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List of works by Jay Shendure

(P3) Next Generation Human Genetics

scientific article

2012 Curt Stern Award Address1 ⬇️

scientific article published on March 7, 2013

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

scientific article published on 03 January 2019

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

scientific article published on 01 March 2019

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

scientific article published on 31 March 2020

A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function

scientific article published on 12 September 2018

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

scientific article

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

scientific article published on 31 July 2015

A brief history of human disease genetics

scientific article published on 08 January 2020

A combination of transcription factors mediates inducible interchromosomal contacts.

scientific article published on 13 May 2019

A combination of transcription factors mediates inducible interchromosomal pairing

A de novo convergence of autism genetics and molecular neuroscience

scientific article

A deep dive into genetic variation

scientific article published in Nature

A general framework for estimating the relative pathogenicity of human genetic variants

scientific article (publication date: March 2014)

A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes

scientific article

A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer

scientific article

A high-coverage genome sequence from an archaic Denisovan individual

scientific article

A homozygous missense variant in type I keratin KRT25 causes autosomal recessive woolly hair

scientific article

A human cell atlas of fetal chromatin accessibility

scientific article published on 01 November 2020

A human cell atlas of fetal gene expression

scientific article published on 01 November 2020

A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues

scientific article published in 2022

A major influence of sex-specific loci on alcohol preference in C57Bl/6 and DBA/2 inbred mice

scientific article published in December 1998

A molecular pathway including Id2, Tbx5, and Nkx2-5 required for cardiac conduction system development

scientific journal article

A new congenital disorder of glycosylation caused by a mutation in SSR4, the signal sequence receptor 4 protein of the TRAP complex

scientific article

A non-active-site SET domain surface crucial for the interaction of MLL1 and the RbBP5/Ash2L heterodimer within MLL family core complexes

scientific article

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

scientific article published on 02 September 2019

A suppressor screen in Mecp2 mutant mice implicates cholesterol metabolism in Rett syndrome

scientific article

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.

scientific article

A systematic evaluation of the design and context dependencies of massively parallel reporter assays

scientific article published on 12 October 2020

A three-dimensional model of the yeast genome

scientific article published on 2 May 2010

ALG1-CDG: Clinical and Molecular Characterization of 39 Unreported Patients

scientific journal article

Accelerating matchmaking of novel dysmorphology syndromes through clinical and genomic characterization of a large cohort

scientific article published on 3 December 2015

Accurate classification of BRCA1 variants with saturation genome editing

scientific article published in Nature

Accurate functional classification of thousands ofBRCA1variants with saturation genome editing

Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules

scientific article

Accurate identification of centromere locations in yeast genomes using Hi-C.

scientific article published on 4 May 2015

Accurate multiplex polony sequencing of an evolved bacterial genome

scientific article

Activation of a cryptic splice site in the mitochondrial elongation factor GFM1 causes combined OXPHOS deficiency.

scientific article

Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis

scientific article

Adaptive gene amplification as an intermediate step in the expansion of virus host range.

scientific article

Adenylate cyclase 1 (ADCY1) mutations cause recessive hearing impairment in humans and defects in hair cell function and hearing in zebrafish

scientific article

Advanced sequencing technologies: methods and goals

scientific article

An Integrated Approach for Prioritizing Causal Variants in Whole Exome and Whole Genome Sequencing

scientific article published in May 2013

An essential cell cycle regulation gene causes hybrid inviability in Drosophila

scientific article

An open-source platform to distribute and interpret data from multiplexed assays of variant effect

An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes ⬇️

scientific journal article

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

scientific article published on 28 November 2012

Analysis of genetic inheritance in a family quartet by whole-genome sequencing

scientific article

Assaying chromosomal inversions by single-molecule haplotyping

scientific article published on June 2006

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Association of MTOR Mutations With Developmental Brain Disorders, Including Megalencephaly, Focal Cortical Dysplasia, and Pigmentary Mosaicism.

scientific article

Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

scientific article published on 30 October 2020

Autosomal dominant multiple pterygium syndrome is caused by mutations in MYH3

Autosomal-Dominant Multiple Pterygium Syndrome Is Caused by Mutations in MYH3.

scientific article

BRCA Testing by Single-Molecule Molecular Inversion Probes

scientific article

Biome representational in silico karyotyping

scientific article

Bipartite structure of the inactive mouse X chromosome

scientific article

CADD: predicting the deleteriousness of variants throughout the human genome

CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions

scientific article published in July 2017

Cancer Genomes on a Shoestring Budget

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

scientific article published on 18 September 2020

Capturing native long-range contiguity by in situ library construction and optical sequencing

scientific article

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

scientific article

Challenges and solutions for gene identification in the presence of familial locus heterogeneity

scientific article

Characterisation of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next-generation sequencing study

scientific article

Characterization of Apparently Balanced Chromosomal Rearrangements from the Developmental Genome Anatomy Project

scientific article published on 5 September 2008

Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project

scientific article published on March 2008

Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy

scientific article published on 08 August 2019

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

scientific article

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

scientific article published on 2 August 2018

Cilia gene mutations cause atrioventricular septal defects by multiple mechanisms

scientific article published on 23 June 2016

Classification and characterization of microsatellite instability across 18 cancer types

scientific article

Comparable specimen collection from both ends of at-home mid-turbinate swabs

scientific article published on 08 December 2020

Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer

scientific article

Complex Minigene Library Vaccination for Discovery of Pre-Erythrocytic Plasmodium T Cell Antigens

scientific article

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

scientific article published on 22 April 2021

Comprehensive single-cell transcriptional profiling of a multicellular organism.

scientific article

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies

scientific article published on 5 December 2017

Computational comparison of two draft sequences of the human genome

scientific article published in February 2001

Computational discovery of sense-antisense transcription in the human and mouse genomes

scientific article

Concurrent genome and epigenome editing by CRISPR-mediated sequence replacement

scientific article published on 18 November 2019

Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence

scientific article published on 27 December 2018

Copy-Number Variation and False Positive Results of Prenatal Screening

scientific article published on December 2015

Copy-number variation and false positive prenatal aneuploidy screening results

scientific article

Correction: A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

scientific article published on 14 April 2017

Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.

scientific article

Corrigendum: Classification and characterization of microsatellite instability across 18 cancer types

scientific article published in October 2017

Corrigendum: Classification and characterization of microsatellite instability across 18 cancer types

scientific article published on 01 April 2018

Corrigendum: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals.

scientific article published on August 2015

Corrigendum: The 4D nucleome project

scientific article published on 22 November 2017

Cryptic transmission of SARS-CoV-2 in Washington State

scientific article published on 06 April 2020

Cryptic transmission of SARS-CoV-2 in Washington state

scientific article published on 10 September 2020

DNA sequencing at 40: past, present and future

scientific article published on 11 October 2017

DPAGT1 Deficiency with Encephalopathy (DPAGT1-CDG): Clinical and Genetic Description of 11 New Patients

scientific article published on 17 August 2018

De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability.

scientific article published in November 2017

De novo Mutations in NALCN Cause a Syndrome of Congenital Contractures of the Limbs and Face with Hypotonia, and Developmental Delay

scholarly preprint article

De novo TBR1 mutations in sporadic autism disrupt protein functions

scientific article

De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes

scientific article

De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay

scientific article

De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome

scientific article

Decoding long nanopore sequencing reads of natural DNA

scientific article

Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes

scientific article

Detection of minimal residual disease in NPM1-mutated acute myeloid leukemia by next-generation sequencing

scientific article

Digital genotyping and haplotyping with polymerase colonies

scientific article

Discovering functional transcription-factor combinations in the human cell cycle

scientific article published on June 2005

Discovery of T cell antigens by high-throughput screening of synthetic minigene libraries

scientific article

Disruptive CHD8 mutations define a subtype of autism early in development

scientific article

Diversity of human copy number variation and multicopy genes

scientific article

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

scientific article published on 04 April 2019

Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform

scientific article published on 01 May 2020

Elevated exopolysaccharide levels in Pseudomonas aeruginosa flagellar mutants have implications for biofilm growth and chronic infections

scientific article published on 12 June 2020

Embryo-scale, single-cell spatial transcriptomics

scientific article

Embryo model completes gastrulation to neurulation and organogenesis

scientific article published in 2022

Encephalopathy caused by novel mutations in the CMP-sialic acid transporter, SLC35A1

Epitope insertion into variable loops of HIV-1 gp120 as a potential means to improve immunogenicity of viral envelope protein

scientific article published on July 1999

Erratum to “Fluorescent in situ sequencing on polymerase colonies” [Anal. Biochem. 320 (2003) 55–65]

scholarly article published in Analytical Biochemistry

Erratum: Corrigendum: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

scientific article published in Nature

Erratum: Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

scholarly article by Brian J O'Roak et al published April 2012 in Nature Genetics

Erratum: Target-enrichment strategies for next-generation sequencing

scholarly article published in Nature Methods

Escape from X inactivation varies in mouse tissues

scientific article

Estimating the human mutation rate using autozygosity in a founder population

scientific article

Evidence for Limited Early Spread of COVID-19 Within the United States, January-February 2020

scientific article published on 05 June 2020

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster

scientific article published on 23 October 2011

Exome sequencing as a tool for Mendelian disease gene discovery

scientific article (publication date: 27 September 2011)

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

scientific article

Exome sequencing identifies SMAD3 mutations as a cause of familial thoracic aortic aneurysm and dissection with intracranial and other arterial aneurysms

scientific article

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers

scientific article

Exome sequencing identifies mutations in CCDC114 as a cause of primary ciliary dyskinesia

scientific article

Exome sequencing identifies the cause of a mendelian disorder

scientific article

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

scientific article (publication date: June 2011)

Exome sequencing in suspected monogenic dyslipidemias

scientific article

Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders

scientific article published on 27 April 2015

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

scientific article

Expanding the Molecular and Clinical Phenotype of SSR4-CDG.

scientific article

Expanding the clinical and genetic heterogeneity of hereditary disorders of connective tissue

scientific article

Expanding the single-cell genomics toolkit

scientific article published on 01 June 2019

Expansion of the spectrum of ITGB6-related disorders to adolescent alopecia, dentogingival abnormalities and intellectual disability

scientific article published on 23 December 2015

Experimental Evolution Identifies Vaccinia Virus Mutations in A24R and A35R That Antagonize the Protein Kinase R Pathway and Accompany Collapse of an Extragenic Gene Amplification

scientific article

Extraordinary molecular evolution in the PRDM9 fertility gene

scientific article published in 2009

FOXE3 mutations predispose to thoracic aortic aneurysms and dissections.

scientific article published on 8 February 2016

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

scientific article published on December 2014

FlashFry: a fast and flexible tool for large-scale CRISPR target design

bioRxiv preprint

FlashFry: a fast and flexible tool for large-scale CRISPR target design.

scientific article published on 5 July 2018

Fluorescent in situ sequencing on polymerase colonies

scientific article

Fragment Length of Circulating Tumor DNA

scientific article (publication date: July 2016)

Functional characterization of enhancer evolution in the primate lineage

scientific article published on 25 July 2018

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity.

scientific article

GABRA1 and STXBP1: novel genetic causes of Dravet syndrome

scientific article published on 12 March 2014

GRIN2A mutations cause epilepsy-aphasia spectrum disorders

scientific article published on 11 August 2013

GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions

article

Genetic Variation Meets Replication Origins

scientific article published on 01 November 2014

Genome evolution in the allotetraploid frog Xenopus laevis

scientific article

Genome interrupted: sequencing of prostate cancer reveals the importance of chromosomal rearrangements

scientific article published on 19 April 2011

Genome sequencing in a case of Niemann-Pick type C

scientific article

Genome sequencing of idiopathic pulmonary fibrosis in conjunction with a medical school human anatomy course

scientific article

Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq

scientific article

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

Genomic Medicine-Progress, Pitfalls, and Promise

scientific article published on 01 March 2019

Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus

scientific article published in 2022

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California ⬇️

scientific article published on 08 June 2020

Genotype-Phenotype correlations in Joubert Syndrome in the Era of Next Generation Sequencing

scientific article published on 13 July 2015

Germline missense variants in the BTNL2 gene are associated with prostate cancer susceptibility

scientific article published on 05 July 2013

Global survey of escape from X inactivation by RNA-sequencing in mouse

scientific article

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

scientific article

Guidelines for investigating causality of sequence variants in human disease

scientific article

Haploinsufficiency of SF3B4, a component of the pre-mRNA spliceosomal complex, causes Nager syndrome

scientific article

Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube.

scientific article

Haplotype-resolved genome sequencing of a Gujarati Indian individual.

scientific article

Haplotype-resolved genome sequencing: experimental methods and applications

scientific article published on 07 May 2015

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

scientific article

High Sensitivity Profiling of Chromatin Structure by MNase-SSP.

scientific article

High-Throughput Single-Cell Sequencing with Linear Amplification

scientific article published on 05 September 2019

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

scientific article

High-resolution comparative analysis of great ape genomes

scientific article published in Science

High-throughput determination of RNA structure by proximity ligation

scientific article published on 3 August 2015

Highly scalable generation of DNA methylation profiles in single cells

scientific article published on 09 April 2018

IFRD1 is a candidate gene for SMNA on chromosome 7q22-q23.

scientific article

Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia

scientific article

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C.

scientific article

Identification of foreign gene sequences by transcript filtering against the human genome

scientific article

Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model

scientific article

Identification of novel HLA class II target epitopes for generation of donor-specific T regulatory cells

scientific article published on 19 September 2012

Identification of sex-specific quantitative trait loci controlling alcohol preference in C57BL/ 6 mice.

scientific article published in June 1996

Identifying Novel Enhancer Elements with CRISPR-Based Screens.

scientific article

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

scientific article

Informed consent for whole genome sequencing: a qualitative analysis of participant expectations and perceptions of risks, benefits, and harms.

scientific article published on 24 April 2012

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay

scientific article published on 23 June 2019

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

scientific article

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

scientific article published on 30 August 2018

Journal club

KIAA0586 is Mutated in Joubert Syndrome

scientific article

LB21. The Seattle Flu Study: A Community-Based Study of Influenza

scientific article published on 23 October 2019

LOX Mutations Predispose to Thoracic Aortic Aneurysms and Dissections.

scientific article published on 12 January 2016

Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

scientific article

Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies

scientific article published on 16 December 2015

Learning the sequence determinants of alternative splicing from millions of random sequences

scientific article published on 22 October 2015

Life after genetics

scientific article published on 29 October 2014

Long-range polony haplotyping of individual human chromosome molecules

scientific article published on 19 February 2006

Long-read sequence assembly of the gorilla genome

scientific article published on April 2016

MAT2A mutations predispose individuals to thoracic aortic aneurysms

scientific article

MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

scientific article published on 6 February 2015

MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing

scientific article

Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation

scientific article published on 21 March 2013

Mammalian target of rapamycin pathway mutations cause hemimegalencephaly and focal cortical dysplasia

scientific article published on 26 February 2015

Mapping 3D genome architecture through in situ DNase Hi-C

scientific article

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

scientific article published on 30 March 2015

Massively Parallel Genetics.

scientific article published on June 2016

Massively multiplex chemical transcriptomics at single-cell resolution

scientific article published on 05 December 2019

Massively multiplex single-cell Hi-C.

scientific article

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

scientific article

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors

Massively parallel exon capture and library-free resequencing across 16 genomes

scientific article

Massively parallel functional dissection of mammalian enhancers in vivo

scientific article

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

scientific article published on 01 September 2019

Massively parallel sequencing and rare disease

scientific article

Massively parallel single-amino-acid mutagenesis

scientific article

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

scientific article published on 04 November 2019

Mechanisms of Interplay between Transcription Factors and the 3D Genome

scientific article published on 11 September 2019

Methods for genomic partitioning

scientific article

Mitral regurgitation as a phenotypic manifestation of nonphotosensitive trichothiodystrophy due to a splice variant in MPLKIP.

scientific article published on 16 February 2016

Mosaicism of the UDP-galactose transporter SLC35A2 causes a congenital disorder of glycosylation

scientific article published on April 2013

Multimodal single-cell analysis reveals distinct radioresistant stem-like and progenitor cell populations in murine glioma

scientific article published on 04 July 2020

Multiplex amplification of large sets of human exons

scientific article

Multiplex assessment of protein variant abundance by massively parallel sequencing

article

Multiplex genome sequencing and analysis

PhD Thesis of Jay Shendure

Multiplex pairwise assembly of array-derived DNA oligonucleotides

scientific article published on 8 November 2015

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing

scientific article published on 7 May 2015

Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders

scientific article

Mutation discovery in mice by whole exome sequencing

scientific article published on 14 September 2011

Mutation of ATF6 causes autosomal recessive achromatopsia

scientific article published on 11 June 2015

Mutations in CSPP1 Cause Primary Cilia Abnormalities and Joubert Syndrome with or without Jeune Asphyxiating Thoracic Dystrophy

Mutations in CSPP1 cause primary cilia abnormalities and Joubert syndrome with or without Jeune asphyxiating thoracic dystrophy

scientific article

Mutations in ECEL1 cause distal arthrogryposis type 5D

scientific article

Mutations in KCTD1 cause scalp-ear-nipple syndrome

scientific article

Mutations in PIEZO2 cause Gordon syndrome, Marden-Walker syndrome, and distal arthrogryposis type 5.

scientific article

Mutations in RSPH1 cause primary ciliary dyskinesia with a unique clinical and ciliary phenotype

scientific article published on March 2014

Mutations in SPAG1 cause primary ciliary dyskinesia associated with defective outer and inner dynein arms

scientific article published on 19 September 2013

Mutations in TBC1D24, a gene associated with epilepsy, also cause nonsyndromic deafness DFNB86.

scientific article published on January 2014

Mutations in the translocon-associated protein complex subunit SSR3 cause a novel congenital disorder of glycosylation

scientific article published on 16 April 2019

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

scientific article

New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis

Next generation sequence analysis for mitochondrial disorders

scientific article published on 23 October 2009

Next-generation human genetics

scientific article published on 14 September 2011

Next-generation human genetics.

scientific article published on 19 September 2011

Non-invasive fetal genome sequencing: opportunities and challenges

scientific article published on 10 August 2012

Noninvasive fetal genome sequencing: a primer

scientific article published on April 2013

Noninvasive whole-genome sequencing of a human fetus.

scientific article

Novel approach to genetic analysis and results in 3000 hemophilia patients enrolled in the My Life, Our Future initiative

scientific article published on 18 May 2017

Novel mutations in the genes TGM1 and ALOXE3 underlying autosomal recessive congenital ichthyosis

scientific article

On the design of CRISPR-based single cell molecular screens

On the design of CRISPR-based single-cell molecular screens

scientific article published on 19 February 2018

Overview of DNA sequencing strategies

scientific article published on January 2008

Overview of DNA sequencing strategies

scientific article published on October 2011

PI3K/AKT pathway mutations cause a spectrum of brain malformations from megalencephaly to focal cortical dysplasia

scientific article

PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution

scientific article published on June 2016

Parallel, tag-directed assembly of locally derived short sequence reads

scientific article

Pathogenic FBN1 variants in familial thoracic aortic aneurysms and dissections

scientific article published on December 2015

Polony DNA sequencing

scientific article

Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses

scientific article (publication date: 17 August 2012)

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

scientific article published on 01 May 2020

Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks

scholarly article published 13 September 2018

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

scientific article published on 26 September 2018

Preliminary support for a “dry swab, extraction free” protocol for SARS-CoV-2 testing via RT-qPCR

scientific article published on 24 April 2020

Primate evolution of the recombination regulator PRDM9

scientific article

Publisher Correction: DNA sequencing at 40: past, present and future

scientific article published on 01 April 2019

Quantification of differential gene expression by multiplexed targeted resequencing of cDNA.

scientific article published on 5 May 2017

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data.

scientific article published in December 2017

RNF213 rare variants in an ethnically diverse population with Moyamoya disease

scientific article published on 2 October 2014

Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections

scientific article

Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions

scientific article published on 28 July 2013

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

scientific article

Rare A2ML1 variants confer susceptibility to otitis media

scientific article

Rare variant associations with waist-to-hip ratio in European-American and African-American women from the NHLBI-Exome Sequencing Project

scientific article published on 13 January 2016

Rare-variant extensions of the transmission disequilibrium test: application to autism exome sequence data

scientific article

Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation

scientific article published on 20 December 2019

Recurrent de novo mutations implicate novel genes underlying simplex autism risk

scientific article

Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections

scientific article published on August 2013

Recurrent somatic loss of TNFRSF14 in classical Hodgkin lymphoma

scientific article

Refining analyses of copy number variation identifies specific genes associated with developmental delay

scientific article

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs

scientific article

Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing

scientific article

Running spell-check to identify regulatory variants

scientific article

SRD5A3-CDG: Expanding the phenotype of a congenital disorder of glycosylation with emphasis on adult onset features. ⬇️

scientific article

Saturation editing of genomic regions by multiplex homology-directed repair

scientific article

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

scientific article published on 08 August 2019

Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing

Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells

scientific article published on 16 September 2019

Sci-fate characterizes the dynamics of gene expression in single cells

scientific article published on 13 April 2020

Selection analyses of insertional mutants using subgenic-resolution arrays

scientific article

Sequencing thoroughbreds.

scientific article

Sex-restricted non-Mendelian inheritance of mouse chromosome 11 in the offspring of crosses between C57BL/6J and (C57BL/6J x DBA/2J)F1 mice

scientific article published in October 1998

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries

scientific article

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain by scGESTALT

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.

scientific article published on 28 March 2018

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

scientific article published on 4 February 2013

Single molecule profiling of alternative pre-mRNA splicing

scientific article

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

scientific article published on 20 December 2019

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

scientific article published on 6 March 2017

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

scientific article

Smash and DASH with Cas9.

scientific article published on 05 March 2016

Somatic mutations in cerebral cortical malformations

scientific article

Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps

scientific article

Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome

scientific article

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

scientific article (publication date: 4 April 2012)

Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer

scientific article published on 29 February 2016

Successes and challenges of using whole exome sequencing to identify novel genes underlying an inherited predisposition for thoracic aortic aneurysms and acute aortic dissections

scientific article

Supervised classification enables rapid annotation of cell atlases

scientific article published on 09 September 2019

Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology

scientific article published on 21 April 2020

Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation

scientific article

Systematic reconstruction of cellular trajectories across mouse embryogenesis

scientific article published on 14 March 2022

TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome

scientific article

Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing

scientific article published in January 2018

Tagmentation-based whole-genome bisulfite sequencing

scientific article

Target-enrichment strategies for next-generation sequencing

scientific article

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs)

scientific article

Targeted capture and massively parallel sequencing of 12 human exomes

scientific article

Targeted enrichment and high-resolution digital profiling of mitochondrial DNA deletions in human brain

scientific article

Targeted enrichment of specific regions in the human genome by array hybridization

scientific article

Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1.

scientific article

The 4D Nucleome Project

scholarly article

The 4D nucleome project

scientific article published on September 2017

The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions.

scientific article published on 24 May 2012

The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

scientific article

The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)

scientific article published on 01 December 2019

The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

scientific article published on 07 March 2020

The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology

scientific article published on 07 October 2020

The beginning of the end for microarrays?

scientific article

The cis-regulatory dynamics of embryonic development at single cell resolution

article

The cis-regulatory dynamics of embryonic development at single-cell resolution

scientific article published on 14 March 2018

The complete genome sequence of a Neanderthal from the Altai Mountains

scientific article

The contribution of de novo coding mutations to autism spectrum disorder

scientific article

The dynamic three-dimensional organization of the diploid yeast genome

scientific article

The expanding scope of DNA sequencing

scientific article

The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis

scientific article published on 20 October 2021

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

scientific article

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

scientific article

The million mutation project: a new approach to genetics in Caenorhabditis elegans

scientific article

The origins, determinants, and consequences of human mutations

scientific article

The power of multiplexed functional analysis of genetic variants.

scientific article published on September 2016

The single-cell transcriptional landscape of mammalian organogenesis

scientific article published on 20 February 2019

Towards a comprehensive catalogue of validated and target-linked human enhancers

scientific article published on 27 January 2020

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

scientific article

Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

scientific article published on 27 November 2020

Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting

scientific article

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

scientific article

Understanding Spatial Genome Organization: Methods and Insights

scientific article

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

scientific article published on 27 January 2018

Variant Interpretation: Functional Assays to the Rescue.

scientific article published in September 2017

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

scientific article published on 30 September 2020

Voices in methods development

scientific article published on 01 October 2019

What Is Your Conceptual Definition of "Cell Type" in the Context of a Mature Organism? ⬇️

scientific article published on 01 March 2017

What's a Genome Worth?

Whole genome prediction for preimplantation genetic diagnosis

scientific article published on 8 April 2015

Whole organism lineage tracing by combinatorial and cumulative genome editing

Whole-exome capture and sequencing identifies HEATR2 mutation as a cause of primary ciliary dyskinesia

scientific article

Whole-genome analysis reveals that mutations in inositol polyphosphate phosphatase-like 1 cause opsismodysplasia

scientific article

Whole-genome sequencing for high-resolution investigation of methicillin-resistant Staphylococcus aureus epidemiology and genome plasticity

scientific article

Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma

scientific article

Whole-organism lineage tracing by combinatorial and cumulative genome editing

scientific article

crisprQTL mapping as a genome-wide association framework for cellular genetic screens

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

scientific article published on 08 July 2020

megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering

scientific article

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