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Nynke L. van Berkum
Researcher at Massachusetts Institute of Technology
Publications - 11
Citations - 12465
Nynke L. van Berkum is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Chromatin & Chromosome conformation capture. The author has an hindex of 9, co-authored 10 publications receiving 10448 citations. Previous affiliations of Nynke L. van Berkum include University of Massachusetts Medical School & University of Massachusetts Amherst.
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Journal ArticleDOI
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman Aiden,Nynke L. van Berkum,Louise Williams,Maxim Imakaev,Tobias Ragoczy,Tobias Ragoczy,Agnes Telling,Agnes Telling,Ido Amit,Bryan R. Lajoie,Peter J. Sabo,Michael O. Dorschner,Richard Sandstrom,Bradley E. Bernstein,Bradley E. Bernstein,Michaël Bender,Mark Groudine,Mark Groudine,Andreas Gnirke,John A. Stamatoyannopoulos,Leonid A. Mirny,Eric S. Lander,Eric S. Lander,Job Dekker +23 more
TL;DR: Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes.
Journal ArticleDOI
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Elphège P. Nora,Bryan R. Lajoie,Edda G. Schulz,Luca Giorgetti,Luca Giorgetti,Luca Giorgetti,Ikuhiro Okamoto,Ikuhiro Okamoto,Ikuhiro Okamoto,Nicolas Servant,Nicolas Servant,Nicolas Servant,Tristan Piolot,Tristan Piolot,Tristan Piolot,Nynke L. van Berkum,Johannes Meisig,John W. Sedat,Joost Gribnau,Emmanuel Barillot,Emmanuel Barillot,Emmanuel Barillot,Nils Blüthgen,Job Dekker,Edith Heard,Edith Heard,Edith Heard +26 more
TL;DR: In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, this study sets the stage for the full genetic dissection of the mouse X-inactivation centre.
Mediator and cohesin connect gene expression and chromatin architecture
Michael H. Kagey,Jamie J. Newman,Steve Bilodeau,Ye Zhan,David A. Orlando,Nynke L. van Berkum,Christopher C. Ebmeier,Jesse Goossens,Peter B. Rahl,Stuart S. Levine,Dylan J. Taatjes,Job Dekker,Richard A. Young +12 more
TL;DR: It is reported that mediator and cohesin physically and functionally connect the enhancers and core promoters of active genes in murine embryonic stem cells.
Journal ArticleDOI
Hi-C: a method to study the three-dimensional architecture of genomes.
Nynke L. van Berkum,Erez Lieberman-Aiden,Louise Williams,Maxim Imakaev,Andreas Gnirke,Leonid A. Mirny,Job Dekker,Eric S. Lander,Eric S. Lander +8 more
TL;DR: Hi-C, an extension of 3C that is capable of identifying long range interactions in an unbiased, genome-wide fashion, is developed, demonstrating that at the megabase scale Hi-C reveals features consistent with a fractal globule conformation.
Journal ArticleDOI
Evidence for transcript networks composed of chimeric RNAs in human cells.
Sarah Djebali,Julien Lagarde,Philipp Kapranov,Vincent Lacroix,Christelle Borel,Jonathan M. Mudge,Cédric Howald,Sylvain Foissac,Catherine Ucla,Jacqueline Chrast,Paolo Ribeca,David C. Martin,Ryan R. Murray,Xinping Yang,Lila Ghamsari,Chenwei Lin,Ian Bell,Erica Dumais,Jorg Drenkow,Michael L. Tress,Josep Lluís Gelpí,Modesto Orozco,Alfonso Valencia,Nynke L. van Berkum,Bryan R. Lajoie,Marc Vidal,John A. Stamatoyannopoulos,Philippe Batut,Alexander Dobin,Jennifer Harrow,Tim Hubbard,Job Dekker,Adam Frankish,Kourosh Salehi-Ashtiani,Alexandre Reymond,Stylianos E. Antonarakis,Roderic Guigó,Thomas R. Gingeras,Thomas R. Gingeras +38 more
TL;DR: Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes.