BOL: Related items

SOWDHAMINI Lab

Sun, 15 Sep 2013 09:19:12 -0500

Genome sequencing projects have enormous potential for benefiting human endeavors. However, just as acquiring a language's vocabulary does not enable one to speak it, databases that list the amino acid composition of proteins do not directly tell us much about these proteins' higher-level structure and function. The most productive way to indirectly exploit these databases has been to start with the small number of proteins that are fully-characterised and to assume that other "similar" proteins will have a related structure and function. Proteins with very similar amino acid sequence are "no-brainers", but the real test, which our group largely focuses on, is to detect the "essential" similarity in proteins whose non-critical sections have experienced random rearrangements during evolution. In such cases functionally similar proteins may have less than 25% sequence overlap.

More @ http://www.ncbs.res.in/sowdhamini/groups_sowdhamini.htm

Research Fellow in Bioinformatics @ Queen's University Belfast -Institute for Global Food Security, School of Biological Sciences

Thu, 17 Oct 2013 04:33:02 -0500

Ref: 13/102900

Available immediately until 30th November 2015, to work on the development of bioinformatics approaches to aid analysis of data derived from the metabolomic profiling of biological matrices. The successful applicant will lead research activities on an FP7 funded EU-wide collaborative project aimed at establishing biomarker-based strategies for high throughput diagnostic screening. Key tasks will involve multivariate analysis of large datasets, bioinformatic-based selection and validation of identified markers, construction of metabolomic spectral profile databases and development of machine learning/database searching approaches amenable to analytical screening techniques. This position will offer the opportunity to travel and undertake work with project collaborators based in the Republic of Ireland and Europe.

Informal enquiries may be directed to Dr Terry McGrath, email: terry.mcgrath@qub.ac.uk.

Anticipated interview date: Thursday 31st October 2013
Salary scale: £30,424 – £39,649 per annum (including contribution points)
Closing date: Monday 21st October 2013

Telephone (028) 90973044 FAX: (028) 90971040 or e-mail on personnel@qub.ac.uk

The University is committed to equality of opportunity and to selection on merit. It therefore welcomes applications from all sections of society and particularly welcomes applications from people with a disability.

Fixed term contract posts are available for the stated period in the first instance but in particular circumstances may be renewed or made permanent subject to availability of funding.

More @ https://hrwebapp.qub.ac.uk/tlive_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=5616943npO&WVID=6273090Lgx&LANG=USA

I-PV: Interactive Protein Sequence Visualization

Jit — Mon, 03 Jul 2017 07:52:51 -0500

I-PV is a interactive data visualization software designed for inspection of protein sequences and mutation information. It is mainly used for Genetics and Bioinformatics. So what exactly makes it standout?

http://i-pv.org/ipv_rec

Address of the bookmark: http://i-pv.org/

JRF @ NATIONAL JALMA INSTITUTE OF LEPROSY AND OTHER MYCOBACTERIAL DISEASES

Mon, 28 Oct 2013 10:42:48 -0500

NATIONAL JALMA INSTITUTE OF LEPROSY AND OTHER MYCOBACTERIAL DISEASES

(INDIAN COUNCIL OF MEDICAL RESEARCH)

P.O BOX 101,
Dr. M. Miyazaki Marg,
Tajganj, Agra - 282001

Applications are invited for a walk-in interview to be held in the Seminar Hall of the on 15th November, 2013, 9:30 am for temporary positions of JRF, Lab Technician and Field attendant in a ICMR funded project entitled "Elucidating the strain differentiation and transmission dynamics of M. leprae through simple sequence repeats ISSR-PCR marker"

1. JRF (one Post)

Essential qualification: Candidates with M.Sc/IVI.Tech or equivalent degree in any life science related subjects with UGC-CSIR/ICMR/DBT-Net qualified

Desirable qualification: Experience in Molecular Biology/Computational Biology will be preferred.

Age. Maximum 28 years as on 11.11.2013. Age relaxation as per GOI rules.

Emoluments: Rs. 6,000 + 20% HRA per Month

2. Lab Technician (One Post)

Essential Qualification: 12th with DMLT/B.SCA4.SC in Life sciences

Desirable qualification: Experience in Molecular Biology/Computational Biology will be preferred.

Age: Maximum 30 years as on 11.11.2013. Age relaxation as per GOI rules.

Emoluments: Rs13,760/ Per Month

3. Field Attendant (One Post)

Essential Qualification: 10th Pass

Desirable Qualification: Experience in field work

Age: Maximum 28 years as on 11.11.2013. Age relaxation as per GOI rules.

Emoluments: Rsl2,040l Per Month

Terms: posts are purely temporary. Appointment will be initially made for a period of one (01) year and may be extended further based on the performance of the candidate up to completion of the project.

Application & Selection procedure: candidates have to appear in the walk-in-interview in person along with an application/CV on plain paper giving details of at educational qualificationq experience and submit photocopies of relevant documents at the time of interview. Selection will be based on the performance of the candidate in the interview' Candidates will not be sent any interview call letter separately. No TA/DA will be paid to the candidate for appearing in the interview. selection is not possible without appearing in the interview. All candidates must report by 9:00am on the date of interview. Advance copy of CV may be sent to m.sarathipartha@gmail.com

Advertisement: http://www.jalma-icmr.org.in/P_S_M_advertisment.pdf

Protein-Protein Interaction Sites Predictions !

Poonam Mahapatra — Wed, 25 Apr 2018 04:53:20 -0500

The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: The interaction partners of a specific protein and the amino acid residues participating in a given PPI. Information about a protein’s interaction partners allows scientists to construct protein interaction networks, such as signaling pathways, which in turn facilitate the understanding of many biological and clinical observations.

Following are the list of tools commonly used to PPIs predictions:

Protein-Protein Interaction Sites

PPISP

A consensus neural network method for predicting protein-protein interaction sites

HOMCOS

A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures

HotPOINT

Prediction of protein interfaces using an empirical model

ISIS

Prediction of interaction hotspots from sequence

KFC server

Automated decision-tree approach to predicting protein-protein interaction hot spots

meta-PPISP

A meta server for predicting protein-protein interaction sites. meta-PPISP is built on three individual web servers: cons-PPISP, PINUP, and Promate

ODA

Identification of optimal surface patches with the lowest docking desolvation energy values

PINUP

Protein binding site prediction with an empirical scoring function

Other Sites (DNA, RNA, Metals)

CHED

Web server for predicting soft metal binding sites in proteins

DBD-Hunter

A knowledge-based method for the prediction of DNA-protein interactions

DISPLAR

Given the structure of a protein known to bind DNA, the method predicts residues that contact DNA using neural network method

iDBPs

Predicts DNA binding proteins for proteins with known 3D structure.

PFplus

A tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

Post-doc in Systems Genetics

Wed, 08 Jan 2014 19:23:37 -0600

Gagneur lab at Gene Center, Ludwig-Maximilians-Universitaet, Munich, Germany

Deadline for applications : January 15, 2014.

Description :

We seek a talented and motivated post-doc to develop computational methods for inferring the molecular basis of genetic diseases by integration of personal omics data. Research topics include: identifying causal mutations of rare disease patients by meta-analysis; inferring disease-causing molecular pathways from genotype, human phenotypes, and omics profile of patient-derived cell lines; and causal inference from longitudinal omics studies of patients. The developed methods will be applied to analyze data from our medical collaborators.

Candidates must either hold a PhD in computational biology or bioinformatics, or hold a PhD in physics, statistics, or applied mathematics with practical experience with high-dimensional data analysis. Experience in quantitative genetics is a plus. Applicants must have a proven publication record and an interest for translational research.

The Gagneur lab is a young, lively and multidisciplinary group with a research focus on systems genetics and gene regulation. It is located at the Gene Center of the LMU (University of Munich), an interdisciplinary institution whose 16 independent research groups investigate the regulation of gene expression at all levels - from the underlying molecular mechanisms to the biological system. The institute is located on the biomedical research campus Munich-Grosshadern, offering a dynamic, interactive and internationally oriented research environment. The dynamism of Munich and the proximity of the Alps provide an excellent quality of life.

The salary is according to the TV-L (German academic salary scale).
Applications including a cover letter, CV, and references must be sent by January 15th 2014 to Julien Gagneur (gagneur@genzentrum.lmu.de)

About the lab: http://www.gagneur.genzentrum.lmu.de

FANTASIA

BioStar — Wed, 20 Aug 2025 02:48:15 -0500

FANTASIA is an advanced pipeline for the automatic functional annotation of protein sequences using state-of-the-art protein language models. It integrates deep learning embeddings and in-memory similarity searches, retrieving reference vectors from a PostgreSQL database with pgvector, to associate Gene Ontology (GO) terms with proteins.

https://www.nature.com/articles/s42003-025-08651-2

Address of the bookmark: https://github.com/CBBIO/FANTASIA

Computer experts in biotechnology laboratory

Jit — Wed, 04 Dec 2013 02:11:43 -0600

Only bioinformatician can understand that multiplication and division are different but same thing :)

Disclaimer: This cartoon is solely designed to create humour and fun, not to offend any computer experts.

Hidden Markov Models, Viterbi Algorithm, Markov Chain Exploration with script

Manisha Mishra — Thu, 14 Nov 2013 13:36:56 -0600

Hidden Markov Models, the Viterbi Algorithm, and CpG Islands (in VB6)

Problem :

The CG island is a stretch of DNA (usually longer than 200 bases) in which the frequency of the CG sequence is higher than other regions. It is also called the CpG island, where "p" simply indicates that "C" and "G" are connected by a phosphodiester bond.

CpG islands are often located around the promoters of housekeeping genes (which are essential for general cell functions) or other genes frequently expressed in a cell. At these locations, the CG sequence is not methylated. By contrast, the CG sequences in inactive genes are usually methylated to suppress their expression. The methylated cytosine may be converted to thymine by accidental deamination. Unlike the cytosine to uracil mutation which is efficiently repaired, the cytosine to thymine mutation can be corrected only by the mismatch repair which is very inefficient. Hence, over evolutionary time scales, the methylated CG sequence will be converted to the TG sequence.

Find step wise explanationand implementation steps at http://dna.cs.byu.edu/bio465/Labs/hmm.shtml

Source code with explanation http://www.tannerhelland.com/1187/hidden-markov-models-viterbi-algorithm-cpg-islands-in-vb6/

Fore detail understanding of HMM read this excellent tutorial http://www.cs.ubc.ca/~murphyk/Software/HMM/labman2.pdf

Viterbi Algo at http://en.wikipedia.org/wiki/Viterbi_path

For firther reading Wiki page http://en.wikipedia.org/wiki/Hidden_Markov_model

On CpG island paper and for indepth understanding http://www.biomedcentral.com/1471-2164/12/S2/S10

If you are more interested in exploring Markov Chain Exploration and understand it with graphical version please visit http://www.planet-source-code.com/vb/scripts/ShowCode.asp?txtCodeId=75049&lngWId=1

Reference:

1.http://www.planet-source-code.com

2. http://www.tannerhelland.com

Scientist Positions @ Gujarat State Biotechnology Mission

Mon, 25 Nov 2013 10:26:39 -0600

Gujarat State Biotechnology Mission invite applications [Online Only] under various projects* namely Gujarat Biodiversity Gene Bank (BioGene), Gujarat Institute of Genomics (GIG), Gujarat Institute of Bioinformatics [GIBS] and Gujarat Institute of Marine Biotechnology. Eligible candidates can Apply through online application portal.

1 Scientist E 3

50,000/-

M.Sc. in Life sciences or Plant Sciences or Biotechnology or Microbiology or Bioinformatics or Ph.D. from a recognized university in any of above subject.

Minimum 8 Yrs. of experience after M.Sc. or 5 Yrs. of experience after Ph.D. in responsible position of work in R & D in the area of genomics/ conservation biotechnology/bioinformatics/Planning/Scientific Administration in Science and technology organization. Highly qualified in the area of modern biology, as evidenced through research experience and proven ability to carry out work in the area of conservation biotechnology. Age limit not exceeding 40yrs.

2 Scientist B 6

30,000/-

M.Sc. in Life sciences or Plant Sciences or Biotechnology or Microbiology or Bioinformatics or Ph.D. from a recognized university in any of above subject shall be preferred.

Minimum 3 Yrs. of experience after M.Sc. in responsible position of work in R & D in the area of genomics/ conservation biotechnology/ bioinformatics /Planning/Scientific Administration in Science and technology organization. Highly qualified in the area of modern biology, as evidenced through research experience and proven ability to carry out work in the area of conservation biotechnology. Age limit not exceeding 35yrs.

The positions are purely on contractual basis for 11 months. Interested candidates can apply online in specified format available at "http://leogen.in/recruit/" The last date of applying is 24th December, 2013. Applications must be submitted online only. Applications submitted in any other format except online prescribed performa will be rejected. Candidates in service must apply through proper channel. Candidates will be required to provide original documents along with duly filled and signed application Performa, as and when called for interview.

For more details please visit the website URL : http://leogen.in/recruit