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Friday, 21 November 2014

Bioinformatics Quiz: Test Your Knowledge of Bioinformatics

Every year Department of Biotechnology  conduct a DBT-JRF BET examination  for BIOTECHNOLOGY and BIOINFORMATICS students,if you consider both part A and Part B then there is  ~15 to 20 questions which are asked from BIOINFORMATICS,because this year BINC(BINC-2015) is also going to conduct in which BIOINFORMATICS play major role;so for these reasons i have decided to consider all BIOINFORMATICS questions,which was asked in DBT-JRF  (2008-2014) Question papers.For that i have prepared "BIOINFORMATICS QUIZ" which not only help you to do good score in  DBT-JRF BET-2015 but it is also useful in BINC-2015(part A MCQs).I have selected All these questions from DBT-JRF  (2008-2014)Question papers;which are available on DBT Website (

 Points to Remember :

  1. Option which is given in BOLD RED colour is a answer of that question.
  2. If you find out any doubt for particular question or you think that answer which is given is not right; please cross check it with DBT Website ( you can inform me on my email:
  3. please send me complete question including all four options and also consider in which option you have doubt and according to you which option should be right and why????....Thanks .

Bioinformatics Quiz: Test Your Knowledge of Bioinformatics

syllabus of Bioinformatics in DBT-JRF BET examination

1. Major Bioinformatics Resources:

  • Sequence databases, Gene Expression database: GEO, SAGE, 3D Structure Database: PDB, NDB, Knowledge driven Databases & utility, Pattern Sequence: InterPro, Prosite, Pfam, ProDom, Gene Ontology

2. Database Searches:

  • Keyword-based searches using tools like ENTREZ and SRS Sequence-based searches: BLAST and FASTA

3. Sequence Analysis, Basic concepts:

  • Sequence similarity, identity and similarity, definitions of homologues, orthologues, paralogues, Tandem and Interspersed repeats, repeat finding.

4. Scoring Matrix,

  • Pairwise sequence alignments, Multiple sequence alignments (MSA), Application in Taxonomy and phylogeny, Comparative genomics.

5. Structural Biology:

  • 3-D structure visualization and simulation, Basic concepts in molecular modeling: different types of computer representations of molecules. External coordinates and Internal Coordinates, Molecular Mechanics, Force fields

6. Proteins:

  • Secondary structure elucidation using Peptide bond, phi, psi and chi torsion angles, Ramachandran map, anatomy of proteins – Hierarchical 12organization of protein structure –like CATH,SCOP, FSSP .

7. DNA & RNA secondary and tertiary structures, t-RNA tertiary structure

8. Classification and comparison of protein 3D structures:

  • Secondary structure prediction: Algorithms viz. Chou Fasman, GOR methods,
  • Tertiary Structure prediction: Fundamentals of the methods for 3D structure prediction (sequence
    similarity/identity of target proteins of known structure, fundamental principles of protein folding etc.
  • Homology/comparative Modeling, fold recognition, threading approaches, and ab initio structure prediction methods. CASP. Computational design of Promoters, Proteins & Enzymes.

9. Application in drug design:

  • Chemical databases like NCI /PUBCHEM. Fundamentals of Receptor-ligand interactions.
  • Structure-based drug design: Identification and Analysis of Binding sites and virtual screening.
  •  Ligand based drug design: Structure Activity Relationship – QSARs & Pharmacophore etc. In silico predictions of drug activity and ADMET.

Thursday, 20 November 2014

PhD @ The University of Luxembourg

The University of Luxembourg has the following vacancy in the Luxembourg Centre for Systems Biomedicine (LCSB)
Doctorale Candidate (PhD student) in Disease Modelling/Chemical Biology (m/f)
  • Fixed-term contract 3 years, 40h/week
  • Employee status (start date: as soon as possible)
  • Ref. I1R-BCM-PAU-14BATD
  • Area:neurodegeneration, yeast disease models, zebrafish disease models, chemical biology

Studying at the University of Luxembourg

Your Role

  • Creation of yeast and zebrafish models of Batten disease (also known as juvenile neuronal ceroid lipofuscinosis (JNCL), the most common neurodegenerative disease in children)
  • Phenotyping of these disease models
  • Chemical modifer screens in both yeast and zebrafish models of Batten disease
  • Initial analysis of the mechanism of action of active small molecules

Your Profile

  • Master in Biomedical Sciences, Biology, Chemistry, Pharmacy, Bioengineering or a related discipline.
  • Strong background in chemistry and molecular biology, as well as some knowledge in bioinformatics are expected.
  • Previous experience with yeast and/or zebrafish will be considered as important asset(s).
  • Flexible regarding research stays abroad.
  • Excellent English writing and speaking skills are required.

We offer

  • Opportunity to participate in the development and integration of the recently created yeast and zebrafish platforms at LCSB.
  • An exciting international research environment.
  • The University offers competitive salaries and is an equal opportunity employer.

Further Information

For further information, please contact:
Dr. Alexander Crawford ( or Dr. Carole Linster (

Applications (in English) should contain the following documents:

  • Cover letter (motivation for this position, past research experience and future interests) mentioning the reference number
  • A detailed curriculum vitae
  • List of publications
  • Names and contact information of three references
  • Please apply online until 31st January, 2015.

Apply for job


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Monday, 17 November 2014

Bioinformatician @ The University of Edinburgh

A bioinformatician with experience of the analysis of microarray datasets is sought for an exciting project to look at stratifying breast cancer patients to ensure they receive the most appropriate treatments. Building upon previous work, the study will involve integration and meta-analysis of large publicly available and local datasets to develop a clinical test that can be routinely used in the clinic. A first degree in biology, mathematics, computer science or related subjects and a higher degree (MSc, MRes or PhD) and/or relevant experience in bioinformatics with programming skills in R, Python or Perl are required. Previous experience of clinical/cancer studies or permutation-based analysis and high performance computing would be a distinct advantage.
The post is funded by an MRC Confidence in Concepts grant for an initial 6 to 9 months, but could be extended for at least another 12 months for the right candidate to work on related projects at the CRUK centre.Informal enquires to

Introduction to the University of Edinburgh

Job Purpose

  • This MRC-funded post will perform permutation-based analysis of published gene expression datasets to establish how many robust molecular subtypes of breast cancer can be identified in order to better stratify patients to ensure they receive the most appropriate treatments.

Main Responsibilities

  • Analyse data generated from laboratory experiments or published datasets based upon research requirements. Monitor progress of experiments, analyse data and advise on the development of future experiments. Collaborate with members of the Applied Bioinformatics of Cancer research group to share and analyse datasets. Manage bioinformatics data archiving
  • Prepare, analyse, collate and interpret data for publication. Present results at scientific meetings and help write manuscripts for publication. Supervision of research students and apply for new research funding in collaboration with PIs
  • Provide assistance and advice in bioinformatics and statistics in support of members of the research team.

Planning and Organising

  • Collaborate with researchers and help guide their work through experimental design and analysis of bioinformatics results
  • Undertake bioinformatic analysis and interpretation of findings relevant to data generated as part of the overall endeavour of the group
  • Learn new skills in keeping with the diversity of the post
  • Undertake manipulations and archive data generated

Problem Solving

  • Solving technical and data analysis problems
  • Finding ways in which the group can work more efficiently, either by the introduction of software or the development of in-house pipelines
  • Ensuring that data and records are of the highest integrity
  • Using bioinformatics applications tailored to researchers needs

Decision Making

  • How to analyse and present bioinformatics information
  • How to set up and implement data management pipelines
  • How to analyse large, complex datasets
  • Prioritisation and allocation of time for different projects.
  • Identify what advice to give researchers, based on the research activity they are undertaking, and what they are trying to achieve, and advising on how to interpret results

Key Contacts/Relationships

  • Head of the research groups and other bioinformaticians and scientists
  • Other researchers in the Edinburgh Cancer Research Unit
  • Computing and bioinformatics staff in the School and in other relevant University establishments
  • Researchers in other centres and institutions out with The University of Edinburgh

Knowledge, Skills and Experience Needed for the Job

  • A first degree in biology, computer science or related subjects and a higher degree (MSc, MRes or PhD) or relevant experience in bioinformatics
  • Relevant experience
  • Experience in the development of bioinformatics applications working with gene based data, SNP data, microarray data and statistics
  • Experience in general bioinformatics and statistics with a background in studying microarrays (methylation arrays, expression arrays, array CGH), SNPs, sequencing, bioinformatics resources e.g. Ensembl, USCS genome browser, etc
  • Experience in programming (e.g. R, Perl, Python, C++, Java) to develop analysis techniques and pipelines for characterising novel datasets
  • Experience of working in a biological laboratory or in a bioinformatics environment
  • Good communication skills, in particular the ability to work productively with scientific researchers
  • Demonstrable organisational and time management skills


  • Work within the Applied Bioinformatics of Cancer research group but interact with other research groups in the Edinburgh Cancer Research Centre and beyond, where required


  • The role is grade UE07 and attracts an annual salary of £31,342 to £37,394 for 35 hours each week. Salary is paid monthly by direct transfer to your Bank or Building Society account, normally on the 28th of the month. Salaries for part-time staff are calculated on the full-time scales, pro-rata to the Standard Working Week.
  • This post is available on a fixed term basis, with a working pattern of 35 hours per week for 6-9 months initially.

Pension Scheme

  • This role is grade UE07 and therefore the post holder is automatically included in membership of the Universities Superannuation Scheme (USS), subject to the USS membership criteria, unless they indicate that they choose not to join the Scheme.

For further information please visit our pensions website

Eligibility to Work

  • In accordance with the Immigration, Asylum and Nationality Act 2006 the University of Edinburgh, as an employer, has a legal responsibility to prevent illegal working and therefore must check that all employees are entitled to work in the United Kingdom (UK).
  • To do so, the University of Edinburgh requires to see original documents evidencing right to work in the UK before commencement of employment and this is normally carried out at interview. Details will be provided in any letter of invitation to interview.
  • For further information on eligibility to work please visit our eligibility to work website
    In the circumstances where the vacancy does not meet the UKBA advertising, salary and/or qualification level criteria for sponsorship the successful applicant must have the existing right to work in the UK.
  • For applicants interested in sponsorship information is available on our Working in the UK website

Application Procedure

All applicants should apply online by clicking the “apply” button at the foot of this page. The application process is quick and easy to follow, and you will receive email confirmation of safe receipt of your application. The online system allows you to submit a CV and other attachments.
Closing date: 05 December 2014 at 5pm.

Interview date

  • We anticipate interviews will be held in the week commencing [insert date]. You will be notified by email whether you have been shortlisted for interview or not.
  • The University reserves the right to vary the candidate information or make no appointment at all. Neither in part, nor in whole does this information form part of any contract between the University and any individual.

Read More/Apply Online

Sunday, 16 November 2014

MRC studentships for 2014/15

MRC studentships (UK and EU applicants who satisfy eligibility requirements)
Each year the MRC funds a number of studentships at the PPU and are awarded for up to a period of 3.5 or 4 years. The first 9 months of 4-year studentships comprise two 4.5-month rotation projects carried out in different research groups, before the final choice of supervisor is made.
We ask potential applicants to note that there are eligibility criteria for these studentships relating to academic qualifications and nationality. However we welcome all applications from UK citizens and EU nationals as they maybe eligible for other sources of funding, see below. Further information regarding eligibility can be found on the main MRC website
The studentship covers University tuition fees and for 2014/15 the tax-free stipend is £20000 per annum, which is joint-funded by the MRC and our commercial fund. Additional benefits of the MRC studentship include reasonable costs of travel to Dundee and an allocation of £2000 to attend conferences and training courses.

External funding sources

  • We also welcome PhD applications from international students as there are studentships available for outstanding applicants who do not meet the eligibility criteria for MRC funded studentships.

Project-specific funding

  • Occasionally we advertise projects that are supported by other funding bodies. Details of this type of funding will be attached to the individual projects that apply.

PhD Applications

Please send a CV with contact details of three referees to, and also include a covering letter indicating which research labs you would like to work in.
  • Please indicate which type of studentship you are applying for a MRC 3.5 or 4 year (includes 2 x 4.5 months of rotation projects) studentship
  • There is no deadline for PhD applications
  • Note that applicants will only be contacted if invited for interview.
  • Professor John Rouse is in charge of student recruitment. He is assisted by Rachel Naismith.

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Saturday, 15 November 2014

Babraham Institute PhD Studentships for 2015

PhD Studentships at the Babraham Institute
Details of PhD Studentships starting at the Babraham Institute in October 2015 are now available and our Group Leaders welcome informal enquiries.
The aim of our Graduate Programme is to train talented individuals for future roles in science and technology or in the communication and wider application of these disciplines. We provide an environment that provides students with a profound knowledge base in one of our research programmes (Epigenetics, Nuclear Dynamics, Lymphocyte Signalling & Development, Signalling) and aims to sharpen critical abilities through exposure to the discipline of hypothesis-driven research.

The role of the Babraham Research Campus

The Institute is fully equipped for state-of-the-art biological research including: innovative molecular biology, stem cell manipulation and transgenics, epigenetics, next generation sequencing, structural studies on chromatin, real-time laser scanning confocal microscopy, monoclonal antibody production, calcium imaging, fluorescence sorting of cells, gene targeting and knockouts, mouse models of disease, mouse behavioural testing, bioinformatics, computational biology, mass spectrometry for proteomics and lipidomics.
  • PhD studentships can be awarded for up to 3.5 or 4 years respectively. In addition, studentships funded by a range of University of Cambridge funding schemes can be held at the Institute. Students will join a thriving scientific community situated on an attractive parkland campus near Cambridge. Our 60 students are all members of University of Cambridge Colleges and participate fully in University social and academic life.
  • A list of potential projects can be found at:
  • As you will see, the person specification states the minimum knowledge, experience and skills required by the Institute to enable the person to do this job. When you are completing the application form you should remember that it will be used in assessing who should be shortlisted and invited for an interview. Please refer to the person specification and state your reasons for applying for the post, relating your knowledge, experience and skills gained either through work or voluntary activities, to the requirements of the job. If you wish to attach a c.v. or supplementary information please feel free to do so. To ensure no conflict of interest may arise, please indicate on your completed application whether or not you are related to any current member of Institute staff.
  • The Babraham Institute aims to promote equality of opportunity for all with the right mix of talent, skills and potential. The Babraham Institute welcomes applications from diverse candidates. Criminal records will be taken into account for recruitment purposes only when the conviction is relevant. Unless the nature of the work demands it, you will not be asked to disclose convictions which are 'spent' under the Rehabilitation of Offenders Act 1974. Having an 'unspent' conviction will not necessarily bar you from employment. This will depend on the circumstances and background to your offence(s).
  • However, all vacancies within our Nursery are exempt from the Rehabilitation of Offenders Act 1974 because the positions entail working with children.
  • The Babraham Institute is continually trying to find ways to reduce its administrative costs, as such we have made the decision not to write to those candidates who have not been shortlisted for interview. Therefore, please be aware that if you have not heard from us within one month of the closing date, you can assume that your application has been unsuccessful.

Apply for Babraham Institute PhD Studentships for 2015


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Friday, 14 November 2014




On behalf of Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, Biotech Consortium India Limited (BCIL) is coordinating a scheme of practical industrial training for B.Tech./ B.E./ M.Sc./ M.Tech./ Advanced Post Graduate Diploma in Bioinformatics and BINC qualified students. The students are placed for training in Bioinformatics & Biotechnology companies willing to impart practical training to these candidates. The training is for a period of six months during which every trainee is paid a stipend of Rs. 8000/- per month. The company is also paid a bench fee to cover expenses towards training. This programme is mutually beneficial to the students and companies as it provides industrial exposure to the students and an opportunity for industry to select prospective manpower. This programme is advantageous for the companies as it gives them an opportunity to assess the performance of the trainees and subject to availability, suitable trainees could be considered for placement.


Read More/Apply Online

Post-doctoral Research Fellow @ The University of Agder

Post-doctoral Research Fellow in Bioinformatics at the Faculty of Engineering and Science.
The University of Agder (UiA) invites applications for a full-time fixed-term appointment as Post-doctoral Research Fellow in Bioinformatics at the Faculty of Engineering and Science, Department of Natural Sciences for a period of two years. The position will mainly be located in Kristiansand, Norway. However, the appointee may be required to stay for a period at the Institute of Marine Research, Flødevigen (IMR). The preferred start date is 1 May 2015 (negotiable with the department).

University of Agder - intro movie

  • The marine group at the Department of Natural Sciences includes 4 professors, 4 associate professors one Post-doc and currently three PhD fellows are associated. The post-doctoral fellow will also benefit from the Center for Coastal Research (CCR), recently established in cooperation with University of Oslo, Institute of Marine Research, GRID-Arendal, NIVA, Telemark University College (
The postdoctoral-fellow will primarily work in an ongoing international project entitled “Adaptation or plasticity as response to large scale translocations and harvesting over a climatic gradient in the marine ecosystem?” funded by the Research Council of Norway (RCN) under the Havkyst programme. This project aims at improving our understanding of adaptive process in marine fish in response to human and climatic stressors. During its development, large datasets will be generated by means of Next-Generation Sequencing (NGS) approaches, focusing the analysis on Rads and transcriptomics data. The candidate will also have the opportunity to get involved in other ongoing projects at CCR as well as to develop own initiatives.
  • The post-doctoral fellow will be expected to take part in a binding cooperation with the research group and contribute to an active research environment that will give opportunities for personal and professional development. The appointee must have the ability to work in a goal-oriented, organised, focused, and independent manner. During the assessment process emphasis will be placed on the applicants’ PhD work, examination results as well as any other previous research and development work. Relevant practical experience, personal suitability and good teamwork skills will also be emphasised.
  • The successful candidate should hold a PhD in bioinformatics, computer science or a closely related field. Applicants with a PhD in marine genomics and strong computational skills or a PhD in medical science and experience in NGS data analysis are also welcome. The qualified candidate should have experience with the major techniques in Bioinformatics. In addition, he/she will be familiar with Linux/Unix systems as well as programming in script-based language, e.g. Python and/or Perl. Teaching experience from college or university level is an advantage as some teaching tasks may be expected.
  • Information about the appointment criteria for a Post-doctoral Research Fellow can be found in the Regulations Concerning Terms and Conditions of Employment for the Post of Post-doctoral Research Fellow, Research Fellow, Research Assistant and Resident, available for downloadhere.
  • The Norwegian public service is committed to reflect the diversity of society and the personnel policy of the University of Agder aims to achieve a balanced workforce. All qualified persons are therefore encouraged to apply for the position irrespective of cultural background, gender, age or disability.
  • Short-listed applicants will be invited for interviews and with permission from the applicant the University will also conduct a reference check before appointment.
  • Appointment is made by the University of Agder’s Appointments Committee for Teaching and Research Positions. The successful applicant will have rights and obligations in accordance with the current regulations for the public service.
The position is remunerated according to the State salary scale, salary plan 17.510, code 1352, scale 24, salary grade 57 -72 (NOK 482.800-639.500). A 2 % compulsory pension contribution to the Norwegian Public Service Pension Fund is deducted from the pay according to current statutory provisions. For information on salary grades, see here.
  • Applicants are asked to submit their application and CV online. Please use the link “Send application”.
The following documentation should be submitted online.
  • Diplomas, transcripts and letters of reference
  • Complete list of scientific publications
  • A description of research interests, background for the problem that the applicant wishes to study and its relevance for the above mentioned project
In addition, the following documents in three hard copies should be submitted to University of Agder, c/o HR Department, att. HR-adviser Richard Lislevand, Post Box 422, NO-4604 Kristiansand, Norway, quoting “Ref. no. 108/14”:
  • Doctoral dissertation
  • A maximum of ten (10) scholarly and other relevant publications which the applicant wishes to include for assessment
The applicant is fully responsible for submitting complete documentation in a sufficient number of copies within the closing date. Without complete documentation we cannot, unfortunately, include you in the assessment process.
The application and all other information must be submitted, preferably in English, but even Norwegian, Danish or Swedish will be accepted.
  • Closing date: 20.12.14.
Further information about the position may be obtained by contacting Associate Professor Enrique Blanco Gonzalez, phone +47 454 96 531, e-mail:, or Personell Adviser Anne Bergit Jørgensen, +47 38 14 11 40, e-mail:
For more information on working at UiA, see here.
  • In accordance with §25(2) of the Freedom of Information Act, applicants may request that they are not identified in the open list of applicants. The University, however, reserves the right to publish the name of applicants. Applicants will be advised of the intention to exercise this right.

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Thursday, 13 November 2014

PhD in bioinformatics @ UCSF

Deadline: Monday, December 1, 2014
The Bioinformatics pathway at UCSF provides a welcoming environment for a diverse student population, including students with disabilities. We encourage students with strong backgrounds in physics, chemistry, biology, mathematics, computer science, or engineering to apply. Read more about our three research areas.
Applicants interested in the emphasis should apply to the Integrative Program in Quantitative Biology (iPQB), which is an umbrella program for graduate studies in Biophysics, Bioinformatics, and Complex Biological Systems.

San Francisco, UCSF Celebrate Mission Bay Science

Admission is based on:

  • Academic excellence.
  • Letters of recommendation.
  • Research experience.
  • Personal interview.
  • Graduate record examination scores.


  • The application for fall 2015 opens in September 2014.
  • The deadline to apply and provide all supporting materials is December 1, 2014.
  • The Admissions Committee reviews all applications and extends invitations to interview. Our interview visit is February 5-6 and February 12-13, 2015. If invited to interview, your basic travel expenses will be covered by the program.
  • Final admissions decisions will be made by March 2015.

Application requirements

  • Prospective students can apply to only one graduate program at UCSF, with the exception of the Joint Graduate Group in BioEngineering, whose application is administered through the University of California, Berkeley.
  • The minimum requirement for application is a bachelor’s degree with a minimum grade point average (GPA) of 3.0.

General GRE

  • We urge you to take the Graduate Record Examination (GRE) during the fall administration dates in order for us to receive scores by December 1. Scores are reported electronically to the UCSF Graduate Division.
  • Please have scores sent to institution code 4840; a department code is not required.
  • UCSF does not have a minimum GRE score requirement.

Subject GRE

  1. General and demographic information
  2. 3 letters of recommendation
  3. Statements
  4. Upload transcripts (instructions can be found on the application)
  • A non-refundable fee of $90 for U.S. citizens and permanent residents or $110 for international applicants is required to finalize your application.

UCSF Mission Bay: A San Francisco Success Story

International applicants

In addition to the information listed above, international applicants must submit TOEFL scores to institution code 4840. Exemptions to this requirement are available. Details: minimum scores and exemptions.
Due to funding restrictions, we're limited in our ability to accept international students—admission is extremely competitive.
Citizens of Mexico are invited to apply for PhD study at UCSF via our collaboration with UC MEXUS - CONACYT. Candidates must complete the UCSF application in addition to following UC MEXUS - CONACYT guildelines.

Student funding

  1. All students admitted to the Biological and Medical Informatics Graduate Program, and its pathway in Bioinformatics, are supported by funding that covers tuition and fees, as well as a stipend for living expenses.
  2. UCSF commits this support for the entire period of a graduate student's PhD training, as long as he or she remains in good standing. Typically it takes five to six years to earn a PhD degree, at a total cost of approximately $250,000.
  3. Of particular importance to students is the annual stipend they receive for living expenses, which is part of this total.
The graduate student stipend for 2014 is $32,500.
UCSF gathers support for graduate student funding in the basic sciences from the following sources, with the majority coming from the National Institutes of Health (NIH) through faculty grants and training grants.
  • National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health Bioinformatics Training Grant
  • National Institute of Biomedical Imaging and Bioengineering (NIBIB) of the National Institutes of Health Integrative Program in Complex Biological System Training Grant
All matriculated students are encouraged to apply for pre-doctoral fellowships.
                                Sources of PhD student support
  • Faculty grants
  • Federal training grants (NIH)
  • UCSF Graduate Division funds
  • UCSF Chancellor's Office funds
  • Internal fellowships
  • External fellowships
  • Endowment gifts for program support and scholarship
  • UCSF School of Pharmacy/School of Medicine funds

Apply Online


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