PUBLICATIONS

LEADING PUBLICATIONS in the field of epigenetics

PUBLICATION HIGHLIGHTS

Found 93 Results
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Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.

Al Bkhetan Z, Kadlof M, Kraft A, Plewczynski D. Methods. 2019 Aug 15;166:83-90. doi: 10.1016/j.ymeth.2019.03.002.

Date Publication: 2019 Type: Seminal publication

McBel-Plnc: A Deep Learning Model for Multiclass Multilabel Classification of Protein-lncRNA Interactions.

Natsuda Navamajiti, Thammakorn Saethang, Duangdao Wichadakul (2019). McBel-Plnc: A deep learning model for multiclass multilabel classification of protein-lncRNA interactions. ICBBE ’19: Proceedings of the 2019 6th International Conference on Biomedical and Bioinformatics Engineering, 21-28. https://doi.org/10.1145/3375923.3375953

Date Publication: 2019 Type: ESR publication

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs.

Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šari? T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A. Cell Stem Cell. 2019 May 2;24(5):736-752.e12. doi:10.1016/j.stem.2019.03.004.

Date Publication: 2019 Type: Seminal publication

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S. Nat Genet. 2019 Apr;51(4):716-727. doi: 10.1038/s41588-019-0359-1.

Date Publication: 2019 Type: Seminal publication

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip.

Bio?anin M, Bues J, Dainese R, Amstad E, Deplancke B. Lab Chip. 2019 Apr 23;19(9):1610-1620. doi:10.1039/c9lc00014c.

Date Publication: 2019 Type: Seminal publication

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer.

Chen W, Schwalie PC, Pankevich EV, Gubelmann C, Raghav SK, Dainese R, Cassano M, Imbeault M, Jang SM, Russeil J, Delessa T, Duc J, Trono D, Wolfrum C, Deplancke B. Nat Commun. 2019 Apr 18;10(1):1809. doi: 10.1038/s41467-019-09803-9.

Date Publication: 2019 Type: Seminal publication

Widespread Enhancer Activity from Core Promoters.

Medina A, Santiago D, Puthier D, Spicuglia S. Wide-spread enhancer activity from core promoters. TiBS. (2018). 43(6):452-468

Date Publication: 2018 Type: Seminal publication

Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules.

Korvigo I, Holmatov M, Zaikovskii A, Skoblov M. Journal of cheminformatics. 2018 Dec;10(1):28.

Date Publication: 2018 Type: ESR publication

PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation.

Cruz-Molina S, Respuela P, Tebartz C, Kolovos P, Nikolic M, Fueyo R, van Ijcken W.F.J, Grosveld F, Frommolt P, Bazzi H, Rada-Iglesias A#. Cell Stem Cell. 2017 May 4;20(5):689-705. PMID:28285903.

Date Publication: 2017 Type: Seminal publication

Genome-wide characterization of mammalian promoters with distal enhancer functions.

Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA, Andrieu-Soler C, Medina-Rivera A, Souaid C, Charbonnier G, Griffon A, Vanhille L, Stephen T, Alomairi J, Martin D, Torres M, Fernandez N, Soler E, van Helden J, Puthier D, Spicuglia S. Nat Genet. (2017). 49(7):1073-1081. PMID: 28581502.

Date Publication: 2017 Type: Seminal publication

GARLIC: A Bioinformatic Toolkit for Etiologically Connecting Diseases and Cell Type-Specific Regulatory Maps.

Nikoli? M, Papantonis A, Rada-Iglesias A#. Hum Mol Genet. 2017 Feb 15;26(4):742-752. PMID:28007912.

Date Publication: 2017 Type: Seminal publication

CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals.

Vanhille L., A. Griffon, M.A. Maqbool, J. Zacarias, L.T.M. Dao, N. Fernandez, B. Ballester, J.C. Andrau, S. Spicuglia. Nat. Comm. 6:6905 (2015)

Date Publication: 2015 Type: Seminal publication

H3K4 tri-methylation provides an epigenetic signature of active enhancers.

Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau J.C, Ferrier P and Spicuglia S EMBO J., 30, 4198–10. (2011).

Date Publication: 2011 Type: Seminal publication

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This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 860002. The information contained in this website reflects only the authors’ view. REA and EC are not responsible for any use that may be made of this information.

PUBLICATIONS

PUBLICATION HIGHLIGHTS

Keywords (title, authors, PMID ...)

Year

Type publication

Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.

McBel-Plnc: A Deep Learning Model for Multiclass Multilabel Classification of Protein-lncRNA Interactions.

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs.

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip.

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer.

Widespread Enhancer Activity from Core Promoters.

Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules.

PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation.

Genome-wide characterization of mammalian promoters with distal enhancer functions.

GARLIC: A Bioinformatic Toolkit for Etiologically Connecting Diseases and Cell Type-Specific Regulatory Maps.

CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals.

H3K4 tri-methylation provides an epigenetic signature of active enhancers.

ENHPATHY highlighted in the Winter issue of EU Research

Pitch my Enhancer in art project in 90 seconds

Current challenges in understanding the role of enhancers in disease

Chronic inflammation decreases HSC fitness by activating the druggable Jak/Stat3 signaling pathway