KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

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The role of CDX2 in Caco-2 cell differentiation

Pascale Anderle Pedone

Background: CDX2 plays a key part in the differentiation of Caco-2 cells, a colon carcinoma derived cell line that undergoes spontaneous differentiation. The effect of CDX2 expression in Caco-2 cells over time in culture has not been studied yet on a genom ...

Elsevier2013

Identification of HMX1 target genes: A predictive promoter model approach

Purpose: A homozygous mutation in the H6 family homeobox 1 (HMX1) gene is responsible for a new oculoauricular defect leading to eye and auricular developmental abnormalities as well as early retinal degeneration (MIM 612109). However, the HMX1 pathway rem ...

Molecular Vision2013

Phosphorylation Regulates FOXC2-Mediated Transcription in Lymphatic Endothelial Cells

Nadine Fournier, Mauro Delorenzi, Nawal Houhou, Yan Agalarov

One of the key mechanisms linking cell signaling and control of gene expression is reversible phosphorylation of transcription factors. FOXC2 is a forkhead transcription factor that is mutated in the human vascular disease lymphedema-distichiasis and plays ...

Amer Soc Microbiology2013

UCNEbase – a database of ultra-conserved non-coding elements and genomic regulatory blocks

Philipp Bucher, Slavica Dimitrieva Janeva

UCNEbase (http://ccg.vital-it.ch/UCNEbase) is a free, web-accessible information resource on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs). It currently covers 4351 such elements in 18 different species. The majority ...

Oxford University Press2013

Corrinoid auxotrophy in the obligate organohalide respiring Dehalobacter restrictus

Christof Holliger, Julien Maillard, Aamani Rupakula Boyanapalli, Kiyan Shabestary

Background Corrinoids are an essential cofactor of reductive dehalogenases, the key enzymes of the environmental-friendly process of organohalide respiration (OHR). Dehalobacter restrictus strain PER-K23 is an obligate OHR bacterium (OHRB) able to conserve ...

2013

The Hourglass and the Early Conservation Models-Co-Existing Patterns of Developmental Constraints in Vertebrates

Pawel Lichocki

Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds to the early con ...

Public Library Science2013

Genomic analyses often involve scanning for potential transcription factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein's DNA-binding specificity, but ...

Nature Publishing Group2013

Protein synthesis is a template polymerization process composed by three main steps: initiation, elongation, and termination. During translation, ribosomes are engaged into polysomes whose size is used for the quantitative characterization of translatome. ...

Public Library of Science2013

Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements

Philipp Bucher, Slavica Dimitrieva Janeva

Motivation: Genomic context analysis, also known as phylogenetic profiling, is widely used to infer functional interactions between proteins but rarely applied to non-coding cis-regulatory DNA elements. We were wondering whether this approach could provide ...

Oxford University Press2012

The genome of Dehalobacter restrictus - high gene redundancy for a restricted metabolism

Christof Holliger, Julien Maillard, Aamani Rupakula Boyanapalli, Hauke Smidt

Organohalide respiration (OHR) is a bacterial anaerobic respiratory metabolism dedicated to use halogenated compounds as terminal electron acceptors. OHR bacteria are strictly anaerobic microorganisms which use reductive dehalogenases (RdhA) as key enzymes ...

2012

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Public Library of Science2013

Nature Publishing Group2013

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data

Vassily Hatzimanikatis

Julien Racle

Evaluation of methods for modeling transcription factor sequence specificity

Yue Zhao

Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements

Philipp Bucher, Slavica Dimitrieva Janeva

Oxford University Press2012