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SUMMARY:An inferred model of the Bacillus subtilis global transcriptional 
 regulatory network
DTSTART:20140616T140000
DTSTAMP:20260428T025032Z
UID:5462382ade0e920282f8b2e4c5465e18511461ecf20cabebad0d38fd
CATEGORIES:Conferences - Seminars
DESCRIPTION:Prof. Patrick Eichenberger\, Department of Biology\, New York 
 University\nWe present a global model of the Bacillus subtilis gene regula
 tion network.  Our model is based on the analysis of two large transcript
 omics datasets (a public dataset from the BaSysBio consortium and our more
  recently collected dataset that includes many time series over a variety 
 of experimental conditio ns). In order to identify potentially causative r
 elationships between transcription regulators (such as DNA binding protein
 s and small regulatory RNAs) and their target genes\, we used an updated v
 ersion of the network inference algorithm Inferelator . Our novel computat
 ional approach integrates previously validated network edges (priors) and 
 estimated transcription factor activities (TFA) to dramatically improve th
 e accuracy of the predictions. Our model currently incorporates 240 putati
 ve regulators and pre dicts 4\,348 regulatory interactions. About a quarte
 r of these interactions are dependent on alternative sigma factors. We sho
 w that a majority of these predictions are supported in microarray experim
 ents comparing wild type to mutant strains (where the gen e encoding the r
 egulator of interest has been knocked out). Our network model will help to
  accelerate the pace of gene function discovery in B. subtilis and other G
 ram - positive species. Initial exploration of the model reveals many gene
 s of previously unkn own function that are co - regulated with other genes
  involved in various aspects of B.  subtilis biology\, including sporulat
 ion\, biofilm formation\, competence\, motility\, stress responses and met
 abolism.  As an example of functional validation of the network p redicti
 ons\, we highlight the characterization of a novel group of sporulation ge
 nes encoding enzymes involved in spore polysaccharide synthesis.\nBio: Aft
 er studying Biochemistry and Molecular Biology\, I obtained my Ph.D. from 
 the University of Geneva in 1997. My doctoral work in the laboratory of Pr
 of. Hans Geiselmann focused on the analysis of mechanisms of transcription
 al activation in the bacterium Escherichia coli. Then\, as a post-doctoral
  fellow\, I moved to the laboratory of Prof. Richard Losick at Harvard\, w
 here I spent six wonderful years investigating various aspects of sporulat
 ion in Bacillus subtilis with a special emphasis on genome-wide identifica
 tion of sporulation genes. I joined NYU Biology’s department as an Assis
 tant Professor in October 2004.
LOCATION:SV 1717a http://map.epfl.ch/?room=sv1717a
STATUS:CONFIRMED
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