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Johan Harmen Gibcus PhD

TitleAssistant Professor
InstitutionUMass Chan Medical School
DepartmentSystems Biology
AddressUniversity of Massachusetts Medical School
55 Lake Ave North
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentSystems Biology


    Collapse Biography 
    Collapse education and training
    University of Groningen, Groningen, , NetherlandsMSBiology
    University of Groningen, Groningen, , NetherlandsPHDPathology

    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.
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    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. Gentien D, Saberi-Ansari E, Servant N, Jolly A, de la Grange P, N?mati F, Liot G, Saule S, Teissandier A, Bourc'his D, Girard E, Wong J, Masliah-Planchon J, Narmanli E, Liu Y, Torun E, Goulancourt R, Rodrigues M, Gaud? LV, Reyes C, Bazire M, Chenegros T, Henry E, Rapinat A, Bohec M, Baulande S, M'kacher R, Jeandidier E, Nicolas A, Ciriello G, Margueron R, Decaudin D, Cassoux N, Piperno-Neumann S, Stern MH, Gibcus JH, Dekker J, Heard E, Roman-Roman S, Waterfall JJ. Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma. Cell Rep. 2023 09 26; 42(9):113132. PMID: 37708024.
      Citations:    Fields:    Translation:HumansCells
    2. Marl?taz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Mart?nez-Garc?a PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, Gonz?lez-Rajal ?, Bogdanovic O, Gibcus JH, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabald?n T, Nakamura T, Tena JJ, Lupi??ez DG, Rokhsar DS, G?mez-Skarmeta JL. The little skate genome and the evolutionary emergence of wing-like fins. Nature. 2023 04; 616(7957):495-503. PMID: 37046085.
      Citations: 5     Fields:    Translation:Animals
    3. Yang L, Akgol Oksuz B, Dekker J, Gibcus JH. Capturing Chromosome Conformation Across Length Scales. J Vis Exp. 2023 01 20; (191). PMID: 36744801.
      Citations:    Fields:    Translation:Cells
    4. Emerson DJ, Zhao PA, Cook AL, Barnett RJ, Klein KN, Saulebekova D, Ge C, Zhou L, Simandi Z, Minsk MK, Titus KR, Wang W, Gong W, Zhang D, Yang L, Venev SV, Gibcus JH, Yang H, Sasaki T, Kanemaki MT, Yue F, Dekker J, Chen CL, Gilbert DM, Phillips-Cremins JE. Cohesin-mediated loop anchors confine the locations of human replication origins. Nature. 2022 06; 606(7915):812-819. PMID: 35676475.
      Citations: 17     Fields:    Translation:HumansCells
    5. Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. Nat Methods. 2021 09; 18(9):1046-1055. PMID: 34480151.
      Citations: 39     Fields:    Translation:HumansCells
    6. Lafontaine DL, Yang L, Dekker J, Gibcus JH. Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. Curr Protoc. 2021 Jul; 1(7):e198. PMID: 34286910.
      Citations: 20     Fields:    Translation:AnimalsCells
    7. 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: 183     Fields:    Translation:HumansAnimalsCells
    8. Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J. A pathway for mitotic chromosome formation. Science. 2018 02 09; 359(6376). PMID: 29348367.
      Citations: 274     Fields:    Translation:AnimalsCells
    9. 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: 662     Fields:    Translation:AnimalsCells
    10. Belaghzal H, Dekker J, Gibcus JH. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods. 2017 07 01; 123:56-65. PMID: 28435001.
      Citations: 127     Fields:    Translation:HumansCells
    11. Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013 Mar 07; 49(5):773-82. PMID: 23473598.
      Citations: 359     Fields:    Translation:HumansAnimalsCells
    12. Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods. 2012 Nov; 58(3):268-76. PMID: 22652625.
      Citations: 408     Fields:    Translation:HumansAnimalsCells
    13. Gibcus JH, Dekker J. The context of gene expression regulation. F1000 Biol Rep. 2012; 4:8. PMID: 22500194.
      Citations:    
    14. Kluiver J, Gibcus JH, Hettinga C, Adema A, Richter MK, Halsema N, Slezak-Prochazka I, Ding Y, Kroesen BJ, van den Berg A. Rapid generation of microRNA sponges for microRNA inhibition. PLoS One. 2012; 7(1):e29275. PMID: 22238599.
      Citations: 65     Fields:    Translation:HumansAnimalsCells
    15. Schrijvers ML, Pattje WJ, Slagter-Menkema L, Mastik MF, Gibcus JH, Langendijk JA, van der Wal JE, van der Laan BF, Schuuring E. FADD expression as a prognosticator in early-stage glottic squamous cell carcinoma of the larynx treated primarily with radiotherapy. Int J Radiat Oncol Biol Phys. 2012 Jul 15; 83(4):1220-6. PMID: 22208968.
      Citations: 12     Fields:    Translation:Humans
    16. Gibcus JH, Kroesen BJ, Koster R, Halsema N, de Jong D, de Jong S, Poppema S, Kluiver J, Diepstra A, van den Berg A. MiR-17/106b seed family regulates p21 in Hodgkin's lymphoma. J Pathol. 2011 Dec; 225(4):609-17. PMID: 21953646.
      Citations: 19     Fields:    Translation:HumansCells
    17. Koster R, di Pietro A, Timmer-Bosscha H, Gibcus JH, van den Berg A, Suurmeijer AJ, Bischoff R, Gietema JA, de Jong S. Cytoplasmic p21 expression levels determine cisplatin resistance in human testicular cancer. J Clin Invest. 2010 Oct; 120(10):3594-605. PMID: 20811155.
      Citations: 105     Fields:    Translation:HumansCells
    18. Tan LP, Wang M, Robertus JL, Schakel RN, Gibcus JH, Diepstra A, Harms G, Peh SC, Reijmers RM, Pals ST, Kroesen BJ, Kluin PM, Poppema S, van den Berg A. miRNA profiling of B-cell subsets: specific miRNA profile for germinal center B cells with variation between centroblasts and centrocytes. Lab Invest. 2009 Jun; 89(6):708-16. PMID: 19349957.
      Citations: 54     Fields:    Translation:HumansCells
    19. Gibcus JH, Tan LP, Harms G, Schakel RN, de Jong D, Blokzijl T, M?ller P, Poppema S, Kroesen BJ, van den Berg A. Hodgkin lymphoma cell lines are characterized by a specific miRNA expression profile. Neoplasia. 2009 Feb; 11(2):167-76. PMID: 19177201.
      Citations: 74     Fields:    Translation:HumansCells
    20. Wildeman MA, Gibcus JH, Hauptmann M, Begg AC, van Velthuysen ML, Hoebers FJ, Mastik MF, Schuuring E, van der Wal JE, van den Brekel MW. Radiotherapy in laryngeal carcinoma: can a panel of 13 markers predict response? Laryngoscope. 2009 Feb; 119(2):316-22. PMID: 19160427.
      Citations: 13     Fields:    Translation:Humans
    21. Gibcus JH, Menkema L, Mastik MF, Hermsen MA, de Bock GH, van Velthuysen ML, Takes RP, Kok K, Alvarez Marcos CA, van der Laan BF, van den Brekel MW, Langendijk JA, Kluin PM, van der Wal JE, Schuuring E. Amplicon mapping and expression profiling identify the Fas-associated death domain gene as a new driver in the 11q13.3 amplicon in laryngeal/pharyngeal cancer. Clin Cancer Res. 2007 Nov 01; 13(21):6257-66. PMID: 17975136.
      Citations: 43     Fields:    Translation:HumansCells
    22. Boelens MC, te Meerman GJ, Gibcus JH, Blokzijl T, Boezen HM, Timens W, Postma DS, Groen HJ, van den Berg A. Microarray amplification bias: loss of 30% differentially expressed genes due to long probe - poly(A)-tail distances. BMC Genomics. 2007 Aug 15; 8:277. PMID: 17697374.
      Citations: 10     Fields:    Translation:HumansCells
    23. Gibcus JH, Kok K, Menkema L, Hermsen MA, Mastik M, Kluin PM, van der Wal JE, Schuuring E. High-resolution mapping identifies a commonly amplified 11q13.3 region containing multiple genes flanked by segmental duplications. Hum Genet. 2007 Apr; 121(2):187-201. PMID: 17171571.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    24. van Rossum AG, Gibcus J, van der Wal J, Schuuring E. Cortactin overexpression results in sustained epidermal growth factor receptor signaling by preventing ligand-induced receptor degradation in human carcinoma cells. Breast Cancer Res. 2005; 7(6):235-7. PMID: 16280034.
      Citations: 5     Fields:    Translation:HumansCells
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