The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

Characterization of Somatically‐Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus)

(2016) Stephanie A. Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

(2016) Rafael D Acemel et al.   NATURE GENETICS

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

Cellular and Molecular Features of Developmentally Programmed Genome Rearrangement in a Vertebrate (Sea Lamprey: Petromyzon marinus)

(2016) Vladimir A. Timoshevskiy et al.   PLoS Genetics

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Lampreys as Diverse Model Organisms in the Genomics Era

(2015) David W. McCauley et al.   BIOSCIENCE

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

(2015) Yuichiro Hara et al.   BMC GENOMICS

Evolution of two prototypic T cell lineages

(2015) Sabyasachi Das et al.   CELLULAR IMMUNOLOGY

Emergence of an Ancestral Glycoprotein Hormone in the Pituitary of the Sea Lamprey, a Basal Vertebrate

(2015) Stacia A. Sower et al.   ENDOCRINOLOGY

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

(2015) Jeramiah J. Smith et al.   GENOME RESEARCH

Bioinformatic Characterization of Genes and Proteins Involved in Blood Clotting in Lampreys

(2015) Russell F. Doolittle   JOURNAL OF MOLECULAR EVOLUTION

Evolution of vertebrates as viewed from the crest

(2015) Stephen A. Green et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates

(2014) Hugo J. Parker et al.   NATURE

Transcriptional Silencing by Polycomb-Group Proteins

(2014) U. Grossniklaus et al.   Cold Spring Harbor Perspectives in Biology

Polycomb complexes in stem cells and embryonic development

(2013) L. Aloia et al.   DEVELOPMENT

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum)

(2013) T. K. Mehta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline In Vivo

(2013) Michael Sachs et al.   Cell Reports

Genetic Consequences of Programmed Genome Rearrangement

(2012) Jeramiah J. Smith et al.   CURRENT BIOLOGY

Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes

(2012) Florent Murat et al.   Genome Biology and Evolution

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species

(2011) J. W. VAN OOIJEN   Genetics Research

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

(2011) MICHAEL R. MILLER et al.   MOLECULAR ECOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution

(2010) Jeramiah J. Smith et al.   CHROMOSOMA

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

(2010) Chris T. Amemiya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes

(2009) V. Ravi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Programmed loss of millions of base pairs from a vertebrate genome

(2009) J. J. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

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

Timing of Genome Duplications Relative to the Origin of the Vertebrates: Did Cyclostomes Diverge before or after?

(2008) S. Kuraku et al.   MOLECULAR BIOLOGY AND EVOLUTION

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE