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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Implication of quality score for de novo transcriptome reconstruction of Illumina reads | RNA-Seq Blog

Implication of quality score for de novo transcriptome reconstruction of Illumina reads | RNA-Seq Blog | Bioinformatics Training | Scoop.it
Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly

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Bioinformatics Training
Bioinformatics, blended with education and health sciences subjects
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Scooped by Pedro Fernandes
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Measuring intra-species diversity using high-throughput sequencing

Measuring intra-species diversity using high-throughput sequencing | Bioinformatics Training | Scoop.it
This practical course aims to show evolutionary biologists and population geneticists the potentials and perils of using high throughput sequencing to estimate intra-species genetic diversity. Participants will have the opportunity to interact with experienced researchers that have successfully applied the technology in a wide variety of high impact studies, and learn from their successes as well as from their failures. Participants will not only listen to theoretical lectures, but will also practice some of the techniques used in those high impact studies. Participants are strongly encouraged to bring their own projects for discussion and experiment novel techniques with their data.
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Registration and abstract deadline:March 31st 2015 !

 

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Bio Databases 2015

Bio Databases 2015 | Bioinformatics Training | Scoop.it
Something interesting happened in 2014. The total number of databases that Nucleic Acids Research (NAR) tracks dropped by three databases! What happened?  Did people quit making databases?  No.

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Pedro Fernandes's insight:

"This year, the “dead” databases (links no longer valid) outnumber the new ones."

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker

Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker | Bioinformatics Training | Scoop.it
Overview We developed a freely available, easy to run implementation of bcbio-nextgen on Amazon Web Services (AWS) using Docker. bcbio is a community developed tool providing validated and scalable...

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Chimps And Gorillas Desperately Need Ebola Vaccine Too – Virus Has Wiped Out A Third Of Them | IFLScience

Chimps And Gorillas Desperately Need Ebola Vaccine Too – Virus Has Wiped Out A Third Of Them | IFLScience | Bioinformatics Training | Scoop.it
There is a side to the Ebola crisis that, perhaps understandably, has received little media attention: the threat it poses to our nearest cousins, the great apes of Africa.

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Cold coddles colds | Science News

Cold coddles colds | Science News | Bioinformatics Training | Scoop.it
Antiviral responses aren’t as effective against common cold viruses in cooler temperatures.

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Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker

Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker | Bioinformatics Training | Scoop.it
Overview We developed a freely available, easy to run implementation of bcbio-nextgen on Amazon Web Services (AWS) using Docker. bcbio is a community developed tool providing validated and scalable...
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Rescooped by Pedro Fernandes from Health and Biomedical Informatics
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Teaching Bioinformatics in Concert

Teaching Bioinformatics in Concert | Bioinformatics Training | Scoop.it
PLOS Collections: Article collections published by the Public Library of Science

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Welcome! — Practical bioinformatics needs survey 1.0 documentation


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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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bioinformatics - fastq-dump using mkfifo to stream data - Biology Stack Exchange

bioinformatics - fastq-dump using mkfifo to stream data - Biology Stack Exchange | Bioinformatics Training | Scoop.it
Biology SE: fastq-dump using mkfifo to stream data http://t.co/UfFVwpxLxH #bioinformatics

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis

MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis | Bioinformatics Training | Scoop.it
ALWAYS check your acronym against other popular bioinformatics software - case in point; we now have another MUSCLE http://t.co/I6Wk1NsfNv

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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METAINTER: meta-analysis of multiple regression models in genome-wide association studies

METAINTER: meta-analysis of multiple regression models in genome-wide association studies | Bioinformatics Training | Scoop.it
RT @genetics_blog: Meta-analysis of multiple regression models in GWAS http://t.co/63TFt8kQnP #bioinformatics

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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The Genome Factory: Minimum standards for bioinformatics command line tools

Minimum standards for bioinformatics command line tools
by @torstenseemann
via @kbradnam and @RoyChaudhuri
http://t.co/0ftRZHMIb4

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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EPGA: de novo assembly using the distributions of reads and insert size

EPGA: de novo assembly using the distributions of reads and insert size | Bioinformatics Training | Scoop.it
RT @SAGRudd: EPGA: de novo assembly using the distributions of reads and insert size http://t.co/OgsLvz71St

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Could Video Feedback Replace the Red Pen?

Could Video Feedback Replace the Red Pen? | Bioinformatics Training | Scoop.it
Stills from a video critique by Monash U.’s Michael Henderson.
Writing useful comments on students’ work can be a fine art.
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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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AtCAST3.0 Update – A web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles | RNA-Seq Blog

AtCAST3.0 Update – A web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles | RNA-Seq Blog | Bioinformatics Training | Scoop.it
In transcriptome experiments, the experimental conditions (e.g., mutants and/or treatments) cause transcriptional changes. Identifying experimental conditions

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Rescooped by Pedro Fernandes from Natural Products Chemistry Breaking News
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Bioinformatics: The Next Frontier of Metabolomics - Analytical Chemistry (ACS Publications)

Bioinformatics: The Next Frontier of Metabolomics - Analytical Chemistry (ACS Publications) | Bioinformatics Training | Scoop.it
Anal Chem. 2015 Jan 6;87(1):147-56. doi: 10.1021/ac5040693. Epub 2014 Nov 20.Bioinformatics: the next frontier of metabolomics.Johnson CH1, Ivanisevic J, Benton HP, Siuzdak G. 

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Building Bioinformatics Solutions: with Perl, R and MySQL

Building Bioinformatics Solutions: with Perl, R and MySQL Offer Price $128.25 ISBN:0199230196 Authors Conrad Bessant, Ian Shadforth, Darren Oakley List Price : $135.00 Availablity Usually ships in 24 hours Publisher : Oxford University Press, USA...

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Vaccines Work. Here Are the Facts.

Vaccines Work. Here Are the Facts. - The Nib - Medium
The risks, the misinformation, and the science behind history’s greatest life saver

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Compression of High Throughput Sequencing Data with Probabilistic de Bruijn Graph « Homolog.us – Bioinformatics

Compression of High Throughput Sequencing Data with Probabilistic de Bruijn Graph « Homolog.us – Bioinformatics | Bioinformatics Training | Scoop.it
@RayanChikhi mentioned in twitter about this new paper –
“A super-efficient de novo read compression algorithm (Leon) from @GuillaumeRizk et al.

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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The Sorghum Transcriptome Database | RNA-Seq Blog

The Sorghum Transcriptome Database | RNA-Seq Blog | Bioinformatics Training | Scoop.it
In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Identifying and correcting errors in draft genomes

Identifying and correcting errors in draft genomes | Bioinformatics Training | Scoop.it
Over the past decade we have seen an exponential increase in the number of sequenced, assembled, and annotated genomes. These these genomes are essential for pretty much any genomics research. If y...

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Genome alignment with graph data structures: a comparison « Homolog.us – Bioinformatics

Genome alignment with graph data structures: a comparison « Homolog.us – Bioinformatics | Bioinformatics Training | Scoop.it
Interesting mathematical paper
Background
Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences.

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations

A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations | Bioinformatics Training | Scoop.it
PLOS Genetics is an open-access

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration | Bioinformatics Training | Scoop.it
PLOS Computational Biology is an open-access

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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MTide – an integrated tool for the identification of miRNA-target interaction in plants | RNA-Seq Blog

MTide – an integrated tool for the identification of miRNA-target interaction in plants | RNA-Seq Blog | Bioinformatics Training | Scoop.it
Small RNA sequencing and degradome sequencing (also known as parallel analysis of RNA ends) have provided rich information on the microRNA (miRNA) and its

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