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Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation.
- Published in:
- Systematic Biology, 2023, v. 72, n. 6, p. 1370, doi. 10.1093/sysbio/syad058
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- Article
MicroRNA Target Identification: Revisiting Accessibility and Seed Anchoring.
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- Genes, 2023, v. 14, n. 3, p. 664, doi. 10.3390/genes14030664
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- Article
Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations.
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- Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.815476
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- Article
Efficiently sparse listing of classes of optimal cophylogeny reconciliations.
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- Algorithms for Molecular Biology, 2022, v. 17, n. 1, p. 1, doi. 10.1186/s13015-022-00206-y
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- Article
BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data.
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- GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac093
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- Article
Efficient hybrid de novo assembly of human genomes with WENGAN.
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- Nature Biotechnology, 2021, v. 39, n. 4, p. 422, doi. 10.1038/s41587-020-00747-w
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- Article
Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions.
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- Bioinformatics, 2020, v. 36, n. 14, p. 4197, doi. 10.1093/bioinformatics/btaa498
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- Article
Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells.
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- Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-70040-y
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- Article
Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility.
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- Algorithms for Molecular Biology, 2020, v. 15, n. 1, p. 1, doi. 10.1186/s13015-020-00174-1
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- Article
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering.
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- BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-020-3377-1
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- Article
MOOMIN – Mathematical explOration of 'Omics data on a MetabolIc Network.
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- Bioinformatics, 2020, v. 36, n. 2, p. 514, doi. 10.1093/bioinformatics/btz584
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- Article
Exploring and Visualizing Spaces of Tree Reconciliations.
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- Systematic Biology, 2019, v. 68, n. 4, p. 607, doi. 10.1093/sysbio/syy075
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- Article
Hydrogen peroxide production and myo‐inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae.
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- Molecular Microbiology, 2018, v. 108, n. 6, p. 683, doi. 10.1111/mmi.13957
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- Article
Fast-SG: an alignment-free algorithm for hybrid assembly.
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- GigaScience, 2018, v. 7, n. 5, p. N.PAG, doi. 10.1093/gigascience/giy048
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- Article
Computing and Listing <italic>st</italic>-Paths in Public Transportation Networks.
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- Theory of Computing Systems, 2018, v. 62, n. 3, p. 600, doi. 10.1007/s00224-016-9747-4
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- Article
OptPipe - a pipeline for optimizing metabolic engineering targets.
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- BMC Systems Biology, 2017, v. 11, p. 1, doi. 10.1186/s12918-017-0515-0
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- Article
How Long Does Wolbachia Remain on Board?
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- Molecular Biology & Evolution, 2017, v. 34, n. 5, p. 1183, doi. 10.1093/molbev/msx073
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- Article
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.
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- Algorithms for Molecular Biology, 2017, v. 12, p. 1, doi. 10.1186/s13015-017-0091-2
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- Article
DegreeCox - a network-based regularization method for survival analysis.
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- BMC Bioinformatics, 2016, v. 17, p. 109, doi. 10.1186/s12859-016-1310-4
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- Publication type:
- Article
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.
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- Nucleic Acids Research, 2016, v. 44, n. 19, p. 1, doi. 10.1093/nar/gkw655
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- Article
Mycoplasma non-coding RNA: identification of small RNAs and targets.
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- BMC Genomics, 2016, v. 17, p. 327, doi. 10.1186/s12864-016-3061-z
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- Article
Enumeration of minimal stoichiometric precursor sets in metabolic networks.
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- Algorithms for Molecular Biology, 2016, v. 11, p. 1, doi. 10.1186/s13015-016-0087-3
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- Article
A Combinatorial Algorithm for Microbial Consortia Synthetic Design.
- Published in:
- Scientific Reports, 2016, p. 29182, doi. 10.1038/srep29182
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- Article
Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling.
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- BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2644-z
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- Article
MEDUSA: a multi-draft based scaffolder.
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- 2015
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- Product Review
A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs.
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- Algorithms for Molecular Biology, 2015, v. 10, n. 1, p. 1, doi. 10.1186/s13015-015-0046-4
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- Article
Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data.
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- BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0594-0
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- Article
Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci.
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- BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1379-6
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- Article
Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci
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- BMC Genomics, 2015, v. 16, n. 1, p. 226, doi. 10.1186/s12864-015-1379-6
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- Article
Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts.
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- Genome Biology & Evolution, 2015, v. 7, n. 3, p. 839, doi. 10.1093/gbe/evv030
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- Article
EUCALYPT: Efficient tree reconciliation enumerator.
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- Algorithms for Molecular Biology, 2015, v. 10, n. 1, p. 1, doi. 10.1186/s13015-014-0031-3
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- Article
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.
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- Bioinformatics, 2014, v. 30, n. 1, p. 61, doi. 10.1093/bioinformatics/btt597
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- Article
Biosynthesis of Vitamins and Cofactors in Bacterium-Harbouring Trypanosomatids Depends on the Symbiotic Association as Revealed by Genomic Analyses.
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- PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0079786
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- Article
Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers.
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- BMC Evolutionary Biology, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2148-13-190
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- Article
Short and long-term genome stability analysis of prokaryotic genomes.
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- BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-309
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- Article
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.
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- Bioinformatics, 2012, v. 28, n. 23, p. 3034, doi. 10.1093/bioinformatics/bts574
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- Article
Structural and dynamical analysis of biological networks.
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- Briefings in Functional Genomics, 2012, v. 11, n. 6, p. 420, doi. 10.1093/bfgp/els030
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- Article
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.
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- Bioinformatics, 2012, v. 28, n. 19, p. 2474, doi. 10.1093/bioinformatics/bts423
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- Article
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
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- BMC Bioinformatics, 2012, v. 13, n. Suppl 6, p. 1, doi. 10.1186/1471-2105-13-S6-S5
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- Article
Sampling solution traces for the problem of sorting permutations by signed reversals.
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- Algorithms for Molecular Biology, 2012, v. 7, n. 1, p. 18, doi. 10.1186/1748-7188-7-18
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- Article
Exploration of the core metabolism of symbiotic bacteria.
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- BMC Genomics, 2012, v. 13, n. 1, p. 438, doi. 10.1186/1471-2164-13-438
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- Article
CycADS: an annotation database system to ease the development and update of BioCyc databases.
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- Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 8, p. 1
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- Article
CycADS: an annotation database system to ease the development and update of BioCyc databases.
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- Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 8, p. 1
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- Publication type:
- Article
Bacterial syntenies: an exact approach with gene quorum.
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- BMC Bioinformatics, 2011, v. 12, n. 1, p. 193, doi. 10.1186/1471-2105-12-193
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- Article
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny.
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- BMC Genomics, 2011, v. 12, n. 1, p. 303, doi. 10.1186/1471-2164-12-303
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- Article
Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata.
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- PLoS Computational Biology, 2010, v. 6, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000904
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- Article
Cassis: detection of genomic rearrangement breakpoints.
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- Bioinformatics, 2010, v. 26, n. 15, p. 1897, doi. 10.1093/bioinformatics/btq301
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- Publication type:
- Article
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.
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- Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W132, doi. 10.1093/nar/gkq312
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- Publication type:
- Article
Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi.
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- BMC Genomics, 2010, v. 11, p. 529, doi. 10.1186/1471-2164-11-529
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- Article
Lossless filter for multiple repeats with bounded edit distance.
- Published in:
- Algorithms for Molecular Biology, 2009, v. 4, p. 1, doi. 10.1186/1748-7188-4-3
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- Article