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SUMMARY:Accurate Quantification of DNA Recognition and Methylation Readout
  by Transcription Factors
DTSTART:20170523T121500
DTEND:20170523T131500
DTSTAMP:20260527T190420Z
UID:4b26bc0351b33573a9d70a3f52b20ef345812dfe15088f6717d060ec
CATEGORIES:Conferences - Seminars
DESCRIPTION:Prof. Harmen J. Bussemaker\, Columbia University\, NYC\, NY (U
 SA)\nBIOENGINEERING SEMINAR\n\nAbstract:\nMutations in non-coding DNA are
  increasingly found to be associated with human disease\, yet we currentl
 y lack robust methods for predicting transcription factor (TF) binding 
 from sequence\, especially at lower affinities. We developed a versatile m
 aximum likelihood framework named No Read Left Behind (NRLB) that fits
  a biophysical model of protein-DNA recognition to sequencing-based in v
 itro TF binding data\, across the full affinity range. NRLB predicts 
 human Max homodimer binding in near-perfect agreement with existing low-t
 hroughput measurements. The model captures the specificity of p53 tetrame
 ric binding sites and discovers multiple binding modes in a single sampl
 e. Additionally\, we confirm that newly-identified low-affinity enhancer 
 binding sites are functional in vivo\, and that their contribution to 
 gene expression matches their predicted affinity. We will also describe Ep
 iSELEX-seq\, our method for quantifying the sensitivity of TF binding to c
 ytosine methylation in a context-specific manner\, and its application to 
 Hox and bZIP complexes as well as p53. Finally\, we will discuss our effor
 ts to decipher the autonomous rules of transcriptional control in human ce
 lls using a massively parallel reporter assay named Survey of Regulatory E
 lements (SuRE)\, coupled with statistical analysis using generalized linea
 r models.\n\nBio:\nExperience\n    Associate Professor\n    Columbia
  University\, NYC\, NY (USA)\n    Professor\, Departments of Biological
  Sciences and Systems Biology\n    Columbia University\, NYC\, NY (USA
 )\n    2014 – Present\n\nEducation\n    Utrecht University (NL)\n
     Doctor of Philosophy (Ph.D.)\, Physics\n    1991 – 1995\n\n 
    Utrecht University (NL)\n    Master's degree\, Physics\n    198
 9 – 1991\n\n    Utrecht University (NL)\n    Bachelor's degree\, P
 hysics\n    1986 – 1989
LOCATION:SV 1717 https://plan.epfl.ch/?room==SV%201717
STATUS:CONFIRMED
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