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edX | HarvardX: Data Analysis for Genomics: PH525x About Video

Data Analysis for Genomics Data Analysis for Genomics will teach students how to harness the wealth of genomics data arising from new technologies, such as m...
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Classes start on April 7th.

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Bioinformatics Training
Bioinformatics, blended with education and health sciences subjects
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GTPB: PHSMCP15 Promoter hunting and systems modelling of cellular pathways - Home

GTPB: PHSMCP15 Promoter hunting and systems modelling of cellular pathways - Home | Bioinformatics Training | Scoop.it
Overview

This course starts by reviewing basic principles of gene regulation and how information is encoded in the huge part of genome - it's so called "non-coding" part. Bioinformatics plays a huge role in exploring how gene regulation works. We will introduce mathematical modelling of cellular pathways and address the interplay between feedback and feed-forward loops of regulation. We will see how a range of modelling techniques can help us to:

- find master regulators
- understand disease mechanisms
- build models for use in precision medicine
- design novel systems for biotechnology

Starting from techniques for the computational prediction of promoters and distant enhancers, we will deal with the analysis of the structure of regulatory regions by identifying binding sites for transcription factors. A complete annotation of a newly sequenced genome has to address the identification of these regions in addition to the classical task of finding genes in terms of coding regions. Regulatory regions determine where, under which conditions and when genes become active. Thus, they are a fundamental part of the definition of the function of a gene. We will have a chance to introduce and acquire *hands-on* practice in next generation sequencing (NGS) techniques for genome-wide epigenetic analyses such as ChIP-seq.

Then we will approach the analysis and modelling of biological systems from several practical angles. Systems biology and modelling are approched here from the interaction and network-based perspectives. We will introduce several pathway databases, such as Reactome, KEGG, TRANSPATH, TRANSFAC, ConsensusPathDB and use these information resources to perform pathway analysis. Next, we will use modelling of biological systems to look at different mathematical modelling strategies, such as Boolean networks and ordinary differential equation systems (ODEs). We will describe computational tools, like Cytoscape and CellDesigner, for the set-up and development of model prototypes and show further tools, such as Copasi, BioUML and PyBioS that can be used for parameter-fitting and sensitivity analysis.

We will follow-on by looking at methods for reconstructing gene regulatory networks from gene expression data. The application of such methods can reveal key nodes in networks as potential biomarkers or drug targets. Dynamic systems modelling will be used to check the consistency of target and biomarker predictions. We will show real examples of application of these methods for identification of disease related biomarkers, drug discovery and personalized medicine.

Special attention will be given to the application of the above mentioned methods in designing novel biological systems, in the growing field of Synthetic Biology.

Methods

Participants will learn about several techniques of finding promoters and enhancers and the principles on which these methods are based on. In the hands-on exercises, several analytical tools will be introduced and the results critically evaluated to assess their reliability. The course sessions will consist of lectures that lay out the conceptual framework as needed, and hands-on exercises, which will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degree of independence. Participants will learn how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how their quality can be assessed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomic and transcriptomic studies.

The course will provide sufficient skills for the participants to address problems using open source software and freely accessible data resources. It will also be a chance to use commercially licensed resources such as TRANSFAC or the geneXplain integrated analytic platform for specific purposes.

Pedro Fernandes's insight:

Learn how to find promoters in NGS data an how to use genes and promoters to produce inferences at the pathway and system levels.

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NIH-Led Effort – Including ISB – Launches Big Data Portal for Alzheimer’s Drug Discovery

NIH-Led Effort – Including ISB – Launches Big Data Portal for Alzheimer’s Drug Discovery | Bioinformatics Training | Scoop.it
The National Institutes of Health announced the launch of a new Alzheimer’s Big Data portal, which includes the first wave of data for use by the research community.
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bionode

Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatic analysis workflows.


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PLOS Pathogens: Catch Me If You Can: The Link between Autophagy and Viruses

PLOS Pathogens: Catch Me If You Can: The Link between Autophagy and Viruses | Bioinformatics Training | Scoop.it

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A Novel Host-Proteome Signature for Distinguishing between Acute Bacterial and Viral Infections

A Novel Host-Proteome Signature for Distinguishing between Acute Bacterial and Viral Infections | Bioinformatics Training | Scoop.it
Bacterial and viral infections are often clinically indistinguishable, leading to inappropriate patient management and antibiotic misuse.

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This 17-Year-Old Has Discovered DNA Mutations That Could Combat HIV And Meningitis

This 17-Year-Old Has Discovered DNA Mutations That Could Combat HIV And Meningitis | Bioinformatics Training | Scoop.it
High schooler Andrew Jin is answering previously unasked questions in biology.

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GTPB - the Gulbenkian Training Programme in Bioinformatics

GTPB - the Gulbenkian Training Programme in Bioinformatics | Bioinformatics Training | Scoop.it

Bioinformatics hands-on training in short fece-to-face courses. GTPB provides skills in...

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Check the events on Facebook (also the past ones)

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GTPB: SMLMC15 - Structural Modelling for Large Macromolecular Complexes - Home

GTPB: SMLMC15 - Structural Modelling for Large Macromolecular Complexes - Home | Bioinformatics Training | Scoop.it
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Overview

We will present a range of techniques to generate, analyse, and optimise models of proteins, RNA, and their complexes. We will talk about new approaches to structure determination of macromolecules and macromolecular complexes. During the practical sessions participants will learn how to use methods for modelling protein and RNA 3D structures such as Modeller and ModeRNA. Also we will focus on methods dedicated to protein-RNA complexes modelling, e.g. by combining data from low-resolution density maps, SAXS and biochemistry. In particular, we will present how to use PyRy3D, a computational tool to build models of macromolecular complexes based on data from various sources.
Participants will be able to bring-in specific biological questions and/or their on data to work with during the course.

Target Audience

The course has been designed for molecular and structural biologists, bioinformaticians and biotechnologists and other scientists interested in modelling of biological complexes. The content is suitable for researchers, both at the graduate and post-graduate levels.
Minimal levels of computer usage skills are required. We anticipate the participants to have a wide diversity of interests in biological complexes and their structures. It is likely that they may also aim at getting involved in generating structural models for complexes of interest, but that does not have to be the case for all the participants: they may, for example, just want to explore publicly available data.

Course Pre-requisites

Graduate level knowledge in Life Sciences, interest in structural biology.

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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis | Bioinformatics Training | Scoop.it
My R/Bioconductor package, DOSE, published in Bioinformatics.



Summary: Disease ontology (DO) annotates human genes in the context of disease.

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A Third Rotary Motor Has Now Been Found in Bacteria

A Third Rotary Motor Has Now Been Found in Bacteria | Bioinformatics Training | Scoop.it
Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution.

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Ed Rybicki's curator insight, March 8, 4:21 PM

They go on a bit about "irreducible complexity", but if yoiu ignore that, it's really interesting: like finding your car has a crankshaft you didn't know about!

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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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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 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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Breaking the Human Genome Code - Opening Pandora's Box - YouTube

Recent technology advances have resulted in the ability to sequence anyone’s genome cheaply and quickly, but we are only just beginning the journey to discov...
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Interesting talk about the present and predictable future  impact of genomics in human health. Win Hide's  inaugural lecture in Sheffield.

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Baliga Lab: A Global Map To Fight Tuberculosis

Baliga Lab: A Global Map To Fight Tuberculosis | Bioinformatics Training | Scoop.it
3 Bullets:
The disease progression of tuberculosis is extremely complex and it’s poorly understood.
ISB and Seattle BioMed researchers have made an important step by developing a comprehensive map of gene regulation in tuberculosis.
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Global migration of influenza A viruses in swine : Nature

The complex and unresolved evolutionary origins of the 2009 H1N1 influenza pandemic exposed major gaps in our knowledge of the global spatial ecology and evolution of influenza A viruses in swine (swIAVs). Here we undertake an expansive phylogenetic analysis of swIAV sequence data and demonstrate that the global live swine trade strongly predicts the spatial dissemination of swIAVs, with Europe and North America acting as sources of viruses in Asian countries. In contrast, China has the world’s largest swine population but is not a major exporter of live swine, and is not an important source of swIAVs in neighbouring Asian countries or globally. A meta-population simulation model incorporating trade data predicts that the global ecology of swIAVs is more complex than previously thought, and the United States and China’s large swine populations are unlikely to be representative of swIAV diversity in their respective geographic regions, requiring independent surveillance efforts throughout Latin America and Asia.


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Emerging Viral Diseases: The One Health Connection: Workshop Summary

Emerging Viral Diseases: The One Health Connection: Workshop Summary | Bioinformatics Training | Scoop.it
In the past half century, deadly disease outbreaks caused by novel viruses of animal origin - Nipah virus in Malaysia, Hendra virus in Australia, Hantavirus in the United States, Ebola virus in Africa, along with HIV (human immunodeficiency virus),...

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burkesquires's curator insight, March 27, 12:17 PM

Download a FREE PDF of the book!

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Ebola’s fast evolution questioned

Ebola’s fast evolution questioned | Bioinformatics Training | Scoop.it
Genome-sequencing study finds the virus evolving more slowly than thought, but others say the focus should be on monitoring the effects of new mutations.

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ISB Launches 3-Year Wilke Lyme Disease Project with $2.13M Funding

ISB Launches 3-Year Wilke Lyme Disease Project with $2.13M Funding | Bioinformatics Training | Scoop.it
Study Utilizes Systems Approaches to Develop Diagnostics and Deeper Understanding of Chronic Lyme PRESS RELEASE, SEATTLE, March 26, 2015 – Institute for Systems Biology (ISB) has received $2.13 million in transformational gifts from Jeff and Liesl...
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The rise of the ‘Data Journal’

The rise of the ‘Data Journal’ | Bioinformatics Training | Scoop.it
The rise of the ‘Data Journal’
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Excellent source of information

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Electronic Health Records (EHR) Market Size, Share, Growth, Analysis And ... - MarketWatch

Electronic Health Records (EHR) Market Size, Share, Growth, Analysis And ... - MarketWatch | Bioinformatics Training | Scoop.it
Electronic Health Records (EHR) Market Size, Share, Growth, Analysis And ...
MarketWatch
Growing demand for digitalization and automation in healthcare is one of the major divers for the growth of electronic health records market.
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GTPB: IB15F Introductory Bioinformatics, First course - Home

GTPB: IB15F Introductory Bioinformatics, First course - Home | Bioinformatics Training | Scoop.it
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with David P Judge, Pedro L Fernandes and Javier Santoyo-Lopez

 

Overview

This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved.

Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products.

This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools.

 

Objectives

The operation of the various programs used in the exercises will be explained, but only to the extent that allows a user to select parameters intelligently and to interpret results.

The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations with a relatively high degree of user independence.

In the training course design, this is intentionally built-in, to allow us to show a wide range of analytical techniques while providing enough experience to break the ice in all of them.

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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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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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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.
Pedro Fernandes's insight:

Registration and abstract deadline:March 31st 2015 !

 

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