Nature Search

Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

The microbial RNA-guided CRISPR/Cas9 system has robust genome-editing activities, but the off-target effects of the Cas9 nuclease have only recently begun to be analysed. Here the authors provide evidence for high specificity of the Cas9 nuclease on targeting of the Tafazzin gene in human-induced pluripotent stem cells and demonstrate the impact of single-nucleotide variations of the human genome on Cas9 specificity.

Luhan Yang
Dennis Grishin
George Church
ResearchOpen Access26 Nov 2014
Nature Communications

Volume: 5, P: 1-6
A highly informative SNP linkage panel for human genetic studies

Sarah Shaw Murray
Arnold Oliphant
Mark S T Hansen
Research21 Oct 2004
Nature Methods

Volume: 1, P: 113-117
Genome-wide mapping of allele-specific protein-DNA interactions in human cells

Nathaniel D Maynard
Jing Chen
Bing Ren
Research16 Mar 2008
Nature Methods

Volume: 5, P: 307-309
Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse

Kerstin Lindblad-Toh
Ellen Winchester
Eric S. Lander
Research01 Apr 2000
Nature Genetics

Volume: 24, P: 381-386
Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays

Joseph G. Hacia
Jian-Bing Fan
Francis S. Collins
Research01 Jun 1999
Nature Genetics

Volume: 22, P: 164-167
Mapping human tissues with highly multiplexed RNA in situ hybridization

Application of multiplexed RNA in situ mapping techniques to human tissues remains challenging. Here, the authors report DART-FISH, a padlock probe-based technology capable of profiling large numbers of genes in centimetre-sized human tissue sections.

Kian Kalhor
Chien-Ju Chen
Kun Zhang
ResearchOpen Access20 Mar 2024
Nature Communications

Volume: 15, P: 1-17
Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development

COBRA1 is a BRCA1-binding protein and, as part of the negative elongation factor, regulates RNA polymerase II pausing and transcription elongation. Here, the authors show that tissue-specific deletion of mouse Cobra1 inhibits postnatal mammary gland development and that the mammary defects can be rescued by additional deletion of Brca1in a DNA repair-independent manner.

Sreejith J. Nair
Xiaowen Zhang
Rong Li
ResearchOpen Access04 Mar 2016
Nature Communications

Volume: 7, P: 1-9
Network analysis reveals crosstalk between autophagy genes and disease genes

Ji-Ye Wang
Wei-Xuan Yao
Jian-Bing Wu
ResearchOpen Access15 Mar 2017
Scientific Reports

Volume: 7, P: 1-9
Dietary components and risk of total, cancer and cardiovascular disease mortality in the Linxian Nutrition Intervention Trials cohort in China

Jian-Bing Wang
Jin-Hu Fan
Christian C. Abnet
ResearchOpen Access04 Mar 2016
Scientific Reports

Volume: 6, P: 1-8
Regulation of adipose oestrogen output by mechanical stress

Aberrant production of oestrogens by adipose stromal cells is a driving factor in oestrogen receptor-positive breast cancer. Here the authors discover that oestrogen synthesis in adipose tissue is regulated by mechanical stress, and reveal how this effect is mediated.

Sagar Ghosh
Keith Ashcraft
Rong Li
Research07 May 2013
Nature Communications

Volume: 4, P: 1-14
Profiling alternative splicing on fiber-optic arrays

Joanne M. Yeakley
Jian-Bing Fan
Xiang-Dong Fu
Research01 Apr 2002
Nature Biotechnology

Volume: 20, P: 353-358
Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis

Marc K. Halushka
Jian-Bing Fan
Aravinda Chakravarti
Research01 Jul 1999
Nature Genetics

Volume: 22, P: 239-247
A second generation human haplotype map of over 3.1 million SNPs

A consortium reports the tripling of the number of genetic markers in Phase II of the International HapMap Project. This map of human genetic variation will continue to revolutionize discovery of susceptibility loci in common genetic diseases, and study of genes under selection in humans.

Kelly A. Frazer (Principal Investigator)
Dennis G. Ballinger
John Stewart
Research18 Oct 2007
Nature

Volume: 449, P: 851-861
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

By testing potential sources of biological signal that drive population-level variation in single-cell gene expression, the PAGODA software enables cells to be characterized on the basis of multiple functionally relevant features such as cell type, signaling state and cell cycle state.

Jean Fan
Neeraj Salathia
Peter V Kharchenko
Research18 Jan 2016
Nature Methods

Volume: 13, P: 241-244
A urine DNA methylation assay for early detection of renal cancer

Tongshuai Shi
Hanzhong Chen
Qingbo Huang
Research17 Mar 2025
Oncogene

Volume: 44, P: 1709-1717
Influence of slope angle on deposit morphology and propagation of laboratory landslides

Yan-Bin Wu
Zhao Duan
Thomas Pähtz
ResearchOpen Access10 Jun 2023
Scientific Reports

Volume: 13, P: 1-15
Highly parallel genomic assays

Fifteen years after the first generation of microarray platforms for highly parallel genomic analysis, intrinsically parallel whole-genome approaches to genotyping, epigenetic profiling and sequencing are being developed. What are the recent key developments that promise to transform the study of human health and disease?

Jian-Bing Fan
Mark S. Chee
Kevin L. Gunderson
Reviews01 Aug 2006
Nature Reviews Genetics

Volume: 7, P: 632-644
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia

José Martin-Subero and colleagues report whole-genome bisulfite sequencing and methylome analysis of two CLLs and three B-cell subpopulations using high-density microarrays on 139 CLLs. They identify widespread hypomethylation in the gene body that is largely associated with intragenic enhancer elements.

Marta Kulis
Simon Heath
José I Martín-Subero
Research14 Oct 2012
Nature Genetics

Volume: 44, P: 1236-1242
The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment

Dick and colleagues map the transcriptional dynamics of human hematopoietic stem cells and early progenitor populations. The authors show that transcriptional programs are extensively shared, extend across lineage-potential boundaries and are not strictly lineage affiliated.

Elisa Laurenti
Sergei Doulatov
John E Dick
Research26 May 2013
Nature Immunology

Volume: 14, P: 756-763
Transarterial chemoembolization with PD-(L)1 inhibitors plus molecular targeted therapies for hepatocellular carcinoma (CHANCE001)

Hai-Dong Zhu
Hai-Liang Li
Gao-Jun Teng
ResearchOpen Access08 Feb 2023
Signal Transduction and Targeted Therapy

Volume: 8, P: 1-10
Circulating cell-free DNA-based methylation patterns for breast cancer diagnosis

Xianyu Zhang
Dezhi Zhao
Da Pang
ResearchOpen Access16 Aug 2021
npj Breast Cancer

Volume: 7, P: 1-8
Mutation in ST6GALNAC5 identified in family with coronary artery disease

Kolsoum InanlooRahatloo
Amir Farhang Zand Parsa
Elahe Elahi
ResearchOpen Access08 Jan 2014
Scientific Reports

Volume: 4, P: 1-8
Genome-wide detection and characterization of positive selection in human populations

Sabeti et al. build on their This paper builds on previous work of detecting selection on human genes, using the many more markers available in the Phase II HapMap project. Three examples of apparent population-specific selection based on geographic area are described, and how these may relate to human biology is discussed.

Pardis C. Sabeti
Patrick Varilly
John Stewart
Research18 Oct 2007
Nature

Volume: 449, P: 913-918
Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

Saiful Islam
Una Kjällquist
Sten Linnarsson
Protocols05 Apr 2012
Nature Protocols

Volume: 7, P: 813-828

Search

Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

A highly informative SNP linkage panel for human genetic studies

Genome-wide mapping of allele-specific protein-DNA interactions in human cells

Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse

Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays

Mapping human tissues with highly multiplexed RNA in situ hybridization

Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development

Network analysis reveals crosstalk between autophagy genes and disease genes

Dietary components and risk of total, cancer and cardiovascular disease mortality in the Linxian Nutrition Intervention Trials cohort in China

Regulation of adipose oestrogen output by mechanical stress

Profiling alternative splicing on fiber-optic arrays

Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis

A second generation human haplotype map of over 3.1 million SNPs

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

A urine DNA methylation assay for early detection of renal cancer

Influence of slope angle on deposit morphology and propagation of laboratory landslides

Highly parallel genomic assays

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia

The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment

Transarterial chemoembolization with PD-(L)1 inhibitors plus molecular targeted therapies for hepatocellular carcinoma (CHANCE001)

Circulating cell-free DNA-based methylation patterns for breast cancer diagnosis

Mutation in ST6GALNAC5 identified in family with coronary artery disease

Genome-wide detection and characterization of positive selection in human populations

Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

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