Publications from 2013
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data, Job Dekker, Marc A. Marti-Renom, and Leonid A. Mirny
Nuclear biology: what's been most surprising, Job Dekker, Joanna Wysocka, Iain Mattaj, Erez Lieberman-Aiden, and Craig PIkaard
The Hierarchy of the 3D Genome, Johan H. Gibcus and Job Dekker
Diet-Induced Developmental Acceleration Independent of TOR and Insulin in C. elegans, Lesley T. MacNeil, Emma Watson, H. Efsun Arda, Lihua Julie Zhu, and Albertha J. M. Walhout
Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome, Rachel Patton McCord, Ashley Nazario-Toole, Haoyue Zhang, Peter Chines, Ye Zhan, Michael Erdos, Francis Collins, Job Dekker, and Kan Cao
Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment, Jennifer E. Phillips-Cremins, Michael E. G. Sauria, Amartya Sanyal, Tatiana I. Gerasimova, Bryan R. Lajoie, Joshua S. K. Bell, Chin-Tong Ong, Tracy A. Hookway, Changying Guo, Yuhua Sun, Michael J. Bland, William Wagstaff, Stephen Dalton, Todd C. McDevitt, Ranjan Sen, Job Dekker, James Taylor, and Victor G. Corces
Complex expression dynamics and robustness in C. elegans insulin networks, Ashlyn D. Ritter, Yuan Shen, Juan Fuxman Bass, Sankarganesh Jeyaraj, Bart Deplancke, Arnab Mukhopadjay, Jian Xu, Monica Driscoll, Heidi A. Tissenbaum, and Albertha J. M. Walhout
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels, Alex M. Tamburino, Sean P. Ryder, and Albertha J. M. Walhout
Handbook of Systems Biology: Concepts and Insights, Albertha J. M. Walhout, Marc Vidal, and Job Dekker
Integration of Metabolic and Gene Regulatory Networks Modulates the C. elegans Dietary Response, Emma Watson, Lesley T. MacNeil, H. Efsun Arda, Lihua Julie Zhu, and Albertha J. M. Walhout
Events from 2012
Understanding the mechanisms of IGF2 gene regulation in hepatocellular carcinoma cells, Amalene Cooper-Morgan, Natalia Naumova, Amartya Sanyal, Bryan R. Lajoie, Job Dekker, and Brian C. Lewis
CTCF and cohesin help neurons raise their self-awareness, Job Dekker
3C-based technologies to study the shape of the genome, Wouter de Laat and Job Dekker
Evidence for transcript networks composed of chimeric RNAs in human cells, Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge, Cedric Howald, Sylvain Foissac, Catherine Ucla, Jacqueline Chrast, Paolo Ribeca, David Marin, Ryan R. Murray, Xinping Yang, Lila Ghamasari, Chenwei Lin, Ian Bell, Erica Dumais, Jorg Drenkow, Michael L. Tress, Josep Lluis Gelpi, Modesto Orozco, Alfonso Valencia, Nynke L. van Berkum, Bryan R. Lajoie, Marc Vidal, John A. Stamatoyannopoulos, Philippe Batut, Alex Dobin, Jennifer Harrow, Tim Hubbard, Job Dekker, Adam Frankish, Kourosh Salehi-Ashtiani, Alexandre Reymond, Stylianos E. Antonarakis, Roderic Guigo, and Thomas R. Gingeras
An integrated encyclopedia of DNA elements in the human genome, Ian Dunham, Ewan Birney, Bryan R. Lajoie, Amartya Sanyal, Xianjun Dong, Melissa Greven, Xinying Lin, Jie Wang, Troy W. Whitfield, Jiali Zhuang, Job Dekker, Zhiping Weng, Gaurav Jain, and ENCODE Project Consortium
Genome architecture and expression, Gary Felsenfeld and Job Dekker
A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans, Huiyun Feng, John S. Reece-Hoyes, Albertha J. M. Walhout, and Ian A. Hope
From cells to chromatin: Capturing snapshots of genome organization with 5C technology, Maria A. Ferraiuolo, Amartya Sanyal, Natalia Naumova, Job Dekker, and Josee Dostie
The context of gene expression regulation, Johan H. Gibcus and Job Dekker
Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Maxim Imakaev, Geoffrey Fudenberg, Rachel Patton McCord, Natalia Naumova, Anton Goloborodko, Bryan R. Lajoie, Job Dekker, and Leonid A. Mirny
MORC family ATPases required for heterochromatin condensation and gene silencing, Guillaume Moissiard, Shawn J. Cokus, Joshua Cary, Suhua Feng, Allison C. Billi, Hume Stroud, Dylan Husmann, Ye Zhan, Bryan R. Lajoie, Rachel Patton McCord, Christopher J. Hale, Wei Feng, Scott D. Michaels, Alison R. Frand, Matteo Pellegrini, Job Dekker, John K. Kim, and Steven E. Jacobsen
An encyclopedia of mouse DNA elements (Mouse ENCODE), Mouse ENCODE Consortium, John A. Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Job Dekker, Bryan R. Lajoie, Gaurav Jain, and Amartya Sanyal
Analysis of long-range chromatin interactions using Chromosome Conformation Capture, Natalia Naumova, Emily M. Smith, Ye Zhan, and Job Dekker
Spatial partitioning of the regulatory landscape of the X-inactivation centre, Elphege P. Nora, Bryan R. Lajoie, Edda G. Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L. van Berkum, Johannes Meisig, John Sedat, Joost Gribnau, Emmanuel Barillot, Nils Bluthgen, Job Dekker, and Edith Heard
Gene-centered yeast one-hybrid assays, John S. Reece-Hoyes and Albertha J. M. Walhout
Yeast one-hybrid assays: A historical and technical perspective, John S. Reece-Hoyes and Albertha J. M. Walhout
The long-range interaction landscape of gene promoters, Amartya Sanyal, Bryan R. Lajoie, Gaurav Jain, and Job Dekker
HiTC : Exploration of High-Throughput 'C' experiments, Nicolas Servant, Bryan R. Lajoie, Elphege P. Nora, Luca Giorgetti, Chongjian Chen, Edith Heard, Job Dekker, and Emmanuel Barillot
Spatial organization of the mouse genome and its role in recurrent chromosomal translocations, Yu Zhang, Rachel Patton McCord, Yu-Jui Ho, Bryan R. Lajoie, Dominic G. Hildebrand, Alince C. Simon, Michael B. Becker, Frederick W. Alt, and Job Dekker
Publications from 2011
Genomics in 2011: challenges and opportunities, David J. Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X. Shirley Liu, Chad L. Myers, Alicia Oshlack, John L. Rinn, and Albertha J. M. Walhout
The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules, Davide Bau, Amartya Sanyal, Bryan R. Lajoie, Emidio Capriotti, Meg Byron, Jeanne B. Lawrence, Job Dekker, and Marc A. Marti-Renom
A stele-enriched gene regulatory network in the Arabidopsis root, Siobhan M. Brady, Lifang Zhang, Molly Megraw, Natalia Julia Martinez, Eric Jiang, Charles S. Yi, Weilin Liu, Anna Zeng, Mallorie Taylor-Teeples, Dahae Kim, Sebastian Ahnert, Uwe Ohler, Doreen Ware, Albertha J. M. Walhout, and Philip N. Benfey
Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants, Federico De Masi, Christian A. Grove, Anastasia Vedenko, Andreu Alibés, Stephen S. Gisselbrecht, Luis Serrano, Martha L. Bulyk, and Albertha J. M. Walhout
Enhanced Y1H assays for Arabidopsis, Allison Gaudinier, Lifang Zhang, John S. Reece-Hoyes, Mallorie Taylor-Teeples, Li Pu, Zhijie Liu, Ghislain Breton, Jose L. Pruneda-Paz, Dahae Kim, Steve A. Kay, Albertha J. M. Walhout, Doreen Ware, and Siobhan M. Brady
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression, Lesley T. MacNeil and Albertha J. M. Walhout
Translocation mapping exposes the risky lifestyle of B cells, Rachel Patton McCord and Job Dekker
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping, John S. Reece-Hoyes, A. Rasim Barutcu, Rachel Patton McCord, Jun Seop Jeong, Lizhi Jiang, Andrew Macwilliams, Xinping Yang, Kourosh Salehi-Ashtiani, David E. Hill, Seth Blackshaw, Heng Zhu, Job Dekker, and Albertha J. M. Walhout
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping, John S. Reece-Hoyes, Alos Diallo, Bryan R. Lajoie, Amanda Kent, Shaleen Shrestha, Sreenath Kadreppa, Colin Pesyna, Job Dekker, Chad L. Myers, and Albertha J. M. Walhout
Chromatin globules: a common motif of higher order chromosome structure, Amartya Sanyal, Davide Bau, Marc A. Marti-Renom, and Job Dekker
Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex, Tomoko M. Tabuchi, Bart Deplancke, Naoki Osato, Lihua Julie Zhu, Inmaculada M. Barrasa, Melissa M. Harrison, Robert H. Horvitz, Albertha J. M. Walhout, and Kirsten A. Hagstrom
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation, Mark A. Umbarger, Esteban Toro, Matthew A. Wright, Gregory J. Porreca, Davide Bau, Sun-Hae Hong, Michael J. Fero, Lihua Julie Zhu, Marc A. Marti-Renom, Harley H. McAdams, Lucy Shapiro, Job Dekker, and George M. Church
Gene-centered regulatory network mapping, Albertha J. M. Walhout
What does biologically meaningful mean? A perspective on gene regulatory network validation, Albertha J. M. Walhout
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression, Kevin C. Wang, Yul W. Yang, Bo Liu, Amartya Sanyal, Ryan Corces-Zimmerman, Yong Chen, Bryan R. Lajoie, Angeline Protacio, Ryan A. Flynn, Rajnish A. Gupta, Joanna Wysocka, Ming Lei, Job Dekker, Jill A. Helms, and Howard Y. Chang
Publications from 2010
Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network., H. Efsun Arda, Stefan Taubert, Lesley T. MacNeil, Colin C. Conine, Ben Tsuda, Marc Van Gilst, Reynaldo Sequerra, Lynn Doucette-Stamm, Keith R. Yamamoto, and Albertha J. M. Walhout
Gene-centered regulatory networks, H. Efsun Arda and Albertha J. M. Walhout
Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease, James E. Bradner, Raymond Mak, Shyam K. Tanguturi, Ralph Mazitschek, Stephen J. Haggarty, Kenneth Ross, Cindy Y. Chang, Jocelyn Bosco, Nathan West, Elizabeth Morse, Katherine Lin, John Paul Shen, Nicholas P. Kwiatkowski, Nele Gheldof, Job Dekker, Daniel J. DeAngelo, Steven A. Carr, Stuart L. Schreiber, Todd R. Golub, and Benjamin L. Ebert
Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene, Nele Gheldof, Emily M. Smith, Tomoko M. Tabuchi, Christoph M. Koch, Ian Dunham, John A. Stamatoyannopoulos, and Job Dekker
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, and Richard A. Young
Sister cohesion and structural axis components mediate homolog bias of meiotic recombination, Keun P. Kim, Beth M. Weiner, Liangran Zhang, Amy Jordan, Job Dekker, and Nancy Kleckner
Integrating one-dimensional and three-dimensional maps of genomes, Natalia Naumova and Job Dekker
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, and Eric S. Lander
Publications from 2009
Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization, Howard Y. Chang, Olivier Cuvier, and Job Dekker
Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening, Barbara D'haene, Catia Attanasio, Diane Beysen, Josee Dostie, Edmond Lemire, Philippe Bouchard, Michael Field, Kristie Jones, Birgit Lorenz, Bjorn Menten, Karen Buysse, Filip Pattyn, Marc Friedli, Catherine Ucla, Colette Rossier, Carine Wyss, Frank Speleman, Anne De Paepe, Job Dekker, Stylianos E. Antonarakis, and Elfride De Baere
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors, Christian A. Grove, Federico De Masi, M. Inmaculada Barrasa, Daniel E. Newburger, Mark J. Alkema, Martha L. Bulyk, and Albertha J. M. Walhout
My5C: web tools for chromosome conformation capture studies, Bryan R. Lajoie, Nynke L. van Berkum, Amartya Sanyal, and Job Dekker
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, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Berstein, M. A. Bender, Mark Groudine, Andreas Gnirke, John A. Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, and Job Dekker
The interplay between transcription factors and microRNAs in genome-scale regulatory networks, Natalia Julia Martinez and Albertha J. M. Walhout
Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions, Adriana Miele, Kerstin Bystricky, and Job Dekker
Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C), Adriana Miele and Job Dekker
Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery, Pranav O. Oza, Sue L. Jaspersen, Adriana Miele, Job Dekker, and Craig L. Peterson
The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors, John S. Reece-Hoyes, Bart Deplancke, M. Inmaculada Barrasa, Julia Hatzold, Ryan B. Smit, H. Efsun Arda, Patricia A. Pope, Jeb Gaudet, Barbara Conradt, and Albertha J. M. Walhout
Determining spatial chromatin organization of large genomic regions using 5C technology, Nynke L. van Berkum and Job Dekker
Getting an edge on human disease, Albertha J. M. Walhout
Publications from 2008
Gene regulation in the third dimension, Job Dekker
Transcription factor functionality and transcription regulatory networks, Christian A. Grove and Albertha J. M. Walhout
A mechanism for Ikaros regulation of human globin gene switching, Janelle R. Keys, Michael R. Tallack, Ye Zhan, Peter Papathanasiou, Christopher Goodnow, Karin M. Gaensler, Merlin Crossley, Job Dekker, and Andrew C. Perkins
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity, Natalia Julia Martinez, Maria C. Ow, M. Inmaculada Barrasa, Molly Hammell, Reynaldo Sequerra, Lynn Doucette-Stamm, Frederick P. Roth, Victor R. Ambros, and Albertha J. M. Walhout
Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity, Natalia Julia Martinez, Maria C. Ow, John S. Reece-Hoyes, M. Inmaculada Barrasa, Victor R. Ambros, and Albertha J. M. Walhout
Long-range chromosomal interactions and gene regulation, Angela Miele and Job Dekker
Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans, Arnab Mukhopadhyay, Bart Deplancke, Albertha J. M. Walhout, and Heidi A. Tissenbaum
The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans, Maria C. Ow, Natalia Julia Martinez, Philip H. Olsen, Howard S. Silverman, M. Inmaculada Barrasa, Barbara Conradt, Albertha J. M. Walhout, and Victor R. Ambros
Publications from 2007
EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression, M. Inmaculada Barrasa, Philippe Vaglio, Fabien Cavasino, Laurent Jacotot, and Albertha J. M. Walhout
Mapping networks of physical interactions between genomic elements using 5C technology, Josee Dostie and Job Dekker
Chromosome conformation capture carbon copy technology, Josee Dostie, Ye Zhan, and Job Dekker
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, ENCODE Project Consortium, Zhiping Weng, and Job Dekker
Quantitative analysis of chromosome conformation capture assays (3C-qPCR), Helene Hagege, Petra Klous, Caroline Braem, Erik Splinter, Job Dekker, Guy Cathala, Wouter de Laat, and Thierry Forne
Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex, Chiara Lanzuolo, Virginie Roure, Job Dekker, Frederic Bantignies, and Valerio Orlando
Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns, John S. Reece-Hoyes, Jane Shingles, Denis Dupuy, Christian A. Grove, Albertha J. M. Walhout, Marc Vidal, and Ian A. Hope
Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network, Vanessa Vermeirssen, M. Inmaculada Barrasa, Cesar A. Hidalgo, Jenny Aurielle B. Babon, Reynaldo Sequerra, Lynn Doucette-Stamm, Albert-Laszlo Barabasi, and Albertha J. M. Walhout
Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping, Vanessa Vermeirssen, Bart Deplancke, M. Inmaculada Barrasa, John S. Reece-Hoyes, H. Efsun Arda, Christian A. Grove, Natalia Julia Martinez, Reynaldo Sequerra, Lynn Doucette-Stamm, Michael R. Brent, and Albertha J. M. Walhout
Publications from 2006
The three 'C' s of chromosome conformation capture: controls, controls, controls, Job Dekker
A gene-centered C. elegans protein-DNA interaction network, Bart Deplancke, Arnab Mukhopadhyay, Wanyuan Ao, Ahmed M. Elewa, Christian A. Grove, Natalia Julia Martinez, Reynaldo Sequerra, Lynn Doucette-Stamm, John S. Reece-Hoyes, Ian A. Hope, Heidi A. Tissenbaum, Susan E. Mango, and Albertha J. M. Walhout
Gateway-Compatible Yeast One-Hybrid Screens, Bart Deplancke, Vanessa Vermeirssen, H. Efsun Arda, Albertha J. M. Walhout, and Natalia Julia Martinez
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements, Josee Dostie, Todd A. Richmond, Ramy A. Arnaout, Rebecca R. Selzer, William L. Lee, Tracey A. Honan, Eric D. Rubio, Anton Krumm, Justin Lamb, Chad Nusbaum, Roland D. Green, and Job Dekker
The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications, Nele Gheldof, Tomoko M. Tabuchi, and Job Dekker
Mapping chromatin interactions by chromosome conformation capture, Adriana Miele, Nele Gheldof, Tomoko M. Tabuchi, Josee Dostie, and Job Dekker
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks, John S. Reece-Hoyes, Bart Deplancke, Jane Shingles, Christian A. Grove, Ian A. Hope, and Albertha J. M. Walhout
Networking at the second Interactome Meeting, Albertha J. M. Walhout
Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping, Albertha J. M. Walhout
C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO, Yamei Wang, Seung Wook Oh, Bart Deplancke, Jianyuan Luo, Albertha J. M. Walhout, and Heidi A. Tissenbaum
Publications from 2005
lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein, Ewa M. Davison, Melissa M. Harrison, Albertha J. M. Walhout, Marc Vidal, and H. Robert Horvitz
C. elegans tubby regulates life span and fat storage by two independent mechanisms, Arnab Mukhopadhyay, Bart Deplancke, Albertha J. M. Walhout, and Heidi A. Tissenbaum
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1, Christopher R. Vakoc, Danielle L. Letting, Nele Gheldof, Tomoyuki Sawado, M. A. Bender, Mark Groudine, Mitchell J. Weiss, Job Dekker, and Gerd A. Blobel
Publications from 2004
A gateway-compatible yeast one-hybrid system, Bart Deplancke, Denis Dupuy, Marc Vidal, and Albertha J. M. Walhout
A first version of the Caenorhabditis elegans Promoterome, Denis Dupuy, Qian-Ru Li, Bart Deplancke, Mike Boxem, Tong Hao, Philippe Lamesch, Reynaldo Sequerra, Stephanie Bosak, Lynn Doucette-Stamm, Ian A. Hope, David E. Hill, Albertha J. M. Walhout, and Marc Vidal
Identification of critical domains and putative partners for the Caenorhabditis elegans spindle component LIN-5, Ridgely Fisk Green, Monique A. Lorson, Albertha J. M. Walhout, Marc Vidal, and Sander van den Heuvel
Evidence for dynamically organized modularity in the yeast protein-protein interaction network, Jing-Dong J. Han, Nicolas Bertin, Tong Hao, Debra S. Goldberg, Gabriel F. Berriz, Lan V. Zhang, Denis Dupuy, Albertha J. M. Walhout, Michael E. Cusick, Frederick P. Roth, and Marc Vidal