Transcription closed and open complex formation coordinate expression of genes with a shared promoter region

Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters

(2018) Fatemeh Behjati Ardakani et al.   Epigenetics & Chromatin

Pervasive coexpression of spatially proximal genes is buffered at the protein level

(2017) Georg Kustatscher et al.   Molecular Systems Biology

Dissecting the stochastic transcription initiation process in liveEscherichia coli

(2016) Jason Lloyd-Price et al.   DNA RESEARCH

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

(2016) Irina O. Vvedenskaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of cell-to-cell variability in divergent gene expression

(2016) Chao Yan et al.   Nature Communications

Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements

(2016) Samuel M. D. Oliveira et al.   PLoS Computational Biology

Free RNA polymerase in Escherichia coli

(2015) Michael Patrick et al.   BIOCHIMIE

Characterizing rate limiting steps in transcription from RNA production times in live cells

(2015) Antti Häkkinen et al.   BIOINFORMATICS

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

Estimation of fluorescence-tagged RNA numbers from spot intensities

(2014) A. Hakkinen et al.   BIOINFORMATICS

Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data

(2014) A. Hakkinen et al.   BIOINFORMATICS

CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli

(2013) Antti Häkkinen et al.   BIOINFORMATICS

Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time

(2012) Leonardo Martins et al.   JOURNAL OF THEORETICAL BIOLOGY

Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells

(2012) Anantha-Barathi Muthukrishnan et al.   NUCLEIC ACIDS RESEARCH

Chromatin is an ancient innovation conserved between Archaea and Eukarya

(2012) Ron Ammar et al.   eLife

Single-Molecule Studies of Transcription: From One RNA Polymerase at a Time to the Gene Expression Profile of a Cell

(2011) Feng Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse

(2011) Antti Häkkinen et al.   JOURNAL OF THEORETICAL BIOLOGY

Direct and indirect effects in the regulation of overlapping promoters

(2011) Kristian Moss Bendtsen et al.   NUCLEIC ACIDS RESEARCH

Translation-Independent Localization of mRNA in E. coli

(2011) K. Nevo-Dinur et al.   SCIENCE

Functional consequences of bidirectional promoters

(2011) Wu Wei et al.   TRENDS IN GENETICS

Potent Transcriptional Interference by Pausing of RNA Polymerases over a Downstream Promoter

(2009) Adam C. Palmer et al.   MOLECULAR CELL

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

(2009) Alfredo Mendoza-Vargas et al.   PLoS One

Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression

(2008) J. M. Pedraza et al.   SCIENCE