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Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks.

Steven M Kelk , Brett G Olivier , Leen Stougie , Frank J Bruggeman
Scientific Reports, 2012, 2, pp.580. ⟨10.1038/srep00580⟩
Journal articles hal-00763439v1

Brief Announcement: Flooding in Dynamic Graphs with Arbitrary Degree Sequence

Hervé Baumann , Pierluigi Crescenzi , Pierre Fraigniaud
26th International Symposium on Distributed Computing, 2012, Salvador, Brazil. pp.417-419
Conference papers hal-00763446v1
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Multichromosomal median and halving problems under different genomic distances

Eric Tannier , Chunfang Zheng , David Sankoff
BMC Bioinformatics, 2009, 10 (1), pp.120. ⟨10.1186/1471-2105-10-120⟩
Journal articles hal-00784456v1

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Milana Frenkel-Morgenstern , Vincent Lacroix , Iakes Ezkurdia , Yishai Levin , Alexandra Gabashvili et al.
Genome Research, 2012, 22 (7), pp.1231-1242. ⟨10.1101/gr.130062.111⟩
Journal articles hal-00744761v1
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The evolution of recombination and genomic structures: a modeling approach.

Alexandra Popa
Bioinformatics [q-bio.QM]. Université Claude Bernard - Lyon I, 2011. English. ⟨NNT : ⟩
Theses tel-00750370v1

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.

Marco Galardini , Alessio Mengoni , Matteo Brilli , Francesco Pini , Antonella Fioravanti et al.
BMC Genomics, 2011, 12, pp.235. ⟨10.1186/1471-2164-12-235⟩
Journal articles hal-00746865v1

Annotation et évolution des familles de transporteurs chez le puceron du pois Acyrthosiphon pisum

N. Parisot
Bio-informatique [q-bio.QM]. 2010
Master thesis hal-00784737v1
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A Fast Discovery Algorithm for Large Common Connected Induced Subgraphs

Alessio Conte , Roberto Grossi , Andrea Marino , Lorenzo Tattini , Luca Versari et al.
WEPA 2019 - Workshop on Enumeration Problems & Applications, Oct 2019, Awaji Island, Japan. pp.1-26
Conference papers hal-02338435v1
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AphidAtlas : avancées récentes

Anthony Bretaudeau , Olivier Dameron , Fabrice Legeai , Yvan Rahbé
BAPOA 2013 MOP, Oct 2013, Montpellier, France
Conference papers hal-00913155v1

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

Kamil Salikhov , Gustavo Sacomoto , Gregory Kucherov
Workshop on Algorithms in Bioinformatics, Sep 2013, Sophia Antipolis, France. 13p
Conference papers hal-00824697v1

A dynamic programming algorithm for the tree mapping problem

C.E. Ferreira , A. S. Freire , G. A. Puglia
Electronic Notes in Discrete Mathematics, 2011, pp.147-152
Journal articles hal-00748779v1

Initial metabolic reconstruction of Klebsiella pneumoniae Kp13, a multidrug resistant pathogen involved in nosocomial outbreaks in Brazil

P. Ivan , Cecilia C. Klein , Ludovic Cottret , Ana T Vasconcelos , Ac Gales et al.
X-meeting, 2011, Florianópolis, Brazil
Conference papers hal-00748781v1

An improved algorithm to enumerate all traces that sort a signed permutation by reversals

Christian Baudet , Zanoni Dias
ACM Symposium on Applied Computing (SAC), Mar 2010, Sierre, Switzerland. pp.1521-1525, ⟨10.1145/1774088.1774416⟩
Conference papers hal-00748579v1

Partial enumeration of solutions traces for the problem of sorting by signed reversals

Christian Baudet , Zanoni Dias
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Aug 2011, Chicago, United States. pp.505--507, ⟨10.1145/2147805.2147884⟩
Conference papers hal-00748607v1
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Motif representation and discovery

A.M. Carvalho
Bioinformatics [q-bio.QM]. Universidade técnica de Lisboa Instituto superior técnico, 2011. English. ⟨NNT : ⟩
Theses tel-00755042v1
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Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract

Mariana Galvao Ferrarini
Bioinformatics [q-bio.QM]. Université Claude Bernard - Lyon I, 2015. English. ⟨NNT : 2015LYO10302⟩
Theses tel-01315159v1
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Identification of metabolic network models from incomplete high-throughput datasets

Sara Berthoumieux , Matteo Brilli , Hidde De Jong , Daniel Kahn , Eugenio Cinquemani et al.
Bioinformatics, 2011, 27 (13), pp.i186-i195. ⟨10.1093/bioinformatics/btr225⟩
Journal articles hal-00793039v1
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Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses

Cecilia C Klein , João M P Alves , Myrna G Serrano , Gregory A Buck , Ana Tereza R Vasconcelos et al.
PLoS ONE, 2013, 8 (11), pp.e79786. ⟨10.1371/journal.pone.0079786⟩
Journal articles hal-00922587v1

Does a parthenogenesis-inducing Wolbachia induce vestigial cytoplasmic incompatibility?

Ken Kraaijeveld , Barbara M Reumer , Laurence Mouton , Natacha Kremer , Fabrice Vavre et al.
The Science of Nature Naturwissenschaften, 2011, 98 (3), pp.175-80. ⟨10.1007/s00114-010-0756-x⟩
Journal articles hal-00746858v1

Reconciliation of metabolites and biochemical reactions for metabolic networks.

Thomas Bernard , Alan Bridge , Anne Morgat , Sébastien Moretti , Ioannis Xenarios et al.
Briefings in Bioinformatics, 2012, 15 (1), pp.123-135. ⟨10.1093/bib/bbs058⟩
Journal articles hal-00764412v1
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Etude structurelle des réseaux : modèles aléatoires, motifs et cycles.

Etienne Birmele
Bio-informatique [q-bio.QM]. Université d'Evry-Val d'Essonne, 2011
Habilitation à diriger des recherches tel-00750375v1

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

Gustavo Akio Tominaga Sacomoto , Vincent Lacroix , Marie-France Sagot
Workshop on Algorithms in Bioinformatics (WABI), Sep 2013, Nice, France
Conference papers hal-00842982v1

Integration of metabolic pathways and host regulation in symbiosis: tyrosine and cuticular protein biosynthesis during the pea aphid embryonic development

Andréane Rabatel , Gérard Febvay , Karen Gaget , Gabrielle Duport , Nadia Bendridi et al.
Sixth International Symposium on Molecular Insect Science, 2011, Amsterdam, Netherlands
Conference papers hal-00748785v1
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Reference-free detection of isolated SNPs

Raluca Uricaru , Guillaume Rizk , Vincent Lacroix , Elsa Quillery , Olivier Plantard et al.
Nucleic Acids Research, 2014, 43 (2), pp.e11. ⟨10.1093/nar/gku1187⟩
Journal articles hal-01083715v1
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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali , Cédric Saule , Cedric Chauve , Yves d'Aubenton-Carafa , Alain Denise et al.
Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩
Journal articles hal-00647725v1
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Exploration et inférence du réseau de régulation de la transcription de la bactérie symbiotique intracellulaire à génome réduit Buchnera aphidicola

Lilia Brinza
Bio-informatique [q-bio.QM]. INSA de Lyon, 2010. Français. ⟨NNT : ⟩
Theses tel-00750363v1
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Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts.

Pierre-Antoine Rollat-Farnier , Diego Santos-Garcia , Qiong Rao , Marie-France Sagot , Francisco J Silva et al.
Genome Biology and Evolution, 2015, 7 (3), pp.839-855. ⟨10.1093/gbe/evv030⟩
Journal articles hal-01139507v1
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Efficient algorithms for the identification of miRNA motifs in DNA sequences

Nuno D Mendes
Bioinformatics [q-bio.QM]. UNIVERSIDADE TECNICA DE LISBOA INSTITUTO SUPERIOR TECNICO, 2011. English. ⟨NNT : ⟩
Theses tel-00750693v1
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Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

Paulo Vieira Milreu , Vicente Acuña , Etienne E. Birmelé , Pierluigi Crescenzi , Alberto Marchetti-Spaccamela et al.
Workshop on Algorithms in Bioinformatics (WABI), Sep 2010, Liverpool, United Kingdom. pp.226-237, ⟨10.1007/978-3-642-15294-8_19⟩
Conference papers hal-00751339v1
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Diversity and dynamics of Wolbachia-host associations in arthropods from the Society archipelago, French Polynesia

Patrícia Martins Simões
Biodiversité. Université Claude Bernard - Lyon I, 2012. Français. ⟨NNT : ⟩
Theses tel-00850707v1