BOL: Related items

Ai-CADD Project @ Kerela University

Tue, 19 Nov 2013 17:48:15 -0600

Applications are invited for the following Positions in the AiCADD project funded by MHRD Govt of India

Last Date for Submitting Application: 25th November 2013

1. Senior Scientist: (01 position)
Pay Scale: Rs.40, 000/-
Qualifications: PhD/ Post Doctoral with Experience in CADD

2. Junior Scientist (10 positions)
Pay Scale: Rs. 22,000/-
Qualifications: MPhil / Masters Degree in Bioinformatics / Computational Biology / CADD / Ayurveda

3. Technical Assistant (01+01 positions)
Pay Scale: Rs.12,000/-
Qualifications: 1. BSc Computer Science/ MCA
Qualifications: 2. MSc Biotechnology / MSc Microbiology

4. Programmer (01 position)
Pay Scale: Rs.20,000/-
Qualifications: MSc Computer Science/ MCA / B Tech (Experience in MATLAB, C, C++) Industrial experience is desirable

5. Teaching Assistant (03 positions)
Pay Scale: Rs.10,000/-
Qualifications: MSc in Bioinformatics

6. Administration Assistant (02 positions)
Pay Scale: Rs.8,000/-
Qualifications: Degree + PGDCA

The Selection process comprises of written test and interview. Positions are purely temporary (initially for the period of one year) and co-terminus with the project. For more details mail to: cbi.uok [at] gmail.com

More detail @ https://sites.google.com/site/centreforbioinformatics/announcements/applicationsinvitedforapplicationforai-caddproject

Scientist-B @ VECTOR CONTROL RESEARCH CENTRE

Tue, 19 Nov 2013 21:19:15 -0600

VECTOR CONTROL RESEARCH CENTRE
(Indian Council of Medical Research)
Indira Nagar Medical Complex
Puducherry-605006

WALK-IN-INTERVIEW

The following vacancies shall be filled purely on adhoc basis under Non-Institutional adhoc project “Bioinformatics in ICMR Institutes” funded by Indian Council of Medical Research at Vector Control Research Centre, Puducherry, to be renewed annually and filled through Walk-in-Interview as indicated below. Candidates who wish to appear for the Walk-in-Interview can download the application format given in the website of Vector Control Research Centre (www.vcrc.res.in). Duly filled in application along with attested copies of certificate should be submitted at time of interview.

Date & Time : 05.12.2013 at 9.00 AM – Scientist-C (Non-Medical)

05.12.2013 at 1.30 PM – Scientist-B (Non-Medical)
06.12.2013 at 9.00 AM – Technical Assistant (Research Assistant)
06.12.2013 at 1.30 PM – Multi Tasking Staff (General)

Place : Vector Control Research Centre, Puducherry

Project entitled : Biomedical Informatics Centres of ICMR

1. Scientist - C (Non-Medical) Number of post – ONE

Essential qualification

B.E./ B. Tech. Degree in Bioinformatics/ Computational Biology from a recognized University with 6 years experience in the relevant field OR

First class Master’s Degree and Ph.D. Degree in Bioinformatics/ Computational Biology from a recognized University OR

First class Master’s Degree in Bioinformatics/ Computational Biology from a recognized University with 4 years R & D experience in the related subjects as mentioned above OR

Second class Master’s Degree + Ph.D. in Bioinformatics/ Computational Biology from a recognized University with 4 years research experience in bio-medical subjects

Age: Not exceeding 40 years Consolidated Salary – Rs.39,960/- p.m. + HRA as
admissible

Desirable qualification (i) Post-doctorate in Bioinformatics/ Computational Biology or M.E. / M. Tech. Degree in Bioinformatics/ Computational Biology from a recognized University for candidates with First Class relevant degree.

(ii) Additional post-doctoral research / teaching experience in Bioinformatics/Computational Biology in recognized Institute(s).

(iii) Knowledge of computer applications or data management

Job requirements i) To apply Bioinformatics / Computational Biology tools in understanding interactions between vectors and parasites/ pathogens and target based development of drug / insecticides.

ii) To assist the investigators to carry out genomic studies on parasites/pathogens/vectors of vector borne diseases

Advertisement: http://vcrc.res.in/Adv_Bio13.pdf

Roslin Bioinformatics Group

Mon, 25 Nov 2013 23:55:25 -0600

Roslin Bioinformatics Group

The Law group provides internal Institute-specific development, training and support roles for data manipulation, sequence analysis and any other aspect of the analysis of biological data using computer systems. Additionally we provide databases and applications supporting the international animal science community, particularly tools and resources for genome mapping.

Head: Andy Law. Members: John Bowman (animal facility database applications), Zen Lu (bioinformatics support), Trevor Paterson (software development)

More @ http://www.bioinformatics.ed.ac.uk/groups/roslin-bioinformatics-group

Finding the Hidden Switches: The Story of KiNext and Protein Kinases

LEGE — Thu, 24 Sep 2026 02:51:28 -0500

Every newly sequenced genome contains thousands of proteins, but identifying what each protein does is a much harder task. Among these proteins are protein kinases, important molecular regulators that control processes such as cell growth, development, metabolism, stress responses, and signaling. Finding these kinases and determining which families they belong to can reveal important clues about how an organism functions and has evolved.

This is where KiNext comes into the picture. Introduced in a 2024 study published in BMC Bioinformatics, KiNext is a computational workflow designed to identify and classify protein kinases from predicted protein sequences. Instead of relying on a single search method, it brings together several approaches, including Hidden Markov Models, sequence alignment, phylogenetic analysis, and structural comparison.

The search begins with a simple question: does a protein contain the characteristics of a kinase? Protein kinases can change considerably during evolution, but important regions of their sequences often retain recognizable patterns. KiNext uses Hidden Markov Models, or HMMs, to detect these patterns. An HMM does not require a protein to be an exact match to a known kinase. Instead, it looks for a statistical sequence signature associated with kinase proteins, making it possible to detect more distant candidates.

Once potential kinases are identified, KiNext takes the analysis further. It distinguishes conventional eukaryotic protein kinases from atypical protein kinases and then attempts to classify them into different kinase groups and families. This distinction is important because simply identifying a protein as a kinase does not tell the complete story. Different kinase families can have very different evolutionary histories and biological functions.

The next stage brings evolution into the picture. KiNext can align kinase sequences and construct phylogenetic trees, allowing researchers to examine how newly identified proteins are related to previously characterized kinases. When sequence evidence alone is difficult to interpret, structural information can provide another clue. The workflow can incorporate AlphaFold-predicted structures and Foldseek-based structural comparisons to investigate whether an unusual protein resembles known kinase structures.

The researchers tested KiNext using two very different organisms: the Pacific oyster, Crassostrea gigas, and the green alga Ostreococcus tauri. In C. gigas, KiNext recovered previously reported kinases while identifying additional candidates. Structural analysis provided further evidence for many of the newly detected proteins. In O. tauri, the workflow similarly recovered most previously reported kinases and identified additional candidates while refining some of their classifications.

What makes KiNext particularly interesting is not just its ability to find kinases, but how the entire analysis is organized. The workflow uses Nextflow, allowing the different computational steps to be connected into a reproducible pipeline. Containers can also help manage software dependencies, making it easier to run the workflow across different computing environments.

This reproducibility becomes increasingly important as the number of available genomes continues to grow. A researcher studying one organism may be able to perform an analysis manually, but repeating the same process across hundreds or thousands of genomes quickly becomes impractical. A standardized workflow provides a way to perform the analysis consistently while keeping track of how the results were generated.

At its core, KiNext demonstrates a broader change taking place in modern genomics. Sequencing a genome provides an enormous amount of information, but the real scientific challenge begins afterward: understanding what all those sequences mean. Protein kinases are only one part of this larger puzzle, yet they are particularly important because they act as molecular switches throughout the cell.

By combining sequence profiles, evolutionary analysis, and structural evidence within a reproducible computational framework, KiNext provides researchers with a systematic way to uncover these molecular switches. Its real value lies not only in finding more kinases, but in making the process scalable, repeatable, and easier to apply to new genomes.

As genome sequencing continues to expand across the tree of life, tools such as KiNext can help turn enormous collections of protein sequences into meaningful biological stories—one kinase at a time.

Postdoc positions in computational biology - Center for Genomic Science - Milan, Italy

Thu, 12 Dec 2013 18:34:47 -0600

Job Description: three postdoc positions in computational biology are available at the Center for Genomic Science in Milan (Italy):

- Development of computational methods to investigate the interplay between epigenetic and genetic layers and their role in tumor progression, by integrating genomic, epigenomic and transcriptional data. PI: Mattia Pelizzola (http://tiny.cc/comEpi)
- Epigenome and transcriptome analysis in mouse models of Hepatocellular Carcinoma. PI: Bruno Amati - Small and long non-coding RNAs in cancer stem cells. PI: Francesco Nicassio

All projects will benefit from the availability of both in-house and publicly available next-generation sequencing datasets. Familiarity with Linux environment, programming skills (especially in R) and a background in either computational biology, or physics/engineering/math will be advantageous.

Deadline for the application January 6th, to apply: http://genomics.iit.it/resources.html

Start date: March 1st, 2014

Duration: 1+2 years

Contact Person (Referent): Mattia Pelizzola

Ref. E-Mail: mattia.pelizzola@iit.it

Tel: 0039-02-94375058
Group Web Page: http://genomics.iit.it

Oldest Hominin DNA Sequenced

Surajeet — Fri, 27 Dec 2013 19:58:31 -0600

Matthias Meyer and his team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have developed new techniques for retrieving and sequencing highly degraded ancient DNA. They then joined forces with Juan-Luis Arsuaga and applied the new techniques to a cave bear from the Sima de los Huesos site. After this success, the researchers sampled two grams of bone powder from a hominin thigh bone from the cave. They extracted its DNA and sequenced the genome of the mitochondria or mtDNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mitochondrial DNA with Neandertals, Denisovans, present-day humans, and apes.

From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominin lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neandertals, about 700,000 years ago. "The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal-derived features," says Matthias Meyer. Considering their age and Neandertal-like features, the Sima hominins were likely related to the population ancestral to both Neandertals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima hominins or their ancestors.

Reference

http://www.sciencedaily.com/releases/2013/12/131204132018.htm

RNA Bioinformatics and High Throughput Analysis Jena

Sat, 09 Nov 2013 20:03:56 -0600

Research Topics:

High Throughput Sequencing Analysis
Comparative Genomics
Identification and Annotation of Non-coding RNAs
Bioinformatic Analysis and System Biology of Viruses
Coevolution of Proteins and RNAs
Algorithmic Bioinformatics
Phylogenetic Analysis

http://www.rna.uni-jena.de/index.php

List of bioinformatics companies and genomics service providers

Rahul Agarwal — Wed, 02 Apr 2014 06:52:28 -0500

Plz check out link for bioinformatics and genomics companies.

Address of the bookmark: http://grouthbio.com/Genome_Software_Service.php

The 2014 CeMM PhD Program

Wed, 05 Feb 2014 06:03:15 -0600

For our next PhD Program starting in October 2014 we are looking for exceptionally motivated PhD candidates with a keen interest in genomics and medicine and a strong interest to work in teams.

The 2014 CeMM PhD Program will focus on two thematic areas: INFECTION and CANCER, that are built on the pillars of epigenetics, bioinformatics and systems biology, chemical biology and the mechanism of action of drugs, high-throughput genetics, genomics and proteomics, and molecular and cell biology.

The choice of this strategic focus rests on the synergies between immunology, infection and cancer in pathophysiological and technological terms. It furthermore reflects the strength of the current CeMM faculty, itself built around the historical and contemporary expertise in immunology and cancer of the Medical University of Vienna.

As a CeMM PhD student you will get the chance to work at the cutting edge of interdisciplinary molecular medicine research and be trained by the entire CeMM and associated faculty to become one of the scientists shaping the future of molecular medicine.
Requirements

To be eligible to enroll in the CeMM PhD Program all candidates are required to have a bachelor’s or master’s degree in medicine, biology, chemistry, bioinformatics, mathematics or any scientific/technical, subject-relevant degree. Candidates do not need to have completed their degree at the time of application, however they must have obtained their final degree certificate by mid-September. The working language at CeMM is English, so excellent written and oral communication skills in English are required.
Timeline

Applications open on 20th January and close on 20th March 2014.
Two references are required to be submitted through the online system by 31st March 2014.
All complete candidate applications are reviewed by the CeMM Faculty in early April.
Selected candidates are invited to a Skype panel interview in late April.
Shortlisted candidates are then invited to Vienna in May for a full interview process, including an opportunity to introduce yourself through a presentation and interview rounds, meet research group members, and attend an informal dinner to get to know the Faculty members and learn more about their research.
Positions are offered by CeMM Faculty in June.
Start of PhD Program: 1st October 2014 .

Contact

Binia Maria Günther, BEd BA
Human Resources Manager
bguenther@cemm.oeaw.ac.at

Catherine Lloyd, Ph.D.
PhD and Postdoc Program Manager
clloyd@cemm.oeaw.ac.at

More Info: www.cemm.oeaw.ac.at/phd-program/application/

JRF @ MANIT

Sun, 02 Feb 2014 03:07:58 -0600

MAULANA AZAD NATIONAL INSTITUTE OF TECHNOLOGY BHOPAL

No. CSE/14/1038

Walk in Interview for the post of JRF under TEQIP-II

SN Department – Qualification Post Graduation – Time

1 Bio-Informatics & Mathematics M.Tech Bio-informatics/M.Sc.* Maths 10.00 AM

2 Biological Sciences M.Sc.* in any branch of Biological Sciences 10.30 AM

3 Chemical Engineering M.Tech Chemical Engineering 11.00 AM

4 Chemistry M.Sc.* Chemistry 11.30 AM

5 Civil Engineering M.Tech Structure/GeoTech. /Water -Resources/Hydraulics/Environment/Transport 12.00 Noon

6 GIS M.Tech GIS/Civil 12.30 PM

7 Computer Science & Engineering M.Tech CSE/Information Security 01.00 PM

8 Electrical Engineering M.Tech Electrical Derives 01.30 PM

9 Electronics & Communication M.Tech Digital Communication 02.00 PM

10 MSME M.Tech Material Science/ Mechanical/Metallurgy 02.30 PM

11 Physics M.Sc.* Physics 03.00 PM

* M.Sc. with NET/GATE qualified

Resume along with one passport size photograph and relevant documents are required at the time of interview

Amount of Fellowship: Rs 18000/-month+ HRA

Duration: 31st Dec 2014 (End of TEQIP-II project)

Date of Interview: 7th February 2014

Venue Institute Committee Room

http://www.manit.ac.in/manitbhopal/Year2014/Recruitment/Advertisement%20JRF.pdf