Tools and tips for scientific tinkers and tailors
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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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Characterization of progressive HIV-associated tuberculosis using 2-deoxy-2-[18F]fluoro-D-glucose positron emission and computed tomography

Nature Medicine | doi:10.1038/nm.4161
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Respect the old but seek out the new: Direct 16S rRNA-seq from bacterial communities

Respect the old but seek out the new: Direct 16S rRNA-seq from bacterial communities | Tools and tips for scientific tinkers and tailors | Scoop.it
I think it’s fair to say that it’s an ongoing struggle to figure out what the heck microbes are doing in their natural environments, and who those microbes are. Clearly, there is no silver bullet t…
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The Genesis Project: New life on exoplanets

The Genesis Project: New life on exoplanets | Tools and tips for scientific tinkers and tailors | Scoop.it
Can life be brought to celestial bodies outside our solar system, which are not permanently inhabitable? A new essay that has been published is trying to deal with this question. Over the last several years, the search for exoplanets has shown that very different types exist leading to new questions and a variety of possible answers.…
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TWiV 405: All the world’s a phage

Vertical transmission of Zika virus by Aedes mosquitoes, and uncovering Earth’s virome by mining existing metagenomic sequence data.
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TWiV 401: Vector victorious

Zika virus spreads in the USA, a Zika virus DNA vaccine goes into phase I trials, and how mosquito bites enhance virus replication and disease.
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An open RNA-Seq data analysis pipeline/tutorial with an example of reprocessing data from a recent Zika virus study | RNA-Seq Blog

RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non
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RACE-Seq – extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing | RNA-Seq Blog

RACE-Seq – extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing | RNA-Seq Blog | Tools and tips for scientific tinkers and tailors | Scoop.it
Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a
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Intestinal flora effects drug response

Intestinal flora effects drug response | Tools and tips for scientific tinkers and tailors | Scoop.it
Intestinal flora has multiple influences on human health, but researchers have revealed that it is also likely to have an effect on the body's response to drugs. Recent research suggests that changes in the intestinal flora, caused by antibacterial and antibiotic drugs or individual differences between people, may have an effect on a person's response…
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Developments in the Polio Vaccine Field: Using cold adaptation to produce safe inactivated vaccine candidates | PLOS Blogs Network

Source: Developments in the Polio Vaccine Field: Using cold adaptation to produce safe inactivated vaccine candidates Poliomyelitis, or polio, is a debilitating childhood disease caused by poliovirus. It has been eliminated from most parts of the world thanks to the extensive use of polio vaccines. However, there are concerns that current vaccines could lead to the reemergence of poliovirus in a polio-free world. It is important to safeguard this eradication by developing safer and more effective strains of polio for use in future vaccine preparations. Earlier this year, PLOS Pathogens published a study in which the authors used cold-adapted virus attenuation (CAVA) to develop temperature-sensitive poliovirus strains, which can be used to produce the next generation of vaccines. While CAVA has been used for other vaccines, it has not been used as a successful tool for poliovirus to date. Why we need new polio vaccine options The poliovirus has been mostly eliminated due to the efforts
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The trouble with PCR duplicates

The trouble with PCR duplicates | Tools and tips for scientific tinkers and tailors | Scoop.it
The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your …
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Single-Cell RNA-Seq Reveals How Zika Virus Causes Fetal Brain Damage | RNA-Seq Blog

Single-Cell RNA-Seq Reveals How Zika Virus Causes Fetal Brain Damage | RNA-Seq Blog | Tools and tips for scientific tinkers and tailors | Scoop.it
Marco Onorati et al. describe the derivation and characterization, including single-cell RNA-seq, of neocortical and spinal cord neuroepithelial stem (NES)
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Introducing Seeq – The Seeq Blog – Medium

Introducing Seeq – The Seeq Blog – Medium | Tools and tips for scientific tinkers and tailors | Scoop.it
tl;dr: We want to make genomics inexpensive, interactive, and fun; get the app at seeq.io.
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Updated phylogeography

Updated phylogeography | Tools and tips for scientific tinkers and tailors | Scoop.it
So, summer has come and gone, and it's time for an updated whole genome molecular clock tree.

Compare this with the "Pre-Zibra phylogeographic summary" posted on Virological in May. The number of new sequences since t…
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Cannibalism, Kuru, and Mad Cows: Prion Disease As a “Choose-Your-Own-Experiment” Case Study to Simulate Scientific Inquiry in Large Lectures

This piece from our Education series uses prion disease as the basis for an active-learning case study that simulates scientific inquiry with a choose-your-own-experiment design. Applicable to courses of any size and subdiscipline of biology.
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Avian Flu Diary: BioRxIv: Zika Virus Replication In Culex Quinquefasciatus In Brazil

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'Adopting' a Pathogen

by Amy Vollmer | Teaching microbiology is a terrific opportunity not just to introduce students to the world of microbes but also to help them to become critical thinkers and life-long learners. The challenges for us teachers are numerous: textbooks are getting thicker, yet the length of the semester is not increasing. How do we balance a sense of history with current discoveries?
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Illumina and FlowJo Partner to Develop and Co-Market a Software Solution for Single Cell Genomics | RNA-Seq Blog

Software for analysis and reporting of single cell data will advance research into cell function, disease progression, and therapeutic response Illumina, Inc
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Avian Flu Diary: ECDC: Epidemiological Update On The Zika Virus & Complications Linked To Infection

Avian Flu Diary: ECDC: Epidemiological Update On The Zika Virus & Complications Linked To Infection | Tools and tips for scientific tinkers and tailors | Scoop.it
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Wait, let me google it. On the fall (and rise?) of human memory.

Wait, let me google it. On the fall (and rise?) of human memory. | Tools and tips for scientific tinkers and tailors | Scoop.it
Ruins of a memory palace Once upon a time, there were no computers. And yet, even in the ancient days when writing was not widespread, people told gigantic tales or recited poems of epic proportion…
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Polio Returns to Nigeria for the First Time in Years

A global eradication campaign hoped to declare Africa polio-free in 2017. Now it will have to vaccinate millions of kids.
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Of microbes and men: Testing the neutral theory with the human microbiome

Of microbes and men: Testing the neutral theory with the human microbiome | Tools and tips for scientific tinkers and tailors | Scoop.it
There is no doubt that one of the hottest current topics in microbiology revolves around the human microbiome. There have been a suite of recent studies we’ve highlighted, on organisms rangin…
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TWiV 403: It’s not easy being vaccine

Experimental plant based poliovirus vaccine, contradictory findings on Flumist, waning efficacy of Zostavax, and a new adjuvanted subunit zoster vaccine.
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Animal viruses with separately packaged RNA segments

Animal viruses with separately packaged RNA segments | Tools and tips for scientific tinkers and tailors | Scoop.it
Multicomponent viruses are commonly found to infect plants and fungi, but only recently have examples of such viruses that infect animals been discovered.
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Researchers report new Zika complication

Researchers report new Zika complication | Tools and tips for scientific tinkers and tailors | Scoop.it
If zika didn't seem scary enough in the media, there is new data showing that there could be a new neurological complication of infection with the Zika virus. "Zika virus infection has become a new emergent neuropathological agent with several neurological complications," notes  Dr. John England. "Outbreaks of Guillain-Barré Syndrome (GBS) associated with Zika virus infections…
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