Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics

PGAP-X: extension on pan-genome analysis pipeline

(2018) Yongbing Zhao et al.   BMC GENOMICS

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

panX: pan-genome analysis and exploration

(2017) Wei Ding et al.   NUCLEIC ACIDS RESEARCH

The Impact of Systems Biology on Bioprocessing

(2017) Kate Campbell et al.   TRENDS IN BIOTECHNOLOGY

Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae

(2017) Renata de A. B. Assis et al.   Scientific Reports

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

(2016) Guy Yachdav et al.   BIOINFORMATICS

Deciphering the regulon of a GntR family regulator via transcriptome and ChIP-exo analyses and its contribution to virulence inXanthomonas citri

(2016) Xiaofeng Zhou et al.   MOLECULAR PLANT PATHOLOGY

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines

(2016) Rafael Nascimento et al.   Scientific Reports

BPGA- an ultra-fast pan-genome analysis pipeline

(2016) Narendrakumar M. Chaudhari et al.   Scientific Reports

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

TheN-Glycan Cluster fromXanthomonas campestrispv.campestris

(2015) Stéphanie Dupoiron et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A quinol oxidase, encoded by cyoABCD, is utilized to adapt to lower O2 concentrations in Rhizobium etli CFN42

(2015) Zachary R. Lunak et al.   MICROBIOLOGY-SGM

Systems Biology for Biologists

(2015) Rachel A. Hillmer   PLoS Pathogens

PanGP: A tool for quickly analyzing bacterial pan-genome profile

(2014) Yongbing Zhao et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Matthew N Benedict et al.   BMC GENOMICS

An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates

(2014) Patrícia Locosque Ramos et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

The Plant Pathogen Xanthomonas campestris pv. campestris Exploits N-Acetylglucosamine during Infection

(2014) A. Boulanger et al.   mBio

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range

(2013) Neha Jalan et al.   BMC GENOMICS

Systems biology in drug discovery and development

(2013) Ellen L. Berg   DRUG DISCOVERY TODAY

Computational solutions for omics data

(2013) Bonnie Berger et al.   NATURE REVIEWS GENETICS

Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

(2013) Hafiz Sohail Naushad et al.   PLoS One

PGAT: a multistrain analysis resource for microbial genomes

(2011) M. J. Brittnacher et al.   BIOINFORMATICS

PGAP: pan-genomes analysis pipeline

(2011) Yongbing Zhao et al.   BIOINFORMATICS

Modulation of Host Immunity by Beneficial Microbes

(2011) Christos Zamioudis et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Solving the Problem: Genome Annotation Standards before the Data Deluge

(2011) William Klimke et al.   Standards in Genomic Sciences

A Decade of Systems Biology

(2010) Han-Yu Chuang et al.   Annual Review of Cell and Developmental Biology

Characterization of Xanthomonas campestris pv. campestris heat shock protein A (HspA), which possesses an intrinsic ability to reactivate inactivated proteins

(2010) Ching-Hsuan Lin et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

(2010) Chad Laing et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae

(2009) Isabelle Pieretti et al.   BMC GENOMICS

New genes of Xanthomonas citri subsp. citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library

(2009) Marcelo L Laia et al.   BMC MICROBIOLOGY

Pattern Recognition Receptors RequireN-Glycosylation to Mediate Plant Immunity

(2009) Heidrun Häweker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Cell Wall-Degrading Esterase of Xanthomonas oryzae Requires a Unique Substrate Recognition Module for Pathogenesis on Rice

(2009) G. Aparna et al.   PLANT CELL

'Omics Data Sharing

(2009) D. Field et al.   SCIENCE