Research Topics
| ALBERTHA WALHOUTSummaryAffiliation: University of Massachusetts Medical School Country: USA Publications
Research Grants
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Detail Information
Publications
A gateway-compatible yeast one-hybrid systemBart Deplancke
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genome Res 14:2093-101. 2004..Taken together, the Gateway-compatible Y1H system will allow the high-throughput identification of protein-DNA interactions and may be a valuable tool to decipher transcription regulatory networks...
Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mappingAlbertha J M Walhout
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genome Res 16:1445-54. 2006....- A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networksJohn S Reece-Hoyes
Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, School of Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
Genome Biol 6:R110. 2005.... - EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expressionM Inmaculada Barrasa
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
BMC Genomics 8:21. 2007..The rapidly increasing amount of protein-DNA interaction data at a genome scale requires a database that facilitates efficient data storage, retrieval and integration... - Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patternsJohn S Reece-Hoyes
Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Clarendon Way, Leeds, LS2 9JT, West Yorkshire, UK
BMC Genomics 8:27. 2007..elegans transcription factor genes was examined, in vivo, with a reporter gene approach... - What does biologically meaningful mean? A perspective on gene regulatory network validationAlbertha J M Walhout
Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Genome Biol 12:109. 2011..Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously... - Gene-centered regulatory networksH Efsun Arda
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
Brief Funct Genomics 9:4-12. 2010..Here, we will discuss gene-centered approaches that we employed to characterize GRNs and describe insights that we have obtained into the global design principles of gene regulation in complex metazoan systems... - Networking at the second Interactome MeetingAlbertha J M Walhout
University of Massachusetts Medical School, Program in Gene Function and Expression and Program in Molecular Medicine, 364 Plantation Street, LRB 605, Worcester, MA 01605, USA
Expert Rev Proteomics 3:477-9. 2006 - Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction networkVanessa Vermeirssen
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genome Res 17:1061-71. 2007..Taken together, we show that a core neuronal C. elegans protein-DNA interaction network possesses TF modules that relate to different functional aspects of the complete network... - A gene-centered C. elegans protein-DNA interaction networkBart Deplancke
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA
Cell 125:1193-205. 2006..We provide additional in vivo evidence for multiple PDIs and illustrate how the PDI network provides insights into metazoan differential gene expression at a systems level... - The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factorsJohn S Reece-Hoyes
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
Nucleic Acids Res 37:3689-98. 2009..Together, our data indicate that there are at least two types of CES-1 target genes and, therefore, that the molecular function of Snail-type TFs is more plastic than previously appreciated... - Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory networkH Efsun Arda
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Mol Syst Biol 6:367. 2010..As NHRs are metabolic sensors that are poised to respond to ligands, this suggests that C. elegans GRNs evolved to enable rapid and adaptive responses to different cues by a concurrence of NHR family expansion and modular GRN wiring... - Transcription factor functionality and transcription regulatory networksChristian A Grove
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
Mol Biosyst 4:309-14. 2008..Here, we discuss the factors that influence TF functionality and, hence, the functionality of the networks in which they operate... - Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegansArnab Mukhopadhyay
Program in Gene Function and Expression, Program in Molecular Medicine, Aaron Lazare Research Building, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
Nat Protoc 3:698-709. 2008..It takes approximately 10-12 d to obtain the worm culture for ChIP; the ChIP procedure is spaced out over a period of 2.5 d with two overnight incubations... - A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacityNatalia J Martinez
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genes Dev 22:2535-49. 2008..This "high flux capacity" suggests that loops provide a mechanism of high information flow for the coordinate and adaptable control of miRNA and TF target regulons... - The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegansMaria C Ow
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genes Dev 22:2520-34. 2008..Therefore, the FLH-1 and FLH-2 proteins likely play a more general role in regulating gene expression in embryos... - C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXOYamei Wang
Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA
Mech Ageing Dev 127:741-7. 2006..Finally, we show that DAF-16/FOXO also physically interacts with the 14-3-3 proteins. These results suggest that C. elegans 14-3-3 proteins can regulate longevity by cooperating with both SIR-2.1 and DAF-16/FOXO... - Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mappingVanessa Vermeirssen
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Nat Methods 4:659-64. 2007..Both strategies outperform library screens in terms of coverage, confidence and throughput. These versatile strategies can be adapted both to TFs in other systems and, likely, to other biomolecules and assays as well... - The interplay between transcription factors and microRNAs in genome-scale regulatory networksNatalia J Martinez
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Bioessays 31:435-45. 2009.... - A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factorsChristian A Grove
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Cell 138:314-27. 2009..For a video summary of this article, see the PaperFlick file available with the online Supplemental Data... - Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activityNatalia J Martinez
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genome Res 18:2005-15. 2008..Finally, our data suggest that post-transcriptional mechanisms contribute to differential miRNA expression. The data and strains described here will provide a valuable guide and resource for the functional analysis of C. elegans miRNAs...
Research Grants
- Identifying transcription factor binding sites in the C. elegans genomeALBERTHA WALHOUT; Fiscal Year: 2009..Since such studies are not feasible at the genome scale in humans or mice, we have chosen the worm (C. elegans) as a model system. ..
- Transcription networks in C elegans organogenesisALBERTHA WALHOUT; Fiscal Year: 2009..Since this is a conserved biological program, these TRNs may provide insights into mammalian differential gene expression as well. ..
- Identifying transcription factor binding sites in the C. elegans genomeALBERTHA JOHANNA WALHOUT; Fiscal Year: 2010..Since such studies are not feasible at the genome scale in humans or mice, we have chosen the worm (C. elegans) as a model system. ..
- Mapping worm fat gene networksALBERTHA WALHOUT; Fiscal Year: 2006..In addition, we recently developed a version of the yeast one-hybrid system that enables us to map fat TF-fat gene interactions in a high-throughput manner. ..
- Gene Regulatory Networks in Development and PhysiologyALBERTHA JOHANNA WALHOUT; Fiscal Year: 2010..Our studies will provide insights into the functions of GRNs during development and in a wide variety of physiological functions such as stress response, metabolism and fighting pathogenic infection. ..