Bioinformatics
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Rescooped by Won Gi Yoo from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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MHCflurry: open-source class I MHC binding affinity prediction

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Via Chris Upton + helpers
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Genome Biology

Genome Biology | Bioinformatics | Scoop.it
Genome Biology covers all areas of biology and biomedicine studied from a genomic and post-genomic perspective. Content includes research, new methods and software tools, and reviews, opinions and commentaries. Areas covered include, but are not limited to: sequence analysis; bioinformatics; insights into molecular, cellular and organismal biology; functional genomics; epigenomics; population genomics; proteomics; comparative biology and evolution; systems and network biology; genomics of disease; and clinical genomics. All content is open access immediately on publication.
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The definition of top-performing algorithms is ontology specific
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Stemformatics - Dataset Search

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

Via Sandrine Palcy
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"Stemformatics is a collaboration between the stem cell and bioinformatics community."
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Sandrine Palcy's curator insight, April 15, 2016 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, 2016 10:51 AM
"Stemformatics is a collaboration between the stem cell and bioinformatics community."
Samuel Viana's curator insight, April 15, 2016 12:53 PM
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.
Rescooped by Won Gi Yoo from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Choosing the right test - Handbook of Biological Statistics


Via Chris Upton + helpers
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어느 정도 통계지식을 가진 상태에서 실험조건에 따라 통계알고리즘을 선택하는데 도움을 주는 표
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Molecular Machinery: A Tour of the Protein Data Bank

Molecular Machinery: A Tour of the Protein Data Bank | Bioinformatics | Scoop.it

Organizes known protein structures into functional categories with visual summary!


Via Kathleen McLeod
Won Gi Yoo's insight:

구조 기능별로 선택하면 해당결과를 애니메이션처럼 보여주는데, fancy하게 잘 만들었음

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Kathleen McLeod's curator insight, October 26, 2015 6:02 PM

Check it out, pretty cool.

Rescooped by Won Gi Yoo from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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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 …

Via Chris Upton + helpers
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나만 바보같은 느낌을 받는 것은 아니었구만 ㅋ

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PLOS Pathogens: Introducing “Research Matters”

PLOS Pathogens: Introducing “Research Matters” | Bioinformatics | Scoop.it

In this issue of PLOS Pathogens, we are introducing a new front matter series to allow individual scientists from the many fields that encompass our community of editors, authors, and readers to comment on why the fundamental research in their labs, and that of their collaborators, matters. The genesis of this idea comes from the apparent gulf between working scientists and the general public that seems to be growing ever wider. In particular, there seems to be an expanding gap between what basic researchers and scientists try to accomplish in terms of scientific advancement, and what nonscientists, such as the lay public and the political world, perceive to be accomplished. This diminishes the deliverables expected as a result of funding basic research, the overall value of science to society, and the rational control of scientific funding. We seek this new Research Matters format for individual scientists to “say” in public how diverse fundamental research into pathogens assures real and compelling impact on public health, human knowledge, and life. Our goal is to evolve a forum for active scientists to speak directly, without filters or publicity agents, about why basic research in their field matters. Over time, we hope to develop a collective voice for our community while still preserving the authentic nature of the individual perspective.

 

 


Via Ed Rybicki
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Rescooped by Won Gi Yoo from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Detection of significant protein coevolution

Motivation: The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals.


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VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data | Bioinformatics | Scoop.it

VirHostNet release 2.0 (http://virhostnet.prabi.fr) is a knowledgebase dedicated to the network-based exploration of virus–host protein–protein interactions. Since the previous VirhostNet release (2009), a second run of manual curation was performed to annotate the new torrent of high-throughput protein–protein interactions data from the literature. This resource is shared publicly, in PSI-MI TAB 2.5 format, using a PSICQUIC web service. The new interface of VirHostNet 2.0 is based on Cytoscape web library and provides a user-friendly access to the most complete and accurate resource of virus–virus and virus–host protein–protein interactions as well as their projection onto their corresponding host cell protein interaction networks. We hope that the VirHostNet 2.0 system will facilitate systems biology and gene-centered analysis of infectious diseases and will help to identify new molecular targets for antiviral drugs design. This resource will also continue to help worldwide scientists to improve our knowledge on molecular mechanisms involved in the antiviral response mediated by the cell and in the viral strategies selected by viruses to hijack the host immune system.


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DrawTree-NDVP 1.0 – Phylogenetics software based on Normalized Descriptor Vector of Protein Sequence

DrawTree-NDVP 1.0 – Phylogenetics software based on Normalized Descriptor Vector of Protein Sequence | Bioinformatics | Scoop.it
DrawTree-NDVP 1.0
:: DESCRIPTION

DrawTree-NDVP (Draw Polytree) is a phylogenetics software based on normalized descriptor vector of proteins.

Via Mel Melendrez-Vallard
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SuRFing the genomics wave: an R package for prioritizing SNPs by functionality

Identifying functional non-coding variants is one of the greatest unmet challenges in genetics.

Via Mel Melendrez-Vallard
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Viruses | Free Full-Text | Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing

Viruses | Free Full-Text | Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing | Bioinformatics | Scoop.it
The complete genome of human cytomegalovirus (HCMV) was elucidated almost 25 years ago using a traditional cloning and Sanger sequencing approach. Analysis of the genetic content of additional laboratory and clinical isolates has lead to a better, albeit still incomplete, definition of the coding potential and diversity of wild-type HCMV strains. The introduction of a new generation of massively parallel sequencing technologies, collectively called next-generation sequencing, has profoundly increased the throughput and resolution of the genomics field. These increased possibilities are already leading to a better understanding of the circulating diversity of HCMV clinical isolates. The higher resolution of next-generation sequencing provides new opportunities in the study of intrahost viral population structures. Furthermore, deep sequencing enables novel diagnostic applications for sensitive drug resistance mutation detection. RNA-seq applications have changed the picture of the HCMV transcriptome, which resulted in proof of a vast amount of splicing events and alternative transcripts. This review discusses the application of next-generation sequencing technologies, which has provided a clearer picture of the intricate nature of the HCMV genome. The continuing development and application of novel sequencing technologies will further augment our understanding of this ubiquitous, but elusive, herpesvirus.

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The Human Virome 

The Human Virome  | Bioinformatics | Scoop.it
Some of our resident viruses may be beneficial.

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Ed Rybicki's curator insight, November 1, 2016 11:23 AM
EXCELLENT article.
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The 7 biggest problems facing science, according to 270 scientists

The 7 biggest problems facing science, according to 270 scientists | Bioinformatics | Scoop.it
These are dark times for science so we asked hundreds of researchers how to fix it.

Via Niklaus Grunwald
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An Introduction to Programming for Bioscientists: A Python-Based Primer

Contemporary biology has largely become computational biology, whether it involves applying physical principles to simulate the motion of each atom in a piece of DNA, or using machine learning algorithms to integrate and mine “omics” data across whole cells (or even entire ecosystems). The ability to design algorithms and program computers, even at a novice level, may be the most indispensable skill that a modern researcher can cultivate. As with human languages, computational fluency is developed actively, not passively. This self-contained text, structured as a hybrid primer/tutorial, introduces any biologist—from college freshman to established senior scientist—to basic computing principles (control-flow, recursion, regular expressions, etc.) and the practicalities of programming and software design. We use the Python language because it now pervades virtually every domain of the biosciences, from sequence-based bioinformatics and molecular evolution to phylogenomics, systems biology, structural biology, and beyond. To introduce both coding (in general) and Python (in particular), we guide the reader via concrete examples and exercises. We also supply, as Supplemental Chapters, a few thousand lines of heavily-annotated, freely distributed source code for personal study.

Via Cindy
Won Gi Yoo's insight:
내용은 둘째치고 논문이 43장짜리..;;;
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Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria. - PubMed - NCBI

Sci Rep. 2015 Dec 2;5:17450. doi: 10.1038/srep17450.

Via Alexander Tyakht
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담석증 환자의 담즙내 메타게놈 분석: 미생물들은 환자-특이적이며, 환자의 담즙은 미생물다양성을 저해.

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Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling | Bioinformatics | Scoop.it
Author Summary Since a protein’s function is largely determined by its structure, predicting a protein’s structure from its amino acid sequence can be very useful to understand its molecular functions and its role in biological pathways. By far the most widely used computational approach for protein structure prediction relies on detecting a homologous relationship with a protein of known structure and using this protein as a template to model the structure of the query protein on it. The bas

Via Chris Upton + helpers
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간단하게 테스트해본 결과, I-TASSER, easyModeller, swiss-model 등보다 훨씬 좋은 3D 구조를 얻을 수 있었다. 약간의 refinement만 하면 개선된 최종 구조 확보가 가능할 듯. 1600aa 서열분석도 가능한지 테스트중.

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How is software development like scientific research?

How is software development like scientific research? | Bioinformatics | Scoop.it
Imagine you have a research question to answer. How do you go about it? You come up with a hypothesis, set your parameters and define your research group. You collect and analyse the data.

Via Mel Melendrez-Vallard
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Rescooped by Won Gi Yoo from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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EpiToolKit—a web-based workbench for vaccine design

EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets.

 


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Promoting an open research culture


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Five ingredients to become a bioinformatician. - atcgeek

Five ingredients to become a bioinformatician. - atcgeek | Bioinformatics | Scoop.it
“ How to become a bioinformatician? Many people, at different career stages, are trying to answer this question, looking for the best path to achieve the required knowledge to become a bioinformatician. Many academic institutions are provided with Bionformatics degrees at undergraduate and postgraduate level, and you can easily find free courses on the internet to get a […”
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Rescooped by Won Gi Yoo from Tools and tips for scientific tinkers and tailors
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Virus entry at a glance

Virus entry at a glance | Bioinformatics | Scoop.it
I'm not normally very keen on infographics - but I like this one:

Source: Yamauchi, Y., and Helenius, A. (2013) Virus entry at a glance. Journal of Cell Science, 126(6): 1289-1295.

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Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges

Computational methods for detecting copy number variations in cancer genome using next generation sequencing http://t.co/CloFfZGyaf

Via Mel Melendrez-Vallard
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