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Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions.
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- Symmetry (20738994), 2024, v. 16, n. 9, p. 1217, doi. 10.3390/sym16091217
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- Article
Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes.
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- Molecular Biology & Evolution, 2022, v. 39, n. 10, p. 1, doi. 10.1093/molbev/msac191
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- Article
Customized strategies for discovering distant ncRNA homologs.
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- Briefings in Functional Genomics & Proteomics, 2009, v. 8, n. 6, p. 451, doi. 10.1093/bfgp/elp035
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Networks in molecular evolution.
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- Complexity, 2002, v. 8, n. 1, p. 34, doi. 10.1002/cplx.10052
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- Article
Canonical approximation of fitness landscapes.
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- Complexity, 1996, v. 2, n. 1, p. 53, doi. 10.1002/(SICI)1099-0526(199609/10)2:1<53::AID-CPLX11>3.0.CO;2-W
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- Article
Evolution of Spliceosomal snRNA Genes in Metazoan Animals.
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- Journal of Molecular Evolution, 2008, v. 67, n. 6, p. 594, doi. 10.1007/s00239-008-9149-6
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Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters: Increased Synonymous Substitution Rate and Asymmetrical Co-divergence of Coding and Non-coding Sequences.
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- Journal of Molecular Evolution, 2005, v. 60, n. 5, p. 665, doi. 10.1007/s00239-004-0252-z
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The Shark HoxN Cluster Is Homologous to the Human HoxD Cluster.
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- Journal of Molecular Evolution, 2004, v. 58, n. 2, p. 212, doi. 10.1007/s00239-003-2545-z
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- Article
Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus.
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- Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-62897-0
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- Article
The Genome of the "Sea Vomit" Didemnum vexillum.
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- Life (2075-1729), 2021, v. 11, n. 12, p. 1377, doi. 10.3390/life11121377
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- Article
SMORE: Synteny Modulator of Repetitive Elements.
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- Life (2075-1729), 2017, v. 7, n. 4, p. 42, doi. 10.3390/life7040042
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The Expansion of Animal MicroRNA Families Revisited.
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- Life (2075-1729), 2015, v. 5, n. 1, p. 905, doi. 10.3390/life5010905
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Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis.
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- Journal of Personalized Medicine, 2023, v. 13, n. 6, p. 924, doi. 10.3390/jpm13060924
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Finding the <italic>K</italic> best synthesis plans.
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- Journal of Cheminformatics, 2018, v. 10, n. 1, p. 1, doi. 10.1186/s13321-018-0273-z
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- Article
Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.
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- Genome Biology & Evolution, 2021, v. 13, n. 8, p. 1, doi. 10.1093/gbe/evab109
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- Article
Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies.
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- Genome Biology & Evolution, 2009, v. 1, p. 85, doi. 10.1093/gbe/evp010
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- Article
Design of Artificial Riboswitches as Biosensors.
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- Sensors (14248220), 2017, v. 17, n. 9, p. 1990, doi. 10.3390/s17091990
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- Article
Structured RNAs and synteny regions in the pig genome.
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- BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-459
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- Article
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations.
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- BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04159-8
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Indirect identification of horizontal gene transfer.
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- Journal of Mathematical Biology, 2021, v. 83, n. 1, p. 1, doi. 10.1007/s00285-021-01631-0
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- Article
Corrigendum to "Best match graphs".
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- Journal of Mathematical Biology, 2021, v. 82, n. 6, p. 1, doi. 10.1007/s00285-021-01601-6
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- Article
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.
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- Journal of Mathematical Biology, 2021, v. 82, n. 3, p. 1, doi. 10.1007/s00285-021-01564-8
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- Article
Best match graphs and reconciliation of gene trees with species trees.
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- Journal of Mathematical Biology, 2020, v. 80, n. 5, p. 1459, doi. 10.1007/s00285-020-01469-y
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Reciprocal best match graphs.
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- Journal of Mathematical Biology, 2020, v. 80, n. 3, p. 865, doi. 10.1007/s00285-019-01444-2
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Best match graphs.
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- Journal of Mathematical Biology, 2019, v. 78, n. 7, p. 2015, doi. 10.1007/s00285-019-01332-9
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Reconstructing gene trees from Fitch’s xenology relation.
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- Journal of Mathematical Biology, 2018, v. 77, n. 5, p. 1459, doi. 10.1007/s00285-018-1260-8
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Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem.
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- Journal of Mathematical Biology, 2018, v. 77, n. 2, p. 313, doi. 10.1007/s00285-017-1197-3
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- Article
Inferring phylogenetic trees from the knowledge of rare evolutionary events.
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- Journal of Mathematical Biology, 2018, v. 76, n. 7, p. 1623, doi. 10.1007/s00285-017-1194-6
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- Article
FORMAN–RICCI CURVATURE FOR HYPERGRAPHS.
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- Advances in Complex Systems, 2021, v. 24, n. 1, p. 1, doi. 10.1142/S021952592150003X
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- Article
NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES.
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- Advances in Complex Systems, 2005, v. 8, n. 2/3, p. 275, doi. 10.1142/S0219525905000427
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- Article
MOLECULAR REPLICATOR DYNAMICS.
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- Advances in Complex Systems, 2003, v. 6, n. 1, p. 47, doi. 10.1142/S0219525903000724
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- Article
Glassy States in a Shaken Sandbox.
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- Advances in Complex Systems, 2001, v. 4, n. 4, p. 429, doi. 10.1142/S0219525901000346
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- Article
Relevant Cycles in Chemical Reaction Networks.
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- Advances in Complex Systems, 2001, v. 4, n. 2/3, p. 207, doi. 10.1142/S0219525901000140
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Call for proposals.
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- Advances in Complex Systems, 1999, v. 2, n. 3, p. 195, doi. 10.1142/S0219525999000230
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RNA In Silico The Computational Biology of RNA Secondary Structures.
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- Advances in Complex Systems, 1999, v. 2, n. 1, p. 65, doi. 10.1142/S0219525999000059
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- Article
Amplitude Spectra of Fitness Landscapes.
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- Advances in Complex Systems, 1998, v. 1, n. 1, p. 39, doi. 10.1142/S0219525998000041
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Molecular Phylogenetics 2014.
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- BioMed Research International, 2015, v. 2015, p. 1, doi. 10.1155/2015/919251
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Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates.
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- Plant Biotechnology Journal, 2022, v. 20, n. 5, p. 944, doi. 10.1111/pbi.13775
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Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair.
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- Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.822304
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- Article
Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.
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- Nucleic Acids Research, 2023, v. 51, n. 11, p. e63, doi. 10.1093/nar/gkad312
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Human pathways in animal models: possibilities and limitations.
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- Nucleic Acids Research, 2021, v. 49, n. 4, p. 1859, doi. 10.1093/nar/gkab012
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TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.
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- Nucleic Acids Research, 2020, v. 48, n. D1, p. D626, doi. 10.1093/nar/gkz994
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- Article
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.
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- Nucleic Acids Research, 2019, v. 47, n. 20, p. 10543, doi. 10.1093/nar/gkz833
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- Article
DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation.
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- Nucleic Acids Research, 2019, v. 47, n. 17, p. 9087, doi. 10.1093/nar/gkz635
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- Article
RNA workbench 2.0: next generation RNA data analysis.
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- Nucleic Acids Research, 2019, v. 47, n. W1, p. W511, doi. 10.1093/nar/gkz353
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- Article
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
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- Nucleic Acids Research, 2017, v. 45, n. W1, p. W560, doi. 10.1093/nar/gkx409
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- Article
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
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- Nucleic Acids Research, 2017, v. 45, n. 8, p. 1, doi. 10.1093/nar/gkw1325
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- Article
Applicability of a computational design approach for synthetic riboswitches.
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- Nucleic Acids Research, 2017, v. 45, n. 7, p. 4108, doi. 10.1093/nar/gkw1267
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- Article
An updated human snoRNAome.
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- Nucleic Acids Research, 2016, v. 44, n. 11, p. 5068, doi. 10.1093/nar/gkw386
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- Article
Optimizing RNA structures by sequence extensions using RNAcop.
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- Nucleic Acids Research, 2015, v. 43, n. 17, p. 8135, doi. 10.1093/nar/gkv813
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- Article