ALBERTHA WALHOUT

Summary

Affiliation: University of Massachusetts Medical School
Country: USA

Publications

  1. pmc A gateway-compatible yeast one-hybrid system
    Bart Deplancke
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 14:2093-101. 2004
  2. ncbi request reprint Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping
    Albertha J M Walhout
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 16:1445-54. 2006
  3. pmc Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network
    H 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
  4. pmc Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants
    Federico De Masi
    Department of Medicine, Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 39:4553-63. 2011
  5. pmc Yeast one-hybrid assays for gene-centered human gene regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1050-2. 2011
  6. pmc Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1059-64. 2011
  7. pmc A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels
    Alex M Tamburino
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    G3 (Bethesda) 3:297-304. 2013
  8. pmc Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters
    Juan I Fuxman Bass
    Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA, Center for Autoimmune Genomics and Etiology CAGE, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA and Divisions of Rheumatology and Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA
    Nucleic Acids Res 42:153-62. 2014
  9. pmc Genetic adaptation to diet preserves longevity
    Albertha J M Walhout
    Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA Electronic address
    Cell Metab 19:177-8. 2014
  10. pmc Genomics in 2011: challenges and opportunities
    David J Adams
    Wellcome Trust Sanger Institute
    Genome Biol 12:137. 2011

Research Grants

  1. Identifying transcription factor binding sites in the C. elegans genome
    ALBERTHA WALHOUT; Fiscal Year: 2009
  2. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2005
  3. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2009
  4. Identifying transcription factor binding sites in the C. elegans genome
    ALBERTHA JOHANNA WALHOUT; Fiscal Year: 2010
  5. Identifying transcription factor binding sites in the C. elegans genome
    ALBERTHA WALHOUT; Fiscal Year: 2009
  6. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2009
  7. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2007
  8. Mapping worm fat gene networks
    ALBERTHA WALHOUT; Fiscal Year: 2006
  9. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2006
  10. Gene Regulatory Networks in Development and Physiology
    ALBERTHA JOHANNA WALHOUT; Fiscal Year: 2010

Collaborators

  • M Inmaculada Barrasa
  • John S Reece-Hoyes
  • Bart Deplancke
  • Heidi Tissenbaum
  • MARC contact VIDAL
  • Ian A Hope
  • Andreu Alibés
  • Victor Ambros
  • Martha L Bulyk
  • Michael Brent
  • MARK ALKEMA
  • Natalia J Martinez
  • Christian A Grove
  • H Efsun Arda
  • Maria C Ow
  • Lynn Doucette-Stamm
  • Reynaldo Sequerra
  • Alex M Tamburino
  • Vanessa Vermeirssen
  • Federico De Masi
  • Juan I Fuxman Bass
  • David J Adams
  • Arnab Mukhopadhyay
  • Yamei Wang
  • Nathan Beittel
  • Akihiro Mori
  • Matthew T Weirauch
  • Sean P Ryder
  • X Shirley Liu
  • Olivier Harismendy
  • Anastasia Vedenko
  • Alicia Oshlack
  • Chad L Myers
  • Luis Serrano
  • John L Rinn
  • Curtis Huttenhower
  • Stephen S Gisselbrecht
  • Bonnie Berger
  • Marc Van Gilst
  • Stefan Taubert
  • Colin C Conine
  • Keith R Yamamoto
  • Ben Tsuda
  • Lesley T MacNeil
  • Daniel E Newburger
  • Barbara Conradt
  • Howard S Silverman
  • Molly Hammell
  • Frederick P Roth
  • Philip H Olsen
  • Jenny Aurielle B Babon
  • César A Hidalgo
  • Albert Laszlo Barabasi
  • Seung Wook Oh
  • Jianyuan Luo

Detail Information

Publications30

  1. pmc A gateway-compatible yeast one-hybrid system
    Bart 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...
  2. ncbi request reprint Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping
    Albertha J M Walhout
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 16:1445-54. 2006
    ....
  3. pmc Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network
    H 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...
  4. pmc Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants
    Federico De Masi
    Department of Medicine, Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 39:4553-63. 2011
    ..Our study provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint for system-level studies of the DNA binding determinants of other TF families in different model organisms and humans...
  5. pmc Yeast one-hybrid assays for gene-centered human gene regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1050-2. 2011
    ..We present Y1H resources, including clones for 988 of 1,434 (69%) predicted human transcription factors, that can be used to detect both known and new interactions between human DNA regions and transcription factors...
  6. pmc Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1059-64. 2011
    ..eY1H assays will be an important tool for mapping gene regulatory networks in Caenorhabditis elegans and other model organisms as well as in humans...
  7. pmc A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels
    Alex M Tamburino
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    G3 (Bethesda) 3:297-304. 2013
    ..wRBP1.0 will provide a significant contribution toward the comprehensive delineation of posttranscriptional regulatory networks and will provide a resource for further studies regulation by RBPs...
  8. pmc Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters
    Juan I Fuxman Bass
    Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA, Center for Autoimmune Genomics and Etiology CAGE, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA and Divisions of Rheumatology and Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA
    Nucleic Acids Res 42:153-62. 2014
    ..Altogether, our data suggest that C. elegans gene regulation may be additive through the combined effects of multiple regulatory regions. ..
  9. pmc Genetic adaptation to diet preserves longevity
    Albertha J M Walhout
    Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA Electronic address
    Cell Metab 19:177-8. 2014
    ....
  10. pmc Genomics in 2011: challenges and opportunities
    David J Adams
    Wellcome Trust Sanger Institute
    Genome Biol 12:137. 2011
    ..What was their favorite paper of 2011? What are the challenges in their particular research area? Who has had the biggest influence on their careers? What advice would they give to young researchers embarking on a career in research?..
  11. pmc A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks
    John 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
    ....
  12. pmc EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression
    M 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...
  13. pmc Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns
    John 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...
  14. ncbi request reprint Networking at the second Interactome Meeting
    Albertha 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
  15. pmc What does biologically meaningful mean? A perspective on gene regulatory network validation
    Albertha 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...
  16. pmc Gene-centered regulatory networks
    H 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...
  17. pmc Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network
    Vanessa 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...
  18. ncbi request reprint A gene-centered C. elegans protein-DNA interaction network
    Bart 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...
  19. pmc The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors
    John 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...
  20. pmc Transcription factor functionality and transcription regulatory networks
    Christian 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...
  21. pmc Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans
    Arnab 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...
  22. ncbi request reprint C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO
    Yamei 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...
  23. pmc A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity
    Natalia 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...
  24. ncbi request reprint Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
    Vanessa 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...
  25. pmc The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans
    Maria 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...
  26. pmc A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors
    Christian 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...
  27. pmc Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
    Natalia 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...
  28. pmc The interplay between transcription factors and microRNAs in genome-scale regulatory networks
    Natalia 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
    ....

Research Grants12

  1. Identifying transcription factor binding sites in the C. elegans genome
    ALBERTHA 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. ..
  2. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2005
    ..Since this is a conserved biological program, these TRNs may provide insights into mammalian differential gene expression as well. ..
  3. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2009
    ..Since this is a conserved biological program, these TRNs may provide insights into mammalian differential gene expression as well. ..
  4. Identifying transcription factor binding sites in the C. elegans genome
    ALBERTHA 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. ..
  5. Identifying transcription factor binding sites in the C. elegans genome
    ALBERTHA 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. ..
  6. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2009
    ..Since this is a conserved biological program, these TRNs may provide insights into mammalian differential gene expression as well. ..
  7. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2007
    ..Since this is a conserved biological program, these TRNs may provide insights into mammalian differential gene expression as well. ..
  8. Mapping worm fat gene networks
    ALBERTHA 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. ..
  9. Transcription networks in C elegans organogenesis
    ALBERTHA WALHOUT; Fiscal Year: 2006
    ..Since this is a conserved biological program, these TRNs may provide insights into mammalian differential gene expression as well. ..
  10. Gene Regulatory Networks in Development and Physiology
    ALBERTHA 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. ..