BOL: Related items

Amity University Bioinformatics Summer Program - Kolkata

eliabrodsky — Tue, 11 Jun 2019 21:27:10 -0500

Registrations are now open for the 2019 Summer Bioinformatics Training program at Amity University, Kolkata. The program will focus on introductory topics for life science students. We will review important history, topics and challenges bioinformatics can help address in the context of basic research, discovery and industry.

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/

alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Jit — Mon, 12 Mar 2018 09:24:40 -0500

Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr

http://www.mdpi.com/2073-4425/8/10/248

Address of the bookmark: http://alienness.sophia.inra.fr/cgi/index.cgi

KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment

Jit — Fri, 19 Oct 2018 09:36:11 -0500

KOBAS 3.0 is a web server for gene/protein functional annotation (Annotate module) and functional gene set enrichment(Enrichment module). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations for each gene based on multiple databases about pathways, diseases, and Gene Ontology. For Enrichment module, it can accept either gene list or gene expression data as input, and generates enriched gene sets, corresponding name, p-value or a probability of enrichment and enrichment score based on results of multiple methods.

Address of the bookmark: http://kobas.cbi.pku.edu.cn/

Gene Finding and Predictions

Poonam Mahapatra — Fri, 26 Aug 2016 07:26:27 -0500

In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by signal, content and homology (protein and cDNA sequences) methods will be employed in order to improve the ab initio results. Weak conservation of Start codons will lead to wrong prediction of initial exons in most cases.

http://genome.crg.es/courses/Bioinformatics2003_genefinding/

Address of the bookmark: http://genome.crg.es/courses/Bioinformatics2003_genefinding/

DeCoSTAR - Detection of Co-evolution

Jit — Fri, 14 Apr 2017 06:27:25 -0500

DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.
Ancestral genes or domains are deduced from reconciled gene trees in a context of birth, speciation, duplication, loss, transfer, which are either given as input or computed with the ecceTERA package, to which DeCoSTAR is integrated. DeCoSTAR constructs parsimonious scenarios of gains and breakages of adjacencies, and contains in particular all the features of previous software DeCo, DeCoLT, ArtDeCo and DeClone. It provides statistical supports on ancestral adjacencies, or the possibility to handle badly assembled genomes.
DeCoSTAR is able to reconstruct the histories of domains inside genes, including gene fusion and fission events, as well as ancestral genome structures for dozens of whole genomes from all kingdoms of life in a few minutes.

Address of the bookmark: http://pbil.univ-lyon1.fr/software/DeCoSTAR/

Research Associate Bioinformatics in IISc Recruitment 2020

Tue, 23 Jun 2020 21:53:34 -0500

Research Associate Bioinformatics in IISc Recruitment 2020

Essential Qualifications: Ph.D. (Bioinformatics/ Biophysics/ Biotechnology or any other stream of biological/ physical sciences) with a minimum of two publications in reputed peer reviewed journals in the area of structural bioinformatics or biophysics or biomolecular modeling/ simulation.

Job description: Development of bioinformatics tools and algorithms/software for structure based analysis of biomolecular systems. Programmatic access to major biomolecular databases using APIs Knowledge based prediction and analysis of biomolecular structure, function and interactions. Docking/simulations for inhibitor design.

Desirable Qualifications (Research Associate/s): i) Strong computer programming skills (in Python/PERL/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment).

ii) Extensive experience in computational analysis of biomolecular structure/interactions and usage of advanced biomolecular simulation softwares. iii) Adequate knowledge of major databases, webservers and softwares in the area of biomolecular structure/function and drug design. iv) Familiarity with Parallel Programming environments and experience in usage of high-end HPC clusters.

The candidates must highlight their experience in above mentioned fields/topics in their CV. Initial appointment will be for a period of 1 year, subject to extension after review of performance.

Emoluments: As per DST, GOI norms and commensurate with experience.

More at https://www.iisc.ac.in/positions-open/

RA at ALAGAPPA UNIVERSITY

Sun, 04 May 2014 23:33:15 -0500

DEPARTMENT OF BIOTECHNOLOGY
(UGC SAP and DST-FIST & PURSE Sponsored Department)
ALAGAPPA UNIVERSITY
(A State University Accredited by NAAC with „A‟ Grade)
Karaikudi - 630 004, India

WALK IN INTERVIEW

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

RA (One Post):

Salary : Rs. 11000 p.m. plus admissible HRA

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf

GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure

Rahul Nayak — Sat, 07 Mar 2020 05:52:20 -0600

GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where presence-absence status of acquired genes is usually confounded by bacterial population structure due to clonal reproduction.

https://www.biorxiv.org/content/10.1101/2020.02.29.970970v1

Address of the bookmark: https://github.com/wanyuac/GeneMates

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

Jit — Mon, 21 Jan 2019 06:50:05 -0600

A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics

Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar (katharinad@gmail.com)

Affiliation: Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, USA

Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genomics. 2014. 15:717.

Usage: Simply execute perl HGTector.pl, or, open GUI.html in a web browser to see a step-by-step wizard.

Download HGTector 0.2.2.

Address of the bookmark: https://github.com/DittmarLab/HGTector

A comprehensive atlas of human gene activity released !!!

Abhimanyu Singh — Tue, 02 Sep 2014 14:20:24 -0500

A large international consortium of researchers has produced the first comprehensive, detailed map of the way genes work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.

We are able to pinpoint the regions of the genome that can be active in a disease and in normal activity, whether it’s in a brain cell, the skin, in blood stem cells or in hair follicles. This is a major advance that will greatly increase our ability to understand the causes of disease across the body.

The research is outlined in a series of papers published March 27, 2014, two in the journal Nature and 16 in other scholarly journals. The work is the result of years of concerted effort among 250 experts from more than 20 countries as part of FANTOM 5 (Functional Annotation of the Mammalian Genome). The FANTOM project, led by the Japanese institution RIKEN, is aimed at building a complete library of human genes.

Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These “switches” — called “promoters” and “enhancers” — are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types.

Referene : www.kurzweilai.net/first-comprehensive-atlas-of-human-gene-activity-released