BOL: Related items

Roth Lab

Tue, 11 Mar 2014 17:43:45 -0500

The Roth Lab seeks insight into biological systems through genome- and proteome-scale experimentation and analysis.

Current computational interests:

Systematic analysis of genetic epistasis to identify redundant or compensatory systems and to reveal order of action in genetic pathways.
Using knockout, knockdown, or overexpression, or other perturbation experiments in combinations of genes in S. cerevisiae, C. elegans or mouse.
Using genome-scale genotyping of natural polymorphisms in S. cerevisiae and human populations.
Alternative splicing and its relationship to protein interaction networks.
Integrating large-scale studies including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns to quantitatively assign function to genes and guide experimentation.

More at http://llama.mshri.on.ca/index.html

Louisiana Biomedical Research Network: Summer Bioinformatics Training Program

eliabrodsky — Wed, 05 Jun 2019 15:30:01 -0500

Louisiana Biomedical Research Network (LBRN) announces registration for it's Summer 2019 Bioinformatics Training Program. The program will be focused on processing, analysis and interpretation of next generation sequecning data for biologists. Learn more:

https://edu.t-bio.info/louisiana-biomedical-research-network-summer-2019-lbrn-bioinformatics-training-program/

Postdoc Position in Computational Biology

Fri, 14 Mar 2014 01:38:49 -0500

The Computational Biology Group of Interdisciplinary Center for
Clinical Research (IZKF) Aachen, RWTH Aachen University Hospital,
Aachen, invites applicants for PhD candidate or postdoctoral position
in computational biology in one of the following topics:

1) Statistical machine learning methods for the analysis of medical
epigenomics data.

2) Sequence analysis algorithms for detection of RNA-DNA interactions.

Applicants should hold a M.Sc . or PhD in Computer Science or related
areas. Experience in the analysis of biological sequences, gene
expression and gene regulation is desirable. The candidate should have
solid programming skills (C, Python and/or R) and acquaintance with
Linux. Experience with high performance computing is a plus. The
working language of the group is English.

The position is based on the German TV-L 13 salary scale, including
all German social benefits (health insurance and pension scheme). The
expected starting date is September 2014. Interested candidates should
send a CV, statement of research interests and the names of three
references to jobs@costalab.org.

More at http://costalab.org/wp/phd-and-postdoc-position-in-computational-biology/

Naegleria fowleri: brain eating amoebae

Neel — Thu, 10 Oct 2019 22:12:03 -0500

Naegleria fowleri is a free living, universally distributed amoeba, which is mostly found in natural, stagnant, warm water bodies such as ponds, lakes, etc. It is also reported to be present even in indoor water bodies, such as swimming pools within a temperature range of 40–45°C.

N. fowleri infects the central nervous system of human body by entering through the nose during swimming and outdoor baths in natural stagnant water bodies, leading to meningoencephalitis. It is a condition of inflammation of cerebral tissues and membranes of the brain and is mostly fatal in nature. Casualties due to N. fowleri infections are reported all across the globe including a few in India but only seven survivors in the entire world have been reported till 2015.

You can find two genome assembly at

https://www.ncbi.nlm.nih.gov/assembly/?term=naegleria%20fowleri

More at https://www.ncbi.nlm.nih.gov/search/all/?term=naegleria+fowleri

BioGeek Fun

Jit — Sun, 16 Mar 2014 06:33:31 -0500

1. A futuristic computational biology student was told to write "It is in my gene!!!" on the board 100 times as a punishment. here's his response -

use warnings;
for ($count=1; $count <=100; $count++) { print "It is in my gene!!!";}

I guess, he is gonna to be a real biogeek. Nice try though. Smart kid.

2. In some perl script I found this
. . . . . .
. . . . . .
# It works for me, only God understood how it is working
while (/(<\/[^>]+>)|(<[^>]+>)|(<[^>]+>)$|([^><]+)/go) {
            $startGene=$1;
            $beginChromosome=$2;

. . . . . .
.. . . . . .
}

3. One more interesting message in Perl found …. It will must tickle you bone :)
open(my $fh, "<", "gene.txt") or kill " Me if you think this is a mistake :$!";

4. From the Perl

while () { # "The Mothership Connection is here!"
print “$_\n”; # Printing the offspring :)

5. Perl message
if ($1) { print “Just found a the error in chromosome !!!, yahoo…”; else { “That is not error, but mutation you moron!”;

6. One genome database curator walk in wine bar asked the bartender:
CREATE TABLE gene IF NOT EXISTS SexOnTheBeach;

Multiple PhD positions

Sun, 09 Feb 2020 03:10:28 -0600

14 PhD positions in the EU Horizon 2020 Marie Skłodowska-Curie Project PRECODE:
International training network which sets a joint research programme to train a new generation of leading scientists in model systems and methods for the development of new therapies for pancreatic cancer (PaCa)

http://precode-project.eu/jobs-board/#1572451761376-39d75f63-c6fb

Jarvis’ laboratory

Tue, 18 Mar 2014 18:53:47 -0500

Dr. Jarvis’ laboratory studies the neurobiology of vocal communication. We want to know how the brain generates, perceives, and learns behavior. We use vocal communication as a model behavior. Emphasis is placed on the molecular pathways involved in the perception and production of learned vocalizations. We use an integrative approach that combines behavioral, anatomical, electrophysiological, and molecular biological techniques. The main animal model used is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations. The overall goal of the research is to advance knowledge of the neural mechanisms for vocal learning and basic mechanisms of brain function.

Lab page: http://jarvislab.net/

Software for genome assembly !

LEGE — Sun, 30 Aug 2020 09:51:38 -0500

List of bioinformatics tools/Software Website References for genome assembly:

1 Falcon https://github.com/PacificBiosciences/pb-assembly

2 Canu assembler http://canu.readthedocs.io/en/latest/index.html

3 Miniasm assembler https://github.com/lh3/miniasm

4 PBJelly scaffolding tool https://sourceforge.net/projects/pb-jelly/

5 ARCS scaffolding tool https://github.com/bcgsc/arcs

6 Redundans reduction and scaffolding tool https://github.com/Gabaldonlab/redundans

7 Arrow error correction https://github.com/PacificBiosciences/ GenomicConsensus

8 PILON error correction https://github.com/broadinstitute/pilon/wiki

9 BUSCO single copy gene markers http://busco.ezlab.org/

10 Bandage graph assembly viewer https://rrwick.github.io/Bandage/

11 Gepard dotter http://cube.univie.ac.at/gepard

12 MUMmer aligner and plotter http://mummer.sourceforge.net/

Professor and Associate Professors (PB-IV) Assistant Professors (PB-III) Job at IIIT, Allahabad

Mon, 31 Mar 2014 08:09:07 -0500

Indian Institute of Information Technology, Allahabad
Devghat, Jhalwa, Allahabad – 211012, Uttar Pradesh, India
E-mail: contact@iiita.ac.in, faculty.applications@iiita.ac.in
Web: www.iiita.ac.in Phone : 0532-2922031/27/67

Applications are invited on prescribed format along with self attested copies of the certificates for Faculty Positions in the following areas:
Sciences – Systems Biology, Computer Aided Drug Designing, Statistics, Applied Mathematics, Applied Physics. BioMedical Engineering – BioMechanics, BioMedical Instrumentation.

Last Date : May 10, 2014

Details are available on our website : http://www.iiita.ac.in

http://www.iiita.ac.in/downloads/announcements/uploads/FACULTY_Advertisement_NO-FS-01_2014130.pdf

Senior Scientist bioinformatics @ Eurofins Genomics India Pvt Ltd, Bengaluru.

Sat, 14 Aug 2021 13:17:36 -0500

Eurofins hiring @ Eurofins Genomics India Pvt Ltd, Bengaluru.

Designation: Senior Scientist bioinformatics
Experience: 8-9 years of experience in bioinformatics analysis of various NGS applications such as WGS, RNASeq, Metagenome, small RNA.

Location: Bangalore

Roles & Responsibilities:
-Develop NGS pipeline for analysis and interpretation of NGS data
-Organizing and managing large scale genomic data
-Should have experience in NGS data analysis, such as WGS, RNASeq, Small RNA, Metagenome (16S, ITS, Whole metagenome)etc.
-Should also have good programming skills in perl or python, PHP,J Query, MySql.
-Manage project timelines and deliverables.
-Implement and execute data processing workflows and automate the pipelines.

If you are interested, please send your profile to me at arpitaghosh@eurofins.com with “Senior Scientist bioinformatics for Genomics” as the subject.