Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms

Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing

(2016) Pedro Seoane-Zonjic et al.   BMC GENOMICS

Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes

(2016) Corinne Biderre-Petit et al.   PLoS One

Capturing protein-coding genes across highly divergent species

(2016) Chenhong Li et al.   BIOTECHNIQUES

PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations

(2015) Min Wang et al.   BMC GENOMICS

Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data

(2015) Pan Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Captured metagenomics: large-scale targeting of genes based on ‘sequence capture’ reveals functional diversity in soils

(2015) Lokeshwaran Manoharan et al.   DNA RESEARCH

Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis

(2015) Roy N. Platt et al.   Genome Biology and Evolution

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing

(2015) Marcin Cieslik et al.   GENOME RESEARCH

Identifying genomic changes associated with insecticide resistance in the dengue mosquitoAedes aegyptiby deep targeted sequencing

(2015) Frederic Faucon et al.   GENOME RESEARCH

The use of museum specimens with high-throughput DNA sequencers

(2015) Andrew S. Burrell et al.   JOURNAL OF HUMAN EVOLUTION

Ancient human genomics: the methodology behind reconstructing evolutionary pathways

(2015) Stephanie Marciniak et al.   JOURNAL OF HUMAN EVOLUTION

Exome and genome sequencing: a revolution for the discovery and diagnosis of monogenic disorders

(2015) H. Stranneheim et al.   JOURNAL OF INTERNAL MEDICINE

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment

(2015) Jessica D. Stephens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

(2015) Michael B Clark et al.   NATURE METHODS

New insights into the performance of human whole-exome capture platforms

(2015) J. Meienberg et al.   NUCLEIC ACIDS RESEARCH

Capturing prokaryotic dark matter genomes

(2015) Cyrielle Gasc et al.   RESEARCH IN MICROBIOLOGY

Mitochondrial Genomes of Giant Deers Suggest their Late Survival in Central Europe

(2015) Alexander Immel et al.   Scientific Reports

Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes

(2015) Bart J.G. Broeckx et al.   Scientific Reports

Performance comparison of four commercial human whole-exome capture platforms

(2015) Daichi Shigemizu et al.   Scientific Reports

Exome Sequencing: Current and Future Perspectives

(2015) Amanda Warr et al.   G3-Genes Genomes Genetics

ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories

(2015) Jinlian Wang et al.   Genome Medicine

Biotechnological applications of functional metagenomics in the food and pharmaceutical industries

(2015) Laura M. Coughlan et al.   Frontiers in Microbiology

Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates

(2015) Marla Trindade et al.   Frontiers in Microbiology

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

(2015) James A. Nicholls et al.   Frontiers in Plant Science

Large-Scale SNP Discovery through RNA Sequencing and SNP Genotyping by Targeted Enrichment Sequencing in Cassava (Manihot esculenta Crantz)

(2015) Wirulda Pootakham et al.   PLoS One

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

(2015) Modhumita Ghosh Dasgupta et al.   PLoS One

Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing

(2015) Robert King et al.   PLoS One

Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition

(2015) Moses M. Muraya et al.   PLoS One

The future of ancient DNA: Technical advances and conceptual shifts

(2014) Michael Hofreiter et al.   BIOESSAYS

Variant detection sensitivity and biases in whole genome and exome sequencing

(2014) Alison M Meynert et al.   BMC BIOINFORMATICS

Design and development of exome capture sequencing for the domestic pig (Sus scrofa)

(2014) Christelle Robert et al.   BMC GENOMICS

ECHS1 mutations in Leigh disease: a new inborn error of metabolism affecting valine metabolism

(2014) Heidi Peters et al.   BRAIN

Solution Hybrid Selection Capture for the Recovery of Functional Full-Length Eukaryotic cDNAs From Complex Environmental Samples

(2014) Claudia Bragalini et al.   DNA RESEARCH

Accurate mitochondrial DNA sequencing using off-target reads provides a single test to identify pathogenic point mutations

(2014) Helen R. Griffin et al.   GENETICS IN MEDICINE

Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

(2014) Jacob A. Tennessen et al.   Genome Biology and Evolution

Selective enrichment of damaged DNA molecules for ancient genome sequencing

(2014) Marie-Theres Gansauge et al.   GENOME RESEARCH

One of the key characteristics of ancient DNA, low copy number, may be a product of its extraction

(2014) Jodi Lynn Barta et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

cDNA Hybrid Capture Improves Transcriptome Analysis on Low-Input and Archived Samples

(2014) Christopher R. Cabanski et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

(2014) David M Wagner et al.   LANCET INFECTIOUS DISEASES

Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies

(2014) Bastien Llamas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus

(2014) Baosheng Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Guidelines for investigating causality of sequence variants in human disease

(2014) D. G. MacArthur et al.   NATURE

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

(2014) Kirsten I. Bos et al.   NATURE

Technology: The $1,000 genome

(2014) Erika Check Hayden   NATURE

Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction

(2014) Ron Do et al.   NATURE

Second-Pandemic Strain of Vibrio cholerae from the Philadelphia Cholera Outbreak of 1849

(2014) Alison M. Devault et al.   NEW ENGLAND JOURNAL OF MEDICINE

A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications

(2014) Alejandro Alemán et al.   NUCLEIC ACIDS RESEARCH

Parallel detection of ancient pathogens via array-based DNA capture

(2014) K. I. Bos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing

(2014) I. M. Henry et al.   PLANT CELL

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grassPanicum virgatum

(2014) Joseph Evans et al.   PLANT JOURNAL

Bovine Exome Sequence Analysis and Targeted SNP Genotyping of Recessive Fertility Defects BH1, HH2, and HH3 Reveal a Putative Causative Mutation in SMC2 for HH3

(2014) Matthew C. McClure et al.   PLoS One

Whole-Exome Sequencing for the Identification of Susceptibility Genes of Kashin–Beck Disease

(2014) Zhenxing Yang et al.   PLoS One

Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome

(2014) Kyriakos Tsangaras et al.   PLoS One

Targeted Sequencing of Large Genomic Regions with CATCH-Seq

(2014) Kenneth Day et al.   PLoS One

Patterns of coding variation in the complete exomes of three Neandertals

(2014) S. Castellano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1)

(2014) Bart J. G. Broeckx et al.   Scientific Reports

Target Capture and Massive Sequencing of Genes Transcribed inMytilus galloprovincialis

(2014) Umberto Rosani et al.   Biomed Research International

Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus

(2014) Sarah Schiessl et al.   Frontiers in Plant Science

Mapping-by-sequencing accelerates forward genetics in barley

(2014) Martin Mascher et al.   GENOME BIOLOGY

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

(2013) Meredith L. Carpenter et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

(2013) Yan Guo et al.   BIOINFORMATICS

Gene Capture Coupled to High-Throughput Sequencing as a Strategy for Targeted Metagenome Exploration

(2013) J. Denonfoux et al.   DNA RESEARCH

Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome

(2013) Darrell L. Dinwiddie et al.   GENOMICS

The promise of whole-exome sequencing in medical genetics

(2013) Bahareh Rabbani et al.   JOURNAL OF HUMAN GENETICS

Comparative Population Genomics of the Ejaculate in Humans and the Great Apes

(2013) Jeffrey M. Good et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)

(2013) Francois Olivier Hebert et al.   MOLECULAR ECOLOGY

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond

(2013) Martin Mascher et al.   PLANT JOURNAL

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations

(2013) Florian Jupe et al.   PLANT JOURNAL

Whole-exome targeted sequencing of the uncharacterized pine genome

(2013) Leandro G. Neves et al.   PLANT JOURNAL

Mitochondrial Phylogenomics of Modern and Ancient Equids

(2013) Julia T. Vilstrup et al.   PLoS One

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

(2013) Brant C. Faircloth et al.   PLoS One

Targeted Enrichment: Maximizing Orthologous Gene Comparisons across Deep Evolutionary Time

(2013) Shannon M. Hedtke et al.   PLoS One

Long-Range Genomic Enrichment, Sequencing, and Assembly to Determine Unknown Sequences Flanking a Known microRNA

(2013) Zhaorong Ma et al.   PLoS One

Genomic DNA Enrichment Using Sequence Capture Microarrays: a Novel Approach to Discover Sequence Nucleotide Polymorphisms (SNP) in Brassica napus L

(2013) Wayne E. Clarke et al.   PLoS One

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

(2013) V. J. Schuenemann et al.   SCIENCE

Finding the lost treasures in exome sequencing data

(2013) David C. Samuels et al.   TRENDS IN GENETICS

Morphological and genetic evidence for early Holocene cattle management in northeastern China

(2013) Hucai Zhang et al.   Nature Communications

A High-Density Gene Map of Loblolly Pine ( Pinus taeda L.) Based on Exome Sequence Capture Genotyping

(2013) Leandro Gomide Neves et al.   G3-Genes Genomes Genetics

Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis

(2013) Mélissa Beaudoin et al.   PLoS Genetics

Microbial Diversity in the Era of Omic Technologies

(2013) Sofia Nikolaki et al.   Biomed Research International

The Role and Challenges of Exome Sequencing in Studies of Human Diseases

(2013) Zuoheng Wang et al.   Frontiers in Genetics

Implications of genetic heterogeneity in cancer

(2012) Michael W. Schmitt et al.   Annals of the New York Academy of Sciences

KASpOD—a web service for highly specific and explorative oligonucleotide design

(2012) Nicolas Parisot et al.   BIOINFORMATICS

Exome sequencing generates high quality data in non-target regions

(2012) Yan Guo et al.   BMC GENOMICS

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

(2012) Lecong Zhou et al.   BMC GENOMICS

Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

(2012) Michael P Mullen et al.   BMC GENOMICS

From genomics to metagenomics

(2012) Narayan Desai et al.   CURRENT OPINION IN BIOTECHNOLOGY

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

Disease gene identification strategies for exome sequencing

(2012) Christian Gilissen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer

(2012) Elise Ruark et al.   NATURE

Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion

(2012) Jeroen R Huyghe et al.   NATURE GENETICS

Mitochondrial genomes gleaned from human whole-exome sequencing

(2012) Ernesto Picardi et al.   NATURE METHODS

Exome RNA sequencing reveals rare and novel alternative transcripts

(2012) Jonatan Halvardson et al.   NUCLEIC ACIDS RESEARCH

Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivumL.)

(2012) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant

(2012) Peter C. Bundock et al.   PLANT BIOTECHNOLOGY JOURNAL

Cultivation of unculturable soil bacteria

(2012) Van H.T. Pham et al.   TRENDS IN BIOTECHNOLOGY

Exome sequencing: Dual role as a discovery and diagnostic tool

(2011) Chee-Seng Ku et al.   ANNALS OF NEUROLOGY

HiSpOD: probe design for functional DNA microarrays

(2011) Eric Dugat-Bony et al.   BIOINFORMATICS

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

The Deciphering Developmental Disorders (DDD) study

(2011) HELEN V FIRTH et al.   DEVELOPMENTAL MEDICINE AND CHILD NEUROLOGY

Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities

(2011) Hikaru Suenaga   ENVIRONMENTAL MICROBIOLOGY

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

(2011) R. D. George et al.   GENOME RESEARCH

Hybrid Capture and Next-Generation Sequencing Identify Viral Integration Sites from Formalin-Fixed, Paraffin-Embedded Tissue

(2011) Eric J. Duncavage et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

(2011) Nicola J. Nadeau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phenotypic and Genomic Analyses of a Fast Neutron Mutant Population Resource in Soybean

(2011) Y.-T. Bolon et al.   PLANT PHYSIOLOGY

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

(2011) V. J. Schuenemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

(2011) N. Agrawal et al.   SCIENCE

Molecular genetic studies of complex phenotypes

(2011) Ali J. Marian   Translational Research

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

(2011) María C. Ávila-Arcos et al.   Scientific Reports

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

(2011) Cyrille Saintenac et al.   GENOME BIOLOGY

Comprehensive comparison of three commercial human whole-exome capture platforms

(2011) Asan et al.   GENOME BIOLOGY

Mutation discovery in mice by whole exome sequencing

(2011) Heather Fairfield et al.   GENOME BIOLOGY

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

(2010) Sébastien Terrat et al.   BMC BIOINFORMATICS

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

(2010) Elizabeth A Worthey et al.   GENETICS IN MEDICINE

Loss-of-function variants in the genomes of healthy humans

(2010) D. G. MacArthur et al.   HUMAN MOLECULAR GENETICS

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

(2010) Sarah B Ng et al.   NATURE GENETICS

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

Repeat subtraction-mediated sequence capture from a complex genome

(2010) Yan Fu et al.   PLANT JOURNAL

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives

(2010) Michael Knapp et al.   Genes

Methods for Genomic Partitioning

(2009) Emily H. Turner et al.   Annual Review of Genomics and Human Genetics

Common vs. rare allele hypotheses for complex diseases

(2009) Nicholas J Schork et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Microdroplet-based PCR enrichment for large-scale targeted sequencing

(2009) Ryan Tewhey et al.   NATURE BIOTECHNOLOGY

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

A comprehensive assay for targeted multiplex amplification of human DNA sequences

(2008) S. Krishnakumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA