In the news

Artificial Transcription Factors – A new class of epigenetic drugs

To date none of the drugs targeting DNA methylation and histone modification are sequence specific, thus the drug may cause genome-wide dysregulation. To increase the specificity of these interactions, ATFs are being developed.

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Imprinting, epigenetic markers and assisted reproductive technologies (ARTs)

Considering the essential role of epigenetic reprogramming during gametogenesis and embryogenesis, the identification and use of epigenetic markers during embryo development may be a useful tool to improve ART efficiency and security.

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Overcoming epigenetic barriers in cloning

The low efficiency of reproductive cloning is attributed to epigenetic barriers that prevent the activation of the zygotic genome. Now, locus-specific demethylation resulted in substantially higher efficiency to produce healthy, fertile cloned mice.

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New single-cell seq technology, novel insight

Extensive clonal diversity generation and mutation rates were proved in aggressive cancer cells by the newly developed nuc-seq method that uses G2/M nuclei to achieve high coverage breadh. The Navin-group provides even more high important findings.

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Common But Just Uncovered Virus in Our Gut

Using a unique sampling approach researchers uncovered a novel bacteriophage in fecal metagenomes. It was found in some 75 percent of published metagenomes, likely infects the Bacteroides and suspectedly is very important in regulating their number.

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Bringing microbial sequencing to hospitals

"Yet pathogen sequencing represents a quick win. Bench-top sequencers that cost around US$125,000 can complete several bacterial genomes in a day, at a cost of around $150 per sample — about twice as much as running some commercial PCR tests."

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Market the microbiom

Pfizer, Janssen, Johnson & Johnson and other large pharmaceutical companies eye the medical potential of manipulating interactions between humans and the bacteria that live in or on the body.

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Oh, dirty money

Researchers have sequenced all the DNA found on about 80 dollar bills from a Manhattan bank. They identified 3,000 types of bacteria in all — though 20% of the non-human DNA they found haven't yet been cataloged in genetic data banks.

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Easy-to-digest biomass could produce far more fuel

Researchers found a gene that changes lignin production, making it easier to break down and therefore sugars are easily extractable from the biomass to turn into fuel.

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A population level analysis gives a new insight into the very early stages of the origin and establishment of genes de novo

Researchers present transcripts that are expressed in D. melanogaster strains they examined, but that corresponded to intergenic sequences of the reference genome, realizing that genes really can arise from formerly noncoding regions of the genome.

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Bottom-up characterization of in vivo cell-type landscapes is possible independently of cell markers or prior knowledge

"Massively parallel single-cell RNA-sequencing was applied to explore cellular heterogeneity within the immune system revealing distinct cellular groupings that corresponded to B cells, macrophages, and dendritic cells."

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Rare variants in a newly identified Alzheimer’s disease risk gene, raising the risk of the disease by around two-fold

A reasearch team used a family-based approach to track down low-frequency Alzheimer’s risk variants, sequencing the exomes of individuals from more than a dozen families impacted by late-onset Alzheimer’s disease.

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Whole genome sequencing not yet practical for the clinical setting

"The day may not be as close as researchers have hoped for, that WGS will be able to provide clinicians with ability to cater treatment plans to individual patients at a molecular level."

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Whole exome sequencing and social media aided in the discovery of a new genetic disease

To define the phenotype associated with a novel autosomal recessive disorder, authors studied a series of eight patients with neurological dysfunction, abnormal tear production, and liver disease.

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What to watch: Emerging technologies

"...therapeutics based on the human microbiome look promising as the vast number of microbes that live in the human gut are now seen to be essential in maintaining health."

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New Antibiotic from a Detrimental Fungus

"The causal agent of ash dieback may soon be providing us with beneficial substances."

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The Surprising Reason Americans Might Be Obese, Anxious and Depressed

"...the theory that certain medical conditions, especially autoimmune ones, may be caused by a changing or declining bacterial environment in the human gut is gaining momentum..."

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Resources

Cancer driver gene catalogue

The Candidate Cancer Gene Database, or CCGD, is designed to house cancer-related information found through transposon mutagenesis studies.

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De Novo Assembly of Human Genome with Only 1.5 GB RAM

The representation of de Bruijn graph plays an important role in de novo assembly bioinformatics, however with huge memory footprint. Recently, a new general data structure has been implemented with space usage of 1.5 GB and a 46% improvement.

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In situ single cell, single molecule RNA sequencing

Cellular localization, phenotype, gene regulation, and environment in situ of RNAs are examinable with the newly combined Fluorescent in situ sequencing (FISSEQ) method.

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Genomes Unzipped provides genetic testing customers with the knowledge and tools they need to make the most of their own genetic data

To review the products currently on offer from genetic testing companies and to illustrate fundamental concepts in genetics, the collaboration shares the results of the scientific analysis of their own genomes.

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Comprehensive review of available bioinformatics tools specific for single cell genomics analysis

Single cell DNA/RNA sequencing data usually have low genome coverage and high amplification bias, which makes bioinformatics analysis challenging.

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Fluigdigm Launches Single-Cell DNA Sequencing Workflow

"An universal sample prep workflow streamlines targeted, whole exome and whole genome sequencing in heterogeneous cell populations and enables researchers to discover and screen somatic mutations, such as SNP, small indels, and translocations."

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One of the world’s fastest supercomputers devoted to life sciences is able to analyze 240 full genomes in about two days

“With this approach, the price for analyzing an entire genome is less than the cost of the looking at just a fraction of genome, bringing the costs of sequencing down to around $1,000 per genome.”

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A human gut microbial gene catalogue established by metagenomic sequencing

This article describes the metagenomic sequencing of 124 samples to discover the human gut microbiome. As the largest metagenomic study up to now, it generated 576.7Gb of sequence data, and catalogued the microbial genes commonly found in the human gut.

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The science of metagenomics: Revealing the Secrets of Our Microbial Planet

This OpenBook explains the biological background of microbial communities, promises of metagenomics, and the challenges of metagenomic data management and analysis.

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Assembling large, complex environmental metagenomes

"We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more computationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies ne

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A Primer on Metagenomics

An excellent overview of the methods and applications of metagenomics in PLOS Computational Biology

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