/10.1186/1748-7188-2-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174486PMC
October 2007

Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.

Bioinformatics 2006 Mar 10;22(6):676-84. Epub 2006 Jan 10.

Department of Bioengineering and Bioinformatics, Moscow State University Moscow, Russia.

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http://dx.doi.org/10.1093/bioinformatics/btk032DOI Listing
March 2006