Bioinformática
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Random DNA + high-tech math = ‘universal microbial diagnostic’

Random DNA + high-tech math = ‘universal microbial diagnostic’ | Bioinformática | Scoop.it

Rice University researchers find way to ID many pathogens with few DNA probes 


Via Integrated DNA Technologies
Samuel Viana's insight:
Cientistas da Universidade de Rice desenvolvem método para acelerar a identificação de bactérias potencialmente perigosas.
Com base em pequenho trechos de DNA e métodos informáticos cientistas desenvolveram formas de reduzir o tempo de idenitificar bactérias potencialmente perigosas.
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Metagenomics pathogen detection tool could change how infectious diseases are diagnosed

Metagenomics pathogen detection tool could change how infectious diseases are diagnosed | Bioinformática | Scoop.it
Scientists at the University of Utah, ARUP Laboratories, and IDbyDNA, Inc., have developed ultra-fast, meta-genomics analysis software called Taxonomer that dramatically improves the accuracy and speed of pathogen detection
Samuel Viana's insight:
O sonho tornado possível graças à metagenómica: determinar computacionalmente o agente infeccioso de uma doença, tudo graças a uma aplicação chamada Taxonomer desenvolvida por cientistas da Universidade de Utah em parceria com laboratórios privados.
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PHD Comics: Microbiomes Explained

PHD Comics: Microbiomes Explained | Bioinformática | Scoop.it
Link to Piled Higher and Deeper
Samuel Viana's insight:
À nossa volta, existem minúsculos organismos com um potencial que ainda mal começámos a entender....
um poderão fazer a diferença entre colonizar um planeta ou talvez mesmo salvar vidas...!
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Stemformatics - Dataset Search

Stemformatics - Dataset Search | Bioinformática | Scoop.it
Datasets from 294 public studies with 4774 human and 1616 mouse samples

Via Sandrine Palcy
Samuel Viana's insight:
As células tronco (em inglês, "stem cells") são muito importantes em biologia do desenvolvimento e na medicina restituitiva uma vez que são capazes de se diferenciar em qualquer tipo de célula no organismo. Num futuro não muito distante, seria possível produzir qualquer tipo de órgão em laboratório o que evitaria o eterno problema de encontrar um dador compatível aquando dos transplantes.
Este portal pretende ser uma porta de entrada para muitos estudos na área, integrando diversas bases de dados provenientes de estudos em feitos em humanos e ratos.
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Sandrine Palcy's curator insight, April 15, 10:48 AM
"Stemformatics is not a substitute for good collaboration between bioinformaticians and stem cell biologists. We think of it as a stepping stone towards that collaboration."
Sandrine Palcy's curator insight, April 15, 10:51 AM
"Stemformatics is a collaboration between the stem cell and bioinformatics community."
Won Gi Yoo's curator insight, August 31, 5:40 AM
"Stemformatics is a collaboration between the stem cell and bioinformatics community."
Rescooped by Samuel Viana from DNA and RNA Research
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Scientists document rare DNA transfer between animals and plants

Scientists document rare DNA transfer between animals and plants | Bioinformática | Scoop.it

Very few cases of natural DNA transfers between animals and plants are documented, according to a Texas A&M AgriLife Research scientist, but recently his team did just that.


Via Integrated DNA Technologies
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Análise da composição bacteriana de amostra de corpos em decomposição permite determinar o momento exacto da morte.

Análise da composição bacteriana de amostra de corpos em decomposição permite determinar o momento exacto da morte. | Bioinformática | Scoop.it
Measuring the microbes that feed on the dead can determine the time of death when maggots and flies fail, Viviane Richter discovers. (Cosmos) - The number of
Samuel Viana's insight:

Através da análise do gene 16S em cadáveres com diferentes estágios de decomposição foi possível estabelecer uma relação entre a composição microbiana e o número de dias desde a morte.

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A Illumina anuncia o seu novo sequenciador - MiniSeq

A Illumina anuncia o seu novo sequenciador - MiniSeq | Bioinformática | Scoop.it
he new system will be superior to competing semiconductor-based sequencing systems with a raw error rate of less than one percent, data quality comparable to that of a HiSeq XTM Sequencing System. With output of approximately 1.2G per run, the platform will be ideal for numerous markets including academic research, oncology, infectious disease, inherited disease, and reproductive health.
Samuel Viana's insight:

A Illumina, líder mundial dos equipamentos de sequenciação lançou o seu novo sequenciador, ao preço mais acessível até agora: cinquenta mil euros.
Destinado a laboratórios de média dimensão como análises clínicas: continuamos no caminho para a sequenciação individual e a medicina personalizada - a Illumina está aí para tornar realidade esse objectivo.
É desta vez que iremos ter um sequnciador mais perto de todos nós ?

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Bacterias de la antártida ayudarían a tratar el cáncer

Bacterias de la antártida ayudarían a tratar el cáncer | Bioinformática | Scoop.it
Bajo las condiciones extremas de los glaciares de la Antártida habitan unas bacterias capaces de sintetizar en su interior nanopartículas fluorescentes que podrían ser utilizadas para marcar células tumorales y rastrear la metástasis de diferentes tipos de cáncer.
Samuel Viana's insight:

Investigadores chilenos encontraram bactérias na Antárctida capazes de produzir pigmentos para identificar células cancerosas.

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Microbial Changes of Decomposition

Microbial Changes of Decomposition | Bioinformática | Scoop.it
The changes that occur to the microbiome upon death may someday be harnessed as a forensic tool.
Samuel Viana's insight:

A análise metagenómica de um cadáver pode ser usada para ter uma ideia do tempo de morte em função da variação das comunidades microbianas ao longo do tempo.

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Not Even Scientists Can Easily Explain P-values

P-values have taken quite a beating lately. These widely used and commonly misapplied statistics have been blamed for giving a veneer of legitimacy to dodgy study results, encouraging bad research …
Samuel Viana's insight:

What Is a P-Value ? How to translate intuitively this concept !? Not even the scientists agree in that...

 

 

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BMC Bioinformatics | Abstract | An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling — quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive.
Samuel Viana's insight:

Num trabalho liderado por um português, este estudo permite determinar até que ponto as actuais pipelines de análise e assemblagem pós-sequenciação pode gerar falsos  SNPs.

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The Cabbages of Doom: Bioinformatics is just like bench science and should be treated as such

The Cabbages of Doom: Bioinformatics is just like bench science and should be treated as such | Bioinformática | Scoop.it

A bad workman blames his tools. A bad life scientist blames bioinformatics. OK, so that’s a little unfair but so is the level of criticism levelled at bioinformatics by people who should know better. If you are a bioinformatician, it is inevitable that you will run up against the question of whether you ever do “real” science.

 

Samuel Viana's insight:

An opinion in which the wet-lab biologists should collaborate with their 'dry-lab' colleagues just like the bioinformaticians.

 

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Ninguém faz realmente ideia da quantidade de micróbios que vivem no chuveiro em nossas casas !!!!

Ninguém faz realmente ideia da quantidade de micróbios que vivem no chuveiro em nossas casas !!!! | Bioinformática | Scoop.it
People across the US are sending in samples from their showers, for science.
Samuel Viana's insight:
Ninguém faz realmente ideia da quantidade de micróbios que vivem no chuveiro em nossas casas !!!!
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Rescooped by Samuel Viana from Python Resources for Bioinformatics
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Virus trading cards

Virus trading cards | Bioinformática | Scoop.it
Deadly but beautiful - The trading cards you probably don’t want to collect.


 

Via burkesquires
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Rescooped by Samuel Viana from DNA and RNA Research
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Bird genome contains 'fossils' of parasites

Bird genome contains 'fossils' of parasites | Bioinformática | Scoop.it

In rare instances, DNA is known to have jumped from one species to another. If a parasite’s DNA jumps to its host’s genome, it could leave evidence of that parasitic interaction that could be found millions of years later – a DNA ‘fossil’ of sorts. An international research team led from Uppsala University has discovered a new type of so-called transposable element that occurred in the genomes of certain birds and nematodes.


Via Integrated DNA Technologies
Samuel Viana's insight:
Trechos de DNA chamados transposões saltaram do DNA de nemátodes como a lombriga para os seus hospedeiros na altura.
Encontram-se certos transposões provenientes de nemátodes no genoma de mamíferos mas essa "infecção" apenas se deu mais recentemente. O que parece provar que os nemátodes apenas foram capazes de parasitar mamíferos mais recentemente do que as aves.
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Scientists Unveil New ‘Tree of Life’

Scientists Unveil New ‘Tree of Life’ | Bioinformática | Scoop.it

Most of the diversity outlined on the new tree has been hiding in plain sight.


Via Integrated DNA Technologies
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Ainda haverá novas bactérias por descobrir ?

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Samuel Viana's insight:

Continuam a serem inventariadas novas espécies de procariotas. Este artigo faz uma revisão do ponto actual de "recenseamento" actual e avança com previsões relativamente à possibilidade de ainda serem encontradas novas espécies.

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A automação chegou aos laboratórios de biotecnologia...

Advancing Biology with an Open-Source Robot - re:form - Medium

A little startup’s big ambitions to improve lab automation and revolutionize life sciences research


Via Integrated DNA Technologies
Samuel Viana's insight:

Um projecto que está recebendo fundos no Kickstartet prometer revolucionar o trabalho de laboratório. Em vez de confiar nos humanos para transferir pequenos quantidades que requerem extrema precisão usando micropipetas, esse trabalho pode ser confiado a um braço robótico baseado em tecnologias de código aberto. Digamos que é uma espécie de 'Bimby' que em vez de servir para cozinhas serve para laboratórios.

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Samuel Viana's comment, January 15, 9:38 AM
This some kind of a 'Bimby' for the wet lab !? Sorry for kidding with the serious stuff, but this my spontaneous reaction...
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Imunoinformática - prever a reacção das células T na possibilidade de fabricar novas vacinas

Imunoinformática - prever a reacção das células T na possibilidade de fabricar novas vacinas | Bioinformática | Scoop.it
Samuel Viana's insight:

O investigador dinamarquês Peter Nielsen encontra-se na senda de predizer a resposta imune dos glóbulos brancos através da predição das proteínas que compõem o vírus.

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Rescooped by Samuel Viana from Viruses and Bioinformatics from Virology.uvic.ca
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SRA Toolkit: the SRA database at your fingertips

SRA Toolkit: the SRA database at your fingertips | Bioinformática | Scoop.it
The Sequence Read Archive (SRA), NCBI’s largest growing repository of molecular data, archives raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS Systems®, Illumina’s Genome Analyzer®, and Complete Genomics® systems.

Researchers commonly use SRA data to make discoveries via comparison of data sets. Data sets can be compared through the SRA web interface, but if you want to integrate these downloads and file conversions into an already existing pipeline, or you simply prefer using a command-line interface, we recommend using the SRA Toolkit.

Via Cindy
Samuel Viana's insight:

O SRA é um formato usado para partilhar data sets. Permite a compressão do dataset de forma a poder ser facilmente partilhado rapidamente.

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Humans may harbor more than 100 genes from other organisms

Humans may harbor more than 100 genes from other organisms | Bioinformática | Scoop.it

You’re not completely human, at least when it comes to the genetic material inside your cells. You—and everyone else—may harbor as many as 145 genes that have jumped from bacteria, other single-celled organisms, and viruses and made themselves at home in the human genome. That’s the conclusion of a new study, which provides some of the broadest evidence yet that, throughout evolutionary history, genes from other branches of life have become part of animal cells.


“This means that the tree of life isn’t the stereotypical tree with perfectly branching lineages,” says biologist Alastair Crisp of the University of Cambridge in the United Kingdom, an author of the new paper. “In reality, it’s more like one of those Amazonian strangler figs where the roots are all tangled and crossing back across each other.”


Scientists knew that horizontal gene transfer—the movement of genetic information between organisms other than parent-to-offspring inheritance—is commonplace in bacteria and simple eukaryotes. The process lets the organisms quickly share an antibiotic-resistance set of genes to adapt to an antibiotic, for instance. But whether genes have been horizontally transferred into higher organisms—like primates—has been disputed. Like in bacteria, it’s been proposed that animal cells could integrate foreign genetic material that’s introduced as small fragments of DNA or carried into cells by viruses. But proving that a bit of DNA in the human genome originally came from another organism is tricky.


Crisp and his colleagues analyzed the genome sequences of 40 different animal species, ranging from fruit flies and roundworms to zebrafish, gorillas, and humans. For each gene in the genomes, the scientists searched existing databases to find close matches—both among other animals and among nonanimals, including plants, fungi, bacteria, and viruses. When an animal’s gene more closely matched a gene from a nonanimal than any other animals, the researchers took a closer look, using computational methods to determine whether the initial database search had missed something.


In all, the researchers pinpointed hundreds of genes that appeared to have been transferred from bacteria, archaea, fungi, other microorganisms, and plants to animals, they report online today in Genome Biology. In the case of humans, they found 145 genes that seemed to have jumped from simpler organisms, including 17 that had been reported in the past as possible horizontal gene transfers.

“I think what this shows it that horizontal gene transfer is not just confined to microorganisms but has played a role in the evolution of many animals,” Crisp says, “perhaps even all animals.


The paper doesn’t give any hints as to how the genes—which now play established roles in metabolism, immune responses, and basic biochemistry—may have been transferred or the exact timeline of the jumps, he says. That will take more work.


Via Dr. Stefan Gruenwald
Samuel Viana's insight:

Cientistas encontraram no nosso próprio genoma  genes que aparentam provir de origens completamente díspares: desde vírus ou fungos.

 

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Microsoft lança ferramenta de encriptação para dados bioinformáticos

Microsoft lança ferramenta de encriptação para dados bioinformáticos | Bioinformática | Scoop.it
Allows researchers to work on data securely.
Samuel Viana's insight:

A Microsoft está às necessidades futura de privacidade nos acessos aos dados bioinformáticos. Cada vez vão existir laboratórios, hospitais que vão trabalhar com dados obtidos de sequenciação e é necessário protegê-los como quaisquer outros dados clínicos.

 

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The five habits of bad bioinformaticians

The five habits of bad bioinformaticians | Bioinformática | Scoop.it
When ever I see bad bioinformatics, a little bit of me dies inside, because I know there is ultimately no reason for it to have happened.  As a community, bioinformaticians are wonderfully open, co...
Samuel Viana's insight:

Cinco maus hábitos que os bioinformáticos reincidem...

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Next-generation genetic sequencing found right diagnosis for Australian 'Mystery Boy'

Next-generation genetic sequencing found right diagnosis for Australian 'Mystery Boy' | Bioinformática | Scoop.it
Mystery Boy Brandon Keesing was incorrectly diagnosed with a degenerative muscular disease until revolutionary genetic sequencing gave him life-changing news.

 

Originally thought that Keesing has a mitochondrial disease, doctors had been wrong all along. Revolutionary advances in genetic sequencing proved he did not have mitochondrial disease at all. "In recent years the capacity to read the genetic code of every single gene — all 20,000 of them in the human body — has reached a point where it is now efficient, accurate, cost-effective to be able to do this," he says.

 

The new technique is called "next generation sequencing" — and where previously it took weeks or months to analyse the code of a single gene, today laboratory computers can decode all 20,000 genes in one go.

 

Almost immediately Westmead Children's Hospital researchers could pinpoint which one of Brandon's genes had a mutation. Professor Christodoulou illustrates how the technique works on a chart. "So here in the unaffected individual we have an 'A'. Here in the affected individual we have a 'G'. And that's precisely where the mistake is," he says.

 

Doctors using next generation sequencing discovered in fact that Brandon had congenital myasthenia — a different genetic disease which also affects the muscles. But although incurable, it is not usually fatal and can be treated with medication.

 

"The name of the gene that we found the mistakes in is called COLQ, and it has a completely different role," Professor Christodoulou says. "It has nothing to do with mitochondrial energy production. "What it is involved in is co-ordinating the communication of nerve cells with the muscle, so that the muscle, when it receives an impulse from a nerve cell, it contracts and relaxes appropriately.

 

"So the problem with the COLQ mistakes is that this process couldn't be co-ordinated properly. And that's what actually led to his progressive problems."

 

Finding that one gene in 20,000 has transformed Brandon's life. A simple drug quickly restored some of his muscle strength. As quickly as he had deteriorated as a toddler, he suddenly began making huge strides.

"We noticed it straight away. By the end of that week he got up off that bed and he walked," she says, wiping away tears. "That was unreal. I'll never forget that day. I was so happy for him and ... I just knew from that he was going to grow, he was going to enjoy his life that much more than what he had before. And he has."

 

Professor Christodoulou says it was a very gratifying outcome for doctors.


Via Dr. Stefan Gruenwald
Samuel Viana's insight:

Quem diria, com a redução de preço das novas tecnologias de sequenciação foi possível diagnosticar correctamente a doença desta rapaz ?

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