BOL: Related items

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/

Gene Ontology Consortium

Jit — Fri, 11 Jan 2019 05:51:02 -0600

The GO knowledgebase is composed of two primary components:

the Gene Ontology (GO), which provides the logical structure of the biological functions (‘terms’) and their relationships to one another, manifested as a directed acyclic graph
the corpus of GO annotations, evidence-based statements relating a specific gene product (a protein, non-coding RNA, or macromolecular complex, which we often refer to as ‘genes’ for simplicity) to a specific ontology term

Together, the ontology and annotations aim to describe a comprehensive model of biological systems. Currently, the GO knowledgebase includes experimental findings from over 140 000 published papers, represented as over 600 000 experimentally-supported GO annotations. These provide the core dataset for additional inference of over 6 million functional annotations for a diverse set of organisms spanning the tree of life.

In addition to this core knowledgebase, GOC resources also include software to edit and perform logical reasoning over the ontologies, web access to the ontology and annotations, and analytical tools that use the GO knowledgebase to support biomedical research.

Address of the bookmark: http://www.geneontology.org/

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

G-NEST: The Gene NEighborhood Scoring Tool

Neel — Fri, 25 Sep 2020 20:09:18 -0500

The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.

Address of the bookmark: https://github.com/dglemay/G-NEST

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

Bioinformatics tools to detect horizontal gene transfer (HGT) in genomes

Jit — Fri, 02 Mar 2018 04:56:23 -0600

Horizontal gene transfer (HGT), the “non-sexual movement of genetic material between two organisms” , is relatively common in prokaryotes and single-celled eukaryotes, but a number of factors combine to make it far rarer in multicellular eukaryotes. In order for a eukaryotic species to gain a gene by HGT, foreign DNA must enter the host nucleus, integrate into the genome, and in more complex organisms it must enter the sequestered germline in order to be transmitted to offspring. Once there, it must not experience strong negative selection, despite potential for genetic incompatibility with the host genome and mismatch between the niche of the donor and the host. Over the longer term, foreign DNA may become “domesticated” in the recipient genome and provide novel function.

Following are the popular tool to detect HGT in genomes:

T-REX / 3.22

HGT detection / download & compile

20525630

RANGER-DTL / 2.0

HGT detection / download binary

22689773

PhyloNet / 3.6.1

HGT detection / download binary

18662388

Jane / 4.01

HGT detection / download binary (!license!)

20181081

TREE-PUZZLE / 5.3.rc16

HGT detection / download & compile

11934758

CONSEL / 0.20

HGT detection / download

11751242

DarkHorse / 1.5 rev170

HGT detection / download & install

17274820

HGTector / 0.2.1

HGT detection / git clone

25159222

EGID / 1.0

HGT detection / download

22355228

GeneMarkS / 4.30

HGT detection / download binary (!license!)

9461475

Assistant Professor in Molecular Synthesis for Drug Discovery and Development @ CBMR, Lucknow

Wed, 30 Oct 2013 06:42:27 -0500

ADVERTISEMENT FOR FACULTY POSITIONS AT CENTRE OF BIOMEDICAL RESEARCH (CBMR), LUCKNOW

Details of the Positions and Pay Structure:

03 Posts for Assistant Professor in Molecular Synthesis for Drug Discovery and Development

Essential Qualifications and Requirements:

1. PhD in Synthetic Organic Chemistry/Medicinal Chemistry with research publications in high quality international journals and first class grade at the preceding degree from recognised University/Institute in India or abroad with consistently good academic record.
2. Three Yrs of Post-doctoral experience in relevant area.
3. Below 35 Yrs of age at the time of application

Desirable Experience: Candidates having strong research background in organic synthesis, total synthesis of structurally complex and medicinally important natural products/drugs related to cancer, neurodegenerative diseases (neurotropically active molecules for Alzheimer's, Parkinson’s, dementia etc) and infectious diseases such as malaria, TB etc. will be preferred.

Interested candidates may apply with:

1. Filled up Application Form (download from CBMR Website: http://www.cbmr.res.in) along with the Cover Letter, Curriculum Vitae including academic record (Bachelor degree onwards), awards, honours, list of Publications and reprints of 5 best publications.
2. Proposed research plan (max 3-4 pages).
3. Names and address (with valid e-mail and Phone number) of at least 3 academic referees.
4. Online Payment Receipt with transaction reference no. of Rs. 1000/- (USD 100 or equivalent foreign currency) on following details.
Account Number: 30054847814 Name: Director, Centre of Biomedical Research
Bank: STATE BANK OF INDIA, SGPGI Campus Branch, LUCKNOW

IFSC Code: SBIN0007789
MICR No: 22602034

Applications can be sent by registered/speed post or by e-mail to the following address:

The Director,
Centre of Biomedical Research (CBMR),
Sanjay Gandhi PGI Campus,
Raebareli Road, Lucknow-226014
e-mail: cbmr.admin@cbmr.res.in,
gp.pandey@cbmr.res.in

More Info:

http://www.cbmr.res.in/career/Advertisement%20for%20the%20post%20of%20Professors%20and%20Assistant%20Professors.pdf

Junior Bioinformatic position

Wed, 26 Aug 2015 05:35:28 -0500

Junior Bioinformatic position in the laboratory of Inflammation and immunology in cardiovascular pathologies at Humanitas:

We are seeking a highly motivated young PhD student with strong interest in high throughput data analysis.
Detailed descriptions of our recent research activities may be found here:
http://www.humanitas-research.org/condorelli-gianluigi-md-phd/

Position is available starting from October/November. A probationary period of one month will be required.

Please send a CV along with a cover letter stating the reasons for applying and contact details of one or more referees to Dr. Paolo Kunderfranco (paolo.kunderfranco@humanitasresearch.it).

gggenes: a ggplot2 extension for drawing gene arrow maps.

BioStar — Tue, 02 Jun 2020 11:43:34 -0500

Install the stable version of gggenes from CRAN:

install.packages("gggenes")

If you want the development version, install it from GitHub:

devtools::install_github("wilkox/gggenes")

More at https://github.com/wilkox/gggenes

Address of the bookmark: http://wilkox.org/gggenes