A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris

Taxonomic reassessment of the Little pocket mouse, Perognathus longimembris (Rodentia, Heteromyidae) of southern California and northern Baja California

(2023) James L. Patton et al.   Therya

Insights into mammalian TE diversity through the curation of 248 genome assemblies

(2023) Austin B. Osmanski et al.   SCIENCE

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

(2023) Marcela Uliano-Silva et al.   BMC BIOINFORMATICS

High-Quality Reference Genome for an Arid-Adapted Mammal, the Banner-Tailed Kangaroo Rat (Dipodomys spectabilis)

(2022) Avril M Harder et al.   Genome Biology and Evolution

Landscape genomics to enable conservation actions: The California Conservation Genomics Project

(2022) H Bradley Shaffer et al.   JOURNAL OF HEREDITY

Haplotype-resolved assembly of diploid genomes without parental data

(2022) Haoyu Cheng et al.   NATURE BIOTECHNOLOGY

A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

(2022) Aryn P Wilder et al.   Genome Biology and Evolution

Understanding climate change response in the age of genomics

(2022) Lesley T. Lancaster et al.   JOURNAL OF ANIMAL ECOLOGY

LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies

(2022) Alaina Shumate et al.   F1000Research

The Dfam community resource of transposable element families, sequence models, and genome annotations

(2021) Jessica Storer et al.   Mobile DNA

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

msRepDB: a comprehensive repetitive sequence database of over 80 000 species

(2021) Xingyu Liao et al.   NUCLEIC ACIDS RESEARCH

Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data

(2020) Joanna E. Handzlik et al.   Scientific Reports

BlobToolKit - Interactive Quality Assessment of Genome Assemblies

(2020) Richard Challis et al.   G3-Genes Genomes Genetics

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

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

(2019) Jay Ghurye et al.   PLoS Computational Biology

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

(2019) Nathan S. Upham et al.   PLOS BIOLOGY

Similar Evolutionary Trajectories for Retrotransposon Accumulation in Mammals

(2017) Reuben M. Buckley et al.   Genome Biology and Evolution

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

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

De Novo Genome and Transcriptome Assembly of the Canadian Beaver ( Castor canadensis )

(2017) Si Lok et al.   G3-Genes Genomes Genetics

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

(2017) Jonas Korlach et al.   GigaScience

P8008 The NCBI Eukaryotic Genome Annotation Pipeline

(2016) F. Thibaud-Nissen et al.   JOURNAL OF ANIMAL SCIENCE

2016 Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education:

(2016) Robert S. Sikes et al.   JOURNAL OF MAMMALOGY

L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes

(2016) Tobias Penzkofer et al.   NUCLEIC ACIDS RESEARCH

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq

(2014) Nicholas J. Marra et al.   MOLECULAR ECOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

SINEBase: a database and tool for SINE analysis

(2012) Nikita S. Vassetzky et al.   NUCLEIC ACIDS RESEARCH

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS