Bioinformatic Core Facility Calanques (BCF-C)

Welcome to the Bioinformatics Core Facility Calanques (BCF-C). Our facility is shared between two Institutes at the Luminy Campus: the TAGC (UMR1090) and the IBDM (UMR7288).

 

 

The BCF-C is a flexible, user-centric Bioinformatics Core Facility, which has 4 core missions:

1) Bioinformatics Methods and Tool Development (external service)

Our associated researchers from the TAGC and the IBDM develop publicly available Bioinformatics Resources designed with the goal to assist wet-lab researchers in data analysis and integration. The application areas of our resources range from working with protein and DNA-sequences to large-scale data analysis and integration, including the integration and analysis of epigenetic and genomic data, as well as methods for network analysis.

All of our resources are publicly available and a comprehensive list of available tools can be found here.

2) User Training in Data Analysis and Code Development (external/internal service)

We organize hand-on workshops for training our users in Bioinformatics data analysis. Next to introductory courses on the theoretical background, we perform hands-on sessions in different data analysis techniques, as well as in code development.

Workshops in Bioinformatics and Data Analysis for Biologists are announced here.

Coding workshops for students and postdocs are announced here.

3) Code Development and Technology Transfer (internal service)

With our experts in coding, we help our researchers in code development, code maintenance and assist them in distributing their code professionally. This ensures the usability, ease-of-installation and longevity of software tools developed by our associated researchers. Furthermore, the source code of the tools developed by our researchers are distributed via shared repositories (gitlab or github).

Note: Though we cannot offer this service to external customers, it helps us to ensure that the tools developed at the TAGC and BCF-C are professionally distributed to the international research community.

Check out the gitlab repository of the BCF-C.

4) Bioinformatics Data Mining and User Support (internal service)

With our experts in Bioinformatics, we provide customized user support to wet-lab researchers in data analysis. Our areas of expertise reach from molecular-level to genome-level Bioinformatics.

 

How to contact us

For any requests, ideas or inquires to the BCF-C, please contact us by using the following e-mail address: contact.bcf@inserm.fr . This e-mail address reaches all members of the BCF-C.

We work in a highly collaborative way and have intensive contact to our users throughout a project. Thus, any project will start with a personal meeting, in which you explain to us your research project and your needs of our support.

Contact:

Scientific and technical leader:

Bianca Habermann

Computational Biology Group (IBDM) and BCF-Calanques (TAGC)
CNRS & Aix-Marseille Université
Case 907 – Parc Scientifique de Luminy
163 Avenue de Luminy
13009 Marseille
France

e-mail: bianca.HABERMANN@univ-amu.fr
phone: +33 (0)4 91 26 92 36

Scientific advisors:

Jacques van Helden, Professor (Aix-Marseille Université)
e-mail: Jacques.van-Helden@univ-amu.fr

Christine Brun, Research Director (CNRS)
email: christine-g.brun@inserm.fr

For associated researchers leading a Bioinformatics research team and contributing to Bioinformatics resource development at the TAGC, please look here.

 

Publications

Methods and Tool Development

2018
Nguyen NTT, Contreras-Moreira B, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D, van Helden J, Medina-Rivera A, Thomas-Chollier M. RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res. 2018 May 2. doi: 10.1093/nar/gky317. [Epub ahead of print] PubMed PMID: 29722874.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. Doi: 10.1093/nar/gkx1126. PubMed PMID: 29140473; PubMed Central PMCID: PMC5753243.

Prytuliak R, Pfeiffer F, Habermann BH. SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data. BMC Bioinformatics. 2018 Jan 26;19(1):24. doi: 10.1186/s12859-018-2020-x. PubMed PMID: 29373955; PubMed Central PMCID: PMC5787307.

2017
Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. Doi: 10.1093/nar/gkx1092. PubMed PMID: 29126285; PubMed Central PMCID: PMC5753247.

Castro-Mondragon JA, Jaeger S, Thieffry D, Thomas-Chollier M, van Helden J. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. Nucleic Acids Res. 2017 Jul 27;45(13):e119. doi: 10.1093/nar/gkx314. PubMed PMID: 28591841; PubMed Central PMCID: PMC5737723.

Castro-Mondragon JA, Rioualen C, Contreras-Moreira B, van Helden J. RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes. Methods Mol. Biol. 2016;1482:297-322. doi: 10.1007/978-1-4939-6396-6_19. PubMed PMID: 27557775.

2016
Contreras-Moreira B, Castro-Mondragon JA, Rioualen C, Cantalapiedra CP, van Helden J. RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes. Methods Mol Biol. 2016;1482:279-95. doi:
10.1007/978-1-4939-6396-6_18. PubMed PMID: 27557774.

Data Mining and User Support

2018

Arechederra M, Daian F, Yim A, Bazai SK, Richelme S, Dono R, Saurin AJ, Habermann BH, Maina F. Hypermethylation of gene body CpG islands predicts high dosage of functional oncogenes in liver cancer. Nat Commun. 2018 Aug 8;9(1):3164. doi: 10.1038/s41467-018-05550-5. PubMed PMID: 30089774; PubMed Central PMCID: PMC6082886.

Spletter ML, Barz C, Yeroslaviz A, Zhang X, Lemke SB, Bonnard A, Brunner E, Cardone G, Basler K, Habermann BH, Schnorrer F. A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle. Elife. 2018 May 30;7. pii: e34058. doi: 10.7554/eLife.34058.

Schmähling S, Meiler A, Lee Y, Mohammed A, Finkl K, Tauscher K, Israel L, Wirth M, Philippou-Massier J, Blum H, Habermann B, Imhof A, Song JJ, Müller J. Regulation and function of H3K36 di-methylation by the trithorax-group protein complex AMC. Development. 2018 Apr 5;145(7). pii: dev163808. Doi: 10.1242/dev.163808.

Donohoe CD, Csordás G, Correia A, Jindra M, Klein C, Habermann B, Uhlirova M. Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture. PLoS Genet. 2018 Mar 1;14(3):e1007241. Doi: 10.1371/journal.pgen.1007241.

Ramírez F, Bhardwaj V, Arrigoni L, Lam KC, Grüning BA, Villaveces J, Habermann B, Akhtar A, Manke T. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat Commun. 2018 Jan 15;9(1):189. doi: 10.1038/s41467-017-02525-w.

2017
Papanikos F, Daniel K, Goercharn-Ramlal A, Fei JF, Kurth T, Wojtasz L, Dereli I, Fu J, Penninger J, Habermann B, Surani A, Stewart AF, Toth A. The enigmatic meiotic dense body and its newly discovered component, SCML1, are dispensable for fertility and gametogenesis in mice. Chromosoma. 2017 Jun;126(3):399-415. Doi: 10.1007/s00412-016-0598-1.

2016
Roth S, Bergmann H, Jaeger M, Yeroslaviz A, Neumann K, Koenig PA, Prazeres da  Costa C, Vanes L, Kumar V, Johnson M, Menacho-Márquez M, Habermann B, Tybulewicz VL, Netea M, Bustelo XR, Ruland J. Vav Proteins Are Key Regulators of Card9 Signaling for Innate Antifungal Immunity. Cell Rep. 2016 Dec 6;17(10):2572-2583. doi: 10.1016/j.celrep.2016.11.018.

Le HQ, Ghatak S, Yeung CY, Tellkamp F, Günschmann C, Dieterich C, Yeroslaviz A, Habermann B, Pombo A, Niessen CM, Wickström SA. Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment. Nat Cell Biol. 2016 Aug;18(8):864-75. doi: 10.1038/ncb3387.

Kowalinski E, Kögel A, Ebert J, Reichelt P, Stegmann E, Habermann B, Conti E. Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex. Mol Cell. 2016 Jul 7;63(1):125-34. doi: 10.1016/j.molcel.2016.05.028.

Nakel K, Bonneau F, Basquin C, Habermann B, Eckmann CR, Conti E. Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity. RNA. 2016 Aug;22(8):1139-45. doi: 10.1261/rna.056598.116.

Crevenna AH, Blank B, Maiser A, Emin D, Prescher J, Beck G, Kienzle C, Bartnik K, Habermann B, Pakdel M, Leonhardt H, Lamb DC, von Blume J. Secretory cargo sorting by Ca2+-dependent Cab45 oligomerization at the trans-Golgi network. JCell Biol. 2016 May 9;213(3):305-14. doi: 10.1083/jcb.201601089.

Braun F, Rinschen MM, Bartels V, Frommolt P, Habermann B, Hoeijmakers JH, Schumacher B, Dollé ME, Müller RU, Benzing T, Schermer B, Kurschat CE. Altered lipid metabolism in the aging kidney identified by three layered omic analysis. Aging (Albany NY). 2016 Mar;8(3):441-57.

Sakakini N, Turchi L, Bergon A, Holota H, Rekima S, Lopez F, Paquis P, Almairac F, Fontaine D, Baeza-Kallee N, Van Obberghen-Schilling E, Junier MP, Chneiweiss H, Figarella-Branger D, Burel-Vandenbos F, Imbert J, Virolle T. A Positive Feed-forward Loop Associating EGR1 and PDGFA Promotes Proliferation and  Self-renewal in Glioblastoma Stem Cells. J Biol Chem. 2016 May 13;291(20):10684-99. doi: 10.1074/jbc.M116.720698.

Leca J., Martinez S., Lac S., Nigri J., Secq V., Rubis M., Bressy C., Sergé A., Lavaut M.-N., Dusetti N., Loncle C., Roques J., Pietrasz D., Bousquet C., Garcia S., Granjeaud S., Ouaissi M., Bachet J.-B., Brun C., Iovanna J.L., Zimmermann P., Vasseur S. and Tomasini R. (2016) Cancer-associated fibroblats-derived annexin A6+ extracellular vesicles support pancreatic cancer aggressiveness. Journal of Clinical Investigations. 2016, 126: 4140-4156. doi: 10.1172/JCI87734.

Group Members

Aurelie Bergon (data analysis specialist)
Christine Brun (scientific leader/advisor)
Bianca Haberman (scientific and technical leader)
Jacques van Helden (scientific leader/advisor)
Edlira Nano (code development and programming specialist, funded by IFB)
Fabrice Lopez (code development and programming specialist)