BOL: Related items

BioCodes/BioScripts

Jit — Tue, 22 Apr 2014 20:53:33 -0500

Over the years most bioinformatics people amass a collection of small utility scripts which make their lives easier. Too often they are kept either in private repositories or as part of a public collection to which noone else can contribute. Biocode is a curated repository of general-use utility scripts.

Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera

Address of the bookmark: https://github.com/jorvis/biocode

Webinar: Wednesday 21 August 2013 at Noon EDT

Jitendra Narayan — Sun, 11 Aug 2013 19:31:56 -0500

This webinar will describe the use of combinatorial pooling to reconstruct gene sequences within BACs. Recent work in barley has shown that this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

http://www.extension.org/pages/67926/upcoming-webinar:-selective-sequencing-through-combinatorial-pooling#.UggsVuHyPqU

Manolis Kellis Lab

Sun, 31 Jan 2016 20:51:06 -0600

A major focus of our lab is understanding the effects of genetic variation on molecular phenotypes and human disease. We develop methods for integrating diverse functional genomic datasets of transcription, chromatin modifications, regulator binding, and their changes across multiple conditions to interpret genetic associations, identify causal variants, and predict the effects of genetic perturbations.

More at http://compbio.mit.edu

Associate Professor - Bio-Informatics at University of Allahabad in Allahabad

Wed, 07 May 2014 00:26:53 -0500

No of vacancies: 01

Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.

i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.

ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.

iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.

v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.

Download application form from website: http://www.allduniv.ac.in/

Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014

For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf

Last Apply Date: 30 May 2014

HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes

Jit — Wed, 17 Jan 2018 05:03:19 -0600

HGT-Finder:

(i) can be used for HGT detection in both prokaryotes and eukaryotes,

(ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and

(iii) is fully automated (requires minimal human intervention), as well as very easy to install and run.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626719/

DNA Replication Process [3D Animation]

Sat, 10 May 2014 04:41:22 -0500

See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/

BioGPS: Spotlight on the Gene Expression Atlas

Jit — Thu, 18 Oct 2018 12:15:12 -0500

BioGPS opened 2016 with a publication in Nucleic Acids Research, right after the New Year holiday. Throughout the year, new designs for the site were being created, reviewed, adjusted, reviewed, adjusted, and more review/adjustments in anticipation of a site redesign for 2017. A Plugin registration Blitz was held in March and April; followed by a Plugin Review Blitz in May. The BioGPS spotlight series was also restarted, with spotlights on BGEE, Intermine, and other Intermine-related plugins.

There were ~910,000 requests made to BioGPS in 2016. Requests to BioGPS peaked in March and at the lowest in December.

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

Bioinformatics PhD at CUK Kerala

Sat, 10 May 2014 20:21:22 -0500

Applications are invited from highly motivated students (UGC-CSIR-JRF) with a background in Genomics/ Biotechnology/ Molecular Microbiology/ Biochemistry and Bioinformatics to pursue research leading to Ph.D. in the following areas;

1. Cancer Genomics

2. Microbial Genetics and Metagenomics

3. Human Infective Diseases

4. Computational Drug Design

Interested candidates may apply to Dr. Ranjith N. Kumavath, Assistant Professor & Head, Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakad (PO), Nileshwar, Kasaragod-671328,Kerala. Email: RNkumavath@gmail.com

ShinyGO v0.61: Gene Ontology Enrichment Analysis + more

Jit — Wed, 03 Jun 2020 08:00:30 -0500

2/3/2020: Now published by Bioinformatics.

11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more.

5/20/2019: V.0.60, Annotation database updated to Ensembl 96. New bacterial and fungal genomes based on STRING-db! Just paste your gene list to get enriched GO terms and othe pathways for over 315 plant and animal species, based on annotation from Ensembl (Release 96), Ensembl plants (R. 43) and Ensembl Metazoa (R. 43). An additional 2031 genomes (including bacteria and fungi) are annotated based on STRING-db (v.10). In addition, it also produces KEGG pathway diagrams with your genes highlighted, hierarchical clustering trees and networks summarizing overlapping terms/pathways, protein-protein interaction networks, gene characterristics plots, and enriched promoter motifs.

Address of the bookmark: http://bioinformatics.sdstate.edu/go/

A Brief Bioinformatics Tutorial

Jit — Wed, 21 May 2014 12:50:09 -0500

This is about how to use a computer to find what is known about a gene of interest and also how to get new insights about it.

The tutorial is divided in three main parts:

In the Sequence part, you will see how to look efficiently for a particular protein sequence, how to blast it against the database of your choice to find homologues, how to perform a multiple alignment of the homologues you've selected and how to edit this alignment.
The Structure part is about molecular visualization, homology modeling and structural domain prediction.
In the Function part, you will be introduced to you 3 useful servers to investigate the function of a protein. i.e. finding interactors, co-expressed genes, see a phylogenetic profile, easily access papers citing your gene etc ...

During all the three parts, we will use the S. cerevisiae VPS36 protein as an example.

Address of the bookmark: http://www.mrc-lmb.cam.ac.uk/rlw/text/bioinfo_tuto/introduction.html