micropan: an R-package for microbial pan-genomics

Estimation of prokaryotic supergenome size and composition from gene frequency distributions

(2014) Alexander E Lobkovsky et al.   BMC GENOMICS

ITEP: An integrated toolkit for exploration of microbial pan-genomes

(2014) Matthew N Benedict et al.   BMC GENOMICS

The discrete Laplace exponential family and estimation of Y-STR haplotype frequencies

(2013) Mikkel Meyer Andersen et al.   JOURNAL OF THEORETICAL BIOLOGY

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

Genomic fluidity: an integrative view of gene diversity within microbial populations

(2011) Andrey O Kislyuk et al.   BMC GENOMICS

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

(2011) Marco Galardini et al.   BMC GENOMICS

Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp. bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production

(2011) Pei Hao et al.   PLoS One

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

(2010) Xiangyu Deng et al.   BMC GENOMICS

Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

(2010) Tristan Lefébure et al.   Genome Biology and Evolution

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Standard operating procedure for computing pangenome trees

(2010) Lars Snipen et al.   Standards in Genomic Sciences

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

(2010) Claudio Donati et al.   GENOME BIOLOGY

Microbial comparative pan-genomics using binomial mixture models

(2009) Lars Snipen et al.   BMC GENOMICS

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Enterococcus faecalis from newborn babies regulate endogenous PPAR  activity and IL-10 levels in colonic epithelial cells

(2008) A. Are et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology