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Nezar Alexander Abdennur PhD

TitleAssistant Professor
InstitutionUMass Chan Medical School
DepartmentGenomics and Computational Biology
AddressUMass Chan Medical School
368 Plantation Street, AS4-1069
Worcester MA 01605
Phone774-455-4376
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentGenomics and Computational Biology

    InstitutionT.H. Chan School of Medicine
    DepartmentSystems Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentSystems Computational and Quantitative Biology


    Collapse Biography 
    Collapse education and training
    University of Ottawa, Ottawa, ON, CanadaBSBiochemistry/Mathematics
    University of Ottawa, Ottawa, ON, CanadaMSBioinformatcis
    Massachusetts Institute of Technology, Cambridge, MA, United StatesPHD

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Scelfo A, Barra V, Abdennur N, Spracklin G, Busato F, Salinas-Luypaert C, Bonaiti E, Velasco G, Bonhomme F, Chipont A, Tijhuis AE, Spierings DCJ, Gu?rin C, Arimondo P, Francastel C, Foijer F, Tost J, Mirny L, Fachinetti D. Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization. J Cell Biol. 2024 04 01; 223(4). PMID: 38376465.
      Citations:    
    2. Huey JD, Abdennur N. Bigtools: a high-performance BigWig and BigBed library in Rust. bioRxiv. 2024 Feb 08. PMID: 38370777.
      Citations:    
    3. 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 01; 40(2). PMID: 38402507.
      Citations:    
    4. Glunk V, Laber S, Sinnott-Armstrong N, Sobreira DR, Strobel SM, Batista TM, Kubitz P, Moud BN, Ebert H, Huang Y, Brandl B, Garbo G, Honecker J, Stirling DR, Abdennur N, Calabuig-Navarro V, Skurk T, Ocvirk S, Stemmer K, Cimini BA, Carpenter AE, Dankel SN, Lindgren CM, Hauner H, Nobrega MA, Claussnitzer M. A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nat Metab. 2023 05; 5(5):861-879. PMID: 37253881.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    5. Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV. Pairtools: from sequencing data to chromosome contacts. bioRxiv. 2023 Feb 15. PMID: 36824968.
      Citations:    
    6. 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. PMID: 36550219.
      Citations: 16     Fields:    Translation:Cells
    7. Reiff SB, Schroeder AJ, Kirli K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, ?zt?rk SU, ?amoglu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022 Nov 02; 13(1):6561. PMID: 36323678.
      Citations: 1     Fields:    
    8. Reiff SB, Schroeder AJ, Kirli K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, ?zt?rk SU, ?amoglu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022 05 02; 13(1):2365. PMID: 35501320.
      Citations: 21     Fields:    Translation:Cells
    9. Wolff J, Abdennur N, Backofen R, Gr?ning B. Scool: a new data storage format for single-cell Hi-C data. Bioinformatics. 2021 08 04; 37(14):2053-2054. PMID: 33135074.
      Citations: 1     Fields:    
    10. Wolff J, Abdennur N, Backofen R, Gr?ning B. Scool: a new data storage format for single-cell Hi-C data. Bioinformatics. 2021 Jun 09; 37(9):1337. PMID: 34002218.
      Citations: 1     Fields:    
    11. Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Ultrastructural Details of Mammalian Chromosome Architecture. Mol Cell. 2020 05 07; 78(3):554-565.e7. PMID: 32213324.
      Citations: 195     Fields:    Translation:HumansAnimalsCells
    12. Abdennur N, Mirny LA. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020 01 01; 36(1):311-316. PMID: 31290943.
      Citations: 223     Fields:    
    13. Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nat Commun. 2019 10 03; 10(1):4486. PMID: 31582744.
      Citations: 18     Fields:    Translation:AnimalsCells
    14. Mirny LA, Imakaev M, Abdennur N. Two major mechanisms of chromosome organization. Curr Opin Cell Biol. 2019 06; 58:142-152. PMID: 31228682.
      Citations: 81     Fields:    Translation:HumansAnimalsCells
    15. Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018 08 24; 19(1):125. PMID: 30143029.
      Citations: 390     Fields:    
    16. Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA. Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc Natl Acad Sci U S A. 2018 07 17; 115(29):E6697-E6706. PMID: 29967174.
      Citations: 255     Fields:    Translation:AnimalsCells
    17. Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA. Emerging Evidence of Chromosome Folding by Loop Extrusion. Cold Spring Harb Symp Quant Biol. 2017; 82:45-55. PMID: 29728444.
      Citations: 105     Fields:    
    18. Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F. Two independent modes of chromatin organization revealed by cohesin removal. Nature. 2017 11 02; 551(7678):51-56. PMID: 29094699.
      Citations: 452     Fields:    Translation:AnimalsCells
    19. Ulianov SV, Galitsyna AA, Flyamer IM, Golov AK, Khrameeva EE, Imakaev MV, Abdennur NA, Gelfand MS, Gavrilov AA, Razin SV. Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure. Epigenetics Chromatin. 2017 07 11; 10(1):35. PMID: 28693562.
      Citations: 9     Fields:    Translation:AnimalsCells
    20. Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell. 2017 May 18; 169(5):930-944.e22. PMID: 28525758.
      Citations: 665     Fields:    Translation:AnimalsCells
    21. Flyamer IM, Gassler J, Imakaev M, Brand?o HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana-Konwalski K. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature. 2017 04 06; 544(7648):110-114. PMID: 28355183.
      Citations: 293     Fields:    Translation:AnimalsCells
    22. Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of Chromosomal Domains by Loop Extrusion. Cell Rep. 2016 05 31; 15(9):2038-49. PMID: 27210764.
      Citations: 759     Fields:    Translation:Cells
    23. Claussnitzer M, Dankel SN, Kim KH, Quon G, Meuleman W, Haugen C, Glunk V, Sousa IS, Beaudry JL, Puviindran V, Abdennur NA, Liu J, Svensson PA, Hsu YH, Drucker DJ, Mellgren G, Hui CC, Hauner H, Kellis M. FTO Obesity Variant Circuitry and Adipocyte Browning in Humans. N Engl J Med. 2015 Sep 03; 373(10):895-907. PMID: 26287746.
      Citations: 629     Fields:    Translation:HumansAnimalsCells
    24. Charlebois DA, Abdennur N, Kaern M. Gene expression noise facilitates adaptation and drug resistance independently of mutation. Phys Rev Lett. 2011 Nov 18; 107(21):218101. PMID: 22181928.
      Citations: 33     Fields:    
    25. Vaillant DC, Copeland SJ, Davis C, Thurston SF, Abdennur N, Copeland JW. Interaction of the N- and C-terminal autoregulatory domains of FRL2 does not inhibit FRL2 activity. J Biol Chem. 2008 Nov 28; 283(48):33750-62. PMID: 18835814.
      Citations: 36     Fields:    Translation:AnimalsCells
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