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Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data

Misbah Razzaq , Loïc Paulevé , Anne Siegel , Julio Saez-Rodriguez , Jérémie Bourdon et al.
PLoS Computational Biology, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩
Journal articles hal-01897020v1
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Mechanically induced development and maturation of human intestinal organoids in vivo

Holly Poling , David Wu , Nicole Brown , Michael Baker , Taylor Hausfeld et al.
Nature Biomedical Engineering, 2018, 2 (6), pp.429 - 442. ⟨10.1038/s41551-018-0243-9⟩
Journal articles hal-01816387v1
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Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models

Méziane Aite , Marie Chevallier , Clémence Frioux , Camille Trottier , Jeanne Got et al.
PLoS Computational Biology, 2018, 14 (5), pp.e1006146. ⟨10.1371/journal.pcbi.1006146⟩
Journal articles hal-01807842v1
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Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming

Lokmane Chebouba , Bertrand Miannay , Dalila Boughaci , Carito Guziolowski
BMC Bioinformatics, 2018, 19 (S2), ⟨10.1186/s12859-018-2034-4⟩
Journal articles hal-01988426v1
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Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota

Raul Tito , Samuel Chaffron , Clara Caenepeel , Gipsi Lima-Mendez , Jun Wang et al.
Journal articles hal-01893208v1
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Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

Dinka Mandakovic , Claudia Rojas , Jonathan Maldonado , Mauricio Latorre , Dante Travisany et al.
Scientific Reports, 2018, 8 (1), pp.5875. ⟨10.1038/s41598-018-23931-0⟩
Journal articles hal-01774624v1
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The Use of Next Generation Sequencing for Improving Food Safety: Translation into practice

Balamurugan Jagadeesan , Peter Gerner-Smidt , Marc Allard , Sébastien Leuillet , Anett Winkler et al.
Food Microbiology, 2018, ⟨10.1016/⟩
Journal articles hal-01934206v1
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Identification of transcription factors involved in the phenotype of a domesticated oleaginous microalgae strain of Tisochrysis lutea

S. Thiriet-Rupert , Gregory Carrier , C. Trottier , Damien Eveillard , B. Schoefs et al.
Algal Research - Biomass, Biofuels and Bioproducts, 2018, 30, pp.59 - 72. ⟨10.1016/j.algal.2017.12.011⟩
Journal articles hal-01677336v1
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Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data

Bertrand Miannay , Stéphane Minvielle , Florence Magrangeas , Carito Guziolowski
BMC Systems Biology, 2018, 12(Suppl3), pp.32 - 32. ⟨10.1186/s12918-018-0551-4⟩
Journal articles inserm-01804825v1
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Logic and Linear programs to understand cancer response

Misbah Razzaq , Lokmane Chebouba , Pierre Le Jeune , Hanen Mhamdi , Carito Guziolowski et al.
Preprints, Working Papers, ... hal-01897036v1
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Complex graphs in biology : problems, algorithms and evaluation

Julien Fradin
Bio-informatique [q-bio.QM]. Université de Nantes, Faculté des sciences et des techniques; Ecole Doctorale MATHSTIC, 2018. Français. ⟨NNT : ⟩
Theses tel-02081176v1
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Scalable and exhaustive screening of metabolic functions carried out by microbial consortia

Clémence Frioux , Enora Fremy , Camille Trottier , Anne Siegel
ECCB - 2018 - 17th European Conference on Computational Biology, Sep 2018, Athènes, Greece. pp.i934-i943
Conference papers hal-01946860v1
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Integrating phosphoproteomic time series data into prior knowledge networks

Misbah Razzaq
Bioinformatics [q-bio.QM]. École centrale de Nantes, 2018. English. ⟨NNT : 2018ECDN0048⟩
Theses tel-02021019v1
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Therapeutic target discovery using Boolean network attractors: improvements of kali

Arnaud Poret , Carito Guziolowski
Royal Society Open Science, 2018, 5 (2), ⟨10.1098/rsos.171852⟩
Journal articles hal-01395079v3