BOL: Related items

Liu Lab

Tue, 04 Feb 2020 06:27:02 -0600

Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

https://liulab-dfci.github.io/software/

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;

BioContainers

Jit — Thu, 20 Feb 2020 05:29:46 -0600

BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics packages (e.g conda) and containers (e.g docker, singularity). BioContainers is based on the popular frameworks Conda, Docker and Singularity.

Address of the bookmark: https://biocontainers.pro/#/

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/

Bioinformatics-focused postdoctoral fellow

Fri, 23 Oct 2020 05:52:52 -0500

Jason Thomas Ladner currently recruiting for a bioinformatics-focused postdoctoral
fellow to join the group at the Pathogen and Microbiome Institute,
Northern Arizona University (http://www7.nau.edu/ladnerlab/). This
will be a multi-year, NIH-funded position focused on the development and
utilization of a novel platform for highly multiplexed antiviral serology,
which utilizes high-throughput sequencing technology.

To apply:
https://hr.peoplesoft.nau.edu/psp/ph92prta/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB.GBL?Page=HRS_APP_JBPST&Action=U&FOCUS=Applicant&SiteId=1&JobOpeningId=604999&PostingSeq=1

For more information, feel free to contact me: jason.ladner@nau.edu

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

bioinformatics workbook

biogeek — Tue, 05 Jan 2021 22:42:32 -0600

This books assumes that the reader has some knowledge of biology and basic understanding of the Unix command line. However, for the beginner, the appendix contains introductory material and tips/tricks for common bioinformatic problems, that is referred to for more information throughout the book.

https://bioinformaticsworkbook.org/

Address of the bookmark: https://bioinformaticsworkbook.org/

Phylogenomics/Phylogenetic website

Aaryan Lokwani — Mon, 07 Apr 2014 02:17:18 -0500

Welcome to phylobabble.org, a discussion forum for phylogenetic theory and applications. The primary goal of this forum is to discuss best practice and new developments in phylogenetics. Although we do have a Troubleshooting category for getting feedback on analyses, this is not a help site for running phylogenetics programs.

A great place to chat about phylogenetics for researchers and the broader community of students and science-interested citizens.

Address of the bookmark: http://phylobabble.org/

Kanthida Lab !

Wed, 28 Apr 2021 02:27:22 -0500

Research Interest:

Bioinformatics

High-throughput and high-dimensional data analysis

Microbiome data analysis (Main focus)

Next-generation and third-generation sequencing data analysis for genomics

Gene expression data analysis

Machine learning for biological data

Biomarkers identification

Database and web-application for biological data

More at
https://sites.google.com/mail.kmutt.ac.th/kanthida-k/home?authuser=0

Scalpel

Shruti Paniwala — Wed, 20 Aug 2014 02:07:58 -0500

A team from Cold Spring Harbor Laboratory has released an algorithm, called Scalpel, for finding insertions and deletions in next generation sequencing data sets. Scalpel, which is open source and available for download on SourceForge, outperformed the popular tools GATK HaplotypeCaller and SOAPindel in test runs on both simulated and real whole human exomes.

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.