We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position.

Referee is a program to calculate a quality score for every position in a genome assembly. This allows for easy filtering of low quality sites for any downstream analysis.

https://github.com/gwct/referee

Address of the bookmark: https://gwct.github.io/referee/#

Orange Bioinformatics provides access to publicly available data, like GEO data sets, Biomart, GO, KEGG, Atlas, ArrayExpress, and PIPAx database. As for the analytics, there is gene selection, quality control, scoring distances between experiments with multiple factors. All features can be combined with powerful visualization, network exploration and data mining techniques from the Orange data mining framework.

Address of the bookmark: https://pypi.python.org/pypi/Orange-Bioinformatics/2.5.34

Responsibilities

Lead teams of scientists in structuring, prototyping, and executing large-scale bioinformatic and other analysis.
Develop novel bioinformatics, statistical, data processing, pathway, data mining and other algorithms to identify biological signals and their clinical correlates in broad kinds of individual and population data.
Develop novel platform-level analytical tools for sequence-based assays (assembly, annotation, variant calling and interpretation, phasing, genome structure, etc.), expression assays (RNAseq and microarray), proteomics, and metabolomics.
Develop statistical models that robustly correlate complex laboratory-derived information with phenotypic and clinical information.
Create scientifically rigorous visualizations, communications, and presentations of results.

Reference @ https://www.google.com/about/careers/search#!t=jo&jid=62095001

Address of the bookmark: http://www.vital-it.ch/

We work in a highly interdisciplinary environment at the interface of Computer Science and Biology. Since its inception, our lab has eagerly engaged in collaborative research partnerships with biological and experimental collaborators, facilitated by our affiliation with the Broad Institute and the Computational and Systems Biology initiative (CSBi) at MIT, our participation in the Epigenome Roadmap, ENCODE, and modENCODE consortia, and by several other ongoing collaborations at MIT, Harvard, and the Harvard Medical School affiliated hospitals.

http://compbio.mit.edu/

There are two options to run ShRec3D (on linuX only so far): the first one uses the Matlab complier runtime environment (MCR), the second one doesn't need any other library to be installed but only works with the latest versions of Linux (equivalent to Fedora 19 and above).

Address of the bookmark: https://sites.google.com/site/julienmozziconacci/#TOC-Downloads

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

Jawaharlal Nehru University has been granted funds by the Department of Biotechnology (DBT), Govt. of India to initiate an Inter-School programme in JNU to strengthen training and research called "DBT-Jawaharlal Nehru University, New Delhi-Interdisciplinary Life Science Programme for Advanced Research and education" with the broad project area entitled "From Molecules to Systems: Exploring biological space using chemical and synthetic biology" cutting across Physical, Chemical and Biological Sciences.

Applications are invited for the following purely temporary posts at various levels in the various Group projects for Research and Technical positions. The project is upto March 2017, but the appointments shall be initially for a period of one year, renewable every year depending on the performance of project staff:

Project Sub-Title: Synthetic Genomics: Making sense out of 'junk' DNA

Senior Research Fellow (SRF) - 01 Post

Qualifications: M.Sc in Bioinformatics, with minimum 2 year research experience, specialization in microRNA, molecular modelling, systems and/or Synthetic biology with publication in the relevant area would be desirable.

Investigator: Prof. Pawan Kumar Dhar

Fellowship: Rs. 14000+30% HRA p.m.

Project Sub-Title: "Structure, function, and dynamics of biomolecules and Molecular engineering"

Postdoctoral Fellow (PDF) - 01 Post

Essential Qualifications: PhD in Science(Bioinformatics/Computational Biology, Physics, Chemistry, Mathematics, & Statistics), specialized in the area of Computational Biology/Structural Bioinformatics/ Quantum Chemistry/Molecular Dynamics & Simulation /Systems Biology , reflected by thesis topics and or publication of papers during PhD and/or Post doctoral experience.

Desirable Qualifications: Computational methods and designing experience in the field of Structure based or ligand based drug design, Chemoinformatics, Programming capabilities as required for developing tools in the computational & systems Biology.

Investigator: Prof. Indira Ghosh, SCIS

Salary: Rs. 22, 000 + 30% HRA

(Note: Revised emoluments shall be payable if Educational Qualifications or Eligibility Criteria as per DST OM No. A.20020/11/97-IFD dated 31-03-2010 are met by the research personnel)

The applications on plain paper indicating name, date of birth/age, address, essential / technical / professional qualifications, experience, research work, should reach the Programme Coordinator on or before 27th August 2015 at the following address:

The Envelop should be marked for the Post applied for. Any clarifications regarding projects may be sought from the respective project investigators as mentioned.

Address for correspondence:
Programme Coordinator
DBT-JNU BUILDER programme
School of Biotechnology
Jawaharlal Nehru University
New Delhi 110067

More at http://www.jnu.ac.in/career/currentjobs.htm

The position is open for immediate appointment and available for two years and then extendable for additional one year. The applicant will be appointed as Research Associate based on qualifications as detailed below:

Research Associate:

-Master’s degree with bioinformatics with at least 2 years of research experience in Next Generation sequencing data analysis as evidence from Fellowship/ Associateship / Training / other engagements.

-Familiarity with bioinformatics tools, database development, programming skills

-Minimum 1 publication in any peer reviewed journal

Salary will be as per ICAR rules and guidelines. Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.

Interested candidates may send a Letter of Interest and CV by email to: keshav@ibioinformatics.org before September 29, 2015.

Working with other members of the TNDRG you will analyse complex genomic and epidemiological datasets, evaluating which computational tools are most suitable. You will contribute to the generation of innovative tools for linking epidemiological and multilevel omics datasets, ensuring that computer programs are written in a form that other collaborators can use and expand.

You will have or be close to completion of a PhD in either: bioinformatics; neuroscience; machine learning; statistics; epidemiology; neurology; or other relevant field. You will have experience programming on either R, Matlab, Python, C++, Java or any other imperative, object oriented or functional language.

Please direct Informal enquiries to Dr Alejo Nevado-Holgado (alejo.nevado-holgado@psych.ox.ac.uk).

You will be required to upload a supporting statement explaining how you meet the selection criteria for the post, a CV, and details of two referees as part of your online application.

The closing date for applications is 12.00 midday on 2 September 2015. Interviews will be held on Tuesday 15 September 2015.

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=118696