---
res:
  bibo_abstract:
  - Transcription factors, by binding to specific sequences on the DNA, control the
    precise spatio-temporal expression of genes inside a cell. However, this specificity
    is limited, leading to frequent incorrect binding of transcription factors that
    might have deleterious consequences on the cell. By constructing a biophysical
    model of TF-DNA binding in the context of gene regulation, I will first explore
    how regulatory constraints can strongly shape the distribution of a population
    in sequence space. Then, by directly linking this to a picture of multiple types
    of transcription factors performing their functions simultaneously inside the
    cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions
    between transcription factors and binding sites that lead to erroneous regulatory
    states -- and understand the constraints this places on the design of regulatory
    systems. I will then develop a generic theoretical framework to investigate the
    coevolution of multiple transcription factors and multiple binding sites, in the
    context of a gene regulatory network that performs a certain function. As a particular
    tractable version of this problem, I will consider the evolution of two transcription
    factors when they transmit upstream signals to downstream target genes. Specifically,
    I will describe the evolutionary steady states and the evolutionary pathways involved,
    along with their timescales, of a system that initially undergoes a transcription
    factor duplication event. To connect this important theoretical model to the prominent
    biological event of transcription factor duplication giving rise to paralogous
    families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription
    factors, a major family in humans, and focus on the patterns of evolution that
    paralogs have undergone in their various protein domains in the recent past. @eng
  bibo_authorlist:
  - foaf_Person:
      foaf_givenName: Roshan
      foaf_name: Prizak, Roshan
      foaf_surname: Prizak
      foaf_workInfoHomepage: http://www.librecat.org/personId=4456104E-F248-11E8-B48F-1D18A9856A87
  bibo_doi: 10.15479/at:ista:th6071
  dct_date: 2019^xs_gYear
  dct_isPartOf:
  - http://id.crossref.org/issn/2663-337X
  dct_language: eng
  dct_publisher: Institute of Science and Technology Austria@
  dct_title: Coevolution of transcription factors and their binding sites in sequence
    space@
...