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.

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Publications from 2006

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

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

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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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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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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

Publications from 2004

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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 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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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

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

Publications from 2003

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A closer look at long-range chromosomal interactions, Job Dekker

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

Publications from 2002

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Capturing chromosome conformation, Job Dekker, Karsten Rippe, Martijn Dekker, and Nancy Kleckner

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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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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

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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

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

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High-throughput yeast two-hybrid assays for large-scale protein interaction mapping, Albertha J. M. Walhout and Marc Vidal

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Protein interaction maps for model organisms, Albertha J. M. Walhout and Marc Vidal

Publications from 2000

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A green fluorescent protein-based reverse two-hybrid system: application to the characterization of large numbers of potential protein-protein interactions, Hideki Endoh, Albertha J. M. Walhout, and Marc Vidal

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Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm, Albertha J. M. Walhout, Simon J. Boulton, and Marc Vidal

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GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes, Albertha J. M. Walhout, Gary F. Temple, Michael A. Brasch, James L. Hartley, Monique A. Lorson, Sander van den Heuvel, and Marc Vidal

Publications from 1999

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Protein interaction mapping in C. elegans using proteins involved in vulval development, Albertha J. M. Walhout, Raffaella Sordella, Xiaowei Lu, James L. Hartley, Gary F. Temple, Michael A. Brasch, Nicolas Thierry-Mieg, and Marc Vidal

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A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens, Albertha J. M. Walhout and Marc Vidal

Publications from 1998

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Sequences flanking the E-box contribute to cooperative binding by c-Myc/Max heterodimers to adjacent binding sites, Albertha J. M. Walhout, P. C. van der Vliet, and H. Th. M. Timmers

Publications from 1997

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c-Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene, Albertha J. M. Walhout, J. M. Gubbels, R. Bernards, P. C. van der Vliet, and H. Th. M. Timmers

Publications from 1993

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E1A functions as a coactivator of retinoic acid-dependent retinoic acid receptor-beta 2 promoter activation, Frank A. E. Kruyt, Gert E. Folkers, Albertha J. M. Walhout, Bas-jan M. van der Leede, and Paul T. van der Saag