2,228 results match your criteria Nature Reviews Genetics [Journal]


Spatial transcriptomics coming of age.

Authors:
Darren J Burgess

Nat Rev Genet 2019 Apr 12. Epub 2019 Apr 12.

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0129-zDOI Listing

Microbial signatures of colorectal cancer.

Authors:
Linda Koch

Nat Rev Genet 2019 Apr 10. Epub 2019 Apr 10.

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0126-2DOI Listing
April 2019
1 Read

Deep learning: new computational modelling techniques for genomics.

Nat Rev Genet 2019 Apr 10. Epub 2019 Apr 10.

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.

As a data-driven science, genomics largely utilizes machine learning to capture dependencies in data and derive novel biological hypotheses. However, the ability to extract new insights from the exponentially increasing volume of genomics data requires more expressive machine learning models. By effectively leveraging large data sets, deep learning has transformed fields such as computer vision and natural language processing. Read More

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http://www.nature.com/articles/s41576-019-0122-6
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http://dx.doi.org/10.1038/s41576-019-0122-6DOI Listing
April 2019
3 Reads

Ancient pathogen genomics as an emerging tool for infectious disease research.

Nat Rev Genet 2019 Apr 5. Epub 2019 Apr 5.

Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.

Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. Read More

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http://dx.doi.org/10.1038/s41576-019-0119-1DOI Listing

Gut microbial structural variation links to human health.

Authors:
Dorothy Clyde

Nat Rev Genet 2019 Apr 5. Epub 2019 Apr 5.

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0124-4DOI Listing

When the elite compete.

Authors:
Linda Koch

Nat Rev Genet 2019 Apr 2. Epub 2019 Apr 2.

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0123-5DOI Listing

A duty to recontact in genetics: context matters.

Nat Rev Genet 2019 Apr 1. Epub 2019 Apr 1.

Department of Medical Humanities, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands.

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http://dx.doi.org/10.1038/s41576-019-0121-7DOI Listing

Clinical metagenomics.

Nat Rev Genet 2019 Mar 27. Epub 2019 Mar 27.

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.

Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health. Read More

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http://dx.doi.org/10.1038/s41576-019-0113-7DOI Listing
March 2019
1 Read

Scanning for determinants of Zika virus host tropism.

Authors:
Dorothy Clyde

Nat Rev Genet 2019 Mar 27. Epub 2019 Mar 27.

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0120-8DOI Listing
March 2019
1 Read

Resolving genetic heterogeneity in cancer.

Nat Rev Genet 2019 Mar 27. Epub 2019 Mar 27.

Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK.

To a large extent, cancer conforms to evolutionary rules defined by the rates at which clones mutate, adapt and grow. Next-generation sequencing has provided a snapshot of the genetic landscape of most cancer types, and cancer genomics approaches are driving new insights into cancer evolutionary patterns in time and space. In contrast to species evolution, cancer is a particular case owing to the vast size of tumour cell populations, chromosomal instability and its potential for phenotypic plasticity. Read More

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http://dx.doi.org/10.1038/s41576-019-0114-6DOI Listing
March 2019
2 Reads
36.978 Impact Factor

Optimizing biological inferences from single-cell data.

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Nat Rev Genet 2019 May;20(5):249

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http://dx.doi.org/10.1038/s41576-019-0118-2DOI Listing
May 2019
1 Read

Author Correction: Regulation of transposable elements by DNA modifications.

Nat Rev Genet 2019 Mar 20. Epub 2019 Mar 20.

Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK.

The originally published article contained an error in Figure 2a: for the left side of the figure part (showing piRNA-directed DNA methylation of mouse transposable elements), DNMT3A/B should have been DNMT3C. The article has now been corrected online. Read More

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http://dx.doi.org/10.1038/s41576-019-0117-3DOI Listing

Switching APOBEC mutation signatures.

Authors:
Darren J Burgess

Nat Rev Genet 2019 May;20(5):253

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0116-4DOI Listing

Regulation of RNA methylation by modified histones.

Authors:
Dorothy Clyde

Nat Rev Genet 2019 May;20(5):254-255

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0115-5DOI Listing

The genetics of convergent evolution: insights from plant photosynthesis.

Nat Rev Genet 2019 Mar 18. Epub 2019 Mar 18.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.

The tree of life is resplendent with examples of convergent evolution, whereby distinct species evolve the same trait independently. Many highly convergent adaptations are also complex, which makes their repeated emergence surprising. In plants, the evolutionary history of two carbon concentrating mechanisms (CCMs) - C and crassulacean acid metabolism (CAM) photosynthesis - presents such a paradox. Read More

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http://dx.doi.org/10.1038/s41576-019-0107-5DOI Listing

Sequencing-based methods and resources to study antimicrobial resistance.

Nat Rev Genet 2019 Mar 18. Epub 2019 Mar 18.

The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.

Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial resistance are imperative for clinical practice to treat resistant infections and for public health efforts to limit the spread of resistance. Technologies such as next-generation sequencing are expanding our abilities to detect and study antimicrobial resistance. Read More

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http://dx.doi.org/10.1038/s41576-019-0108-4DOI Listing

Enhancers assemble!

Authors:
Linda Koch

Nat Rev Genet 2019 May;20(5):255

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0112-8DOI Listing

Old cogs, new tricks: the evolution of gene expression in a chromatin context.

Nat Rev Genet 2019 May;20(5):283-297

Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

Sophisticated gene-regulatory mechanisms probably evolved in prokaryotes billions of years before the emergence of modern eukaryotes, which inherited the same basic enzymatic machineries. However, the epigenomic landscapes of eukaryotes are dominated by nucleosomes, which have acquired roles in genome packaging, mitotic condensation and silencing parasitic genomic elements. Although the molecular mechanisms by which nucleosomes are displaced and modified have been described, just how transcription factors, histone variants and modifications and chromatin regulators act on nucleosomes to regulate transcription is the subject of considerable ongoing study. Read More

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http://dx.doi.org/10.1038/s41576-019-0105-7DOI Listing

The ethics of sequencing infectious disease pathogens for clinical and public health.

Nat Rev Genet 2019 Mar 15. Epub 2019 Mar 15.

Wellcome Centre for Ethics and Humanities and Ethox Centre, University of Oxford, Oxford, UK.

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http://www.nature.com/articles/s41576-019-0109-3
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http://dx.doi.org/10.1038/s41576-019-0109-3DOI Listing
March 2019
2 Reads

Cytosine base editors go off-target.

Nat Rev Genet 2019 May;20(5):254-255

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0110-xDOI Listing

Balancing uncertainty with patient autonomy in precision medicine.

Nat Rev Genet 2019 May;20(5):251-252

Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/s41576-019-0111-9DOI Listing

Regulation of transposable elements by DNA modifications.

Nat Rev Genet 2019 Mar 12. Epub 2019 Mar 12.

Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK.

Maintenance of genome stability requires control over the expression of transposable elements (TEs), whose activity can have substantial deleterious effects on the host. Chemical modification of DNA is a commonly used strategy to achieve this, and it has long been argued that the emergence of 5-methylcytosine (5mC) in many species was driven by the requirement to silence TEs. Potential roles in TE regulation have also been suggested for other DNA modifications, such as N6-methyladenine and oxidation derivatives of 5mC, although the underlying mechanistic relationships are poorly understood. Read More

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http://dx.doi.org/10.1038/s41576-019-0106-6DOI Listing

Coming full circle in cancer.

Authors:
Darren J Burgess

Nat Rev Genet 2019 Apr;20(4):191

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0104-8DOI Listing

3D genome shows its stripes in gene-rich regions.

Nat Rev Genet 2019 Apr;20(4):192-193

Associate Editor, Nature Communications, .

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http://dx.doi.org/10.1038/s41576-019-0102-xDOI Listing

Getting the drop on chromatin interaction.

Authors:
Linda Koch

Nat Rev Genet 2019 Apr;20(4):192-193

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0103-9DOI Listing
April 2019
1 Read

Telomeres and telomerase: three decades of progress.

Nat Rev Genet 2019 May;20(5):299-309

Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.

Many recent advances have emerged in the telomere and telomerase fields. This Timeline article highlights the key advances that have expanded our views on the mechanistic underpinnings of telomeres and telomerase and their roles in ageing and disease. Three decades ago, the classic view was that telomeres protected the natural ends of linear chromosomes and that telomerase was a specific telomere-terminal transferase necessary for the replication of chromosome ends in single-celled organisms. Read More

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http://dx.doi.org/10.1038/s41576-019-0099-1DOI Listing

A new Cas in town.

Authors:
Linda Koch

Nat Rev Genet 2019 Apr;20(4):193

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0101-yDOI Listing

Induced pluripotent stem cells in disease modelling and drug discovery.

Nat Rev Genet 2019 Feb 8. Epub 2019 Feb 8.

Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.

The derivation of induced pluripotent stem cells (iPSCs) over a decade ago sparked widespread enthusiasm for the development of new models of human disease, enhanced platforms for drug discovery and more widespread use of autologous cell-based therapy. Early studies using directed differentiation of iPSCs frequently uncovered cell-level phenotypes in monogenic diseases, but translation to tissue-level and organ-level diseases has required development of more complex, 3D, multicellular systems. Organoids and human-rodent chimaeras more accurately mirror the diverse cellular ecosystems of complex tissues and are being applied to iPSC disease models to recapitulate the pathobiology of a broad spectrum of human maladies, including infectious diseases, genetic disorders and cancer. Read More

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http://dx.doi.org/10.1038/s41576-019-0100-zDOI Listing
February 2019
1 Read

Integrative single-cell analysis.

Nat Rev Genet 2019 May;20(5):257-272

New York Genome Center, New York, NY, USA.

The recent maturation of single-cell RNA sequencing (scRNA-seq) technologies has coincided with transformative new methods to profile genetic, epigenetic, spatial, proteomic and lineage information in individual cells. This provides unique opportunities, alongside computational challenges, for integrative methods that can jointly learn across multiple types of data. Integrated analysis can discover relationships across cellular modalities, learn a holistic representation of the cell state, and enable the pooling of data sets produced across individuals and technologies. Read More

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http://dx.doi.org/10.1038/s41576-019-0093-7DOI Listing

The long and the short of it.

Authors:
Linda Koch

Nat Rev Genet 2019 Mar;20(3):131

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0098-2DOI Listing

Learning the language of splicing.

Authors:
Dorothy Clyde

Nat Rev Genet 2019 Mar;20(3):132-133

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0097-3DOI Listing

Chromatin accessibility and the regulatory epigenome.

Nat Rev Genet 2019 Apr;20(4):207-220

Department of Genetics, Stanford University, Stanford, CA, USA.

Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. Read More

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http://dx.doi.org/10.1038/s41576-018-0089-8DOI Listing
April 2019
1 Read

Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data.

Nat Rev Genet 2019 May;20(5):310

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

During typesetting of this article, errors were inadvertently introduced to the hyperlinked URLs of some of the clustering tools in table 1 (Seurat, CIDR, pcaReduce and mpath), as well as to the numbering of the bold-text annotations in the reference list. The article has now been corrected online. The editors apologize for this error. Read More

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http://dx.doi.org/10.1038/s41576-019-0095-5DOI Listing
May 2019
2 Reads

Human protein mutagens found via bacteria.

Authors:
Darren J Burgess

Nat Rev Genet 2019 Mar;20(3):132-133

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0096-4DOI Listing
March 2019
1 Read

Baby sequencing steps.

Authors:
Linda Koch

Nat Rev Genet 2019 Mar;20(3):133

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-019-0094-6DOI Listing
March 2019
2 Reads

Genomic imprinting disorders: lessons on how genome, epigenome and environment interact.

Nat Rev Genet 2019 Apr;20(4):235-248

Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania 'Luigi Vanvitelli', Caserta; Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso' CNR, Napoli, Italy.

Genomic imprinting, the monoallelic and parent-of-origin-dependent expression of a subset of genes, is required for normal development, and its disruption leads to human disease. Imprinting defects can involve isolated or multilocus epigenetic changes that may have no evident genetic cause, or imprinting disruption can be traced back to alterations of cis-acting elements or trans-acting factors that control the establishment, maintenance and erasure of germline epigenetic imprints. Recent insights into the dynamics of the epigenome, including the effect of environmental factors, suggest that the developmental outcomes and heritability of imprinting disorders are influenced by interactions between the genome, the epigenome and the environment in germ cells and early embryos. Read More

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http://www.nature.com/articles/s41576-018-0092-0
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http://dx.doi.org/10.1038/s41576-018-0092-0DOI Listing
April 2019
11 Reads

A great-ape view of the gut microbiome.

Nat Rev Genet 2019 Apr;20(4):195-206

Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.

Humans assemble a specialized microbiome from a world teeming with diverse microorganisms. Comparison to the microbiomes of great apes provides a dimension that is indispensable to understanding how these microbial communities form, function and change. This evolutionary perspective exposes not only how human gut microbiomes have been shaped by our great-ape heritage but also the features that make humans unique, as exemplified by an expansive loss of bacterial and archaeal diversity and the identification of microbial lineages that have co-diversified with their hosts. Read More

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http://dx.doi.org/10.1038/s41576-018-0085-zDOI Listing
April 2019
2 Reads

Challenges in unsupervised clustering of single-cell RNA-seq data.

Nat Rev Genet 2019 May;20(5):273-282

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

Single-cell RNA sequencing (scRNA-seq) allows researchers to collect large catalogues detailing the transcriptomes of individual cells. Unsupervised clustering is of central importance for the analysis of these data, as it is used to identify putative cell types. However, there are many challenges involved. Read More

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http://dx.doi.org/10.1038/s41576-018-0088-9DOI Listing
May 2019
3 Reads

The role of sex in the genomics of human complex traits.

Nat Rev Genet 2019 Mar;20(3):173-190

Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.

Nearly all human complex traits and disease phenotypes exhibit some degree of sex differences, including differences in prevalence, age of onset, severity or disease progression. Until recently, the underlying genetic mechanisms of such sex differences have been largely unexplored. Advances in genomic technologies and analytical approaches are now enabling a deeper investigation into the effect of sex on human health traits. Read More

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http://www.nature.com/articles/s41576-018-0083-1
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http://dx.doi.org/10.1038/s41576-018-0083-1DOI Listing
March 2019
15 Reads

Genome editing for disease locus dissection.

Authors:
Darren J Burgess

Nat Rev Genet 2019 Feb;20(2):67

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-018-0091-1DOI Listing
February 2019
19 Reads

Mechanisms regulating zygotic genome activation.

Nat Rev Genet 2019 Apr;20(4):221-234

Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.

Following fertilization, the two specified gametes must unite to create an entirely new organism. The genome is initially transcriptionally quiescent, allowing the zygote to be reprogrammed into a totipotent state. Gradually, the genome is activated through a process known as the maternal-to-zygotic transition, which enables zygotic gene products to replace the maternal supply that initiated development. Read More

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http://dx.doi.org/10.1038/s41576-018-0087-xDOI Listing
April 2019
1 Read

Synthetic readers and writers for mammalian chromatin.

Nat Rev Genet 2019 Feb;20(2):68-69

Associate Editor, Nature Communications, .

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http://dx.doi.org/10.1038/s41576-018-0090-2DOI Listing
February 2019
1 Read

Deciphering bacterial epigenomes using modern sequencing technologies.

Nat Rev Genet 2019 Mar;20(3):157-172

Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Read More

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http://dx.doi.org/10.1038/s41576-018-0081-3DOI Listing
March 2019
2 Reads

Proximity-CLIP - close encounters of the RNA kind.

Authors:
Linda Koch

Nat Rev Genet 2019 Feb;20(2):68-69

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-018-0086-yDOI Listing
February 2019
2 Reads

Integrating behavioural health tracking in human genetics research.

Nat Rev Genet 2019 Mar;20(3):129-130

Center for Behavioral Intervention Technologies, Northwestern University, Chicago, IL, USA.

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http://dx.doi.org/10.1038/s41576-018-0078-yDOI Listing
March 2019
1 Read

Risk loci for ADHD.

Authors:
Dorothy Clyde

Nat Rev Genet 2019 Feb;20(2):69

Nature Reviews Genetics, .

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http://dx.doi.org/10.1038/s41576-018-0084-0DOI Listing
February 2019
1 Read

Harnessing genomic information for livestock improvement.

Nat Rev Genet 2019 Mar;20(3):135-156

Queensland Alliance for Agriculture and Food Innovation (QAAFI), Queensland Bioscience Precinct, The University of Queensland, Brisbane, Queensland, Australia.

The world demand for animal-based food products is anticipated to increase by 70% by 2050. Meeting this demand in a way that has a minimal impact on the environment will require the implementation of advanced technologies, and methods to improve the genetic quality of livestock are expected to play a large part. Over the past 10 years, genomic selection has been introduced in several major livestock species and has more than doubled genetic progress in some. Read More

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http://dx.doi.org/10.1038/s41576-018-0082-2DOI Listing
March 2019
1 Read

The value of genetic testing for family health history of adopted persons.

Authors:
Thomas May

Nat Rev Genet 2019 Feb;20(2):65-66

Elson S. Floyd College of Medicine, Washington State University, Vancouver, WA, USA.

Lack of family health history experienced by most adopted persons can represent a marked disadvantage. This Comment discusses the role of genetic testing in filling this informational gap and the challenges that need to be overcome. Read More

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http://dx.doi.org/10.1038/s41576-018-0080-4DOI Listing
February 2019
1 Read

Clinical epigenetics: seizing opportunities for translation.

Nat Rev Genet 2019 Feb;20(2):109-127

Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.

Biomarker discovery and validation are necessary for improving the prediction of clinical outcomes and patient monitoring. Despite considerable interest in biomarker discovery and development, improvements in the range and quality of biomarkers are still needed. The main challenge is how to integrate preclinical data to obtain a reliable biomarker that can be measured with acceptable costs in routine clinical practice. Read More

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http://dx.doi.org/10.1038/s41576-018-0074-2DOI Listing
February 2019
1 Read

Testing the generality of non-genetic inheritance.

Authors:
Darren J Burgess

Nat Rev Genet 2019 Jan;20(1)

Nature Reviews Genetics, .

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http://www.nature.com/articles/s41576-018-0079-x
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http://dx.doi.org/10.1038/s41576-018-0079-xDOI Listing
January 2019
4 Reads