Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.pex-1336/v1]Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.pex-1336/v1]Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.pex-1336/v1]Ison J, Ienasescu H, Rydza E, Chmura P, Rapacki K, Gaignard A, Schwämmle V, van Helden J, Kalaš M, Ménager H.
biotoolsSchema: a formalized schema for bioinformatics software description.
Gigascience. 2021 Jan 27;10(1):giaa157. doi: 10.1093/gigascience/giaa157.

Eric Charpentier, Marine Cornec, Solenne Dumont, Dimitri Meistermann, Philippe Bordron, Laurent David, Richard Redon, Stéphanie Bonnaud, Audrey Bihouée
3’ RNA sequencing for robust and low-cost gene expression profiling.
Research Square, 28 January 2021, doi: 10.21203/rs.3.pex-1336/v1

M Lefebvre, A Gaignard, M Folschette, J Bourdon, C Guziolowski.
Large-scale regulatory and signaling network assembly through linked open data.
Database, Volume 2021, 2021, baaa113, doi: 10.1093/database/baaa113

Mutala LB, Deleine C, Karakachoff M, Dansette D, Ducoin K, Oger R, Rousseau O, Podevin J, Duchalais E, Fourquier P, Thomas WEA, Gourraud PA, Bennouna J, Brochier C, Gervois N, Bossard C, Jarry A.
The Caspase-1/IL-18 Axis of the Inflammasome in Tumor Cells: A Modulator of the Th1/Tc1 Response of Tumor-Infiltrating T Lymphocytes in Colorectal Cancer.
Cancers (Basel). 2021 Jan 7;13(2):E189. doi: 10.3390/cancers13020189.

Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron
MiBiOmics: An interactive web application for multi-omics data exploration and integration
BMC Bioinformatics 22, 6 (2021)  doi: 10.1186/s12859-020-03921-8


Bakker M et al.Bakker, M.K., van der Spek, R.A.A., van Rheenen, W. et al.
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors.
Nat Genet 52, 1303–1313 (2020). doi: 10.1038/s41588-020-00725-7

A. Nouri, F. Autrusseau, R. Bourcier, A. Gaignard, V. L’allinec, C. Menguy, J. Véziers, H. Desal, G. Loirand, R. Redon,
Characterization of 3D bifurcations in micro-scan and MRA-TOF images of cerebral vasculature for prediction of intra-cranial aneurysms.
Computerized Medical Imaging and Graphics, Volume 84, 2020,101751,ISSN 0895-6111 . doi: 10.1016/j.compmedimag.2020.101751

Rousseau O, Karakachoff M, Gaignard A, Bellanger L, Bijlenga P, Constant Dit Beaufils P, L'Allinec V, Levrier O, Aguettaz P, Desilles JP, Michelozzi C, Marnat G, Vion AC, Loirand G, Desal H, Redon R, Gourraud PA, Bourcier R; ICAN Investigators.
Location of intracranial aneurysms is the main factor associated with rupture in the ICAN population.
J Neurol Neurosurg Psychiatry. 2020 Oct 23:jnnp-2020-324371. doi: 10.1136/jnnp-2020-324371.

Lecomte E, Saleun S, Bolteau M, Guy-Duché A, Adjali O, Blouin V, Penaud-Budloo M, Ayuso E.
The SSV‐Seq 2.0 PCR‐Free Method Improves the Sequencing of Adeno‐Associated Viral Vector Genomes Containing GC‐Rich Regions and Homopolymers.
Biotechnology Journal (2020) ISSN: 1860-6768 Online ISSN: 1860-7314. doi: 10.1002/biot.202000016

Gaël Castel, Dimitri Meistermann, Betty Bretin, Julie Firmin, Justine Blin, Sophie Loubersac, Alexandre Bruneau, Simon Chevolleau, Stéphanie Kilens, Caroline Chariau, Anne Gaignerie, Quentin Francheteau, Harunobu Kagawa, Eric Charpentier, Léa Flippe, Valentin François--Campion, Sandra Haider, Bianca Dietrich, Martin Knöfler, Takahiro Arima, Jérémie Bourdon, Nicolas Rivron, Damien Masson, Thierry Fournier, Hiroaki Okae, Thomas Fréour, Laurent David.
Induction of Human Trophoblast Stem Cells from Somatic Cells and Pluripotent Stem Cells,
Cell Reports,Volume 33, Issue 8,2020,108419,ISSN 2211-1247. doi: 10.1016/j.celrep.2020.108419

Jean-Baptiste Alberge, Florence Magrangeas, Mirko Wagner, Soline Denié, Catherine Guérin-Charbonnel, Loïc Campion, Michel Attal, Hervé Avet-Loiseau, Thomas Carell, Philippe Moreau, Stéphane Minvielle, Aurélien A. Sérandour
DNA hydroxymethylation reveals transcription regulation networks and prognostic signatures in multiple myeloma
Clin Epigenet 12, 163 (2020). doi: 10.1186/s13148-020-00953-y

Alban Gaignard, Hala Skaf-Molli, Khalid Belhajjame
Findable and reusable workflow data products: A genomic workflow case study
Semantic Web Journal, IOS Press, 2020, pp.1-13. doi:10.3233/SW-200374

Vincent l'Allinec, Stéphanie Chatel, Matilde Karakachoff, Emmanuelle Bourcereau, Zeineb Es-Salah-Lamoureux, Alban Gaignard et al.
Prediction of Unruptured Intracranial Aneurysm Evolution: The UCAN Project
Neurosurgery, 2020 July 1;87(1):150-156. doi:10.1093/neuros/nyaa093

Huet S, Pouvreau J-B, Delage E, Delgrange S, Marais C, Bahut M, Delavault P, Simier P and Poulin L
Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota
Front. Plant Sci., 17 July 2020. doi: 10.3389/fpls.2020.01075

Patin J, Castro C, Steenman M, Hivonnait A, Carcouët A, Tessier A, Lebreton J, Bihouée A, Donnart A, Le Marec H, Baró I, Charpentier F, Derangeon M.
Gap-134, a Connexin43 activator, prevents age-related development of ventricular fibrosis in Scn5a+/- mice.
Pharmacol Res 2020;104922. doi:10.1016/j.phrs.2020.104922

Chénais B, Cornec M, Dumont S, Marchand J, Blanckaert V
Transcriptomic Response of Breast Cancer Cells MDA-MB-231 to Docosahexaenoic Acid: Downregulation of Lipid and Cholesterol Metabolism Genes and Upregulation of Genes of the Pro-Apoptotic ER-Stress Pathway
Int J Environ Res Public Health 2020;17. doi: 10.3390/ijerph17103746

Antoine Roquilly, Cedric Jacqueline, Marion Davieau, Alice Mollé, Abderrahmane Sadek, Cynthia Fourgeux, Paul Rooze, Alexis Broquet, Barbara Misme-Aucouturier, Tanguy Chaumette, Mickael Vourc'h, Raphael Cinotti, Nadege Marec, Vanessa Gauttier, Hamish E G McWilliam, Frederic Altare, Jeremie Poschmann, Jose A Villadangos, Karim Asehnoune
Alveolar macrophages are epigenetically altered after inflammation, leading to long-term lung immunoparalysis
Nat Immunol. 2020 Jun;21(6):636-648. Epub 2020 May 18. doi: 10.1038/s41590-020-0673-x

Carolane Seiller, Sophie Maiga, Cyrille Touzeau, Céline Bellanger, Charlotte Kervoëlen, Géraldine Descamps, Laurent Maillet, Philippe Moreau, Catherine Pellat-Deceunynck, Patricia Gomez-Bougie, Martine Amiot
Dual targeting of BCL2 and MCL1 rescues myeloma cells resistant to BCL2 and MCL1 inhibitors associated with the formation of BAX/BAK hetero-complexes
Cell Death Dis. 2020 May 5;11(5):316. doi: 10.1038/s41419-020-2505-1

Morgane Frapin, Simon Guignard, Dimitri Meistermann, Isabelle Grit, Valentine S. Moullé, Vincent Paillé, Patricia Parnet, Valérie Amarger
Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus
Nutrients. 2020 May 19;12(5):E1464. doi: 10.3390/nu12051464

Aude Saint Pierre, Joanna Giemza, Isabel Alves, Matilde Karakachoff, Marinna Gaudin, Philippe Amouyel, Jean-François Dartigues, Christophe Tzourio, Martial Monteil, Pilar Galan, Serge Hercberg, Iain Mathieson, Richard Redon, Emmanuelle Génin, Christian Dina
The Genetic History of France 
Eur J Hum Genet. 2020 Feb 10. doi: 10.1038/s41431-020-0604-1 

Thu Ha Pham, Lecomte S, Le Guevel R, Lardenois A, Evrard B, Chalmel F, Ferriere F, Balaguer P, Efstathiou T, Pakdel F
Characterization of Glyceollins as Novel Aryl Hydrocarbon Receptor Ligands and Their Role in Cell Migration
International Journal of Molecular Sciences, 2020, 21, 1368. doi: 10.3390/ijms21041368

Rabé M, Dumont S, Álvarez-Arenas A, Janati H, Belmonte-Beitia J, Calvo G, Thibault-Carpentier C, Séry Q, Chauvin C, Joalland N, Briand F, Blandin S, Scotet E, Pecqueur C, Clairambault J, Oliver L, Perez-Garcia V, Nadaradjane A, Cartron P-F, Gratas C, Vallette F
Identification of a transient state during the acquisition of temozolomide resistance in glioblastoma
Cell Death & Disease, volume 11, 2020. doi: 10.1038/s41419-019-2200-2

Fatima-Zahra Boujdad, Alban Gaignard, Mario Südholt, Wilmer Garzón-Alfonso, Luis Daniel Benavides Navarro, Richard Redon
On distributed collaboration for biomedical analyses
CCGrid-Life 2019 Workshop on Clusters, Clouds and Grids for Life Sciences, May 2019, Larnaca, Cyprus. pp.1-10, doi:10.1109/CCGRID.2019.00079

Maxime Folschette, Kirsley Chennen, Alban Gaignard, Richard Redon, Hala Skaf-Molli, et al.
INEX-MED: a Knowledge Graph to explore and link heterogeneous bio-medical data
JOBIM 2019, Jul 2019, Nantes, France. https://hal.archives-ouvertes.fr/hal-02330809v1

Anass Nouri, Florent Autrusseau, Romain Bourcier, Alban Gaignard, Vincent l'Allinec, et al.
3D bifurcations characterization for intra-cranial aneurysms prediction
SPIE Medical Imaging, Feb 2019, San Diego, CA, United States. doi:10.1117/12.2504626

Montassier E, Al-Ghalith G, Mathé C, Le Bastard Q, Douillard V, Garnier A, Guimon R, Raimondeau B, Touchefeu Y, Duchalais E, Vince N, Limou S, Gourraud PA, Laplaud D, Nicot A, Soulillou JP, Berthelot L
Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome
Front Immunol. 2019; 10: 3000. doi: 10.3389/fimmu.2019.03000

Le Bastard Q, Vangay P, Batard E, Knights D, Montassier E
US immigration is associated with rapid and persistent acquisition of antibiotic resistance genes in the gut
Clinical Infectious Diseases (Nov 2019). doi: 10.1093/cid/ciz1087

Nadjet Belbachir, Vincent Portero, Zeina R Al Sayed, Jean-Baptiste Gourraud, Florian Dilasser, Laurence Jesel, Hongchao Guo, Haodi Wu, Nathalie Gaborit, Christophe Guilluy
RRAD mutation causes electrical and cytoskeletal defects in cardiomyocytes derived from a familial case of Brugada syndrome
European Heart Journal, Volume 40, Issue 37, 1 October 2019, Pages 3081–3094. doi:10.1093/eurheartj/ehz308

Leroy T, Louvet J-M, Lalanne C,Le Provost G, Labadie K, Aury J-M, Delzon S, Plomion C, Kremer A
Adaptive introgression as a driver of local adaptation to climate in European white oaks
New Phytologist (2019). doi: 10.1111/nph.16095

Leroy T, Rougemont Q, Dupouey JL, Bodenes C, Lalanne C, Belser C, Labadie K, Le Provost G, Aury JM, Kremer A, Plomion C
Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers
New Phytologist (2019). doi: 10.1111/nph.16039

Leveque X, Hochane M, Geraldo F, Dumont S, Gratas C, Oliver L, Gaignier C, Trichet V, Layrolle P, Heymann D, Herault O, Vallette F, Olivier C
Low‐dose pesticide mixture induces accelerated mesenchymal stem cells aging in vitro
STEM CELLS 9999:00–00. doi: 10.1002/stem.3014

Thériault S, Dina C, Messika-Zeitoun D, Le Scouarnec S, Capoulade R, Gaudreault N, Rigade S, Li Z, Simonet F, Lamontagne M, Clavel MA, Arsenault B, Boureau A-S, Lecointe S, Baron E, Bonnaud S, Karakachoff M, Charpentier E, Fellah I, Roussel J-C, Verhoye JP, Baufreton C, Probst V, Roussel R, D.E.S.I.R. Study Group, Redon R, Dagenais F, Pibarot P, Mathieu P, Le Tourneau T, Bossé Y, JJ Schott
Genetic association analyses highlight IL6, ALPL, and NAV1 as three new susceptibility genes underlying calcific aortic valve stenosis
Circulation: Genomic and Precision Medicine. 2019;12. doi: 10.1161/CIRCGEN.119.002617

Guimbretiere G, Le Scouarnec S, Rigade S, Boureau AS, Cueff C, Capoulade R, Dina C, Mérot J, Schott JJ, Le Tourneau T
Phenotypic and genotypic approach of a large family with early onset tricuspid aortic valve sclerosis-stenosis: A multimodality evaluation
Archives of Cardiovascular Diseases Supplements, January 2019  11(1):66-67. doi: 10.1016/j.acvdsp.2018.10.145


Tessoulin B, Moreau-Aubry A, Descamps G, Gomez-Bougie P, Maïga S, Gaignard A, Chiron D, Ménoret E, Le Gouill S, Moreau P, Amiot M, Pellat-Deceunynck C
Whole-exon sequencing of human myeloma cell lines shows mutations related to myeloma patients at relapse with major hits in the DNA regulation and repair pathways
J Hematol Oncol. 2018 Dec 13;11(1):137 | doi: 10.1186/s13045-018-0679-0
Persyn E, Redon R, Bellanger L, Dina C
The impact of a fine-scale population stratification on rare variant association test results
PLOS One 13(12): e0207677, December 2018 | doi: https://doi.org/10.1371/journal.pone.0207677

M Lenglet, F Robriquet, K Schwarz, C Camps, A Couturier, D Hoogewijs, A Buffet, S J. L. Knight, S Gad, S Couvé, F Chesnel, M Pacault, P Lindenbaum, S Job, S Dumont, T Besnard, M Cornec, H Dreau, M Pentony, E Kvikstad, S Deveaux, N Burnichon, S Ferlicot, M Vilaine, JM Mazzella, F Airaud, C Garrec, L Heidet, S Irtan, E Mantadakis, K Bouchireb, K-M Debatin, R Redon, S Bezieau, B Bressac-de Paillerets, BT Teh, F Girodon, M-L Randi, M Caterina Putti, V Bours, R Van Wijk, J R. Göthert, A Kattamis, N Janin, C Bento, J C. Taylor, Y Arlot-Bonnemains, S Richard, A-P Gimenez-Roqueplo, H Cario and B Gardie
Identification of a new VHL exon and complex splicing alterations in familial erythrocytosis or von Hippel-Lindau disease
Blood 2018 132:469-483, September 2018 | doi: https://doi.org/10.1182/blood-2018-03-838235

Eric Charpentier, Audrey Bihouee, Dimitri Meistermann, Stephanie Kilens, Lea Flippe, Solenne Dumont, Audrey Donnart,Marine Cornec, Laurent David, Richard Redon
3’seq-RP : A low cost high throughput digital sequencing technique to evaluate gene expression profiles
Journées Ouvertes en BioInformatique et Mathématiques (JOBIM2018, Poster).
Chebouba L, Boughaci D, Guziolowski C
Proteomics Versus Clinical Data and Stochastic Local Search Based Feature Selection for Acute Myeloid Leukemia Patients' Classification
Journal of Medical Systems, 2018https://doi.org/10.1007/s10916-018-0972-z

Dumont S, Le Pennec S, Donnart A, Teusan R, Steenman M, Chevalier C, Houlgatte R and Savagner F
Transcriptional orchestration of mitochondrial homeostasis in a cellular model of PGC-1-related coactivator-dependent thyroid tumor
Oncotarget, 2018 Mar 23;9(22):15883-15894 | https://doi.org/10.18632/oncotarget.24633 

Dinka Mandakovic, Claudia Rojas, Jonathan Maldonado, Mauricio Latorre, Dante Travisany, Erwan Delage, Audrey Bihouée, Géraldine Jean, Francisca P. Díaz, Beatriz Fernández-Gómez, Pablo Cabrera, Alexis Gaete, Claudio Latorre, Rodrigo A. Gutiérrez, Alejandro Maass, Verónica Cambiazo, Sergio A. Navarrete, Damien Eveillard & Mauricio González
Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
Scientific Reports volume 8, Article number: 5875 (2018) | https://doi.org/10.1038/s41598-018-23931-0

L Chebouba, B Miannay, D Boughaci, C Guziolowski
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming
BMC Bioinformatics, March 2018 19(Suppl 2):59 | https://doi.org/10.1186/s12859-018-2034-4

Espitia O, Chatelais M, Steenman M, Charrier C, Maurel B, Georges S, Houlgatte R, Verrecchia F, Ory B, Lamoureux F, Heymann D, Gouëffic Y, Quillard T
Implication of molecular vascular smooth muscle cell heterogeneity among arterial beds in arterial calcification.
PLOS One, January 26, 2018 | https://doi.org/10.1371/journal.pone.0191976

Kilens S, Meistermann D, Moreno D, Chariau C, Gaignerie A, Reignier A, Lelièvre Y, Casanova M, Vallot C, Nedellec S, Flippe L, Firmin J, Song J, Charpentier E, Lammers J, Donnart A, Marec N, Deb W, Bihouée A, Le Caignec C, Pecqueur C, Redon R, Barrière P, Bourdon J, Pasque V, Soumillon M, Mikkelsen TS, Rougeulle C, Fréour T, David L and The Milieu Intérieur Consortium
Parallel derivation of isogenic human primed and naive induced pluripotent stem cells.
Nat Commun. 2018 Jan 24;9(1):360 | https://doi.org/10.1038/s41467-017-02107-w

S. Bézie, D. Meistermann, L. Boucault, S. Kilens, J. Zoppi, E. Autrusseau, A. Donnart, V. Nerrière-Daguin, F. Bellier-Waast, E. Charpentier, F. Duteille, L. David, I. Anegon and C. Guillonneau
Ex vivo expanded human non-cytotoxic CD8+CD45RClow/- tregs efficiently delay skin graft rejection and GVHD in humanized mice.
Front Immunol, 24 January 2018 | https://doi.org/10.3389/fimmu.2017.02014

R Danger, PJ Royer, D Reboulleau, E Durand, J Loy, A Tissot, P Lacoste, A Roux, M Reynaud-Gaubert, C Gomez, R Kessler, S Mussot, C Dromer, O Brugière, JF Mornex, R Guillemain, M Dahan, C Knoop, K Botturi, A Foureau, C Pison, A Koutsokera, L Nicod, S Brouard, A Magnan and  The COLT and SysCLAD Consortia
Blood Gene Expression Predicts Bronchiolitis Obliterans Syndrome
Front. Immunol., 11 January 2018 | https://doi.org/10.3389/fimmu.2017.01841
Bourcier R, Le Scouarnec S, Bonnaud S, Karakachoff M, Bourcereau E, Heurtebise-Chrétien S, Menguy C, Dina C, Simonet F, Moles A, Lenoble C, Lindenbaum P, Chatel S, Isidor B, Génin E, Deleuze JF, Schott JJ
Rare Coding Variants in ANGPTL6 Are Associated with Familial Forms of Intracranial Aneurysm
The American Journal of Human Genetics, Volume 102, Issue 1, 4 January 2018, Pages 133–141 | https://doi.org/10.1016/j.ajhg.2017.12.006

M. Lefebvre, J. Bourdon, C. Guziolowski, A. Gaignard.
Regulatory and signaling network assembly through linked open data
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM2017, demo paper).

Y. Lelievre, A. Bihouée, E. Charpentier, A. Gaignard, S. Souchet and D. Vintache
Developing and sharing reproducible bioinformatics pipelines: best practices,
Journées Ouvertes en BioInformatique et Mathématiques (JOBIM2017, Poster).

A. Gaignard, K. Belhajjame, H. Skaf-Molli.
SHARP: Harmonizing cross-workflow provenance
Semantic Web solutions for large-scale biomedical data analytics (SeWebMeDA ‘17), full day workshop at ESWC2017, Portoroz, Slovenia.

A. Gaignard, K. Belhajjame, H. Skaf-Molli.
SHARP: Harmonizing Galaxy and Taverna workflow provenance
Sematic Web solutions for large-scale biomedical data analytics (SeWebMeDA ‘17), full day workshop at ESWC2017, Portoroz, Slovenia. Demo paper

P. Lindenbaum, R. Redon
bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.
Küry S, van Woerden GM, Besnard T, Proietti Onori M, Latypova X, Towne MC, Cho MT, Prescott TE, Ploeg MA, Sanders S, Stessman HAF, Pujol A, Distel B, Robak LA, Bernstein JA, Denommé-Pichon AS, Lesca G, Sellars EA, Berg J, Carré W, Busk ØL, van Bon BWM, Waugh JL, Deardorff M, Hoganson GE, Bosanko KB, Johnson DS, Dabir T, Holla ØL, Sarkar A, Tveten K, de Bellescize J, Braathen GJ, Terhal PA, Grange DK, van Haeringen A, Lam C, Mirzaa G, Burton J, Bhoj EJ, Douglas J, Santani AB, Nesbitt AI, Helbig KL, Andrews MV, Begtrup A, Tang S, van Gassen KLI, Juusola J, Foss K, Enns GM, Moog U, Hinderhofer K, Paramasivam N, Lincoln S, Kusako BH, Lindenbaum P, Charpentier E, Nowak CB, Cherot E, Simonet T, Ruivenkamp CAL, Hahn S, Brownstein CA, Xia F, Schmitt S, Deb W, Bonneau D, Nizon M, Quinquis D, Chelly J, Rudolf G, Sanlaville D, Parent P, Gilbert-Dussardier B, Toutain A, Sutton VR, Thies J, Peart-Vissers LELM, Boisseau P, Vincent M, Grabrucker AM, Dubourg C; Undiagnosed Diseases Network, Tan WH, Verbeek NE, Granzow M, Santen GWE, Shendure J, Isidor B, Pasquier L, Redon R, Yang Y, State MW, Kleefstra T, Cogné B; GEM HUGO; Deciphering Developmental Disorders Study, Petrovski S, Retterer K, Eichler EE, Rosenfeld JA, Agrawal PB, Bézieau S, Odent S, Elgersma Y, Mercier S
De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability.
Am J Hum Genet, Nov, 2017 | https://doi.org/10.1016/j.ajhg.2017.10.003
Nicol B, Salou M, Vogel I, Garcia A, Dugast E, Morille J, Kilens S, Charpentier E, Donnart A, Nedellec S, Jacq-Foucher M, Le Frère F, Wiertlewski S, Bourreille A, Brouard S, Michel L, David L, Gourraud PA, Degauque N, Nicot AB, Berthelot L, Laplaud DA.
An intermediate level of CD161 expression defines a novel activated, inflammatory, and pathogenic subset of CD8+ T cells involved in multiple sclerosis.
J Autoimmun, Oct 2017 | https://doi.org/10.1016/j.jaut.2017.10.005

Oizel K, Chauvin C, Oliver L, Gratas C, Geraldo F, Jarry U, Scotet E, Rabe M, Alves-Guerra MC, Teusan R, Gautier F, Loussouarn D, Compan V, Martinou JC, Vallette F and Pecqueur C
Efficient mitochondrial glutamine targeting prevails over glioblastoma metabolic plasticity.
Clinical Cancer Research, July, 2017 | https://doi.org/10.1158/1078-0432.CCR-16-3102

Persyn E, Karakachoff M, Le Scouarnec S, Le Clézio C, Campion D, Schott J-J, Redon R, Bellanger L, Dina C
DoEstRare: A statistical test to identify local enrichments in rare genomic variants associated with disease.
PLOS, July 2017 | https://doi.org/10.1371/journal.pone.0179364
Penaud-Budloo M, Lecomte E, Guy-Duché A, Saleun S, Roulet A, Lopez-Roques C, Tournaire B, Cogné B, Léger A, Blouin V, Lindenbaum P, Moullier P, Ayuso E
Accurate identification and quantification of DNA species by next-generation sequencing in adeno-associated viral vectors produced in insect cells.
Human Gene Therapy Methods, May 2017 | https://doi.org/10.1016/j.omtm.2018.01.002

Kambarev S, Corvec S, Chauty A, Marion E, Marsollier L, Pecorari F
Draft Genome Sequence of Mycobacterium ulcerans S4018 Isolated from a Patient with an Active Buruli Ulcer in Benin, Africa.
Genome Announc. April 2017 vol. 5 no. 17 e00248-17 | https://doi.org/10.1128/genomeA.00248-17

Maniangou B, Legrand N, Alizadeh M, Guyet U, Willem C, David G, Charpentier E, Walencik A, Retiere C, Gagne K
KIR allele determination using Next Generation Sequencing technology.
Frontiers in Immunology, Apr 2017 | https://doi.org/10.3389/fimmu.2017.00547

Renson P, Fablet C, Le Dimna M, Mahé S, Touzain F, Blanchard Y, Paboeuf F, Rose N, Bourry O
Preparation for emergence of an Eastern European porcine reproductive and respiratory syndrome virus (PRRSV) strain in Western Europe: immunization with modified live virus vaccines or a field strain confers partial protection.
Veterinary Microbiology (2017) | https://doi.org/10.1016/j.vetmic.2017.04.021

Cohen-Boulakia S, Belhajjame K, Collin O, Chopard J, Froidevaux C, Gaignard A, Hinsen K, Larmande P, LeBras Y, Lemoine F, Mareuil F, Ménager H, Pradal C and Blanchet C
Scientific workflows for computational reproducibility in the life sciences : Status, challenges and opportunities.
Future Generation Computer Systems (2017) | http://dx.doi.org/10.1016/j.future.2017.01.012
Picarda E, Bézie S, Boucault L, Autrusseau E, Kilens S, Meistermann D, Martinet B, Daguin V, Donnart A, Charpentier E, David L, Anegon I and Guillonneau C
Transient antibody targeting of CD45RC induces transplant tolerance and potent antigen-specific regulatory T cells.
JCI Insight 2017 | http://dx.doi.org/10.1172/jci.insight.90088
Riou R, Bressollette-Bodin C, Boutoille D, Katia Gagne, Rodallec A, Lefebvre M, Raffi F, Senitzer D, Imbert-Marcille B-M and Retière C
Severe symptomatic primary HCMV infection despite effective innate and adaptive immune responses.
J. Virol. JVI.02245-16; Accepted manuscript Dec 2016
Leroy T, Roux C, Villate L, Bodénès C, Romiguier J, Paiva J, Dossat C, Aury J-M, Plomion C and Antoine Kremer
Extensive recent secondary contacts between four European white oak species.
New Phytologist 2017 Accepted 21 Nov 2016

Vincent Portero, Solena Le Scouarnec, Zeineb EsSalahLamoureux, Sophie Burel, JeanBaptiste Gourraud, Stéphanie Bonnaud, Pierre Lindenbaum, Floriane Simonet, Jade Violleau, Estelle Baron, Eléonore Moreau, Carol Scott, Stéphanie Chatel, Gildas Loussouarn, Thomas O'Hara, Philippe Mabo, Christian Dina, Hervé Le Marec, JeanJacques Schott, Vincent Probst, Isabelle Baró, Céline Marionneau, Flavien Charpentier, Richard Redon
Dysfunction of the VoltageGated K+ Channel 2 Subunit in a Familial Case of Brugada Syndrome.
Journal of the American Heart Association. 2016;5:e003122

Sanchez-Castro M, Eldjouzi H, Charpentier E, Busson PF, Hauet Q, Lindenbaum P, Delasalle-Guyomarch B, Baudry A, Pichon O, Pascal C, Lefort B, Bajolle F, Pezard P, Schott JJ, Dina C, Redon R, Gournay V, Bonnet D, Le Caignec C.
Search for Rare Copy-Number Variants in Congenital Heart Defects Identifies Novel Candidate Genes and a Potential Role for FOXC1 in Patients With Coarctation of the Aorta.
Circ Cardiovasc Genet. 2016 Feb
Rimbert A, Pichelin M, Lecointe S, Marrec M, Le Scouarnec S, Barrak E, Croyal M, Krempf M, Le Marec H, Redon R, Schott JJ, Magré J, Cariou B.
Identification of novel APOB mutations by targeted next-generation sequencing for the molecular diagnosis of familial hypobetalipoproteinemia.
Atherosclerosis, 2016
Isidor B, Küry S, Rosenfeld JA, Besnard T, Schmitt S, Joss S, Davies SJ, Lebel RR, Henderson A, Schaaf CP, Streff HE, Yang Y, Jain V, Chida N, Latypova X, Caignec CL, Cogné B, Mercier S, Vincent M, Colin E, Bonneau D, Denommé AS, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Piton A, Dina C, Donnart A, Lindenbaum P, Charpentier E, Redon R, Iemura K, Ikeda M, Tanaka K, Bézieau S.
De Novo Truncating Mutations in the kinetochore-microtubules attachment gene CHAMP1 Cause Syndromic Intellectual Disability.
Hum Mutat. 2016 Jan 11

Daumy X, Amarouch MY, Lindenbaum P, Bonnaud S, Charpentier E, Bianchi B, Nafzger S, Baron E, Fouchard S, Thollet A, Kyndt F, Barc J, Le Scouarnec S, Makita N, Le Marec H, Dina C, Gourraud JB, Probst V, Abriel H, Redon R, Schott JJ
Targeted resequencing identifies TRPM4 as a major gene predisposing to progressive familial heart block type I.
International Journal of Cardiology (2016)
Lecomte E, Tournaire B, Cogné B, Dupont JB, Lindenbaum P, Martin-Fontaine M, Broucque F, Robin C, Hebben M, Merten OW, Blouin V, François A, Redon R, Moullier P, Léger A.
Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing.
Mol Ther Nucleic Acids. 2015 Oct 27

Karakachoff M, Duforet-Frebourg N, Simonet F, Le Scouarnec S, Pellen N, Lecointe S, Charpentier E, Gros F, Cauchi S, Froguel P, Copin N; D.E.S.I.R. Study Group, Le Tourneau T, Probst V, Le Marec H, Molinaro S, Balkau B, Redon R, Schott JJ, Blum MG, Dina C; D E S I R Study Group.
Fine-scale human genetic structure in Western France.
Eur J Hum Genet. 2015 Jun
Le Scouarnec S, Karakachoff M, Gourraud JB, Lindenbaum P, Bonnaud S, Portero V, Duboscq-Bidot L, Daumy X, Simonet F, Teusan R, Baron E, Violleau J, Persyn E, Bellanger L, Barc J, Chatel S, Martins R, Mabo P, Sacher F, Haïssaguerre M, Kyndt F, Schmitt S, Bézieau S, Le Marec H, Dina C, Schott JJ, Probst V, Redon R.
Testing the burden of rare variation in arrhythmia-susceptibility genes provides new insights into molecular diagnosis for Brugada syndrome.
Hum Mol Genet. 2015 May 15;24(10):2757-63.
Béziau DM, Barc J, O'Hara T, Le Gloan L, Amarouch MY, Solnon A, Pavin D, Lecointe S, Bouillet P, Gourraud JB, Guicheney P, Denjoy I, Redon R, Mabo P, le Marec H, Loussouarn G, Kyndt F, Schott JJ, Probst V, Baró I.
Complex Brugada syndrome inheritance in a family harbouring compound SCN5A and CACNA1C mutations.
Basic Res Cardiol. 2014 Nov
Chesné J, Danger R, Botturi K, Reynaud-Gaubert M, Mussot S, Stern M, Danner-Boucher I, Mornex JF, Pison C, Dromer C, Kessler R, Dahan M, Brugière O, Le Pavec J, Perros F, Humbert M, Gomez C, Brouard S, Magnan A; COLT Consortium.
Systematic analysis of blood cell transcriptome in end-stage chronic respiratory diseases.
PLoS One. 2014 Oct 20
Lindenbaum P. and Redon R.
mod_bio: Apache modules for Next-Generation sequencing data.
Bioinformatics. 2014 Sept 4
Shy D, Gillet L, Ogrodnik J, Albesa M, Verkerk AO, Wolswinkel R, Rougier JS, Barc J, Essers MC, Syam N, Marsman RF, van Mil AM, Rotman S, Redon R, Bezzina CR, Remme CA, Abriel H.
PDZ domain-binding motif regulates cardiomyocyte compartment-specific NaV1.5 channel expression and function.
Circulation. 2014 Jul 8
Cogné B, Snyder R, Lindenbaum P, Dupont JB, Redon R, Moullier P, Leger A.
NGS library preparation may generate artifactual integration sites of AAV vectors.
Nat Med. 2014 Jun

Mercier S, Küry S, Shaboodien G, Houniet DT, Khumalo NP, Bou-Hanna C, Bodak N, Cormier-Daire V, David A, Faivre L, Figarella-Branger D, Gherardi RK, Glen E, Hamel A, Laboisse C, Le Caignec C, Lindenbaum P, Magot A, Munnich A, Mussini JM, Pillay K, Rahman T, Redon R, Salort-Campana E, Santibanez-Koref M, Thauvin C, Barbarot S, Keavney B, Bézieau S, Mayosi BM.
Mutations in FAM111B Cause Hereditary Fibrosing Poikiloderma with Tendon Contracture, Myopathy, and Pulmonary Fibrosis.
Am J Hum Genet. 2013 Dec 5

Bezzina CR, Barc J, Mizusawa Y, Remme CA, Gourraud JB, Simonet F, Verkerk AO, Schwartz PJ, Crotti L, Dagradi F, Guicheney P, Fressart V, Leenhardt A, Antzelevitch C, Bartkowiak S, Schulze-Bahr E, Zumhagen S, Behr ER, Bastiaenen R, Tfelt-Hansen J, Olesen MS, Kääb S, Beckmann BM, Weeke P, Watanabe H, Endo N, Minamino T, Horie M, Ohno S, Hasegawa K, Makita N, Nogami A, Shimizu W, Aiba T, Froguel P, Balkau B, Lantieri O, Torchio M, Wiese C, Weber D, Wolswinkel R, Coronel R, Boukens BJ, Bézieau S, Charpentier E, Chatel S, Despres A, Gros F, Kyndt F, Lecointe S, Lindenbaum P, Portero V, Violleau J, Gessler M, Tan HL, Roden DM, Christoffels VM, Le Marec H, Wilde AA, Probst V, Schott JJ, Dina C, Redon R.
Common variants at SCN5A-SCN10A and HEY2 are associated with Brugada syndrome, a rare disease with high risk of sudden cardiac death
Nat Genet. 2013 Aug 28;45(9):1044-9. 
Colman H, Le Berre-Scoul C, Hernandez C, Pierredon S, Bihouée A, Houlgatte R, Vagner S, Rosenberg AR, Féray C.
Genome-wide analysis of host mRNA translation during hepatitis C virus infection.
J Virol. 2013 Apr 3.

Feuerstein P, Puard V, Chevalier C, Teusan R, Cadoret V, Guerif F, Houlgatte R, Royere D.

Genomic assessment of human cumulus cell marker genes as predictors of oocyte developmental competence : impact of various experimental factors.
PLoS One. 2012

Cuccuini W, Briere J, Mounier N, Voelker HU, Rosenwald A, Sundstrom C, Cogliatti S, Hirchaud E, Ysebaert L, Bron D, Soulier J, Gaulard P, Houlgatte R, Gisselbrecht C, Thieblemont C.
MYC+ diffuse large B-cell lymphoma is not salvaged by classical R-ICE or R-DHAP followed by BEAM plus autologous stem cell transplantation.
Blood. 2012 May 17

Thieblemont C, Briere J, Mounier N, Voelker HU, Cuccuini W, Hirchaud E, Rosenwald A, Jack A, Sundstrom C, Cogliatti S, Trougouboff P, Boudova L, Ysebaert L, Soulier J, Chevalier C, Bron D, Schmitz N, Gaulard P, Houlgatte R, Gisselbrecht C.
The germinal center/activated B-cell subclassification has a prognostic impact for response to salvage therapy in relapsed/refractory diffuse large B-cell lymphoma : a bio-CORAL study.
J Clin Oncol. 2011 Nov 1

Quillé ML, Carat S, Quéméner-Redon S, Hirchaud E, Baron D, Benech C, Guihot J, Placet M, Mignen O, Férec C, Houlgatte R, Friocourt G.
High-throughput analysis of promoter occupancy reveals new targets for Arx, a gene mutated in mental retardation and interneuronopathies.
PLoS One. 2011 ;6(9):e25181

Baron D, Dubois E, Bihouée A, Teusan R, Steenman M, Jourdon P, Magot A, Péréon Y, Veitia R, Savagner F, Ramstein G, Houlgatte R.
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns.
BMC Genomics. 2011 Feb 16
Baron D, Bihouée A, Teusan R, Dubois E, Savagner F, Steenman M, Houlgatte R, Ramstein G.
MADGene : retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets.
Bioinformatics. 2011 Mar 1


Orozco-Solís R, Matos RJ, Guzmán-Quevedo O, Lopes de Souza S, Bihouée A, Houlgatte R, Manhães de Castro R, Bolaños-Jiménez F.
Nutritional programming in the rat is linked to long-lasting changes in nutrient sensing and energy homeostasis in the hypothalamus.
PLoS One. 2010 Oct 21

Carat S, Houlgatte R, Bourdon J.
A parallel scheme for comparing transcription factor binding sites matrices.
J Bioinform Comput Biol. 2010 Jun

Lamirault G, Meur NL, Roussel JC, Cunff MF, Baron D, Bihouée A, Guisle I, Raharijaona M, Ramstein G, Teusan R, Chevalier C, Gueffet JP, Trochu JN, Léger JJ, Houlgatte R, Steenman M.
Molecular risk stratification in advanced heart failure patients.
J Cell Mol Med. 2010 Jun