The Program in Systems Biology was established as a new interdisciplinary research program at UMass Medical School in 2012. The goal of systems biology as a field is to understand biological processes at a systems level rather than at the level of individual molecules. Systems biology capitalizes on technological advances in the areas of genomics and high-throughput instrumentation, with strong links to computational biology, math, statistics and bioinformatics. Leading the new program as co-directors are Job Dekker, PhD, professor of biochemistry & molecular pharmacology and molecular medicine and a member of the Program in Gene Function and Expression; and Marian Walhout, PhD, professor of molecular medicine. This collection showcases the journal articles, book chapters, and other publications and presentations written by faculty and researchers of the Program in Systems Biology at the University of Massachusetts Medical School.

Follow

Publications from 2014

PDF

Transcriptional regulation of Caenorhabditis elegans FOXO/DAF-16 modulates lifespan, Ankita Bansal, Eun-Soo Kwon, Darryl Conte Jr., Haibo Liu, Michael J. Gilchrist, Lesley T. MacNeil, and Heidi A. Tissenbaum

PDF

Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters, Juan I. Fuxman Bass, Alex M. Tamburino, Akihiro Mori, Nathan Beittel, Matthew T. Weirauch, John S. Reece-Hoyes, and Albertha J. M. Walhout

Link

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription, Luca Giorgetti, Rafael Galupa, Elphege P. Nora, Tristan Piolot, France Lam, Job Dekker, Guido Tiana, and Edith Heard

PDF

Defining functional DNA elements in the human genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, and ENCODE Project Consortium

PDF

Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6, Wan-Ju Liu, John S. Reece-Hoyes, Albertha J. M. Walhout, and David M. Eisenmann

Link

A nanoparticle-based combination chemotherapy delivery system for enhanced tumor killing by dynamic rewiring of signaling pathways, Stephen W. Morton, Michael J. Lee, Zhou J. Deng, Erik C. Dreaden, Elise Siouve, Kevin E. Shopsowitz, Nisarg J. Shah, Michael B. Yaffe, and Paula T. Hammond

Link

Genetic adaptation to diet preserves longevity, Albertha J. M. Walhout

Link

Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits, Emma Watson, Lesley T. MacNeil, Ashlyn D. Ritter, L. Safak Yilmaz, Adam P. Rosebrock, Amy A. Caudy, and Albertha J. M. Walhout

Link

Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy, Emma Watson and Albertha J. M. Walhout

Link

Determination and inference of eukaryotic transcription factor sequence specificity, Matthew T. Weirauch, Ally Yang, Mihai Albu, Atina G. Cote, Alejandro Montenegro-Montero, Philipp Drewe, Hamed S. Najafabadi, Samuel A. Lambert, Ishminder Mann, Kate Cook, Hong Zheng, Alejandra Goity, Harm van Bakel, Jean-Claude Lozano, Mary Galli, Mathew G. Lewsey, Eryong Huang, Tuhin Mukherjee, Xiaoting Chen, John S. Reece-Hoyes, Sridhar Govindarajan, Gad Shaulsky, Albertha J. M. Walhout, Francois-Yves Bouget, Gunnar Ratsch, Luis F. Larrondo, Joseph R. Ecker, and Timothy R. Hughes

Link

Worms, bacteria, and micronutrients: an elegant model of our diet, L. Safak Yilmaz and Albertha J. M. Walhout

Publications from 2013

Link

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data, Job Dekker, Marc A. Marti-Renom, and Leonid A. Mirny

Link

Biological techniques: Chromosomes captured one by one, Job Dekker and Leonid A. Mirny

Link

Nuclear biology: what's been most surprising, Job Dekker, Joanna Wysocka, Iain Mattaj, Erez Lieberman-Aiden, and Craig Pikaard

Link

The bromodomain protein Brd4 insulates chromatin from DNA damage signalling, Scott R. Floyd, Michael E. Pacold, Qiuying Huang, Scott M. Clarke, Fred C. Lam, Ian G. Cannell, Bryan D. Bryson, Jonathan Rameseder, Michael J. Lee, Emily J. Blake, Anna Fydrych, Richard Ho, Benjamin A. Greenberger, Grace C. Chen, Amanda Maffa, Amanda M. Del Rosario, David E. Root, Anne E. Carpenter, William C. Hahn, David M. Sabatini, Clark C. Chen, Forest M. White, James E. Bradner, and Michael B. Yaffe

Link

Using networks to measure similarity between genes: association index selection, Juan I. Fuxman Bass, Alos Diallo, Justin Nelson, Juan M. Soto, Chad L. Myers, and Albertha J. M. Walhout

Link

The Hierarchy of the 3D Genome, Johan H. Gibcus and Job Dekker

Link

High-throughput genome scaffolding from in vivo DNA interaction frequency, Noam Kaplan and Job Dekker

PDF

Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny, Satyendra Kumar, Robert Wuerffel, Ikbel Achour, Bryan R. Lajoie, Ranjan Sen, Job Dekker, Ann J. Feeney, and Amy L. Kenter

PDF

Food, pathogen, signal: The multifaceted nature of a bacterial diet, Lesley T. MacNeil and Albertha J. M. Walhout

Link

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

PDF

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

Link

Organization of the mitotic chromosome, Natalia Naumova, Maxim Imakaev, Geoffrey Fudenberg, Ye Zhan, Bryan R. Lajoie, Leonid A. Mirny, and Job Dekker

Link

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?, Elphege P. Nora, Job Dekker, and Edith Heard

Link

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

Link

Extensive Rewiring and Complex Evolutionary Dynamics in a C. elegans Multiparameter Transcription Factor Network, John S. Reece-Hoyes, Carles Pons, Alos Diallo, Akihiro Mori, Shaleen Shrestha, Sreenath Kadreppa, Justin Nelson, Stephanie Diprima, Amelie Dricot, Bryan R. Lajoie, Philippe Souza Moraes Ribeiro, Matthew T. Weirauch, David E. Hill, Timothy R. Hughes, Chad L. Myers, and Albertha J. M. Walhout

Link

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

PDF

Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments, Vlad Seitan, Andre Faure, Ye Zhan, Rachel Patton McCord, Bryan R. Lajoie, Elizabeth Ing-Simmons, Boris Lenhard, Luca Giorgetti, Edith Heard, Amanda Fisher, Paul Flicek, Job Dekker, and Matthias Merkenschlager

PDF

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

Link

Handbook of Systems Biology: Concepts and Insights, Albertha J. M. Walhout, Marc Vidal, and Job Dekker

Link

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

Publications from 2012

PDF

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

PDF

CTCF and cohesin help neurons raise their self-awareness, Job Dekker

Link

3C-based technologies to study the shape of the genome, Wouter de Laat and Job Dekker

PDF

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

PDF

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

Link

Genome architecture and expression, Gary Felsenfeld and Job Dekker

Link

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

Link

From cells to chromatin: Capturing snapshots of genome organization with 5C technology, Maria A. Ferraiuolo, Amartya Sanyal, Natalia Naumova, Job Dekker, and Josee Dostie

PDF

The context of gene expression regulation, Johan H. Gibcus and Job Dekker

Link

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

Link

Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks, Michael J. Lee, Albert S. Ye, Alexandra K. Gardino, Anne Margriet Heijink, Peter K. Sorger, Gavin MacBeath, and Michael B. Yaffe

Link

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

Link

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

Link

Analysis of long-range chromatin interactions using Chromosome Conformation Capture, Natalia Naumova, Emily M. Smith, Ye Zhan, and Job Dekker

Link

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

Link

Gene-centered yeast one-hybrid assays, John S. Reece-Hoyes and Albertha J. M. Walhout

Link

Yeast one-hybrid assays: A historical and technical perspective, John S. Reece-Hoyes and Albertha J. M. Walhout

PDF

The long-range interaction landscape of gene promoters, Amartya Sanyal, Bryan R. Lajoie, Gaurav Jain, and Job Dekker

Link

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

PDF

Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress, Andrea R. Tentner, Michael J. Lee, Gerry J. Ostheimer, Leona D. Samson, Douglas A. Lauffenburger, and Michael B. Yaffe

Link

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

Link

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

Link

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

PDF

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

PDF

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

Link

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

Link

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression, Lesley T. MacNeil and Albertha J. M. Walhout

Link

Translocation mapping exposes the risky lifestyle of B cells, Rachel Patton McCord and Job Dekker

Link

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

Link

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

Link

Chromatin globules: a common motif of higher order chromosome structure, Amartya Sanyal, Davide Bau, Marc A. Marti-Renom, and Job Dekker

PDF

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

Link

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

Link

Gene-centered regulatory network mapping, Albertha J. M. Walhout

PDF

What does biologically meaningful mean? A perspective on gene regulatory network validation, Albertha J. M. Walhout

Link

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

PDF

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

Link

Gene-centered regulatory networks, H. Efsun Arda and Albertha J. M. Walhout

PDF

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

PDF

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

Link

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

Link

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

PDF

Integrating one-dimensional and three-dimensional maps of genomes, Natalia Naumova and Job Dekker

Link

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

Link

Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization, Howard Y. Chang, Olivier Cuvier, and Job Dekker

PDF

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

Link

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

Link

My5C: web tools for chromosome conformation capture studies, Bryan R. Lajoie, Nynke L. van Berkum, Amartya Sanyal, and Job Dekker

Link

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

Link

The interplay between transcription factors and microRNAs in genome-scale regulatory networks, Natalia Julia Martinez and Albertha J. M. Walhout

PDF

Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions, Adriana Miele, Kerstin Bystricky, and Job Dekker

Link

Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C), Adriana Miele and Job Dekker

Link

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

PDF

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

Link

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase, Matthew P. Torres, Michael J. Lee, Feng Ding, Carrie Purbeck, Brian Kuhlman, Nikolay V. Dokholyan, and Henrik G. Dohlman

Link

Determining spatial chromatin organization of large genomic regions using 5C technology, Nynke L. van Berkum and Job Dekker

PDF

Getting an edge on human disease, Albertha J. M. Walhout

Publications from 2008

Link

Gene regulation in the third dimension, Job Dekker

Link

Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction, Job Dekker

PDF

Transcription factor functionality and transcription regulatory networks, Christian A. Grove and Albertha J. M. Walhout

Link

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

Link

Coactivation of G protein signaling by cell-surface receptors and an intracellular exchange factor, Michael J. Lee and Henrik G. Dohlman

PDF

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

PDF

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

Link

Long-range chromosomal interactions and gene regulation, Angela Miele and Job Dekker

Link

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

PDF

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

PDF

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

PDF

GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p, Job Dekker