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Gene Expression, Synteny, and Local Similarity in Human Noncoding Mutation Rates.
- Published in:
- Molecular Biology & Evolution, 2004, v. 21, n. 10, p. 1820, doi. 10.1093/molbev/msh181
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- Article
Evidence That the Human X Chromosome Is Enriched for Male-Specific but not Female-Specific Genes.
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- Molecular Biology & Evolution, 2003, v. 20, n. 7, p. 1113, doi. 10.1093/molbev/msg131
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- Article
Local Similarity in Evolutionary Rates Extends over Whole Chromosomes in Human-Rodent and Mouse-Rat Comparisons: Implications for Understanding the Mechanistic Basis of the Male Mutation Bias.
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- Molecular Biology & Evolution, 2001, v. 18, n. 11, p. 2032, doi. 10.1093/oxfordjournals.molbev.a003744
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- Article
Horizontal gene transfer depends on gene content of the host.
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- Bioinformatics, 2005, v. 21, p. ii222, doi. 10.1093/bioinformatics/bti1136
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- Article
Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39840-4
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- Article
A general model to predict small molecule substrates of enzymes based on machine and deep learning.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38347-2
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- Article
sybil - Efficient constraint-based modelling in R.
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- BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-125
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- Article
Minimal regulatory spaces in yeast genomes.
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- BMC Genomics, 2011, v. 12, n. 1, p. 320, doi. 10.1186/1471-2164-12-320
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- Article
Optimal density of bacterial cells.
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- PLoS Computational Biology, 2023, v. 19, n. 6, p. 1, doi. 10.1371/journal.pcbi.1011177
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- Article
Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth.
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- PLoS Computational Biology, 2023, v. 19, n. 6, p. 1, doi. 10.1371/journal.pcbi.1011156
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- Article
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R.
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- Molecular Biology & Evolution, 2014, v. 31, n. 7, p. 1929, doi. 10.1093/molbev/msu136
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- Article
Plant and Animal Glycolate Oxidases Have a Common Eukaryotic Ancestor and Convergently Duplicated to Evolve Long-Chain 2-Hydroxy Acid Oxidases.
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- Molecular Biology & Evolution, 2014, v. 31, n. 5, p. 1089, doi. 10.1093/molbev/msu041
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- Publication type:
- Article
Younger Genes Are Less Likely to Be Essential than Older Genes, and Duplicates Are Less Likely to Be Essential than Singletons of the Same Age.
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- Molecular Biology & Evolution, 2012, v. 29, n. 7, p. 1703, doi. 10.1093/molbev/mss014
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- Article
Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years.
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- Molecular Biology & Evolution, 2008, v. 25, n. 3, p. 559, doi. 10.1093/molbev/msm283
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- Article
Chance and necessity in the evolution of minimal metabolic networks.
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- Nature, 2006, v. 440, n. 7084, p. 667, doi. 10.1038/nature04568
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- Article
An integrated view of protein evolution.
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- Nature Reviews Genetics, 2006, v. 7, n. 5, p. 337, doi. 10.1038/nrg1838
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- Article
The evolutionary dynamics of eukaryotic gene order.
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- Nature Reviews Genetics, 2004, v. 5, n. 4, p. 299, doi. 10.1038/nrg1319
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- Article
Adaptive evolution of complex innovations through stepwise metabolic niche expansion.
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- Nature Communications, 2016, v. 7, n. 5, p. 11607, doi. 10.1038/ncomms11607
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- Article
Energy efficiency trade-offs drive nucleotide usage in transcribed regions.
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- Nature Communications, 2016, v. 7, n. 4, p. 11334, doi. 10.1038/ncomms11334
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- Article
Coexpression of Linked Gene Pairs Persists Long after Their Separation.
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- Genome Biology & Evolution, 2011, v. 3, p. 565, doi. 10.1093/gbe/evr049
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- Article
Transcriptional Coupling of Neighboring Genes and Gene Expression Noise: Evidence that Gene Orientation and Noncoding Transcripts Are Modulators of Noise.
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- Genome Biology & Evolution, 2011, v. 3, p. 320, doi. 10.1093/gbe/evr025
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- Article
Co-expression of neighbouring genes inArabidopsis: separating chromatin effects fromdirect interactions.
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- BMC Genomics, 2010, v. 11, p. 178, doi. 10.1186/1471-2164-11-178
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- Article
Horizontally transferred genes cluster spatially and metabolically.
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- Biology Direct, 2015, v. 10, p. 1, doi. 10.1186/s13062-015-0102-5
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- Article
An integrated approach to characterize genetic interaction networks in yeast metabolism.
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- Nature Genetics, 2011, v. 43, n. 7, p. 656, doi. 10.1038/ng.846
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- Article
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.
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- Nature Genetics, 2005, v. 37, n. 12, p. 1372, doi. 10.1038/ng1686
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- Article
A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships.
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- PLoS Computational Biology, 2024, v. 20, n. 5, p. 1, doi. 10.1371/journal.pcbi.1012100
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- Article
Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal.
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- PLoS Computational Biology, 2017, v. 13, n. 4, p. 1, doi. 10.1371/journal.pcbi.1005494
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- Article
Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets.
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- PLoS Computational Biology, 2016, v. 12, n. 8, p. 1, doi. 10.1371/journal.pcbi.1005036
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- Article
On the optimality of the enzyme–substrate relationship in bacteria.
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- PLoS Biology, 2021, v. 19, n. 10, p. 1, doi. 10.1371/journal.pbio.3001416
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- Article
Deep learning allows genome-scale prediction of Michaelis constants from structural features.
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- PLoS Biology, 2021, v. 19, n. 10, p. 1, doi. 10.1371/journal.pbio.3001402
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- Article
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.
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- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07652-6
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- Article
Understanding the Degradation of Hominid Gene Control.
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- 2006
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- Publication type:
- Letter
BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation.
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- Bioinformatics, 2018, v. 34, n. 18, p. 3205, doi. 10.1093/bioinformatics/bty299
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- Article
Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast.
- Published in:
- Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-47935-6
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- Article
Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR.
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- Frontiers in Microbiology, 2019, p. 1, doi. 10.3389/fmicb.2019.02254
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- Article
The protein translation machinery is expressed for maximal efficiency in Escherichia coli.
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- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-18948-x
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- Article
The Effects of Network Neighbours on Protein Evolution.
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- PLoS ONE, 2011, v. 6, n. 4, p. 1, doi. 10.1371/journal.pone.0018288
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- Article
A Gene's Ability to Buffer Variation Is Predicted by Its Fitness Contribution and Genetic Interactions.
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- PLoS ONE, 2011, v. 6, n. 3, p. 1, doi. 10.1371/journal.pone.0017650
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- Article
Clustering of housekeeping genes provides a unified model of gene order in the human genome.
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- Nature Genetics, 2002, v. 31, n. 2, p. 180, doi. 10.1038/ng887
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- Article
Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes.
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- PLoS Biology, 2009, v. 7, n. 3, p. e1000048, doi. 10.1371/journal.pbio.1000048
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- Article
Evidence for Widespread Degradation of Gene Control Regions in Hominid Genomes.
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- PLoS Biology, 2005, v. 3, n. 2, p. 1, doi. 10.1371/journal.pbio.0030042
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- Article
Evidence for Widespread Degradation of Gene Control Regions in Hominid Genomes.
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- PLoS Biology, 2005, v. 3, n. 1, p. 1, doi. 10.1371/journal.pbio.0030042
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- Publication type:
- Article
Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome.
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- Proteomics, 2010, v. 10, n. 6, p. 1297, doi. 10.1002/pmic.200900414
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- Article
Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers.
- Published in:
- Scientific Reports, 2017, p. 40294, doi. 10.1038/srep40294
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- Publication type:
- Article
Network reduction methods for genome-scale metabolic models.
- Published in:
- Cellular & Molecular Life Sciences, 2020, v. 77, n. 3, p. 481, doi. 10.1007/s00018-019-03383-z
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- Article
An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes.
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- PLoS Genetics, 2021, v. 17, n. 11, p. 1, doi. 10.1371/journal.pgen.1009939
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- Article
Modeling photosynthetic resource allocation connects physiology with evolutionary environments.
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- Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-94903-0
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- Article
Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. W1, p. W270, doi. 10.1093/nar/gkz357
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- Article
MVP: a microbe--phage interaction database.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. D1, p. D700, doi. 10.1093/nar/gkx1124
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- Article
Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees.
- Published in:
- Nucleic Acids Research, 2016, v. 44, n. W1, p. W236, doi. 10.1093/nar/gkw370
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- Publication type:
- Article