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Network-based function prediction and interactomics: The case for metabolic enzymes

Metabolic engineering, 2011, Vol.13 (1), p.1-10

2011

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Predicting Functional Interactions Among Genes in Prokaryotes by Genomic Context

Advances in experimental medicine and biology, 2015, Vol.883, p.97

2015

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GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways

Nucleic acids research, 2008-07, Vol.36 (Web Server issue), p.W176-W180

2008

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Functional impact of IBS-D microbiota on the gut-brain axis

Brain, behavior, and immunity, 2015-10, Vol.49, p.e41-e41

2015

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Isolation and characterization of genetic variability in bacteria with β-hemolytic and antifungal activity isolated from the rhizosphere of Medicago truncatula plants

Genetics and molecular research, 2014-07, Vol.13 (3), p.4967-4975

2014

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The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective

Nucleic acids research, 2012-08, Vol.40 (15), p.7104-7112

2012

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partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons

Proceedings of the National Academy of Sciences - PNAS, 2006-03, Vol.103 (10), p.3834-3839

2006

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A powerful non-homology method for the prediction of operons in prokaryotes

Bioinformatics, 2002-07, Vol.18 Suppl 1 (1), p.S329-S336

2002

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Operons in Escherichia coli: Genomic Analyses and Predictions

Proceedings of the National Academy of Sciences - PNAS, 2000-06, Vol.97 (12), p.6652-6657

2000

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Whole-Genome Expression Profiling Defines the HrpL Regulon of Pseudomonas syringae pv. tomato DC3000, Allows de novo Reconstruction of the Hrp cis Clement, and Identifies Novel Coregulated Genes

Molecular plant-microbe interactions, 2006-11, Vol.19 (11), p.1167-1179

2006

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A comparative genomics approach to prediction of new members of regulons

Genome research, 2001-04, Vol.11 (4), p.566-584

2001

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Conservation of DNA curvature signals in regulatory regions of prokaryotic genes

Nucleic acids research, 2003-12, Vol.31 (23), p.6770-6777

2003

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Conservation of adjacency as evidence of paralogous operons

Nucleic acids research, 2004-01, Vol.32 (18), p.5392-5397

2004

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Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons

Nucleic acids research, 2005-01, Vol.33 (8), p.2521-2530

2005

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Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes

Molecular biology and evolution, 2004-10, Vol.21 (10), p.1884-1894

2004

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Open resource metagenomics: a model for sharing metagenomic libraries

Standards in genomic sciences, 2011-11, Vol.5 (2), p.203-210

2011

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Transcription unit conservation in the three domains of life: a perspective from Escherichia coli

Trends in genetics, 2001-04, Vol.17 (4), p.175-177

2001

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The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments

Genome biology, 2003, Vol.4 (6), p.R36-R36

2003

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The disulfide bridges of toxin 2 from the scorpion Centruroides noxius Hoffmann and its three-dimensional structure calculated using the coordinates of variant 3 from Centruroides sculpturatus

FEBS letters, 1994-06, Vol.347 (1), p.59-62

1994

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A new method of solution for the occupancy problem and its application to operon size prediction

Journal of theoretical biology, 2004-04, Vol.227 (3), p.315-322

2004

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Microbial computational genomics of gene regulation

Pure and applied chemistry, 2002-01, Vol.74 (6), p.899-905

2002

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Escherichia coli TEM1 β-lactamase in CTAB reverse micelles: exchange/diffusion-limited catalysis

FEBS letters, 1999-10, Vol.459 (1), p.111-114

1999

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Expanding the UniFrac Toolbox

PloS one, 2016-09, Vol.11 (9), p.e0161196-e0161196

2016

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Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

PloS one, 2021-11, Vol.16 (11), p.e0255262-e0255262

2021

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VIR.II: a new interface with the antibody sequences in the Kabat database

BioSystems, 2001-07, Vol.61 (2), p.125-131

2001

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Network-based function prediction and interactomics: The case for metabolic enzymes

Predicting Functional Interactions Among Genes in Prokaryotes by Genomic Context

GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways

Functional impact of IBS-D microbiota on the gut-brain axis

Isolation and characterization of genetic variability in bacteria with β-hemolytic and antifungal activity isolated from the rhizosphere of Medicago truncatula plants

The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective

partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons

A powerful non-homology method for the prediction of operons in prokaryotes

Operons in Escherichia coli: Genomic Analyses and Predictions

Whole-Genome Expression Profiling Defines the HrpL Regulon of Pseudomonas syringae pv. tomato DC3000, Allows de novo Reconstruction of the Hrp cis Clement, and Identifies Novel Coregulated Genes

A comparative genomics approach to prediction of new members of regulons

Conservation of DNA curvature signals in regulatory regions of prokaryotic genes

Conservation of adjacency as evidence of paralogous operons

Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons

Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes

Open resource metagenomics: a model for sharing metagenomic libraries

Transcription unit conservation in the three domains of life: a perspective from Escherichia coli

The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments

The disulfide bridges of toxin 2 from the scorpion Centruroides noxius Hoffmann and its three-dimensional structure calculated using the coordinates of variant 3 from Centruroides sculpturatus

A new method of solution for the occupancy problem and its application to operon size prediction

Microbial computational genomics of gene regulation

Escherichia coli TEM1 β-lactamase in CTAB reverse micelles: exchange/diffusion-limited catalysis

Expanding the UniFrac Toolbox

Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

VIR.II: a new interface with the antibody sequences in the Kabat database

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