Towards plant pangenomics

micropan: an R-package for microbial pan-genomics

(2015) Lars Snipen et al.   BMC BIOINFORMATICS

Ten years of pan-genome analyses

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

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

(2015) Fei Liu et al.   BMC GENOMICS

SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips

(2014) Shoshana Marcus et al.   BIOINFORMATICS

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

(2014) Yongbing Zhao et al.   BIOINFORMATICS

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

(2014) Matthew N Benedict et al.   BMC GENOMICS

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage

(2014) Ke Lin et al.   BMC GENOMICS

Structural variations in plant genomes

(2014) R. K. Saxena et al.   Briefings in Functional Genomics

Phenotypic and Genotypic Analysis of Clostridium difficile Isolates: a Single-Center Study

(2014) Y. Zhou et al.   JOURNAL OF CLINICAL MICROBIOLOGY

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat

(2014) Kaitao Lai et al.   PLANT BIOTECHNOLOGY JOURNAL

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones

(2014) Ramani Baddam et al.   Scientific Reports

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

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

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

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

High presence/absence gene variability in defense-related gene clusters of Cucumis melo

(2013) Víctor M González et al.   BMC GENOMICS

Genome-wide patterns of large-size presence/absence variants in sorghum

(2013) Li-Min Zhang et al.   Journal of Integrative Plant Biology

Presence–Absence Variation in A. thaliana Is Primarily Associated with Genomic Signatures Consistent with Relaxed Selective Constraints

(2013) Stephen J. Bush et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pan genome of the phytoplankton Emiliania underpins its global distribution

(2013) Betsy A. Read et al.   NATURE

GenomeRing: alignment visualization based on SuperGenome coordinates

(2012) A. Herbig et al.   BIOINFORMATICS

Variation of presence/absence genes among Arabidopsis populations

(2012) Shengjun Tan et al.   BMC EVOLUTIONARY BIOLOGY

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

Copy Number Variation Affecting the Photoperiod-B1 and Vernalization-A1 Genes Is Associated with Altered Flowering Time in Wheat (Triticum aestivum)

(2012) Aurora Díaz et al.   PLoS One

A Papaver somniferum 10-Gene Cluster for Synthesis of the Anticancer Alkaloid Noscapine

(2012) T. Winzer et al.   SCIENCE

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

The genetic integrity of bacterial species: the core genome and the accessory genome, two different stories

(2012) Bo Segerman   Frontiers in Cellular and Infection Microbiology

PGAP: pan-genomes analysis pipeline

(2011) Yongbing Zhao et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Detection of copy number variations in rice using array-based comparative genomic hybridization

(2011) Ping Yu et al.   BMC GENOMICS

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

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

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

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

(2010) Claudio Donati et al.   GENOME BIOLOGY

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Copy number variants, diseases and gene expression

(2009) C. N. Henrichsen et al.   HUMAN MOLECULAR GENETICS

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

(2009) K. L. McNally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Comparative genomics: the bacterial pan-genome

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

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE