BOL: Related items

Research Scientist – National Institute of Cholera and Enteric Diseases

Wed, 22 Oct 2014 10:26:46 -0500

The following post is to be filled up on purely temporary basis under the project entitled "Second phase of Task Force Biomedical Informatics Center of ICMR" under Dr. Santasabuj Das, Scientist 'D' of this Institute:-

01. Scientist II 01
Essential: Ph.D. degree in Life Sciences from a recognized university along with a minimum of 2 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

OR
Ph.D. degree in Bioinformatics from a recognized university.

OR
M.Sc. in Bioinformatics from a recognized university along with a minimum of 3 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

Desirable:
Thorough Knowledge about In silico genome analysis and comparative genomics.
Experience with in silico identification of novel virulence factors of pathogens, host-pathogen interactions and Systems Biology.
Additional Postdoctoral research experience in relevant subjects from a recognized institutions.

Rs. 44,000/- p.m. (consolidated) plus 30% HRA

Below 40 years

Applications along with Bio-Data containing detail work experience and full list of publications may be sent via email tosantasabujdas@yahoo.com latest by October 27, 2014.

Short-listed candidates will be called via email for an interview to be held at the institute in the second week of November, 2014.

Advertisement: www.niced.org.in/placements.htm

Mulan: MUltiple sequence Local AligNment and conservation visualization tool

Rahul Nayak — Thu, 20 Jul 2017 08:02:32 -0500

Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines refine and tba tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic graphical interface to align and visualize conservation profiles for evolutionarily distant and closely related species.

Input formats, automated data upload from the UCSC Genome Browser, gene annotation, annotation of repetitive elements, and progress report were previously described in the zPicture instructions and we refer the users to these materials for more details. This introduction is mainly focused on some novel features unique to the Mulan.

Address of the bookmark: https://mulan.dcode.org/mulanInstructions.php

Celebrating Crystallography - An animated adventure

Fri, 31 Oct 2014 15:59:00 -0500

NEW: Now with French or Spanish subtitles (click on the 'Captions' icon to select). Plus... Watch the French language version here: https://www.youtube.com/watch?v=PvLu7BOsJhM X-ray crystallography is arguably one of the greatest innovations of the twentieth century, but not that many people know what it is or how it came about. Join us on an animated journey through the 100 year history of crystallography -- from the pioneering work of William and Lawrence Bragg in 1913 to the surface of Mars! Narrated by structural biologist Stephen Curry and produced by animation company 12foot6, the film explores the extraordinary history of crystallography. To date 28 Nobel Prizes have been awarded to projects related to the field and X-ray crystallography remains the foremost technique in determining the structures of a huge range of complex molecules. This film was produced in celebration of the Bragg Centenary and was funded by STFC. Watch more science videos on the amazing Ri Channel: http://richannel.org Watch more animations from 12foot6: http://12foot6.com/ The Ri is on Twitter: http://twitter.com/ri_science and Facebook: http://www.facebook.com/royalinstitution Subscribe for the latest science videos: http://richannel.org/newsletter

ACANA: An accurate and consistent alignment tool for DNA sequences

Jit — Wed, 06 Dec 2017 09:45:29 -0600

ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements.

Address of the bookmark: https://www.niehs.nih.gov/research/resources/software/biostatistics/acana/index.cfm

Postdoctoral fellowship in Bioinformatics

Sat, 08 Nov 2014 14:41:14 -0600

A two-year post-doctoral position is available in the Biocomputing group of the Sapienza University led by Anna Tramontano to work on either genomics research or structural bioinformatics, focusing on the study of relevant biomedical problems.
The ideal candidate should be motivated and talented, hold a PhD degree, have good programming skills, a grasp of statistical methods and an understanding of biology.
Experience in the development of computational biology methods would be an added value.

Good communication skills and fluency in spoken and written English are required.
Please apply sending a curriculum vitae, the names of at least two referees and a letter of motivation describing past experience and future goals to anna.tramontano@uniroma1.it with subject: “Application for post-doctoral position November 2014 YOUR LAST NAME”

Deadline: No later than November 28th, 2014.
Duration: 2 years

Salary on grant: Commeasured to the experience of the candidate
Contact Person (Referent): Anna Tramontano
Ref. E-Mail: anna.tramontano@uniroma1.it
Group Web Page: http:/www.biocomputing.it

SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences

Jit — Thu, 21 Dec 2017 08:26:57 -0600

SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (also called SMASH). For visualization, SMASH outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values (only value varies). The following image, illustrating the information maps between human and chimpanzee for the several chromosomes, depicts an example:

Address of the bookmark: https://github.com/pratas/smash

Centre for Systems Biology & Bioinformatics, Panjab University vacancy of Research Fellow

Wed, 12 Nov 2014 06:18:54 -0600

Applications are invited along with complete bio-data and attested copies of certificates of qualifications, experience etc. for the one post of
Research Fellow and one post of Program Assistant under PURSE Grant of the University in Centre for Systems Biology & Bioinformatics, UIEAST, Panjab University, Chandigarh which is tenable till the period of the project

Essential Qualification
For Research Fellow:-
M.Sc. in Systems Biology and Bioinformatics / Life
Sciences with minimum 55% marks.
Preference will be given to NET/GATE/ICMR qualified candidates without fellowship however, candidates who have cleared the Panjab University Ph.D. entrance test in Systems Biology & Bioinformatics will also be eligible.

Applications should be reach on or before 19-11-2014 in the office of the undersigned. Interview will be held on 21-11-2014 in the office of the Coordinator, Centre for Systems Biology & Bioinformatics, South Campus, Block-3, Sector-25, Panjab University, Chandigarh. No TA/DA will be paid.

more at http://jobs.puchd.ac.in/includes/jobs/2014/20141110143634-Advertisement.pdf

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

Jit — Thu, 19 Apr 2018 08:06:03 -0500

Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap

Bioinformatics JRF/RA/SRF position at Institute of Cytology and Preventive Oncology (ICPO)

Wed, 19 Nov 2014 20:16:32 -0600

Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301

Candidates having the below mentioned qualifications may appear for walk in interview at ICPO on 2nd December 2014 between 10.00 AM and 12:00 PM under the below time bound projects under Dr. Subhash M. Agarwal, Scientist C. The post is purely temporary and co-terminus with the project.

Research Assistant (One)
25650/- consolidated
Discovery of EGFR secondary mutant inhibitors using structure based screening approach (ICMR)
Duration: 7 months

Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record.

Desirable: Experience in scripting and molecular docking.

Below 30 years

Junior Research Fellow (One)

16,000 + 30% HRA = Rs. 20800/-

Identification of novel inhibitors targeting EGFR using an integrated ligand and structure based approach (DBT)

Duration: 9 months

Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record. Candidates with CSIR-UGC / ICMR, NET qualification will be preferred

Desirable: Experience in scripting, QSAR and molecular docking.

Below 28 years

Interested eligible candidates may send their applications with Bio-data by email at (smagarwal@gmail.com) or by post addressed to Dr. Subhash M Agarwal, Scientist C, Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301 so as to reach latest by 1st December, 2014. The candidates may appear for interview at ICPO along with 3 copies of CV, photo and relevant certificates of qualifications in original and reprints of publications at the time of interview. It should be noted that No TA/DA will be paid for the walk in Interview.

Advertisement: www.icpo.org.in/advt-walk-in-interview.docx

BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data

Jit — Thu, 31 May 2018 09:35:23 -0500

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC. https://github.com/lh3/bfc

Address of the bookmark: https://github.com/lh3/bfc