An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis)

(2022) Allison K Miller et al.   JOURNAL OF HEREDITY

Pervasive male-biased expression throughout the germline-specific regions of the sea lamprey genome supports key roles in sex differentiation and spermatogenesis

(2022) Tamanna Yasmin et al.   Communications Biology

Significantly improving the quality of genome assemblies through curation

(2021) Kerstin Howe et al.   GigaScience

A transcriptomic pipeline adapted for genomic sequence discovery of germline restricted sequence in zebra finch, Taeniopygia guttata

(2021) Kathryn C Asalone et al.   Genome Biology and Evolution

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

(2021) Yoichiro Nakatani et al.   Nature Communications

100 years of sea lampreys above Niagara Falls: A reflection on what happened and what we learned

(2021) Jill Wingfield et al.   JOURNAL OF GREAT LAKES RESEARCH

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

Supernumerary B chromosomes of Aegilops speltoides undergo precise elimination in roots early in embryo development

(2020) Alevtina Ruban et al.   Nature Communications

Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey

(2020) Jon E. Hess et al.   MOLECULAR ECOLOGY

Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution

(2020) Ting Zhu et al.   Molecular Ecology Resources

Programmed DNA Elimination in Vertebrates

(2020) Jeramiah J. Smith et al.   Annual Review of Animal Biosciences

Germline-restricted chromosome (GRC) is widespread among songbirds

(2019) Anna A. Torgasheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Programmed DNA elimination of germline development genes in songbirds

(2019) Cormac M. Kinsella et al.   Nature Communications

Germline-Specific Repetitive Elements in Programmatically Eliminated Chromosomes of the Sea Lamprey (Petromyzon marinus)

(2019) Vladimir A. Timoshevskiy et al.   Genes

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

(2018) Jeramiah J. Smith et al.   NATURE GENETICS

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

Comparative genome analysis of programmed DNA elimination in nematodes

(2017) Jianbin Wang et al.   GENOME RESEARCH

gEVAL — a web-based browser for evaluating genome assemblies

(2016) William Chow et al.   BIOINFORMATICS

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

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

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

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

(2016) Mihaela Pertea et al.   Nature Protocols

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

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Programmed DNA elimination in multicellular organisms

(2014) Jianbin Wang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The lamprey: A jawless vertebrate model system for examining origin of the neural crest and other vertebrate traits

(2014) Stephen A. Green et al.   DIFFERENTIATION

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

(2013) Jeramiah J Smith et al.   NATURE GENETICS

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

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

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

(2012) Jia-Ming Chang et al.   BMC BIOINFORMATICS

Genetic Consequences of Programmed Genome Rearrangement

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

Contrasting demographic histories of European and North American sea lamprey (Petromyzon marinus) populations inferred from mitochondrial DNA sequence variation

(2012) Martin J. Genner et al.   MARINE AND FRESHWATER RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Whole chromosome elimination and chromosome terminus elimination both contribute to somatic differentiation in Taiwanese hagfish Paramyxine sheni

(2010) Noriko F. Kojima et al.   CHROMOSOME RESEARCH

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

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

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS