Section: Publications

Postdoctoral Position Available

Marian Walhout, Ph.D.

Academic Role: Associate Professor

Faculty Appointment(s) In:
   Program in Gene Function and Expression
   Program in Molecular Medicine

Other Affiliation(s):
   Interdisciplinary Graduate Program

Representative Publications

2009

Grove, CA, F deMasi, MI Barrasa, DE Newburger, MJ Alkema, ML Bulyk and AJM Walhout (2009).  A multi-parameter network reveals extensive divergence between C. elegans bHLH transcription factors.  Cell, in press

Reece-Hoyes, JS, B Deplancke, MI Barrasa, J Hatzold, RB Smit, HE Arda, PA Pope, J Gaudet, B Conradt and AJM Walhout (2009).  The C. elegans snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors.  Nuc. Acids Res., Epub ahead of print April 16.

Martinez, NJ and AJM Walhout (2009). The interplay between transcription factors and microRNAs in genome-scale regulatory networks.  BioEssays, 31: 435-445.

2008

Martinez, NJ, MC Ow, JS Reece-Hoyes, MI Barrasa, VR Ambros and AJM Walhout (2008). Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity.  Genome Res., 18: 2005-2015.

Martinez, NJ, MC Ow, MI Barrasa, M Hammell, R Sequerra, L Doucette-Stamm, FP Roth, V Ambros and AJM Walhout (2008).  A C. elegans genome-scale microRNA network contains composite feedback loops with high flux capacity. Genes Dev., 22: 2535-2549.

Ow, MC, NJ Martinez, P Olsen, S Silverman, MI Barrasa, B Conradt, AJM Walhout and V Ambros (2008). The FLYWCH transcription factors FLH-1, FLH-2 and FLH-3 repress embryonic expression of microRNA genes in C. elegans. Genes Dev., 22: 2520-2534.

Grove, CA and AJM Walhout (2008). Transcription factor functionality and transcription regulatory networks. Mol. Biosyst., 4: 309-314.

Mukhopadhyay, A, B Deplancke, AJ Walhout and HA Tissenbaum (2008). Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat. Protocols, 3: 698-709.

2007

Vermeirssen, V, B Deplancke, MI Barrasa, JS Reece-Hoyes, HE Arda, CA Grove, NJ Martinez, R Sequerra, L Doucette-Stamm, MR Brent and AJ Walhout (2007). Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat. Methods, 4: 659-664.

Vermeirssen, V, MI Barrasa, CA Hidalgo, JA Babon, R Sequerra, L Doucette-Stamm, AL Barabasi and AJ Walhout (2007). Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res., 17: 1061-1071.

Barrasa, MI, P Vaglio, F Cavasino, L Jacotot and AJ Walhout (2007). EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics, 8: 21.

Reece-Hoyes, JS, J Shingles, D Dupuy, CA Grove, AJ Walhout, M Vidal and IA Hope (2007). Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics, 8: 27.

2006

Deplancke, B, V Vermeirssen, HE Arda, NJ Martinez and AJ Walhout (2006). Gateway-compatible yeast one-hybrid screens. CSH Protocols (online journal).

Walhout, AJ (2006) Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res., 16: 1445-1454.

Walhout, AJ (2006) Networking at the second Interactome Meeting. Expert Rev Proteomics, 3: 477-479.

Wang, Y, SW Oh, B Deplancke, J Luo, AJ Walhout and HA Tissenbaum (2006). C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO. Mech Ageing and Dev., 127: 741-747.

Deplancke, B, A Mukhopadhyay, W Ao, AE Elewa, CA Grove, NJ Martinez, R Sequerra, L Doucette-Stamm, JS Reece-Hoyes, IA Hope, HA Tissenbaum, SE Mango and AJ Walhout (2006). A gene-centered C. elegans protein-DNA interaction network. Cell, 125: 1192-1205.

2005

Mukhopadhyay, A, B Deplanke, AJ Walhout and HA Tissenbaum. 2005. C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metabolism, 2: 35-42.

Davison, EM, MM Harrison, AJ Walhout, M Vidal and B Horvitz. 2005. lin-8, which antagonizes C. elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein. Genetics, 171: 1017-1031.

Walhout, AJ and SJ Boulton. 2005. Biochemistry and Molecular Biology. Wormbook, eds. The C. elegans Research Community, WormBook, http://www.wormbook.org

Reece-Hoyes*, JS, B Deplancke*, J Shingles, CA Grove, IA Hope and AJ Walhout. 2005. A compendium of C. elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biology, 6: R110. (* indicates co-first author)

2004

Fisk Green, R, M Lorson, AJ Walhout, M Vidal and S van den Heuvel. 2004. Identification of critical domains and putative partners for the Caenorhabditis elegans spindle component LIN-5. Molecular Genetics and Genomics, 271: 532-544.

Han, JD, N Bertin, T Hao, DS Goldberg, GF Berriz, LV Zhang, D Dupuy, AJ Walhout, ME Cusick, FP Roth and M Vidal. 2004. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430: 88-93.

Dupuy, D, QR Li, B Deplancke, M Boxem, T Hao, P Lamesch, R Sequerra, S Bosak, L Doucettte-Stamm, IA Hope, DE Hill, AJ Walhout and M Vidal. 2004. A first version of the Caenorhabditis elegans promoterome. Genome Research, 14: 2169-2175.

Deplancke, B, D Dupuy, M Vidal and AJ Walhout. 2004. A Gateway-compatible yeast one-hybrid system. Genome Research, 14: 2093-2101.

2003

Ge, H, AJ Walhout and M Vidal. 2003. Integrating "omic" information: a bridge between genomics and systems biology. Trends in Genetics, 19: 551-560.

2002

Walhout, AJ, J Reboul, O Shtanko, N Bertin, P Vaglio, H Ge, H Lee, L Doucette-Stamm, KC Gunsalus, AJ Schetter, DG Morton, KJ Kemphues, V Reinke, SK Kim, F Piano and M Vidal. 2002. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Current Biology, 12: 1952-1958.

2001

Walhout, AJ and M Vidal. 2001. Protein interaction maps for model organisms. Nature Reviews Molecular Cell Biology 2: 55-62.

Walhout, AJ and M Vidal. 2001. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24: 297-306.

Davy, A, P Bello, N Thierry-Mieg, P Vaglio, J Hitti, L Doucette-Stamm, D Thierry-Mieg, J Reboul, S Boulton, AJ Walhout, O Coux and M Vidal. 2001. A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Reports, 2: 821-828.

2000

Walhout, AJ, R Sordella, MA Brasch, G Temple, JL Hartley, N Thierry-Mieg and M Vidal. 2000. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287: 116-122.

Walhout, AJ, G Temple, MA Brasch, JL Hartley, MA Lorson, S van den Heuvel and M Vidal. 2000. GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods in Enzymology, “Chimeric genes and proteins” 328: 575-592.

Endoh, H, AJ Walhout and M Vidal. 2000. A green fluorescent protein-based reverse two-hybrid system: application to the characterization of large numbers of potential protein-protein interactions. Methods in Enzymology, "Chimeric genes and proteins" 328: 74-88.

Walhout, AJ, SJ Boulton and M Vidal. 2000. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17: 88-94.

1999

Walhout, AJ and M Vidal.  1999. A Genetic Strategy to Eliminate Self-Activator Baits Prior to High-Throughput Yeast Two-Hybrid Screens. Genome Res. 9: 1128-1134.

1998

Walhout M, H Endoh, W Wong, N Thierry-Mieg and M Vidal. 1998. A model of elegance. Am. J. Hum. Gen., 63: 955-961.

Phone: 508-856-4364
E-mail: Marian.Walhout@umassmed.edu
Keywords: Organisms - C. elegans, Systems Biology, Gene Expression, Protein-DNA recognition

More on Marian Walhout's Research Research | Publications | Rotations | Personnel | Biography View All Sections on One Page

Postdoctoral Position Available A postdoctoral position is available to study in this laboratory.  Please contact Dr. Walhout for additional details.