Publications related to Coding region

The Genetics of Transcription Factor DNA Binding Variation

Bart Deplancke, Vincent Roland Julien Gardeux, Daniel Alpern

Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-DNA binding motifs. Variable TF-DNA interactions are therefore increasingly considered as key ...

Elsevier2016

An Optimization Based Coupling Method For Multiscale Problems

Assyr Abdulle, Alexander Shapeev

A new multiscale coupling method is proposed for elliptic problems with highly oscillatory coefficients with a continuum of scales in a subset of the computational domain and scale separation in complementary regions of the computational domain. A disconti ...

Society for Industrial and Applied Mathematics2016

Olfactory receptor pseudo-pseudogenes

Matteo Dal Peraro, Benoîte Bargeton

Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes(1). Although certain pseudogene-derived RNAs have regulatory roles(2), and some pseudogene fragments are tr ...

Nature Publishing Group2016

A two-state activation mechanism controls the histone methyltransferase Suv39h1

Beat Fierz

Specialized chromatin domains contribute to nuclear organization and regulation of gene expression. Gene-poor regions are di- and trimethylated at lysine 9 of histone H3 (H3K9me2 and H3K9me3) by the histone methyltransferase Suv39h1. This enzyme harnesses ...

Nature Publishing Group2016

Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

Denis Duboule, Jozsef Zakany, Guillaume Andrey, Leonardo Beccari, Anamaria Necsulea, Edgardo Rodriguez Carballo, Virginie Marcet

Vertebrate Hox genes encode transcription factors operating during the development of multiple organs and structures. However, the evolutionary mechanism underlying this remarkable pleiotropy remains to be fully understood. Here, we show that Hoxd8 and Hox ...

National Academy of Sciences2016

Stratification and therapeutic potential of PML in metastatic breast cancer

Evaristo Jose Planet Letschert

Patient stratification has been instrumental for the success of targeted therapies in breast cancer. However, the molecular basis of metastatic breast cancer and its therapeutic vulnerabilities remain poorly understood. Here we show that PML is a novel tar ...

Nature Publishing Group2016

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

Jiri Vanicek, Ray Marcel Marin Florez, Miroslav Sulc

The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/ ...

Oxford University Press2015

MATHICSE Technical Report: An optimization based coupling method for multiscale problems

Assyr Abdulle, Alexander Shapeev

A new multiscale coupling method is proposed for elliptic problems with highly oscillatory coefficients with a continuum of scales in a subset of the computational domain and scale separation in complementary regions of the computational domain. A disconti ...

MATHICSE2015

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

Anamaria Necsulea

Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs h ...

Oxford Univ Press2015

TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation

Michele De Palma, Mario Leonardo Squadrito

Despite its importance during viral or bacterial infections, transcriptional regulation of the interferon-beta gene (Ifnb1) in activated macrophages is only partially understood. Here we report that TRIM33 deficiency results in high, sustained expression o ...

Nature Publishing Group2015

Coding region

The Genetics of Transcription Factor DNA Binding Variation

An Optimization Based Coupling Method For Multiscale Problems

Olfactory receptor pseudo-pseudogenes

A two-state activation mechanism controls the histone methyltransferase Suv39h1

Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

Stratification and therapeutic potential of PML in metastatic breast cancer

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

MATHICSE Technical Report: An optimization based coupling method for multiscale problems

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation

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Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

The Genetics of Transcription Factor DNA Binding Variation

Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

Olfactory receptor pseudo-pseudogenes

A two-state activation mechanism controls the histone methyltransferase Suv39h1

Stratification and therapeutic potential of PML in metastatic breast cancer

An Optimization Based Coupling Method For Multiscale Problems

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation

MATHICSE Technical Report: An optimization based coupling method for multiscale problems