Computational pan-genomics: status, promises and challenges

PanTools: representation, storage and exploration of pan-genomic data

(2016) Siavash Sheikhizadeh et al.   BIOINFORMATICS

Read mapping on de Bruijn graphs

(2016) Antoine Limasset et al.   BMC BIOINFORMATICS

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis

(2016) Wouter van Rheenen et al.   NATURE GENETICS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Graphical pan-genome analysis with compressed suffix trees and the Burrows–Wheeler transform

(2015) Uwe Baier et al.   BIOINFORMATICS

HapCol: accurate and memory-efficient haplotype assembly from long reads

(2015) Yuri Pirola et al.   BIOINFORMATICS

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

KMC 2: fast and resource-frugal k-mer counting

(2015) Sebastian Deorowicz et al.   BIOINFORMATICS

Pan-Tetris: an interactive visualisation for Pan-genomes

(2015) André Hennig et al.   BMC BIOINFORMATICS

Genome assembly using Nanopore-guided long and error-free DNA reads

(2015) Mohammed-Amin Madoui et al.   BMC GENOMICS

Biological and Therapeutic Impact of Intratumor Heterogeneity in Cancer Evolution

(2015) Nicholas McGranahan et al.   CANCER CELL

Ten years of pan-genome analyses

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

The Origin of Land Plants: A Phylogenomic Perspective

(2015) Bojian Zhong et al.   Evolutionary Bioinformatics

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays

(2015) A. C. Y. Mak et al.   GENETICS

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

(2015) Brigitte Boeckmann et al.   Genome Biology and Evolution

Building a Pan-Genome Reference for a Population

(2015) Ngan Nguyen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

(2015) Murray Patterson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Data analysis: Create a cloud commons

(2015) Lincoln D. Stein et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

(2015) Colin S Cooper et al.   NATURE GENETICS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Haplotype-resolved genome sequencing: experimental methods and applications

(2015) Matthew W. Snyder et al.   NATURE REVIEWS GENETICS

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

(2015) Tyler S. Alioto et al.   Nature Communications

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic

(2015) Richard J. Hall et al.   Frontiers in Microbiology

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

(2015) Alastair Crisp et al.   GENOME BIOLOGY

A Brief Review of Software Tools for Pangenomics

(2015) Jingfa Xiao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Robustness of Massively Parallel Sequencing Platforms

(2015) Pınar Kavak et al.   PLoS One

Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)

(2014) R. Durbin   BIOINFORMATICS

Journaled string tree--a scalable data structure for analyzing thousands of similar genomes on your laptop

(2014) R. Rahn et al.   BIOINFORMATICS

Comparative assembly hubs: Web-accessible browsers for comparative genomics

(2014) Ngan Nguyen et al.   BIOINFORMATICS

Probabilistic single-individual haplotyping

(2014) V. Kuleshov   BIOINFORMATICS

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

(2014) Shoshana Marcus et al.   BIOINFORMATICS

GATB: Genome Assembly & Analysis Tool Box

(2014) Erwan Drezen et al.   BIOINFORMATICS

Genome alignment with graph data structures: a comparison

(2014) Birte Kehr et al.   BMC BIOINFORMATICS

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

(2014) Bas E Dutilh et al.   BMC GENOMICS

Indexing Graphs for Path Queries with Applications in Genome Research

(2014) Jouni Siren et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The ctenophore genome and the evolutionary origins of neural systems

(2014) Leonid L. Moroz et al.   NATURE

Guidelines for investigating causality of sequence variants in human disease

(2014) D. G. MacArthur et al.   NATURE

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Data use under the NIH GWAS Data Sharing Policy and future directions

(2014)   NATURE GENETICS

Whole-genome sequence variation, population structure and demographic history of the Dutch population

(2014) Laurent C Francioli et al.   NATURE GENETICS

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Comparative primate genomics: emerging patterns of genome content and dynamics

(2014) Jeffrey Rogers et al.   NATURE REVIEWS GENETICS

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

Indexes of Large Genome Collections on a PC

(2014) Agnieszka Danek et al.   PLoS One

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic

(2014) Mark Eppinger et al.   mBio

Whole-genome haplotyping approaches and genomic medicine

(2014) Gustavo Glusman et al.   Genome Medicine

Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology

(2014) Timothy D Read et al.   Genome Medicine

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

(2014) Emily Berger et al.   PLoS Computational Biology

Viral Quasispecies Assembly via Maximal Clique Enumeration

(2014) Armin Töpfer et al.   PLoS Computational Biology

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

(2014) Mark de Been et al.   PLoS Genetics

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Haplotype assembly in polyploid genomes and identical by descent shared tracts

(2013) Derek Aguiar et al.   BIOINFORMATICS

Short read alignment with populations of genomes

(2013) L. Huang et al.   BIOINFORMATICS

DSK: k-mer counting with very low memory usage

(2013) G. Rizk et al.   BIOINFORMATICS

Mobilomics in Saccharomyces cerevisiae strains

(2013) Giulia Menconi et al.   BMC BIOINFORMATICS

Discovering motifs that induce sequencing errors

(2013) Manuel Allhoff et al.   BMC BIOINFORMATICS

Explaining microbial phenotypes on a genomic scale: GWAS for microbes

(2013) B. E. Dutilh et al.   Briefings in Functional Genomics

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

An archaeal origin of eukaryotes supports only two primary domains of life

(2013) Tom A. Williams et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

(2013) Alex R. Hastie et al.   PLoS One

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

(2013) Emma S. Mace et al.   Nature Communications

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

(2013) István Bartha et al.   eLife

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Rules of Engagement: Molecular Insights from Host-Virus Arms Races

(2012) Matthew D. Daugherty et al.   Annual Review of Genetics

GenomeRing: alignment visualization based on SuperGenome coordinates

(2012) A. Herbig et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1

(2012) J. M. Carlson et al.   JOURNAL OF VIROLOGY

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

DNA sequencing with nanopores

(2012) Grégory F Schneider et al.   NATURE BIOTECHNOLOGY

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

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

(2012) Zamin Iqbal et al.   NATURE GENETICS

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

(2012) Ester Falconer et al.   NATURE METHODS

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

(2012) Christine M. Malboeuf et al.   NUCLEIC ACIDS RESEARCH

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Efficient counting of k-mers in DNA sequences using a bloom filter

(2011) Páll Melsted et al.   BMC BIOINFORMATICS

Estimation of rearrangement phylogeny for cancer genomes

(2011) C. D. Greenman et al.   GENOME RESEARCH

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Cactus Graphs for Genome Comparisons

(2011) Benedict Paten et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Emerging Knowledge from Genome Sequencing of Crop Species

(2011) Delfina Barabaschi et al.   MOLECULAR BIOTECHNOLOGY

The importance of phase information for human genomics

(2011) Ryan Tewhey et al.   NATURE REVIEWS GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Single Virus Genomics: A New Tool for Virus Discovery

(2011) Lisa Zeigler Allen et al.   PLoS One

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

A Survey of Combinatorial Methods for Phylogenetic Networks

(2010) Daniel H. Huson et al.   Genome Biology and Evolution

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Storage and Retrieval of Highly Repetitive Sequence Collections

(2010) Veli Mäkinen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Visualizing genomes: techniques and challenges

(2010) Cydney B Nielsen et al.   NATURE METHODS

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

High-resolution human genome structure by single-molecule analysis

(2010) B. Teague et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

(2009) Bas E. Dutilh et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

(2008) Shannon J. Williamson et al.   PLoS One