BOL: Related items

Experimental Scientific Officer (Bioinformatics)

Fri, 27 Sep 2013 11:09:44 -0500

Closing Date: 8 October 2013

Salary: £27,854 - £29,541, with progression to £36,298

You will perform cutting edge computational biology within the Faculty of Medical Sciences, with a particular focus on the Northern Institute for Cancer Research (NICR), and contribute to the delivery of Faculty wide programmes of training, analytical services and skill transfer between Faculty Institutes.

You will have a relevant first degree or equivalent qualifications and/or experience in a relevant scientific/technical role, together with previous specialist experience at a senior level in bioinformatics. A PhD is desirable.

This position is part of the Bioinformatics Support Unit but physically located for the majority of the time in the NICR buildings.

Tenable for three years.

Informal enquiries to unit head Dr Simon Cockell: 0191 222 7253; simon.cockell@ncl.ac.uk

For more information visit @ https://www15.i-grasp.com/fe/tpl_newcastle02.asp?s=4A515F4E5A565B1A&jobid=50667,2552984041&key=70203469&c=725434237887&pagestamp=sepghtjhowdqpsxuyn

You can also find several other jobs @http://bsu.ncl.ac.uk/support/recruitment/

GOLD:Genomes Online Database

Jit — Wed, 26 Jul 2017 07:49:29 -0500

GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

Paolo Ruggerone Lab

Tue, 01 Oct 2013 14:15:53 -0500

Efflux pumps (RND family)

Functioning of efflux systems in Gram-negative bacteria
Determinants of the compound-efflux system interactions
Action of inhibitors on efflux systems
Structural and dynamical features of the efflux systems

TatA
Assembly of the TatA system
Study of the dynamical features of the charge zipper

Methods
Setup of a kinetic Monte Carlo (KMC) scheme to study the flux of antibiotics through porins and efflux systems
Setup of protocol to integrate MD results in a ligand-based approach

Viral inhibitors
Interactions of selected compounds with RNA-dependent RNA polymerases (RdRps) of HCV and BVDV
Assessment of the role of mutations in RdRps
Antimicrobial peptides

Interactions of antimicrobial peptides with membranes: structure and dynamics
Interactions between antimicrobial peptides in the presence of different membranes
Protein-protein interactions
Effects of mutations

Lab Page
http://www.dsf.unica.it/~paolo/Site/Home.html

coursera genome assembly tutorial

Jit — Sat, 25 Nov 2017 08:57:25 -0600

Solutions to Coursera Genome Sequencing (Bioinformatics II)

Address of the bookmark: https://github.com/iansealy/coursera-assembly

Bergman Lab

Thu, 03 Oct 2013 17:20:09 -0500

Broad area of research:

Genome Annotation and Functional Genomics

Bergman Lab is actively engaged in the development and application of computational methods to improve the annotation of functional biological features in genome sequences. Bergman Lab work focuses on improving annotation of non-protein-coding regions of the genome including conserved noncoding sequences (CNSs), cis-regulatory modules (CRMs), transcription factor binding sites (TFBSs), transposable elements (TEs) and noncoding RNA (ncRNA) genes. Current projects include improving the (i) annotation of TEs in the fly and yeast genomes, (ii) annotation of CRMs and TFBSs in the fly genome, and (iii) analysis of transposon knockout collections in flies. Research in this area is supported by the EC FP7 programme.

Genome and Molecular Evolution
Text and Data Mining

More @ http://bergmanlab.smith.man.ac.uk/

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

Jit — Wed, 06 Dec 2017 02:08:14 -0600

An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/cope

The anatomy of successful computational biology software

Jitendra Narayan — Thu, 10 Oct 2013 11:53:08 -0500

Creators of software widely used in computational biology discuss the factors that contributed to their success

Nature Biotechnology spoke with Altschul and several other originators of computational biology software programs widely used today (Table 1). The conversations explored what makes certain software tools successful, the unique challenges of developing them for biological research and how the field of computational biology, as a whole, can move research agendas forward. What follows is an edited compilation of interviews.

Detail @ http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html

News Source @ Nature

Mash: fast genome and metagenome distance estimation using MinHash

Jit — Tue, 12 Dec 2017 17:30:12 -0600

Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is available in and GCC >= 4.8 and OSX >= 10.7.

See http://mash.readthedocs.org for more information.

Address of the bookmark: https://github.com/marbl/Mash/releases

Network Analysis @ Indian Statistical Institute

Wed, 16 Oct 2013 08:06:50 -0500

Indian Statistical Institute Kolkata invites applications for the following posts

2013 Oct Advertisement from Indian Statistical Institute

Post: Network Analysis

No. of Positions: 01

Educational Qualifications:

Candidate should have passed BE/B.Tech Or Equivalent in Computer Science / Electrical Engineering / Electronics / Information Technology / Bioinformatics / Biotechnology with throughout first Class
Experience:

(details of experience required)
Pay Scale: INR Rs.16000-20000/-P.M.

Walk-In-Interview : 22 Oct 2013 at 10:30 AM

Download Official Notification:
http://www.isical.ac.in/JobApplicationFiles/MIU_0310201311433700.pdf

Troyanskaya Lab

Fri, 18 Oct 2013 10:57:40 -0500

In our research, we combine computational methods with an experimental component in a unified effort to develop comprehensive descriptions of genetic systems of cellular controls, including those whose malfunctioning becomes the basis of genetic disorders, such as cancer, and others whose failure might produce developmental defects in model systems.

Research Interest
Genomic Data Integration

Microarray Analysis

Gene and Protein Function Prediction

Detection and Analysis of Chromosomal Abnormalities and Functional Evolution

Integration of Computation and Experiments

Identification of Biological Networks and Pathways

Evaluation and Validation of Computational Predictions

Scalable Visualization-Based Data Analysis

More @ http://reducio.princeton.edu/cm/
PI page @ http://reducio.princeton.edu/cm/ogt