المؤلفون: Abdennur, Nezar, Fudenberg, Geoffrey, Flyamer, Ilya, Galitsyna, Aleksandra, Goloborodko, Anton, Imakaev, Maxim, Venev, Sergey

مصطلحات موضوعية: bioinformatics, genomics, ranges, intervals, dataframes, pandas, numpy, Python

العلاقة: https://github.com/open2c/bioframe/tree/v0.7.2Test; https://dx.doi.org/10.5281/zenodo.3897573Test

الإتاحة: https://doi.org/10.5281/zenodo.1217390410.5281/zenodo.3897573Test

المؤلفون: Abdennur, Nezar, Goloborodko, Anton, Imakaev, Maxim, Kerpedjiev, Peter, Fudenberg, Geoffrey, Oullette, Scott, Lee, Soohyun, Strobelt, Hendrik, Gehlenborg, Nils, Mirny, Leonid A.

مصطلحات موضوعية: bioinformatics, genomics, Hi-C, sparse, matrix, format, Python, out-of-core

العلاقة: https://github.com/open2c/cooler/tree/v0.10.1Test; https://dx.doi.org/10.5281/zenodo.597976Test

الإتاحة: https://doi.org/10.5281/zenodo.1200145110.5281/zenodo.597976Test

المؤلفون: Abdennur, Nezar, Abraham, Sameer, Fudenberg, Geoffrey, Flyamer, Ilya M, Galitsyna, Aleksandra A, Goloborodko, Anton, Imakaev, Maxim, Oksuz, Betul A, Venev, Sergey V, Xiao, Yao

المساهمون: Genomics and Computational Biology, Systems Biology

المصدر: PLoS computational biology ; 20 ; 5 ; e1012067 ; United States

مصطلحات موضوعية: Genomics, Invertebrate genomics, Eigenvectors, Genome analysis, Chromosome mapping, Chromosome pairs, Meiosis, Yeast

العلاقة: PLoS Computational Biology; https://doi.org/10.1371/journal.pcbi.1012067Test; Open2C; Abdennur N, Abraham S, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Oksuz BA, Venev SV, Xiao Y. Cooltools: Enabling high-resolution Hi-C analysis in Python. PLoS Comput Biol. 2024 May 6;20(5):e1012067. doi:10.1371/journal.pcbi.1012067. PMID: 38709825; PMCID: PMC11098495.; http://hdl.handle.net/20.500.14038/53545Test

الإتاحة: https://doi.org/10.1371/journal.pcbi.101206720.500.14038/53545Test
https://hdl.handle.net/20.500.14038/53545Test

المؤلفون: Abdennur, Nezar, Fudenberg, Geoffrey, Flyamer, Ilya M, Galitsyna, Aleksandra A, Goloborodko, Anton, Imakaev, Maxim, Venev, Sergey V

المساهمون: Genomics and Computational Biology, Program in Bioinformatics and Integrative Biology, Systems Biology

المصدر: PLoS computational biology ; 20 ; 5 ; e1012164 ; United States

مصطلحات موضوعية: Genomics, Sequence alignment, Data processing, DNA libraries, DNA fragment ligation, Quality control, Chromosome pairs, Computer software

العلاقة: This article is based on a previously available preprint in bioRxiv, https://doi.org/10.1101/2023.02.13.528389Test.; PLoS Computational Biology; https://doi.org/10.1371/journal.pcbi.1012164Test; Open2C; Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV. Pairtools: From sequencing data to chromosome contacts. PLoS Comput Biol. 2024 May 29;20(5):e1012164. doi:10.1371/journal.pcbi.1012164. PMID: 38809952; PMCID: PMC11164360.; http://hdl.handle.net/20.500.14038/53544Test

الإتاحة: https://doi.org/10.1371/journal.pcbi.101216420.500.14038/5354410.1101/2023.02.13.528389Test
https://hdl.handle.net/20.500.14038/53544Test

المؤلفون: Scelfo, Andrea, Barra, Viviana, Abdennur, Nezar, Spracklin, George, Busato, Florence, Salinas-Luypaert, Catalina, Bonaiti, Elena, Velasco, Guillaume, Bonhomme, Frédéric, Chipont, Anna, Tijhuis, Andréa, Spierings, Diana C.J., Guérin, Coralie, Arimondo, Paola B, Francastel, Claire, Foijer, Floris, Tost, Jӧrg, Mirny, Leonid, Fachinetti, Daniele

المساهمون: Biologie Cellulaire et Cancer, Institut Curie Paris -Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Palermo - University of Palermo, University of Massachusetts Medical School Worcester (UMASS), University of Massachusetts System (UMASS), Massachusetts Institute of Technology (MIT), Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre épigénétique et destin cellulaire (EDC), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Chimie biologique épigénétique - Epigenetic Chemical Biology (EpiCBio), Institut Pasteur Paris (IP)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Curie Paris, University of Groningen Groningen, Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM), D. Fachinetti receives salary support from the Centre National de la Recherche Scientifique and has received support for this project by Centre National de la Recherche Scientifique, Institut Curie, and Fondation ARC pour la recherche sur le cancer “ARC labellisation program 2019”. A. Scelfo was supported by AIRC and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 800924., We thank all the members of the Daniele Fachinetti team for the discussion and Edith Pfister (UMass Chan Medical School, Worcester, MA, USA) for editing the manuscript. We thank Hélöise Muller from Ines Drinnenberg’s laboratory (Institut Curie, Paris, France) for advice and sharing reagents. We also acknowledge the Flow Cytometry Core Facility and the Cell and Tissue Imaging Facility (member of the French National Research Infrastructure France-BioImaging ANR10-INBS-04) of the Institut Curie and the DIMONEHEALT2019 equipment grant (project EpiK to Paola Arimondo).

المصدر: ISSN: 0021-9525.

مصطلحات موضوعية: [CHIM]Chemical Sciences

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/38376465; pasteur-04472433; https://pasteur.hal.science/pasteur-04472433Test; https://pasteur.hal.science/pasteur-04472433/documentTest; https://pasteur.hal.science/pasteur-04472433/file/jcb_202307026.pdfTest; PUBMED: 38376465; PUBMEDCENTRAL: PMC10876481

الإتاحة: https://doi.org/10.1083/jcb.202307026Test
https://pasteur.hal.science/pasteur-04472433Test
https://pasteur.hal.science/pasteur-04472433/documentTest
https://pasteur.hal.science/pasteur-04472433/file/jcb_202307026.pdfTest

المؤلفون: Abdennur, Nezar, Fudenberg, Geoffrey, Flyamer, Ilya M, Galitsyna, Aleksandra A, Goloborodko, Anton, Imakaev, Maxim, Venev, Sergey

المساهمون: Genomics and Computational Biology, Systems Biology

المصدر: Bioinformatics (Oxford, England) ; 40 ; 2 ; United States ; England

مصطلحات موضوعية: genomic intervals, Python, Python libraries, dataframes

العلاقة: Bioinformatics; https://doi.org/10.1093/bioinformatics/btae088Test; Open2C; Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev S. Bioframe: operations on genomic intervals in Pandas dataframes. Bioinformatics. 2024 Feb 1;40(2):btae088. doi:10.1093/bioinformatics/btae088. PMID: 38402507; PMCID: PMC10903647.; http://hdl.handle.net/20.500.14038/53268Test; Bioinformatics (Oxford, England)

الإتاحة: https://doi.org/10.1093/bioinformatics/btae088Test
https://doi.org/20.500.14038/53268Test
https://hdl.handle.net/20.500.14038/53268Test

المؤلفون: Abdennur, Nezar(Nezar Alexander)

مرشدي الرسالة: Leonid Mirny., Massachusetts Institute of Technology. Computational and Systems Biology Program., Massachusetts Institute of Technology. Computational and Systems Biology Program

مصطلحات موضوعية: Computational and Systems Biology Program.

وصف الملف: 166 pages; application/pdf

الإتاحة: https://hdl.handle.net/1721.1/122537Test

المؤلفون: Huey, Jack, Abdennur, Nezar

المساهمون: Genomics and Computational Biology, Morningside Graduate School of Biomedical Sciences, Program in Molecular Medicine, Systems Biology, Jack Huey

المصدر: bioRxiv : the preprint server for biology ; United States

مصطلحات موضوعية: Genomics, file formats, software library

العلاقة: bioRxiv; https://doi.org/10.1101/2024.02.06.579187Test; Huey JD, Abdennur N. Bigtools: a high-performance BigWig and BigBed library in Rust. bioRxiv [Preprint]. 2024 Feb 8:2024.02.06.579187. doi:10.1101/2024.02.06.579187. PMID: 38370777; PMCID: PMC10871241.; http://hdl.handle.net/20.500.14038/53269Test; bioRxiv : the preprint server for biology

الإتاحة: https://doi.org/10.1101/2024.02.06.579187Test
https://doi.org/20.500.14038/53269Test
https://hdl.handle.net/20.500.14038/53269Test

المؤلفون: Abdennur, Nezar, Goloborodko, Anton, Imakaev, Maxim, Kerpedjiev, Peter, Fudenberg, Geoffrey, Oullette, Scott, Lee, Soohyun, Strobelt, Hendrik, Gehlenborg, Nils, Mirny, Leonid A.

مصطلحات موضوعية: bioinformatics, genomics, Hi-C, sparse, matrix, format, Python, out-of-core

العلاقة: https://github.com/open2c/cooler/tree/v0.9.2Test; https://dx.doi.org/10.5281/zenodo.597976Test

الإتاحة: https://doi.org/10.5281/zenodo.799267910.5281/zenodo.597976Test
https://zenodo.org/record/7992679Test

المؤلفون: Spracklin, George, Abdennur, Nezar, Imakaev, Maxim, Chowdhury, Neil, Pradhan, Sriharsa, Mirny, Leonid A, Dekker, Job

المساهمون: Program in Bioinformatics and Integrative Biology, Systems Biology

المصدر: Nature structural & molecular biology ; 30 ; 1 ; 38 ; 51 ; United States

مصطلحات موضوعية: Biophysics, Computational biology and bioinformatics, Epigenomics, Nuclear organization, Systems biology

العلاقة: Nature Structural & Molecular Biology; https://doi.org/10.1038/s41594-022-00892-7Test; Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny LA, Dekker J. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nat Struct Mol Biol. 2023 Jan;30(1):38-51. doi:10.1038/s41594-022-00892-7. Epub 2022 Dec 22. PMID: 36550219; PMCID: PMC9851908.; http://hdl.handle.net/20.500.14038/52871Test

الإتاحة: https://doi.org/10.1038/s41594-022-00892-7Test
https://doi.org/20.500.14038/52871Test
https://hdl.handle.net/20.500.14038/52871Test