BIstrO

Adress
300 boulevard Sébastien Brant 67412 Illkirch
Structure(s)
CNRS
Unit:
UMR7357
Regional Center
IFB North East
Website
BIstrO
Scientific leader
Thompson Julie
Technical leader
Cognat Valérie
Certificat(s)
  • ISO 9001
Annual visits:
10 200 an
Unique visits:
1 800 an
Quotes:
1
Latest update:
Not documented

PlantRNA

Description

Database of annotated tRNA sequences from plants.
Cognat et al, Nucleic Acids Res. 2013 41: D273-D279.

Access conditions

Free Web access : http://plantrna.ibmp.cnrs.fr/

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
7
Latest update:
01-07-2006

CYPedia

Description

Database of P450 cytochromes from plants.
Ehlting J, et al. BMC Plant Biol. 2008 8:47; Ehlting J, et al. Biochem Soc Trans 2006, 34:1192-1198

Access conditions

Free Web access : http://www-ibmp.u-strasbg.fr/~CYPedia/

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
22
Latest update:
01-02-2014

Orthoinspector

Description

Database describing orthology/inparalogy relations and a suite of tools to exploit these data.
Linard et al. BMC Bioinformatics. 2011 12:11

Access conditions

Free Web or download access

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
1
Latest update:
01-02-2012

EvoluCode

Description

Evolutionary barcodes, representing evolutionary histories of the complete human proteome at the vertebrate scale.
Linard et al. Evol Bioinform Online. 2012 8:61-77

Access conditions

Free Web access

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
78
Latest update:
01-12-2011

BAliBASE

Description

Database of multiple sequence alignments, used as a benchmark for the comparative evaluation of algorithms.
Prosdocimi et al. PLoS One. 2011 6(3):e18093.  (538)

Access conditions

Free Web or download access.

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Latest update:
01-06-2013

GxDB

Description

Database of transcriptomic data with automatic and standardized analyses.
Poidevin et al. 2014 Manuscript in preparation

Access conditions

Free Web access after user identification.

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Latest update:
Not documented

MousePat

Description

Analysis of the expression of nuclear receptors in the brains of adult mice. Collection of qPCR and in situ hybridization results.
Gofflot et al. Cell, 2007 131, 405-41.

Access conditions

Free Web access : www.ics-mci.fr/mousepat

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Latest update:
01-11-2015

MouseCre

Description

Database of CreERT2 lines of the ICS, with their characterization in different tissues and organs.

Access conditions

Free Web access : www.ics-mci.fr/mousecre

Annual visits:
10 000 an
Unique visits:
8 000 an
Quotes:
Not documented
Latest update:
Not documented

ICS Mouse Zoo

Description

Database of genetically modified mice lines generated by the ICS. Standardized database of mouse models compatible with international standards, also including phenotypic parameters and metadata. These data are exchanged with the reference centres in the field and we develop statistical analyses in line with our data capture.

Access conditions

www.ics-mci.fr/en/resources-and-technologies/eucomm-lines/
www.ics-mci.fr/en/resources-and-technologies/nuclear-receptor-zoo
www.ics-mci.fr/en/resources-and-technologies/phenomin-lines

Annual visits:
Not documented
Unique visits:
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Quotes:
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Latest update:
Not documented

dbSTAR

Description

A reference DataBase of human STructural vARiation from sequencing data

Access conditions

Téléchargement libre. http://dbstar.lbgi.fr/dbstar/

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
21
Downloads:
Not documented

Assemble2

Description

Assemble2 allows the design of RNA 2D structures interactively, creation and assembly of the corresponding RNA 3D modules directly in UCSF Chimera. The available services include 2D prediction, a database of structural motifs, 3D alignment of RNA sequences and annotation of 3D structures.
Jossinet et al. Bioinformatics. 2010 26:2057-9

Access conditions

Free Web access

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

GETEC

Description

ANALYSIS OF SEQUENCES
Determination of evolutionary analytical solutions for genetic motifs based on the substitution, insertion, and deletion as a function of time or the sequence length, as well as in the direct time direction (past-present) or in the reverse time direction (present-past)
Bernard et al. 2014 (submitted)

Access conditions
No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
21
Downloads:
Not documented

Macsims

Description

ANALYSIS OF SEQUENCES
MACSIMS is an information management system for data related to multiple alignments that combines protein structural and functional knowledge with ab initio predictions.
Thompson et al. BMC Bioinformatics. 2006 318

Access conditions

Free access web site

Annual visits:
Not documented
Unique visits:
1 584 an
Quotes:
6
Downloads:
Not documented

MSDA

Description

A software suite and databases for the interpretation of data from proteomic analyses by mass spectrometry (database search tools, de novo sequencing pipeline, extraction of protein functional annotations, extraction of spectra based on spectral quality criteria,...).
Carapito et al. Proteomics. 2014 14:1014-1019.

Access conditions

Free Web access

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

NGS-QC Generator

Description

ANALYSIS OF THE DATA NGS - QUALITY CONTROL OF READINGS
Universal quality control system for ChIP-seq and NGS 'enrichment-based' data (www.ngs-qc.org). The NGS-QC database hosts QC descriptors for 6066 publicly available data sets.
Mendoza-Parra et al. A quality control system for profiles obtained by ChIP sequencing Nucleic Acids Res. 2013 41:e196.
 
NB : content continuously updated to maintain coverage of all public data sets

Access conditions

Free Web access for the academic research community. Premium access is also available on request.

Annual visits:
Not documented
Unique visits:
280 an
Quotes:
Not documented
Downloads:
Not documented

GalaxEast

Description

The objective of GalaxEast (http://www.galaxeast.fr) is to provide a reliable public Galaxy instance, with guaranteed availability and accessibility. GalaxEast offers a catalogue of about a hundred tools, mainly for handling of sequencing data (ChIP-seq, RNA-seq and DNAseq) high speed. The addition of proteomic and spectroscopy data analysis tools is planned for 2014. The tools come from both the official Galaxy toolshed and the developments of bioinformaticians from the local community. The new tools will be made available in the platform toolshed. The platform has a wiki that allows users to find documentation and request the addition of new tools and genomes.

Access conditions

Open access for the French academic research community.
Access facilitated via rapid connexions (eg : Osiris, Renater)

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

PipeAlign

Description

An online workflow for Multiple Sequence Alignment.

Plewniak F, et al. PipeAlign: A new toolkit for protein family analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3829-32.
Access conditions

http://galaxy.bioinfo-bistro.fr/galaxy/

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

OrthoInspector

Description

Rapid detection of orthology and inparalogy relations.

Linard B, et al. OrthoInspector: comprehensive orthology analysis and visual exploration. BMC Bioinformatics. 2011 Jan 10;12:11.
Access conditions

http://bioinfo-bistro.fr/orthoinspector/

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

GETEC

Description

Genome Evolution by Transformation, Expansion and Contraction.

Access conditions

http://icube-bioinfo.u-strasbg.fr/webMathematica/GETEC/Accueil.jsp

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

VaRank

Description

Comprehensive workflow for annotating and ranking SNVs and indels from next generation sequencing data.

Geoffroy V, et al. VaRank: a simple and powerful tool for ranking genetic variants. PeerJ 2015 3:e796

Access conditions

Source code avaiilable : http://www.lbgi.fr/VaRank/

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

EASEA Cloud

Description

EASEA (EAsy Specification of Evolutionary Algorithms) is an Artificial Evolution platform to implement evolutionary algorithms.

Collet P, et al. EASEA : un langage de spécification pour les algorithmes évolutionnaires. [Rapport de recherche] RR-4218, INRIA. 2001.

Access conditions

Available at http://easea.unistra.fr/easea/index.php/EASEA_platform

Domains of activity
  • Biomedical
  • Agri-food
  • Environment
  • Biotechnology
  • Biology
Description of expertise domains
• Integrative Plant Biology (silencing, epigenetics, pathogen-host interactions, cell cycle,...) 
• Rare genetic diseases (ciliopathies, retinopathies, myopathies,...) structural, functional, comparative genomics
• Development of quantitative methods based on mass spectrometry and their application to biological systems
• Non-coding RNA: architecture, mechanisms of evolution, and roles in pathogenicity
• Study of micro-organisms adapted to extreme environmental conditions
• Trans-disciplinary research at the interface of biology, biochemistry, physics, and medicine

 

 

The BISTRO platform regroups several bioinformatics platforms/services in various research institutes in Strasbourg:

 

Molecular Genetics, Genomics, Microbiology (GMGM)

The study of microorganisms adapted to extreme environmental conditions can reveal unsuspected microbial capabilities. Their understanding, including metabolic functions and biofilm formation involved in the adaptation to specific conditions is a major objective of environmental microbiology. We study these microbial adaptation mechanisms in ecosystems contaminated by toxic elements at 3 levels: (i) isolation of new strains and characterization of their metabolic properties, (ii) study of the adaptive response to toxic metals in laboratory conditions, (iii) study of environments contaminated to understand the functioning of the in-situ microbial communities.

 

Institute of Molecular and Cellular Biology (IBMC)

 

The "evolution of yeast non-coding RNA" team focuses on the role and evolution of ncRNA in biological mechanisms. These RNA have been known for a long time, but it was thought they were only "infrastructural components" of the translational machinery, leftovers of an ancestral "all RNA" world: ribosomal RNA, transfer RNA, intron RNA, as well as small nucleolar RNA. Through experimental and bioinformatics approaches, we are particularly interested in: (i) the study of structure-function relationships in certain families of ncRNA (ribosomes, riboswitches,...), (ii) the identification and the study of new ncRNA involved in pathogenicity mechanisms in certain yeast species.

 

Institute of Plant Molecular Biology (IBMP)

The research activity is dedicated to the study of the fundamental mechanisms of plant life, with applications including notably in the biotechnology or medical research fields. The studied areas are very diverse: (i) biosynthesis of bioactive molecules (involved in the development of materials, cosmetics, aromas or drugs) and their regulation, (ii) plant viruses, (iii) large regulatory pathways enabling the development and reproduction of plants and adaptation to their environment, (iv) the biogenesis of organelles, chloroplasts, and mitochondria, essential for the cells’ energy production and whose malfunction can cause highly deleterious effects with respect to cellular life.

 

Laboratory of engineering science, computer science and imaging (ICube)

The Complex systems and Translational Bioinformatics (CSTB), covers a broad spectrum of research in computer science: integrative bioinformatics and genomics, theoretical bioinformatics, data mining, knowledge engineering, and stochastic optimization. In the bioinformatics field, we focus primarily on the field of health, notably the study of rare genetic diseases, and the understanding of patho-physiological mechanisms involved in these diseases. These mechanisms often have a potential interest for the understanding of biological processes altered in more common diseases, such as obesity, diabetes or cancer.

 

Institute of Genetics and Molecular and Cellular Biology (IGBMC)

The objective of the Institute is to develop interdisciplinary research at the interface of biology, biochemistry, physics and medicine. We explore very diverse themes, combining basic and applied research in the field of health. The research work also concerns very diverse topics, ranging from structural analysis of proteins in human genetics, stem cells, biophysics and epigenetics. The scientific results have already allowed significant progress, notably in the understanding of many human diseases such as certain cancers or rare genetic diseases.

 

Mouse Clinic Institute (ICS - IGBMC)

The ICS IT service has strong computer expertise in the development of data processing protocols related to genetically modified mice: development of tools for phenotyping data capture, appropriate statistical analyses, procedures for interfacing with external resources. They are also developing integrative analyses of these data by cross-referencing them with available public resources (MGI, EMMA...).

 

Institut Pluridisciplinaire Hubert Curien (IPHC)

The goal of the “bioorganic mass spectrometry laboratory” (LSMBO) is the structural determination of macromolecules, mainly proteins, without any structural ambiguity at the atomic level. In proteomics, we focus on improving the description of structures (from identification to complete characterization), including post-translational modifications. Specific objectives include the description of non-covalent complexes and we are developing supra-molecular MS. We have applied this very innovative methodology to the analysis of biological complexes measuring several millions of Daltons, paving the way for a ‘complexomics’ that can be used in biology in the same way as proteomics.

Keywords:
  • NGS data analysis
  • Sequence analysis
  • Machine learning
  • Data curation
  • Genomics: Chips
  • Proteomics

Formation professionnelle

No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Clinique de la souris

Description

CNRS on-going training courses: participation in a general training course on mouse models, with 2 x 1 hour modules: Current phenotyping databases and tools; Statistical analyses of phenotyping.

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Workshop, introduction to JalView editor

Description

in collaboration with the developers of Jalview

Access conditions

Open access after registration

No website documented
Trainees:
15 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Galaxy : packages and workflow deploiement.

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
8 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Infrastructure informatique distribuée de France Grilles: Grilles et Cloud

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
10 trainees / year
Training time:
5 day(s) / year
No upcoming session scheduled

Spectrométrie de masse, analyse protéomique et interprétation des données

Description
Not documented
Access conditions
Not documented

Formation universitaire

No website documented
Trainees:
65 trainees / year
Training time:
2 day(s) / year
No upcoming session scheduled

Analyse protéomique à haut débit, interprétation des données, ESBS / TPS, Strasbourg Illkirch

Description
Not documented
Access conditions
Not documented
Users distribution
International
0 %
National
0 %
Regional
0 %
Local
0%
Explanation about this distribution:
The exact distribution of users of the diverse services offered by the platform partners is currently difficult to estimate. However, we distinguish three categories of services:

• available only to local users, such as the computing power of BioImage servers and the associated bioinformatics tools, as well as the project hosting and support in terms of data processing or software development.
• available only to the French academic community. This includes the local Galaxy instance (GalaxEast), offering a catalogue of a hundred tools for manipulation of high throughput sequencing data (ChIP-seq, RNA - seq and DNAseq), proteomics and spectroscopy data. 
• available to the international academic community. The majority of the databases and software are freely available online via websites listed on bioinfo-bistro.fr.

Platform's own projects

BioImage
- Participation in TerpFactory project (LabCom programme): data analysis on the BioImage computing server. Installation of tools and analysis protocols. Project with PAT private company, Nancy.

Collaborations
National projets

BioImage
- Participation in French ANRs

International and European projects

ICS
- Numerous European projects focused on the generation and phenotyping of mouse models: EUMORPHIA (2002-2006), EUMODIC (2007-2012), EUCOMM (2006-2010), CASIMIR (2007-2010), EMMA (2009 /), IMPC (2011 /). Active role in several workpackages: advice on IT architectures to be installed, statistical analyses, data export.

Projects with industry
ICS

- Collaboration established in 2003 for data exchange and specification of phenotyping database for MERCK.

Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )

• Organisation of Strasbourg bioinformatics meetings: 2 / year. Thematic exchanges.
• Organisation of « bioinfo » seminars: 3 / year (presentation of tools, IT infrastructure, …).
• Organisation of GalaxEast (Galaxy) workgroup, with thte goal of sharing tools developed by bioinformaticians in Strasbourg with the scientific community
• Participation in "Strasbourg microbiology federation meetings", 2 / year
• Participation in organisation of ECCB 2014 conference in Strasbourg

Internal publications

Thompson, JD. Statistics for Bioinformatics: Methods for Multiple Sequence Alignment. ISTE Press 2016

External publications
Cébron A, Arsène-Ploetze F, Bauda P, Bertin PN, Billard P, Carapito C, Devin S, Goulhen-Chollet F, Poirel J, Leyval C. Rapid impact of phenanthrene and arsenic on bacterial community structure and activities in sand batches. Microb Ecol. 2014 67:129-44.

Erbs E, Faget L, Scherrer G, Matifas A, Filliol D, Vonesch JL, Koch M, Kessler P, Hentsch D, Birling MC, Koutsourakis M, Vasseur L, Veinante P, Kieffer BL, Massotte D. A mu-delta opioid receptor brain atlas reveals neuronal co-occurrence in subcortical networks. Brain Struct Funct. 2014 Mar 13.

Fève M, Saliou JM, Zeniou M, Lennon S, Carapito C, Dong J, Van Dorsselaer A, Junier MP, Chneiweiss H, Cianférani S, Haiech J, Kilhoffer MC. Comparative Expression Study of the Endo-G Protein Coupled Receptor (GPCR) Repertoire in Human Glioblastoma Cancer Stem-like Cells, U87-MG Cells and Non Malignant Cells of Neural Origin Unveils New Potential Therapeutic Targets. PLoS One. 2014 9:e91519

Juste C, Kreil DP, Beauvallet C, Guillot A, Vaca S, Carapito C, Mondot S, Sykacek P, Sokol H, Blon F, Lepercq P, Levenez F, Valot B, Carré W, Loux V, Pons N, David O, Schaeffer B, Lepage P, Martin P, Monnet V, Seksik P, Beaugerie L, Ehrlich SD, Gibrat JF, Van Dorsselaer A, Doré J. Bacterial protein signals are associated with Crohn's disease. Gut. 2014

Rejón JD, Delalande F, Schaeffer-Reiss C, Carapito C, Zienkiewicz K, de Dios Alché J, Isabel Rodríguez-García M, Van Dorsselaer A, Castro AJ. The plant stigma exudate: A biochemically active extracellular environment for pollen germination? Plant Signal Behav. 2014;9. pii: e28274.

Scheidecker S, Etard C, Pierce NW, Geoffroy V, Schaefer E, Muller J, Chennen K, Flori E, Pelletier V, Poch O, Marion V, Stoetzel C, Strähle U, Nachury MV, Dollfus H. Exome sequencing of Bardet-Biedl syndrome patient identifies a null mutation in the BBSome subunit BBIP1 (BBS18). J Med Genet. 2014 51(2):132-6.

Schwenzer H, Scheper GC, Zorn N, Moulinier L, Gaudry A, Leize E, Martin F, Florentz C, Poch O, Sissler M. Released selective pressure on a structural domain gives new insights on the functional relaxation of mitochondrial aspartyl-tRNA synthetase. Biochimie. 2014 100:18-26

Bruneaux M, Mary J, Verheye M, Lecompte O, Poch O, Jollivet D, Tanguy A. Detection and characterisation of mutations responsible for allele-specific protein thermostabilities at the Mn-superoxide dismutase gene in the deep-sea hydrothermal vent polychaete Alvinella pompejana. J Mol Evol. 2013 76:295-310

Levasseur A, Paganini J, Dainat J, Thompson JD, Poch O, Pontarotti P, Gouret P. . The chordate proteome history database. Evol Bioinform Online. 2012 437-47

Hashem Y, des Georges A, Fu J, Buss SN, Jossinet F, Jobe A, Zhang Q, Liao HY, Grassucci RA, Bajaj C, Westhof E, Madison-Antenucci S, Frank J. High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature. 2013 494:385-9

Mendoza-Parra MA, Van Gool W, Mohamed Saleem MA, Ceschin DG, Gronemeyer H. A quality control system for profiles obtained by ChIP sequencing Nucleic Acids Res. 2013; 41: e196

Miguet L, Lennon S, Baseggio L, Traverse-Glehen A, Berger F, Perrusson N, Chenard MP, Galoisy AC, Eischen A, Mayeur-Rousse C, Maar A, Fornecker L, Herbrecht R, Felman P, Van Dorsselaer A, Carapito C, Cianférani S, Mauvieux L. Cell-surface expression of the TLR homolog CD180 in circulating cells from splenic and nodal marginal zone lymphomas. Leukemia. 2013 27:1748-50

Plumel MI, Wasselin T, Plot V, Strub JM, Van Dorsselaer A, Carapito C, Georges JY, Bertile F. Mass spectrometry-based sequencing and SRM-based quantitation of two novel vitellogenin isoforms in the leatherback sea turtle (Dermochelys coriacea). J Proteome Res. 2013 12:4122-35

Rejón JD, Delalande F, Schaeffer-Reiss C, Carapito C, Zienkiewicz K, de Dios Alché J, Rodríguez-García MI, Van Dorsselaer A, Castro AJ. Proteomics profiling reveals novel proteins and functions of the plant stigma exudate. J Exp Bot. 2013 64:5695-705.

Ayadi A, Birling MC, Bottomley J, Bussell J, Fuchs H, Fray M, Gailus-Durner V, Greenaway S, Houghton R, Karp N, Leblanc S, Lengger C, Maier H, Mallon AM, Marschall S, Melvin D, Morgan H, Pavlovic G, Ryder E, Skarnes WC, Selloum M, Ramirez-Solis R, Sorg T, Teboul L, Vasseur L, Walling A, Weaver T, Wells S, White JK, Bradley A, Adams DJ, Steel KP, Hrabě de Angelis M, Brown SD, Herault Y. Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project. Mamm Genome. 2012 23(9-10):600-10.

Carapito C, Aebersold R. Targeted proteomics. Proteomics. 2012 12:1073

Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C, Barillot E. ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics. 2012 28:3147-9.

De Craene JO, Ripp R, Lecompte O, Thompson JD, Poch O, Friant S. Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism. BMC Genomics. 2012 13:297.

Halter D, Goulhen-Chollet F, Gallien S, Casiot C, Hamelin J, Gilard F, Heintz D, Schaeffer C, Carapito C, Van Dorsselaer A, Tcherkez G, Arsène-Ploetze F, Bertin PN. In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis. ISME J. 2012 6:1391-402

Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Niméus-Malmström E, Rinner O, Aebersold R. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med. 2012 4:142ra94.

Huck O, Al-Hashemi J, Poidevin L, Poch O, Davideau J-L , Tenenbaum H, Amar S. Identification and Characterization of miRNA differentially expressed in macrophages exposed to Porphyromonas gingivalis infection. Infection and Immunity (in press)


Schartner V, Romero NB, Donkervoort S, Treves S, Munot P, Pierson TM, Dabaj I, Malfatti E, Zaharieva I, Zorzato F, Neto OA, Brochier G, Lornage X, Eymard B, Taratuto AL, Böhm J, Gonorazky H, Ramos-Platt L, Feng L, Phadke R, Bharucha-Goebel D, Sumner CJ, Bui MT, Lacene E, Beuvin M, Labasse C, Dondaine N, Schneider R, Thompson J, Boland A, Deleuze JF, Matthews E, Pakleza AN, Sewry CA, Biancalana V, Quijano-Roy S, Muntoni F, Fardeau M, Bönnemann CG, Laporte J. Dihydropyridine receptor (DHPR) congenital myopathy. Acta Neuropathologica, Springer Verlag (Germany) (in press)


Kole K, Berdugo N, Da Silva C, Aït-Ali N, Blond F, Poidevin L, Ripp R, Fontaine V, Wincker P, Zack D, Sahel J, Poch O, Léveillard T. Identification of an alternative splicing product of the Otx2 gene expressed in the neural retina and retinal pigmented epithelial cells, PLoS ONE 2016 11: e0150758


Krupina K, Kleiss C, Metzger T, Fournane S, Schmucker S, Hofmann K, Fischer B, Paul N, Porter I, Raffelsberger W, Poch O, Swedlow J, Brino L, Sumara I. Ubiquitin Receptor Protein UBASH3B Drives Aurora B Recruitment to Mitotic Microtubules, Developmental Cell 2016, 36:63-78

Publications with the hosting laboratory
Linard B, Allot A, Schneider R, Morel C, Ripp R, Bigler M, Thompson JD, Poch O, Lecompte O. OrthoInspector 2.0: Software and database updates. Bioinformatics. 2015 31(3):447-8.

Benard E, Lèbre S, Michel CJ, GETEC: Genome Evolution by Transformation, Expansion and Contraction. 2014 (submitted).

Bermejo-Das-Neves C, Nguyen HN, Poch O, Thompson JD. A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). BMC Bioinformatics. 2014 15:111

Carapito C, Burel A, Guterl P, Walter A, Varrier F, Bertile F, Van Dorsselaer A. MSDA, a proteomics software suite for in-depth Mass Spectrometry Data Analysis using grid computing. Proteomics. 2014 14:1014-9

Bedez F, Linard B, Brochet X, Ripp R, Thompson JD, Moras D, Lecompte O, Poch O. Functional insights into the core-TFIIH from a comparative survey. Genomics. 2013 101:178-86

Bleykasten-Grosshans C, Friedrich A, Schacherer J. Genome-wide analysis of intraspecific transposon diversity in yeast. BMC Genomics. 2013 14:399

Cognat V, Pawlak G, Duchêne AM, Daujat M, Gigant A, Salinas T, Michaud M, Gutmann B, Giegé P, Gobert A, Maréchal-Drouard L. PlantRNA, a database for tRNAs of photosynthetic eukaryotes. Nucleic Acids Res. 2013 41:D273-9

Lehmann J, Jossinet F, Gautheret D. A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders. Nucleic Acids Res. 2013 41:5494-502

Mendoza-Parra MA, Van Gool W, Ceschin DG, Gronemeyer H. A quality control system for profiles obtained by massive parallel sequencing; Nucleic Acid Research 2013 41(21):e196. (patented)

Mendoza-Parra MA, Nowicka M, Van Gool W, Gronemeyer H. Characterising ChIP-seq binding patterns by model-based peak shape deconvolution; BMC Genomics 2013 26; 14: 834

Nguyen H, Luu TD, Poch O, Thompson JD. Knowledge discovery in variant databases using inductive logic programming Bioinform Biol Insights. 2013 7:119-31

Bertaccini D, Vaca S, Carapito C, Arsène-Ploetze F, Van Dorsselaer A, Schaeffer-Reiss C. An improved stable isotope N-terminal labeling approach with light/heavy TMPP to automate proteogenomics data validation: dN-TOP. J Proteome Res. 2013 12:3063-70.

De Luis A, Markmann K, Cognat V, Holt DB, Charpentier M, Parniske M, Stougaard J, Voinnet O. Two microRNAs linked to nodule infection and nitrogen-fixing ability in the legume Lotus japonicus. Plant Physiol. 2012 160:2137-54

Friedrich A, Jung PP, Hou J, Neuvéglise C, Schacherer J. Comparative mitochondrial genomics within and among yeast species of the Lachancea genus. PLoS One. 2012 7:e47834

Linard B, Nguyen NH, Prosdocimi F, Poch O, Thompson JD. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. Evol Bioinform Online. 2012 8:61-77

Jung PP, Friedrich A, Reisser C, Hou J, Schacherer J. Mitochondrial genome evolution in a single protoploid yeast species. G3 (Bethesda). 2012 Sep;2(9):1103-11.

Jung PP, Friedrich A, Reisser C, Hou J, Schacherer J. Mitochondrial genome evolution in a single protoploid yeast species. G3 (Bethesda). 2012 Sep;2(9):1103-11.

Luu TD, Rusu AM, Walter V, Ripp R, Moulinier L, Muller J, Toursel T, Thompson JD, Poch O, Nguyen H. MSV3d: database of human MisSense Variants mapped to 3D protein structure. Database (Oxford). 2012 bas018

Prosdocimi F, Linard B, Pontarotti P, Poch O, Thompson JD. Controversies in modern evolutionary biology: the imperative for error detection and quality control. BMC Genomics. 2012 13:5

E. Benard, S. Lèbre, C. J. Michel, Genome Evolution by Transformation, Expansion and Contraction (GETEC) Biosystems, 2015
Geoffroy V, Pizot C, Redin C, Piton A, Vasli N, Stoetzel C, Blavier A, Laporte J, Muller J. VaRank: a simple and powerful tool for ranking genetic variants. PeerJ. 2015
 


Khenoussi W, Vanhoutrève R, Poch O, Thompson JD. SIBIS: a Bayesian model for inconsistent protein sequence estimation. Bioinformatics. 2014


Allot A, Anno YN, Poidevin L, Ripp R, Poch O, Lecompte O. PARSEC: PAtteRn SEarch and Contextualization. Bioinformatics. 2013 29:2643-4.


Romand R, Ripp R, Poidevin L, Boeglin M, Geffers L, Dollé P, Poch O. Integrated annotation and analysis of in situ hybridization images using the ImAnno system: application to the ear and sensory organs of the fetal mouse. PLoS One. 10:e0118024.


Arsène-Ploetze, F., Bertin, P.N., and Carapito, C. Proteomic tools to decipher microbial community structure and functioning., Environ Sci Pollut Res Int. 2015 22(18), 13599-612.


Vaca Jacome, A.-S., Rabilloud, T., Schaeffer-Reiss, C., Rompais, M., Ayoub, D., Lane, L., Bairoch, A., Van Dorsselaer, A., and Carapito, C. N-terminome analysis of the human mitochondrial proteome., Proteomics. 2015 15(14), 2519-2524.


Ethuin, P., Marlard, S., Delosiere, M., Carapito, C., Delalande, F., Van Dorsselaer, A., Dehaut, A., Lencel, V., Duflos, G., and Grard, T. Differentiation between fresh and frozen–thawed sea bass (Dicentrarchus labrax) fillets using two-dimensional gel electrophoresis, Food Chemistry 2015 176:294-301.


Schnell, G., Boeuf, A., Westermann, B., Jaulhac, B., Lipsker, D., Carapito, C., Boulanger, N., and Ehret-Sabatier, L. Discovery and targeted proteomics on cutaneous biopsies infected by borrelia to investigate lyme disease., Mol Cell Proteomics 2015 14(5), 1254-64.


Wasselin, T., Zahn, S., Le Maho, Y., Van Dorsselaer, A., Raclot, T., and Bertile, F. Exacerbated oxidative stress in the fasting liver according to fuel partitioning, Proteomics 2014 14(16), 1905-1921.


Plumel, M.I., Stier, A., Thiersé, D., Van Dorsselaer, A., Criscuolo, F., and Bertile, F. Litter size manipulation in laboratory mice: an example of how proteomic analysis can uncover new mechanisms underlying the cost of reproduction, Frontiers in Zoology 2014 11(41).


Stoetzel, C., S. Bar, J.O. De Craene, S. Scheidecker, C. Etard, J. Chicher, J.R. Reck, I. Perrault, V. Geoffroy, K. Chennen, U. Strahle, P. Hammann, S. Friant, and H. Dollfus, A mutation in VPS15 (PIK3R4) causes a ciliopathy and affects IFT20 release from the cis-Golgi. Nat Commun, 2016. 7: p. 13586.


Prasad, M.K., V. Geoffroy, S. Vicaire, B. Jost, M. Dumas, S. Le Gras, M. Switala, B. Gasse, V. Laugel-Haushalter, M. Paschaki, B. Leheup, D. Droz, A. Dalstein, A. Loing, B. Grollemund, M. Muller-Bolla, S. Lopez-Cazaux, M. Minoux, S. Jung, F. Obry, V. Vogt, J.L. Davideau, T. Davit-Beal, A.S. Kaiser, U. Moog, B. Richard, J.J. Morrier, J.P. Duprez, S. Odent, I. Bailleul-Forestier, M.M. Rousset, L. Merametdijan, A. Toutain, C. Joseph, F. Giuliano, J.C. Dahlet, A. Courval, M. El Alloussi, S. Laouina, S. Soskin, N. Guffon, A. Dieux, B. Doray, S. Feierabend, E. Ginglinger, B. Fournier, M. de la Dure Molla, Y. Alembik, C. Tardieu, F. Clauss, A. Berdal, C. Stoetzel, M.C. Maniere, H. Dollfus, and A. Bloch-Zupan, A targeted next-generation sequencing assay for the molecular diagnosis of genetic disorders with orodental involvement. J Med Genet, 2016. 53(2): p. 98-110.


Scheidecker, S., C. Etard, L. Haren, C. Stoetzel, S. Hull, G. Arno, V. Plagnol, S. Drunat, S. Passemard, A. Toutain, C. Obringer, M. Koob, V. Geoffroy, V. Marion, U. Strahle, P. Ostergaard, A. Verloes, A. Merdes, A.T. Moore, and H. Dollfus, Mutations in TUBGCP4 alter microtubule organization via the gamma-tubulin ring complex in autosomal-recessive microcephaly with chorioretinopathy. Am J Hum Genet, 2015. 96(4): p. 666-74.


Vanhoutreve R, Kress A, Legrand B, Gass H, Poch O, Thompson JD. LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system. BMC Bioinformatics. 2016;17:271.


Aouled El Haj S, Elloumi M, Thompson JD. Discovery of motifs in biological sequences, in Pattern Recognition, S. Ramakrishnan (Eds.), Ramakrishnan, 2016

Development

A patent application has been filed (EP123406478.4) describing the use of the NGS-QC system and the software has been registered at the APP (Paris). In addition, the NGS-QC generator system is currently supported by SATT-Conectus Alsace in the framework of a maturation process that aims to transform this concept into a start-up specialized in the certification of antibodies dedicated to NGS applications.

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