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. This collection showcases the journal articles and other publications written by faculty and researchers of the Program in Systems Biology at the University of Massachusetts Medical School.

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Publications from 2012

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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 (Nature methods, 9-2-2012)

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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 (Genome biology, 8-13-2012)

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Yeast one-hybrid assays: A historical and technical perspective, John S. Reece-Hoyes and Albertha J. M. Walhout (Methods (San Diego, Calif.), 8-3-2012)

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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 (Science (New York, N.Y.), 6-15-2012)

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

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Hi-C: A comprehensive technique to capture the conformation of genomes, Jon-Matthew Belton, Rachel Patton McCord, Johan H. Gibcus, Natalia Naumova, Ye Zhan, and Job Dekker

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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

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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 (Nature, 5-17-2012)

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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 (Cell, 5-11-2012)

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Genome architecture and expression, Gary Felsenfeld and Job Dekker (Current opinion in genetics and development, 4-10-2012)

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

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

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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 (Cell, 3-2-2012)

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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 (Gene, 2-15-2012)

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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 (Molecular systems biology, 1-31-2012)

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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 (PloS one, 1-4-2012)

Publications from 2011

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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 (Genome biology, 12-28-2011)

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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

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

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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 (Nature methods, 10-30-2011)

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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

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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

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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

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

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

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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

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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

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

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

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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

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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

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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 (Nature structural and molecular biology)

Publications from 2010

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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

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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

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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

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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

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

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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

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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

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

Publications from 2009

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

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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

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

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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

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

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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

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

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

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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

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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

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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 (The Journal of biological chemistry, 3-27-2009)

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

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

Publications from 2008

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

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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

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

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Prolonged signaling at the parathyroid hormone receptor by peptide ligands targeted to a specific receptor conformation, Makoto Okazaki, Sebastien Ferrandon, Jean-Pierre Vilardaga, Mary L. Bouxsein, John T. Potts, and Thomas James Gardella

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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

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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

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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

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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

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Gene regulation in the third dimension, Job Dekker

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

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Coactivation of G protein signaling by cell-surface receptors and an intracellular exchange factor, Michael J. Lee and Henrik G. Dohlman (Current biology : CB, 2-12-2008)

Publications from 2007

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Chromosome conformation capture carbon copy technology, Josee Dostie, Ye Zhan, and Job Dekker

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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

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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

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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

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

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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

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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

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Mapping networks of physical interactions between genomic elements using 5C technology, Josee Dostie and Job Dekker

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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

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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

Publications from 2006

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Networking at the second Interactome Meeting, Albertha J. M. Walhout

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Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping, Albertha J. M. Walhout

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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

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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

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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

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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

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Mapping chromatin interactions by chromosome conformation capture, Adriana Miele, Nele Gheldof, Tomoko M. Tabuchi, Josee Dostie, and Job Dekker

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The three 'C' s of chromosome conformation capture: controls, controls, controls, Job Dekker

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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

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Gateway-Compatible Yeast One-Hybrid Screens, Bart Deplancke, Vanessa Vermeirssen, H. Efsun Arda, Albertha J. M. Walhout, and Natalia Julia Martinez

Publications from 2005

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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

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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

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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

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Differential regulation of G protein alpha subunit trafficking by mono- and polyubiquitination, Yuqi Wang, Louis A. Marotti Jr., Michael J. Lee, and Henrik G. Dohlman (The Journal of biological chemistry, 1-7-2005)

Publications from 2004

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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

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A gateway-compatible yeast one-hybrid system, Bart Deplancke, Denis Dupuy, Marc Vidal, and Albertha J. M. Walhout

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A mechanical basis for chromosome function, Nancy Kleckner, Denise Zickler, Gareth H. Jones, Job Dekker, Ruth Padmore, Jim Henle, and John N. Hutchinson

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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

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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

Publications from 2003

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Integrating 'omic' information: a bridge between genomics and systems biology, Hui Ge, Albertha J. M. Walhout, and Marc Vidal

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A closer look at long-range chromosomal interactions, Job Dekker (Trends in biochemical sciences, 6-27-2003)

Publications from 2002

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Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline, Albertha J. M. Walhout, Jerome Reboul, Olena Shtanko, Nicolas Bertin, Philippe Vaglio, Hui Ge, Hongmei Lee, Lynn Doucette-Stamm, Kristin C. Gunsalus, Aaron J. Schetter, Diane G. Morton, Kenneth J. Kemphues, Valerie Reinke, Stuart K. Kim, Fabio Piano, and Marc Vidal

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Integrated version of reverse two-hybrid system for the postproteomic era, Hideki Endoh, Sylvie Vincent, Yves Jacob, Eleonore Real, Albertha J. M. Walhout, and Marc Vidal

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Capturing chromosome conformation, Job Dekker, Karsten Rippe, Martijn Dekker, and Nancy Kleckner (Science (New York, N.Y.), 2-16-2002)

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MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans, Nancy N. Huang, Darcy E. Mootz, Albertha J. M. Walhout, Marc Vidal, and Craig P. Hunter

Publications from 2001

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A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome, Anne Davy, Paul Bello, Nicolas Thierry-Mieg, Philippe Vaglio, Joseph Hitti, Lynn Doucette-Stamm, Danielle Thierry-Mieg, Jerome Reboul, Simon J. Boulton, Albertha J. M. Walhout, Olivier Coux, and Marc Vidal