BOL: Related items

Bioinformatics group at Boku University

Thu, 12 Dec 2013 17:53:10 -0600

The Bioinformatics group at Boku University has two main areas of interest, underpinning a common goal, the study of complex systems in living organisms. To overcome the engineered redundancies and combinatorial effects prevalent in higher eukaryotes, novel views augmenting the classical gene by gene approaches are required. We combine

1. Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and
2. Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)

Lab page @ http://bioinf.boku.ac.at/

Free math books

Manisha Mishra — Thu, 12 Dec 2013 19:38:34 -0600

Bioinformatics require some match skills, therefore I decided to provide this wonderful math eBooks links to the BOL community.

Please add ur links/bookmarks in comment section.

Address of the bookmark: http://physicsdatabase.com/free-math-books/

DNA is packaged in a chromosome experiment

Mon, 23 Sep 2013 18:01:12 -0500

For more information, log on to- http://shomusbiology.weebly.com/ Download the study materials here- http://shomusbiology.weebly.com/bio-materials.html A nucleosome is the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around four histone protein cores.[1] This structure is often compared to thread wrapped around a spool.[2] Nucleosomes form the fundamental repeating units of eukaryotic chromatin,[3] which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter). Nucleosomes are folded through a series of successively higher order structures to eventually form a chromosome; this both compacts DNA and creates an added layer of regulatory control, which ensures correct gene expression. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosomes were observed as particles in the electron microscope by Don and Ada Olins [4] and their existence and structure (as histone octamers surrounded by approximately 200 base pairs of DNA) were proposed by Roger Kornberg.[5][6] The role of the nucleosome as a general gene repressor was demonstrated by Lorch et al. in vitro [7] and by Han and Grunstein in vivo.

Bioinformatics software for biologists in the genomics era

Poonam Mahapatra — Sun, 22 Dec 2013 17:31:05 -0600

The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/23/14/1713.full

How I discovered DNA - James Watson

Fri, 18 Oct 2013 11:30:26 -0500

View full lesson: http://ed.ted.com/lessons/james-watson-on-how-he-discovered-dna Nobel laureate James Watson opens TED2005 with the frank and funny story of how he and his research partner, Francis Crick, discovered the structure of DNA. Talk by James Watson.

JRF @ PONDICHERRY UNIVERSITY

Fri, 03 Jan 2014 16:48:56 -0600

PONDICHERRY UNIVERSITY

CENTRE FOR BIOINFORMATICS

PUDUCHERRY

Applications are invited for one Project Assistant to work in the UGC sponsored Research Award "Molecular Docking and Dynamics studies to understand the interacting mechanism of oncogenic 101 protein with its cellular proteins".

The duration for the fellowship is 12months only with consolidated pay ofRs. 5,000 per month.

Application on plain paper with following details: Name, Address, Data of Birth, Father's Name, Nationality, Educational Qualification (SSLC onwards-enclose attested copies of certificate) and Researcb Experience may be addressed to Dr. R. Krishna, Principle Investigator (PI), UGC Research Award, Centre for Bioinformatics, Pondicherry University, Pondicherry - 605 014.

Application should reach in January 261h , 2013.

Essential Qualification: M.Sc. in Bioinformatics/Biophysics with good academic record.

Qualification for Project Fellow:

M.Sc in Bioinformatics/Biophysics.

The person to be considered for appointment as Project Fellow must have second class master degree with a minimum of 55% marks in the subject concerned or a related subject.

The candidate to be appointed as Project Fellows should be below thc age of40 years at the time of appointment.

Desirable Qualification for this Project: Research Experience in Small/Macromolecule Crystallography and Structural Bioinformatics.

For more details, refer the web site: www.pondiuni.edu.in/sites/default/files/BIC-311213.pdf

DNA testing companies around the globe !

Jit — Thu, 13 Jul 2017 04:44:03 -0500

It was realized in the 1940s that DNA molecules are passed down through the generations of a family. In 1953 Watson and Crick elucidated the chemical structure of this molecule as a twisted ladder (a ‘helix’) made of two strands. DNA occurs in all the cells of our body, it is our blueprint! The strands of DNA contain information in the form of a code, which in turn determines our individual traits and characteristics. This code, the genetic code, is the order of four types of DNA building block. When the two strands of DNA separate, each building block (‘base’) accurately templates a corresponding base on the newly made strand of DNA so that information is not lost but is instead duplicated and preserved.

Testing for similarities between DNA (deoxyribonucleic acid) samples from two people allows family relationships to be established – or disproved – to an extraordinarily high degree of certainty. A common use for a DNA test is to establish if a man is the biological father of a child; this is known as a paternity test. However, there are other uses for the science of DNA testing (also called genotyping), these include forensic analysis of human DNA samples, and tracking relationships amongst domesticated animals.

The order in which the bases occur in DNA is referred to as the DNA sequence. Each person is unique and just as people differ in their fingerprints, they also have a unique and slightly different DNA sequence. Half of a person’s DNA is received from their mother, and half is received from the father. However, while fingerprints have no value for establishing family relationships, the minor variations in DNA sequence are extraordinarily useful for this purpose. All cells of our body contain DNA, skin cells from the lining of the cheek provide a simple and convenient source of material.

DNA is purified from these cells and the minor variations are read out as a type of bar-code by a machine. When the net DNA ‘barcodes’ from family members are lined up next to each other it becomes clear when a child is related to biological parents because half the stripes in the bar-code like signature will line up with those of the mother, and half will line up with those of the father. On the other hand, in the absence of a biological relationship, the DNA signatures from a child and from a potential parent are not found to have 50% in common. It may be appreciated that DNA testing is the most convenient and scientifically accurate method of determining relationships between people.

Following are the list of companies who qssist in DNA testing:

DNA testing companies

23andMe (admixture, adoption, deep ancestry, genealogy) (health and trait reports also available in some countries)
24 genetics (admixture, exome sequencing, health, paternity, pharmacogenetics, whole genome sequencing) A company catering for the Spanish market
African Ancestry (deep ancestry)
AfricanDNA (FTDNA affiliate) (admixture, deep ancestry, genealogy)
AncestrybyDNA (admixture, deep ancestry)
AncestryDNA, a subsidiary of Ancestry.com (admixture, adoption, genealogy)
Atlas Biomed (deep ancestry, diet, health and traits, sport) A test catering for the Russian market
BritainsDNA (formerly Ethnoancestry) (admixture, deep ancestry)
Centrillion Biosciences (aka TribeCode) (admixture, deep ancestry)
CymruDNAWales - see BritainsDNA
Dante Labs (exome sequencing, health, whole genome sequencing) A test aimed at the European market
DNA Ancestry and Family Origin (FTDNA affiliate in the Middle East) (admixture, adoption, deep ancestry, full mtDNA sequencing, genealogy)
DNA Consultants (admixture, deep ancestry)
DNA Tribes (admixture)
DNA Worldwide (formerly a FTDNA partner. See also Living DNA)
Ethnoancestry - see BritainsDNA
Family Tree DNA (admixture, adoption, deep ancestry, full mtDNA sequencing, genealogy, Y chromosome sequencing)
Full Genomes Corporation (whole genome sequencing, Y-chromosome sequencing)
Gene by Gene - the parent company of Family Tree DNA which now incorporates the companies previously known as DNA Traits, DNA DTC and DNA Findings (research, health, exome sequencing, whole genome sequencing)
Genebase (deep ancestry, genealogy)
GenoTek (admixture, genealogy, diet and fitness, family planning, health, talents and sports) A company catering for the Russian market
Genographic Project (admixture, deep ancestry)
Genos Research Inc (DTC whole exome sequencing; consumer focused healthcare big data spin out from Complete Genomics; Note: no genetic genealogy focus or tools)
Guardiome (admixture, whole genome sequencing and interpretation)
Helix (exome sequencing) US supplier of the Genographic Project Geno 2.0 Next Generation test
iGENEA (FTDNA affiliate) (admixture, deep ancestry, genealogy)
IrelandsDNA - See BritainsDNA (formerly Ethnoancestry)
MyDNA Global - a new name for BritainsDNA
Living DNA (admixture, deep ancestry) See also DNA Worldwide
MyHeritage DNA (admixture, genealogy)
Oxford Ancestors (deep ancestry)
Roots for Real (admixture, deep ancestry)
ScotlandsDNA - (formerly Ethnoancestry) (admixture, deep ancestry)
Sorenson Genomics (laboratory services)
Sure Genomics (whole genome sequencing and interpretation)
TribeCode See Centrillion Biosciences
Veritas Genetics (whole genome sequencing and interpretation)
Xcode (Diet and Fitness, Precision medicine, Genotyping, Sequencing, Interpretation)
YorkshiresDNA - See BritainsDNA (formerly Ethnoancestry)
WeGene (admixture, deep ancestry, health, sports, traits) A test tailored for the East Asian market
YSEQ (custom Y-SNPs, Y-STRs, SNP panels, whole genome sequencing)

FACULTY POSITIONS AT IIIT-ALLAHABAD

Thu, 23 Jan 2014 06:19:34 -0600

OPENINGS OF FACULTY POSITIONS AT IIIT-ALLAHABAD

(Under Tenure-Track Model)

Open Advt. No IIITA/DIC/16012014

IIIT-Allahabad has several Openings for the Faculty positions at the Assistant Professor level.

It is a regular tenure-track faculty positions for 3-5 years in teaching and research. A regular faculty is expected to engage heavily in research and teaching. The eligibility criteria for regular faculty positions are similar as in IITs. For an Assistant Professor position, a candidate must have a PhD (in IT/Computer Science &/or Engineering/Electrical, Electronics &/or Communication Engineering/etc; for interdisciplinary areas the PhD may be in an appropriate field), plus three years experience. However, for PhDs from a well known University/Institute (e.g. IITs/IISc/TIFR/ISI in India or well known research universities across the world), and a good research/academic record, the 3 years experience requirement may be waived.

The pay scale for faculty is same as in IITs. Other benefits include initiation research grant, travel support, book grant, professional society membership, etc., and personal benefits such as medical/LTC, on campus subsidized family housing with excellent modern infrastructural facilities.

Areas of Interest

IIIT-Allahabad aims to build strong research groups in important and emerging areas in CS/IT/ECE as well as in emerging interdisciplinary areas, and applications are invited in all these areas. Some of the areas of special interest, besides strengthening the existing research areas, are : Software Engineering, Theoretical Computer Science, Cyber Physical Systems, Robotics, Network science, Digital Media, Computational neuroscience, Machine learning, Healthcare informatics, Computational Biology, Communications networks (both at hardware and protocol levels), Circuits (including VLSI, analog, low power, etc), Energy systems and technologies, Biomedical electronics and systems, Computer Architecture, signal/image processing, Embedded and control systems.

Application Process

Interested candidates can apply by sending their detailed CV with list of publications clearly mentioning Journal names and citation index with three references through email entitled “Faculty positions at IIIT Allahabad” to faculty.applications@iiita.ac.in. Do not send your applications in any other email addresses. Applications will be considered regularly, hence there is no deadline for applying.

Important Clarifications on Eligibility

A PhD in CS/IT (or other disciplines, as announced) is the minimum expected requirement for an Assistant Professor.

Advertisement: http://iiita.ac.in/pub/Faculty-Position-IIITA1.pdf

D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way

Jit — Mon, 11 Jun 2018 09:41:22 -0500

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. http://dgenies.toulouse.inra.fr/

Address of the bookmark: http://dgenies.toulouse.inra.fr/

Scientist Positions at Rajiv Gandhi Centre for Biotechnology

Thu, 06 Feb 2014 23:18:49 -0600

Rajiv Gandhi Centre for Biotechnology

An Autonomous National Institute under Government of India,
Ministry of Science & Technology
Department of Biotechnology

No: RGCB/ Advt./2014/1
January 24, 2014

Scientist Positions

Group Leader in Computational Biology/Bioinformatics
A highly motivated and innovative individual who will pursue basic research, solve biological problems with emphasis on computational and quantitative experimental methods and build active bridges to translational research. The scientist will also provide computational biology support to analyze complex data sets generated by RGCB scientists and collaborators.

Location: Thiruvananthapuram (Trivandrum)

The above positions will be at the E-II, F or equivalent levels. For senior applicants with an outstanding track record, an option of a contract career path for research excellence at Scientist G or H equivalent level can also be discussed. All positions will initially be for 5 years. Essential and desired qualifications as well as other relevant details for all the above positions are posted on the RGCB website (http://www.rgcb.res.in). The last date for receiving applications is March 14, 2014.

Sd/-
Director

Rajiv Gandhi Centre for Biotechnology
Thycaud, P.O., Poojappura,
Thiruvananthapuram, Kerala, India-695 014
Ph.: 91-471-2529400 (30 Lines), 2347975, 2348104, 2348753, 2345899
Fax: 91-471-2348096, 2346333

More at http://rgcb.res.in/jobs.html