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List of works by Cedric Notredame

1. Multichannel Sequence Analysis Applied to Social Science Data

article

3DCoffee: combining protein sequences and structures within multiple sequence alignments

scientific article published in July 2004

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment

scientific article published on July 2004

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

A field guide for the compositional analysis of any-omics data

scientific article published on 01 September 2019

A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis

scientific article published on January 2010

A user-friendly web portal for T-Coffee on supercomputers

scientific article

AMPA: an automated web server for prediction of protein antimicrobial regions.

scientific article published on 3 November 2011

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.

scientific article

APDB: a web server to evaluate the accuracy of sequence alignments using structural information

scientific article published on October 2006

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

scientific article

Alignathon: a competitive assessment of whole-genome alignment methods

scientific article

An improved understanding of TNFL/TNFR interactions using structure-based classifications

scientific article published on 11 July 2012

BlastR--fast and accurate database searches for non-coding RNAs

scientific article

Breen et al. reply

scientific article published in Nature

CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis.

scientific article published on 27 September 2015

CaspR: a web server for automated molecular replacement using homology modelling

scientific article published on July 2004

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

scientific article published on 6 July 2010

Computing multiple sequence/structure alignments with the T-coffee package

scientific article published in February 2004

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

scientific article

Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite proliferation and viability

scientific article

Detecting and comparing non-coding RNAs in the high-throughput era

scientific article published on 24 July 2013

Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations

scientific article

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

scientific article

Epistasis as the primary factor in molecular evolution

scientific article published on 14 October 2012

Evolutionary Footprints Reveal Insights into Plant MicroRNA Biogenesis.

scientific article

Exploiting parallelism on progressive alignment methods

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

scientific article

Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift

scientific article published on October 2015

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

scientific article

Extinction and reinstatement of an operant responding maintained by food in different models of obesity

scientific article published on 28 December 2017

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

scientific article

Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions

scientific article

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

scientific article

Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani

scientific article published on 6 November 2017

High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools

article published in 2015

How Much Does It Cost?

How should we measure proportionality on relative gene expression data?

scientific article

Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance

scientific article

Improved definition of the mouse transcriptome via targeted RNA sequencing

scientific article published on May 2016

Improving multiple sequence alignment biological accuracy through genetic algorithms

Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words

scientific article

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

scientific article published on 06 February 2019

Large multiple sequence alignments with a root-to-leaf regressive method

scientific article published on 02 December 2019

Long noncoding RNAs with enhancer-like function in human cells

scientific article (publication date: October 2010)

M-Coffee: combining multiple sequence alignment methods with T-Coffee

scientific article

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

scientific article published in 2010

Multiple sequence alignment modeling: methods and applications

scientific article

Nextflow enables reproducible computational workflows

scientific article

Nextflow, an efficient tool to improve computation numerical stability in genomic analysis

scientific article published in January 2017

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments

scientific article

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases

scientific article published on 22 April 2016

Performance analysis of computational approaches to solve Multiple Sequence Alignment

Pharmacological assessment defines Leishmania donovani casein kinase 1 as a drug target and reveals important functions in parasite viability and intracellular infection

scientific article published on 23 December 2013

Predicting phenotypic traits of prokaryotes from protein domain frequencies

scientific article

Principal Component Analysis of the Effects of Environmental Enrichment and (-)-epigallocatechin-3-gallate on Age-Associated Learning Deficits in a Mouse Model of Down Syndrome

scientific article

R-Coffee: a method for multiple alignment of non-coding RNA

scientific article

R-Coffee: a web server for accurately aligning noncoding RNA sequences

scientific article

Recent evolutions of multiple sequence alignment algorithms

scientific article

Recent progress in multiple sequence alignment: a survey

scientific article (publication date: 2002)

Recovering accuracy methods for scalable consistency library

SAGA: sequence alignment by genetic algorithm

scientific article

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

scientific article

STRIKE: evaluation of protein MSAs using a single 3D structure

scientific article published on 28 October 2011

Scalability and accuracy improvements of consistency-based multiple sequence alignment tools

Segment-based multiple sequence alignment

scientific article

Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets

scientific article

T-Coffee: A novel method for fast and accurate multiple sequence alignment

scientific article (publication date: 8 September 2000)

T-Coffee: Tree-based consistency objective function for alignment evaluation

scientific article published in January 2014

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

scientific article

T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors

scientific article published on 13 May 2010

T-RMSD: a web server for automated fine-grained protein structural classification ⬇️

scientific article published on May 28, 2013

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction

scientific article (publication date: June 2014)

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

scientific article

Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments

scientific article

Ten steps to get started in Genome Assembly and Annotation

scientific article published on 05 February 2018

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

scientific article

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods

scientific article published on 25 May 2007

The iRMSD: a local measure of sequence alignment accuracy using structural information

scientific article

The impact of Docker containers on the performance of genomic pipelines

scientific article

The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences

scientific article published on November 2011

Third Report on Chicken Genes and Chromosomes 2015.

scientific article published on 14 July 2015

Time-course and dynamics of obesity-related behavioral changes induced by energy-dense foods in mice.

scientific article published on 10 January 2018

Transcript profiling of jasmonate-elicited Taxus cells reveals a β-phenylalanine-CoA ligase.

scientific article published on 21 April 2015

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

scientific article

Use of ChIP-Seq data for the design of a multiple promoter-alignment method

scientific article

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

scientific article published on November 2011

Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time.

scientific article

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