Conservative route to genome compaction in a miniature annelid

The Genome of Caenorhabditis bovis

(2020) Lewis Stevens et al.   CURRENT BIOLOGY

Extreme Genome and Nervous System Streamlining in the Invertebrate Parasite Intoshia variabili

(2020) George S. Slyusarev et al.   CURRENT BIOLOGY

Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

(2020) Vasavi Sundaram et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Widespread patterns of gene loss in the evolution of the animal kingdom

(2020) Cristina Guijarro-Clarke et al.   Nature Ecology & Evolution

Gene gain and loss across the metazoan tree of life

(2020) Rosa Fernández et al.   Nature Ecology & Evolution

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Deeply conserved synteny resolves early events in vertebrate evolution

(2020) Oleg Simakov et al.   Nature Ecology & Evolution

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans

(2019) Ferdinand Marlétaz et al.   CURRENT BIOLOGY

Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements

(2019) Magali Naville et al.   CURRENT BIOLOGY

Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

(2019) J. Blommaert et al.   BMC GENOMICS

KEGG Mapper for inferring cellular functions from protein sequences

(2019) Minoru Kanehisa et al.   PROTEIN SCIENCE

Broad North Atlantic distribution of a meiobenthic annelid – against all odds

(2019) Katrine Worsaae et al.   Scientific Reports

A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum

(2019) Fedor S. Sharko et al.   PLoS One

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Multiple large-scale gene and genome duplications during the evolution of hexapods

(2018) Zheng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent evolution of the ladder-like ventral nerve cord in Annelida

(2018) Conrad Helm et al.   Frontiers in Zoology

Xenacoelomorph Neuropeptidomes Reveal a Major Expansion of Neuropeptide Systems during Early Bilaterian Evolution

(2018) Daniel Thiel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

Prevalence of Mutation-Prone Microhomology-Mediated End Joining in a Chordate Lacking the c-NHEJ DNA Repair Pathway

(2018) Wei Deng et al.   CURRENT BIOLOGY

mTOR as a central hub of nutrient signalling and cell growth

(2018) Joungmok Kim et al.   NATURE CELL BIOLOGY

Comparative genomics of the major parasitic worms

(2018)   NATURE GENETICS

DNA Repair in Drosophila : Mutagens, Models, and Missing Genes

(2017) Jeff Sekelsky   GENETICS

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies

(2017) Venkat Talla et al.   Genome Biology and Evolution

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

(2017) Cibele G. Sotero-Caio et al.   Genome Biology and Evolution

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

High diversity in neuropeptide immunoreactivity patterns among three closely related species of Dinophilidae (Annelida)

(2017) Alexandra Kerbl et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

(2017) Sabrina M. Schiemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of genome size evolution in birds and mammals

(2017) Aurélie Kapusta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

(2017) Yuki Yoshida et al.   PLOS BIOLOGY

DNA Repair in Drosophila : Mutagens, Models, and Missing Genes

(2017) Jeff Sekelsky   GENETICS

Evolution of bird genomes-a transposon's-eye view

(2016) Aurélie Kapusta et al.   Annals of the New York Academy of Sciences

The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity

(2016) Arnau Sebé-Pedrós et al.   CELL

The Compact Body Plan of Tardigrades Evolved by the Loss of a Large Body Region

(2016) Frank W. Smith et al.   CURRENT BIOLOGY

Comparison of neuromuscular development in two dinophilid species (Annelida) suggests progenetic origin of Dinophilus gyrociliatus

(2016) Alexandra Kerbl et al.   Frontiers in Zoology

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae)

(2016) Alexandra Kerbl et al.   EvoDevo

The developmental basis for the recurrent evolution of deuterostomy and protostomy

(2016) José M. Martín-Durán et al.   Nature Ecology & Evolution

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The Evolution of Annelids Reveals Two Adaptive Routes to the Interstitial Realm

(2015) Torsten Hugo Struck et al.   CURRENT BIOLOGY

Nervous system development in lecithotrophic larval and juvenile stages of the annelid Capitella teleta

(2015) Néva P Meyer et al.   Frontiers in Zoology

Articulating “Archiannelids”: Phylogenomics and Annelid Relationships, with Emphasis on Meiofaunal Taxa

(2015) Sónia C.S. Andrade et al.   MOLECULAR BIOLOGY AND EVOLUTION

Trans-Splicing and Operons in Metazoans: Translational Control in Maternally Regulated Development and Recovery from Growth Arrest

(2015) Gemma B. Danks et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

(2015) Thomas C. Boothby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Evolutionary conservation of the eumetazoan gene regulatory landscape

(2014) M. Schwaiger et al.   GENOME RESEARCH

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements

(2013) Guojun Yang   BMC BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

AnIn-silicoGenomic Survey to Annotate Genes Coding for Early Development-Relevant Signaling Molecules in the Pearl Oyster,Pinctada fucata

(2013) Davin H. E. Setiamarga et al.   ZOOLOGICAL SCIENCE

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The normal development of Platynereis dumerilii (Nereididae, Annelida)

(2011) Antje HL Fischer et al.   Frontiers in Zoology

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

Extensive Chordate and Annelid Macrosynteny Reveals Ancestral Homeobox Gene Organization

(2011) J. H. L. Hui et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Hippo pathway in organ size control, tissue regeneration and stem cell self-renewal

(2011) Bin Zhao et al.   NATURE CELL BIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Ras-ERK and PI3K-mTOR pathways: cross-talk and compensation

(2011) Michelle C. Mendoza et al.   TRENDS IN BIOCHEMICAL SCIENCES

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

(2010) F. Denoeud et al.   SCIENCE

Loss of the insulator protein CTCF during nematode evolution

(2009) Peter Heger et al.   BMC MOLECULAR BIOLOGY

Mammalian cell-cycle regulation: several Cdks, numerous cyclins and diverse compensatory mechanisms

(2009) A Satyanarayana et al.   ONCOGENE

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

Malin: maximum likelihood analysis of intron evolution in eukaryotes

(2008) M. Csuros   BIOINFORMATICS

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

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

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

(2008) Pierre Abad et al.   NATURE BIOTECHNOLOGY

The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

(2008) Christoph Dieterich et al.   NATURE GENETICS

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Spliceosomal introns as tools for genomic and evolutionary analysis

(2008) M. Irimia et al.   NUCLEIC ACIDS RESEARCH

Genomic Organization and Expression Demonstrate Spatial and Temporal Hox Gene Colinearity in the Lophotrochozoan Capitella sp. I

(2008) Andreas C. Fröbius et al.   PLoS One