Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

(2019) Weizhi Song et al.   Microbiome

New approaches for metagenome assembly with short reads

(2019) Martin Ayling et al.   BRIEFINGS IN BIOINFORMATICS

High proportions of bacteria are culturable across major biomes

(2019) Adam C. Martiny   ISME Journal

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

(2019) Kerrin Mendler et al.   NUCLEIC ACIDS RESEARCH

De novo gene birth

(2019) Stephen Branden Van Oss et al.   PLoS Genetics

virMine: automated detection of viral sequences from complex metagenomic samples

(2019) Andrea Garretto et al.   PeerJ

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data

(2019) Krithika Arumugam et al.   Microbiome

Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories

(2019) Alon Shaiber et al.   mBio

RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss

(2018) Mukul S Bansal et al.   BIOINFORMATICS

A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting

(2018) Sarah M. Hücker et al.   BMC EVOLUTIONARY BIOLOGY

Homologous Recombination and Transposon Propagation Shape the Population Structure of an Organism from the Deep Subsurface with Minimal Metabolism

(2018) Alexander J Probst et al.   Genome Biology and Evolution

A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments

(2018) Jacob H. Munson-McGee et al.   ISME Journal

Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes

(2018) Cintia P. J. Rua et al.   MICROBIAL ECOLOGY

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

Single-cell metagenomics: challenges and applications

(2018) Yuan Xu et al.   Protein & Cell

AMBER: Assessment of Metagenome BinnERs

(2018) Fernando Meyer et al.   GigaScience

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins

(2018) Deyvid Amgarten et al.   Frontiers in Genetics

High-quality genome sequences of uncultured microbes by assembly of read clouds

(2018) Alex Bishara et al.   NATURE BIOTECHNOLOGY

The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase

(2018) Sonja Vanderhaeghen et al.   Scientific Reports

MinION-based long-read sequencing and assembly extends theCaenorhabditis elegansreference genome

(2017) John R. Tyson et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

panX: pan-genome analysis and exploration

(2017) Wei Ding et al.   NUCLEIC ACIDS RESEARCH

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

(2017) John Vollmers et al.   PLoS One

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria

(2017) Rochelle M. Soo et al.   SCIENCE

MetaSort untangles metagenome assembly by reducing microbial community complexity

(2017) Peifeng Ji et al.   Nature Communications

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains

(2017) Gil Ron et al.   Nature Communications

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

(2017) Feiqiao Brian Yu et al.   eLife

Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers

(2017) Tommy Harding et al.   Frontiers in Microbiology

HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities

(2017) Weizhi Song et al.   PeerJ

Variant profiling of evolving prokaryotic populations

(2017) Markus Zojer et al.   PeerJ

The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange

(2017) Andrew S. Lang et al.   Annual Review of Virology

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly

(2016) Tomàs Llorens–Marès et al.   ISME Journal

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

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

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

No evidence for extensive horizontal gene transfer in the genome of the tardigradeHypsibius dujardini

(2016) Georgios Koutsovoulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

(2016) Christopher L. Hemme et al.   mBio

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

A Functional Bacterium-to-Plant DNA Transfer Machinery of Rhizobium etli

(2016) Benoît Lacroix et al.   PLoS Pathogens

Computational methods for predicting genomic islands in microbial genomes

(2016) Bingxin Lu et al.   Computational and Structural Biotechnology Journal

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

(2015) Eric D. Becraft et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting

(2015) Lea Fellner et al.   BMC EVOLUTIONARY BIOLOGY

Horizontal gene transfer in an acid mine drainage microbial community

(2015) Jiangtao Guo et al.   BMC GENOMICS

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

(2015) A. C. Y. Mak et al.   GENETICS

Read clouds uncover variation in complex regions of the human genome

(2015) Alex Bishara et al.   GENOME RESEARCH

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

Origin, dynamics, and implications of extracellular DNA pools in marine sediments

(2015) Andrea Torti et al.   Marine Genomics

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

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

(2015) Nicholas J Loman et al.   NATURE METHODS

New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation

(2015) Aoife McLysaght et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

(2015) Kema Malki et al.   Virology Journal

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

(2015) Stephen Nayfach et al.   PLoS Computational Biology

Inferring Horizontal Gene Transfer

(2015) Matt Ravenhall et al.   PLoS Computational Biology

Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota

(2015) Guanhui Bao et al.   Frontiers in Microbiology

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Omega: an Overlap-graph de novo Assembler for Metagenomics

(2014) Bahlul Haider et al.   BIOINFORMATICS

DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads

(2014) Gökhan Yavaş et al.   BMC GENOMICS

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

(2014) Qiyun Zhu et al.   BMC GENOMICS

Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

(2014) Gavin C Conant et al.   CURRENT OPINION IN PLANT BIOLOGY

A first look at the Oxford Nanopore MinION sequencer

(2014) Alexander S. Mikheyev et al.   Molecular Ecology Resources

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

(2014) Natalie Ward et al.   PLoS One

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India

(2014) Johan Bengtsson-Palme et al.   Frontiers in Microbiology

Gene Loss and Adaptation to Hominids Underlie the Ancient Origin of HIV-1

(2013) Lucie Etienne et al.   Cell Host & Microbe

Lateral Gene Transfer of Family A DNA Polymerases between Thermophilic Viruses, Aquificae, and Apicomplexa

(2013) Thomas W. Schoenfeld et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

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

Understanding Bacteriophage Specificity in Natural Microbial Communities

(2013) Britt Koskella et al.   Viruses-Basel

Bacterial Adaptation through Loss of Function

(2013) Alison K. Hottes et al.   PLoS Genetics

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome

(2012) Conor J Meehan et al.   BMC MICROBIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Evolution of Viral Proteins Originated De Novo by Overprinting

(2012) Niv Sabath et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

(2012) V. J. Denef et al.   SCIENCE

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Intercellular Nanotubes Mediate Bacterial Communication

(2011) Gyanendra P. Dubey et al.   CELL

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements

(2011) Erik Kristiansson et al.   PLoS One

Bacteriophages and their genomes

(2011) Graham F Hatfull et al.   Current Opinion in Virology

Bacterial Exchange via Nanotubes: Lessons Learned from the History of Molecular Biology

(2011) Thomas A. Ficht   Frontiers in Microbiology

GLOOME: gain loss mapping engine

(2010) O. Cohen et al.   BIOINFORMATICS

cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data

(2010) Fengfeng Zhou et al.   BIOINFORMATICS

Third Generation DNA Sequencing: Pacific Biosciences' Single Molecule Real Time Technology

(2010) Alice McCarthy   CHEMISTRY & BIOLOGY

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

(2010) Christopher L Hemme et al.   ISME Journal

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

Detecting genomic islands using bioinformatics approaches

(2010) Morgan G. I. Langille et al.   NATURE REVIEWS MICROBIOLOGY

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions

(2010) Benjamin Schuster-Böckler et al.   PLoS One

Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities

(2010) J. Jacob Parnell et al.   PLoS One

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes

(2009) Aditi Kanhere et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic and metagenomic analysis of Verrucomicrobia in former  agricultural grassland soil

(2009) Anna Kielak et al.   FEMS MICROBIOLOGY ECOLOGY

Detection of 140 clinically relevant antibiotic-resistance genes in the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to selected antibiotics

(2009) R. Szczepanowski et al.   MICROBIOLOGY-SGM

Reconciling Ecological and Genomic Divergence among Lineages of Listeria under an "Extended Mosaic Genome Concept"

(2009) K. A. Dunn et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of long-distance horizontal gene transfer on prokaryotic genome size

(2009) O. X. Cordero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

New dimensions of the virus world discovered through metagenomics

(2009) David M. Kristensen et al.   TRENDS IN MICROBIOLOGY

Estimating the extent of horizontal gene transfer in metagenomic sequences

(2008) Javier Tamames et al.   BMC GENOMICS

CoastalSynechococcusmetagenome reveals major roles for horizontal gene transfer and plasmids in population diversity

(2008) B. Palenik et al.   ENVIRONMENTAL MICROBIOLOGY

De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae

(2008) J. Cai et al.   GENETICS

Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns

(2008) J. R. Zaneveld et al.   MICROBIOLOGY-SGM

The Epidemic of Antibiotic-Resistant Infections: A Call to Action for the Medical Community from the Infectious Diseases Society of America

(2007) B. Spellberg et al.   CLINICAL INFECTIOUS DISEASES