Evaluating the performance of targeted sequence capture, RNA‐Seq, and degenerate‐primer PCR cloning for sequencing the largest mammalian multigene family

The Birth and Death of Olfactory Receptor Gene Families in Mammalian Niche Adaptation

(2018) Graham M Hughes et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating the Performance of De Novo Assembly Methods for Venom-Gland Transcriptomics

(2018) Matthew Holding et al.   Toxins

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

(2018) M. Lisandra Zepeda Mendoza et al.   Nature Ecology & Evolution

The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly

(2018) Matthew D. MacManes   PeerJ

Long-read sequence capture of the haemoglobin gene clusters across codfish species

(2018) Siv Nam Khang Hoff et al.   Molecular Ecology Resources

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Evolving Neural and Genetic Architecture of Vertebrate Olfaction

(2016) Daniel M. Bear et al.   CURRENT BIOLOGY

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

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

De novo transcriptome assembly facilitates characterisation of fast-evolving gene families, MHC class I in the bank vole (Myodes glareolus)

(2016) M Migalska et al.   HEREDITY

Family-assisted inference of the genetic architecture of major histocompatibility complex variation

(2016) A. Gaigher et al.   Molecular Ecology Resources

Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird

(2016) Aleksandra Biedrzycka et al.   Molecular Ecology Resources

Olfactory receptor pseudo-pseudogenes

(2016) Lucia L. Prieto-Godino et al.   NATURE

Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

(2016) Kamil Witek et al.   NATURE BIOTECHNOLOGY

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

A generalized birth and death process for modeling the fates of gene duplication

(2015) Jing Zhao et al.   BMC EVOLUTIONARY BIOLOGY

Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini)

(2015) Philipp Brand et al.   BMC EVOLUTIONARY BIOLOGY

Multi-copy venom genes hidden in de novo transcriptome assemblies, a cautionary tale with the snakelocks sea anemone Anemonia sulcata (Pennant, 1977)

(2015) Jason Macrander et al.   TOXICON

Deep Sequencing of the Murine Olfactory Receptor Neuron Transcriptome

(2015) Ninthujah Kanageswaran et al.   PLoS One

Do you smell what I smell? Genetic variation in olfactory perception

(2014) Darren W. Logan   BIOCHEMICAL SOCIETY TRANSACTIONS

The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms

(2014) Peter A Larsen et al.   BMC GENOMICS

Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

(2014) A. D. Yoder et al.   Genome Biology and Evolution

Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals

(2014) Yoshihito Niimura et al.   GENOME RESEARCH

A Cluster of Olfactory Receptor Genes Linked to Frugivory in Bats

(2014) Sara Hayden et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata)

(2014) Jackie Lighten et al.   Molecular Ecology Resources

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Profiling of Olfactory Receptor Gene Expression in Whole Human Olfactory Mucosa

(2014) Christophe Verbeurgt et al.   PLoS One

Vampire bats exhibit evolutionary reduction of bitter taste receptor genes common to other bats

(2014) W. Hong et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Functional promiscuity in a mammalian chemosensory system: extensive expression of vomeronasal receptors in the main olfactory epithelium of mouse lemurs

(2014) Philipp Hohenbrink et al.   Frontiers in Neuroanatomy

The Olfactory Transcriptomes of Mice

(2014) Ximena Ibarra-Soria et al.   PLoS Genetics

Using Illumina next generation sequencing technologies to sequence multigene families inde novospecies

(2013) Graham M. Hughes et al.   Molecular Ecology Resources

The missense of smell: functional variability in the human odorant receptor repertoire

(2013) Joel D Mainland et al.   NATURE NEUROSCIENCE

Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing

(2013) Caroline Flegel et al.   PLoS One

First evidence for functional vomeronasal 2 receptor genes in primates

(2012) P. Hohenbrink et al.   Biology Letters

Olfactory Receptor Multigene Family in Vertebrates: From the Viewpoint of Evolutionary Genomics

(2012) Yoshihito Niimura   CURRENT GENOMICS

Transcriptomes of Mouse Olfactory Epithelium Reveal Sexual Differences in Odorant Detection

(2012) Meng-Shin Shiao et al.   Genome Biology and Evolution

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats

(2011) Elena O. Gracheva et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Adaptive evolution of young gene duplicates in mammals

(2009) M. V. Han et al.   GENOME RESEARCH

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Ecological adaptation determines functional mammalian olfactory subgenomes

(2009) S. Hayden et al.   GENOME RESEARCH

Extensive Copy-Number Variation of the Human Olfactory Receptor Gene Family

(2008) Janet M. Young et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution

(2008) Yehudit Hasin et al.   PLoS Genetics