Tools and tips for scientific tinkers and tailors
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Biome | Bioinformatics for biologists

Biome | Bioinformatics for biologists | Tools and tips for scientific tinkers and tailors | Scoop.it
The 4273π operating system for Raspberry Pi computers has been developed to facilitate an in-depth bioinformatics course for biologists | Research published by BioMed Central
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Tools and tips for scientific tinkers and tailors
Next gen sequencing, bioinformatics, virology, microbiology, genomes, zoonoses, workshops, conferences, all-around science geekery
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Collaboration keeps your research program alive | Small Pond Science

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Get Rid of the Noise – Targeted Depletion Approach for RNA-Seq | RNA-Seq Blog

In this webinar, researchers from NuGEN describe a novel method for targeted depletion of unwanted transcripts in RNA-Seq libraries. The proprietary Insert
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The Rise Of Superbugs: How Bacteria Defeat Antibiotics

News stations are constantly warning us about the threats of climate change, hackers, and another season of Fuller House , but what doesn'
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RNA sequencing of archived dried blood spots | RNA-Seq Blog

RNA sequencing of archived dried blood spots | RNA-Seq Blog | Tools and tips for scientific tinkers and tailors | Scoop.it
Neonatal dried blood spots (DBS) are routinely collected on standard Guthrie cards for all-comprising national newborn screening programs for inborn errors of
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The Myth of "Darwin's Body-Snatchers" - Neuroskeptic

The Myth of "Darwin's Body-Snatchers" - Neuroskeptic | Tools and tips for scientific tinkers and tailors | Scoop.it
Did Charles Darwin’s thirst for skulls contribute to the near-extinction of the Aboriginal Tasmanian people? If you believe certain creationists, Darwin sought examples of Tasmanian skulls in order to prove that this unfortunate race was a ‘missing link’ between humans and apes. However, according to John van Wyhe in a new paper called Darwin’s body-snatchers?, …
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Identifying stably expressed genes from multiple RNA-Seq data sets

Identifying stably expressed genes from multiple RNA-Seq data sets | Tools and tips for scientific tinkers and tailors | Scoop.it
We examined RNA-Seq data on 211 biological samples from 24 different Arabidopsis experiments carried out by different labs. We grouped the samples according to tissue types, and in each of the groups, we identified genes that are stably expressed across biological samples, treatment conditions, and experiments. We fit a Poisson log-linear mixed-effect model to the read counts for each gene and decomposed the total variance into between-sample, between-treatment and between-experiment variance components. Identifying stably expressed genes is useful for count normalization and differential expression analysis. The variance component analysis that we explore here is a first step towards understanding the sources and nature of the RNA-Seq count variation. When using a numerical measure to identify stably expressed genes, the outcome depends on multiple factors: the background sample set and the reference gene set used for count normalization, the technology used for measuring gene expression, and the specific numerical stability measure used. Since differential expression (DE) is measured by relative frequencies, we argue that DE is a relative concept. We advocate using an explicit reference gene set for count normalization to improve interpretability of DE results, and recommend using a common reference gene set when analyzing multiple RNA-Seq experiments to avoid potential inconsistent conclusions.
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RNA sequencing highlights problems with gene expression in clones | RNA-Seq Blog

It has been 20 years since Dolly the sheep was successfully cloned in Scotland, but cloning mammals remains a challenge. A new study by researchers from the U.S
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New Lyme Disease Vaccine Heads to Clinical Trial | History of Vaccines

New Lyme Disease Vaccine Heads to Clinical Trial | History of Vaccines | Tools and tips for scientific tinkers and tailors | Scoop.it
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Single-cell RNA-Seq charts a molecular map of the brain | RNA-Seq Blog

The human brain is made up of billions of cells. We do not know the identity or exact function of countless thousands of them since comprehensive efforts to
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Roche Abruptly Breaks Off PacBio Partnership

This morning was a solid block of meetings, but in a pause I checked my phone and saw the shocking headline: Roche Diagnostics had suddenl
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Making authentic science accessible—the benefits and challenges of integrating bioinformatics into a high-school science curriculum

Despite the central place held by bioinformatics in modern life sciences and related areas, it has only recently been integrated to a limited extent into high-school teaching and learning programs. Here we describe the assessment of a learning environment entitled ‘Bioinformatics in the Service of Biotechnology’.... Analysis of students’ affective outcomes revealed positive attitudes toward bioinformatics and the learning environment, as well as their perception of the teacher’s role. Insights from this analysis yielded implications and recommendations for curriculum design, classroom enactment, teacher education and research. For example, we recommend teaching bioinformatics in an integrative and comprehensive manner, through an inquiry process, and linking it to the wider science curriculum.


Via Cindy
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Is the long read sequencing war already over?

My enthusiasm for nanopore sequencing is well known; we have some awesome software for working with the data; we won a grant to support this work; and we successfully assembled a tricky bacterial g…
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10X Genomics updates

10X Genomics updates | Tools and tips for scientific tinkers and tailors | Scoop.it
We had a seminar form 10X Genomics today to present some of the most recent updates on their systems and chemistry. The new chemistry fo
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New Technology for Single Cell RNA-Seq | RNA-Seq Blog

New Technology for Single Cell RNA-Seq | RNA-Seq Blog | Tools and tips for scientific tinkers and tailors | Scoop.it
Dolomite Bio has launched a new Injection Valve and Sample Loop for single cell RNA sequencing workflows. This option enables straightforward, gentle
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A Necessary Retelling of the Smallpox Vaccine Story | PLOS Blogs Network

A Necessary Retelling of the Smallpox Vaccine Story | PLOS Blogs Network | Tools and tips for scientific tinkers and tailors | Scoop.it
Source: A Necessary Retelling of the Smallpox Vaccine Story A curious confluence of events unfolded Tuesday night. Just hours before President Obama uttered the powerful “science and reason matter” in his farewell address, Robert F. Kennedy Jr. announced that the incoming president had tapped him to head a committee on vaccine safety. RFK Jr. is not a pediatric immunologist nor an epidemiologist, but a vocal “vaccine skeptic.” Although the PEOTUS dialed back on the purported appointment shortly after social media erupted, a tweet from March 28, 2014 makes his analysis of the history and science of vaccines clear: Healthy young child goes to doctor, gets pumped with massive shot of many vaccines, doesnt feel good and changes – AUTISM. Many such cases! As a child I devoured books on the history of medicine. One of my favorite stories was how Edward Jenner developed the first vaccine, testing an approach that had been used for centuries. Knowing his story made me understand why my little
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Illumina’s announces new sequencers: NovaSeq Series

Illumina’s announces new sequencers: NovaSeq Series | Tools and tips for scientific tinkers and tailors | Scoop.it
Illumina announced new sequencers, NovaSeq 5000 and 6000, that could potentially reduces the cost of human genome sequencing to $100 in the future. The NovaSeq sequencing systems, which are built f…
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Evolutionary Clues in 17th-Century Smallpox Genome

Evolutionary Clues in 17th-Century Smallpox Genome | Tools and tips for scientific tinkers and tailors | Scoop.it
By Michelle Ziegler Smallpox is one of those diseases long believed to have an ancient pedigree, the suspected culprit of legendary epidemics. Yet, so far, smallpox hasn't made a big impression in ancient DNA surveys. If it was truly endemic throughout the Old World before 1492, so much so that it pops up in the…
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Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensivel
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Phylogeny of the elves illustrates why we need to sample elf DNA immediately

Phylogeny of the elves illustrates why we need to sample elf DNA immediately | Tools and tips for scientific tinkers and tailors | Scoop.it
Last year for Christmas Eve, Dominic Evangelista reconstructed the evolutionary history of elves and elf-like fantasy creatures in a tour-de-force of nerd crossover. Seriously, go read that piece i…
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I do not think it means what you think it means: “relic DNA” can obscure microbial diversity studies

I do not think it means what you think it means: “relic DNA” can obscure microbial diversity studies | Tools and tips for scientific tinkers and tailors | Scoop.it
Although microbes are small, they play an important part in both biogeochemical cycles in the ocean as well as on land. However, as they are not so easy to observe by eye, and in many cases can’t b…
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Vertical flow array chips reliably identify cell types from single-cell mRNA sequencing experiments | RNA-Seq Blog

Vertical flow array chips reliably identify cell types from single-cell mRNA sequencing experiments | RNA-Seq Blog | Tools and tips for scientific tinkers and tailors | Scoop.it
Hitachi, Ltd. (TSE: 6501) announced the development of a compact 1-mm square chip that can efficiently analyze small amounts of various genetic material,
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Summary and talks/slides from Workshop on the Microbiome of the International Space Station

Summary and talks/slides from Workshop on the Microbiome of the International Space Station | Tools and tips for scientific tinkers and tailors | Scoop.it
Just a quick post here that all the information (including slides and videos) from a really interesting CASIS sponsored workshop are online.  The topic relates to the most extreme built environment…
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Researchers use single-cell RNA-Seq to unlock genetic code of diseased lung cells | RNA-Seq Blog

Researchers use single-cell RNA-Seq to unlock genetic code of diseased lung cells | RNA-Seq Blog | Tools and tips for scientific tinkers and tailors | Scoop.it
A new study has determined the genetic codes of healthy and diseased human lung cells, a finding that may allow doctors to better diagnose and follow idiopathic
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“Mysterious” Non-protein-coding RNAs Play Important Roles In Gene Expression 

“Mysterious” Non-protein-coding RNAs Play Important Roles In Gene Expression  | Tools and tips for scientific tinkers and tailors | Scoop.it

In cells, DNA is transcribed into RNAs that provide the molecular recipe for cells to make proteins. Most of the genome is transcribed into RNA, but only a small proportion of RNAs are actually from the protein-coding regions of the genome.


Via Integrated DNA Technologies
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Single-cell barcoding and sequencing using droplet microfluidics | RNA-Seq Blog

Single-cell barcoding and sequencing using droplet microfluidics | RNA-Seq Blog | Tools and tips for scientific tinkers and tailors | Scoop.it
Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput
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Altruistic viruses

Altruistic viruses | Tools and tips for scientific tinkers and tailors | Scoop.it
A virophage called mavirus has been found to integrate into the genome of its host and behaves like an inducible antiviral defense system.
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