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Thursday, 30 October 2014

The most cited Bioinformatics papers of all time

nature
The discovery of high-temperature superconductors, the determination of DNA’s double-helix structure, the first observations that the expansion of the Universe is accelerating — all of these breakthroughs won Nobel prizes and international acclaim. Yet none of the papers that announced them comes anywhere close to ranking among the 100 most highly cited papers of all time.
Citations, in which one paper refers to earlier works, are the standard means by which authors acknowledge the source of their methods, ideas and findings, and are often used as a rough measure of a paper’s importance.
  • Fifty years ago, Eugene Garfield published the Science Citation Index (SCI), the first systematic effort to track citations in the scientific literature. To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time. (See the full list at Web of Science Top 100.xls or the interactive graphic, below.) The search covered all of Thomson Reuter’s Web of Science, an online version of the SCI that also includes databases covering the social sciences, arts and humanities, conference proceedings and some books. It lists papers published from 1900 to the present day.

The paper mountain

Bioinformatics

  • The rapid expansion of genetic sequencing since Sanger’s contribution has helped to boost the ranking of papers describing ways to analyse the sequences. A prime example is BLAST (Basic Local Alignment Search Tool), which for two decades has been a household name for biologists wanting to work out what genes and proteins do. Users simply have to open the program in a web browser and plug in a DNA, RNA or protein sequence. Within seconds, they will be shown related sequences from thousands of organisms — along with information about the function of those sequences and even links to relevant literature. So popular is BLAST that versions8, 9 of the program feature twice on the list, at spots 12 and 14.
But owing to the vagaries of citation habits, BLAST has been bumped down the list by Clustal, a complementary programme for aligning multiple sequences at once. Clustal allows researchers to describe the evolutionary relationships between sequences from different organisms, to find matches among seemingly unrelated sequences and to predict how a change at a specific point in a gene or protein might affect its function. A 1994 paper10 describing ClustalW, a user-friendly version of the software, is currently number 10 on the list. A 1997 paper11on a later version called ClustalX is number 28.
  • The team that developed ClustalW, at the European Molecular Biology Laboratory in Heidelberg, Germany, had created the program to work on a personal computer, rather than a mainframe. But the software was transformed when Julie Thompson, a computer scientist from the private sector, joined the lab in 1991. “It was a program written by biologists; I’m trying to find a nice way to say that,” says Thompson, who is now at the Institute of Genetics and Molecular and Cellular Biology in Strasbourg, France. Thompson rewrote the program to ready it for the volume and complexity of the genome data being generated at the time, while also making it easier to use.
The teams behind BLAST and Clustal are competitive about the ranking of their papers. It is a friendly sort of competition, however, says Des Higgins, a biologist at University College Dublin, and a member of the Clustal team. “BLAST was a game-changer, and they’ve earned every citation that they get.”
  • Here Nature tours some of the key methods that tens of thousands of citations have hoisted to the top of science’s Kilimanjaro — essential, but rarely thrust into the limelight.
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The most cited bioinformatics papers of all time:

Rank: 10 Citations: 40,289
Clustal W:
improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson, J. D., Higgins, D. G. & Gibson, T. J
Nucleic Acids Res. 22, 4673–4680 (1994).
Rank: 12 Citations: 38,380
Basic local alignment search tool.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J.
J. Mol. Biol. 215, 403–410 (1990).
Rank: 14 Citations: 36,410
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs.
Altschul, S. F. et al.
Nucleic Acids Res. 25, 3389–3402 (1997).
Rank: 20 Citations: 30,176
The neighbor-joining method: A new method for reconstructing phylogenetic trees.
Saitou, N. & Nei, M.
Mol. Biol. Evol. 4, 406–425 (1987).
Rank: 28 Citations: 24,098
The CLUSTAL_X Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G.
Nucleic Acids Res. 25, 4876–4882 (1997).
Rank: 41 Citations: 21,373
Confidence limits on phylogenies: an approach using the bootstrap
Felsenstein, J.
Evolution 39, 783–791 (1985).
Rank: 45 Citations: 18,286
MEGA4:
Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Tamura, K., Dudley, J., Nei, M. & Kumar, S.
Mol. Biol. Evol. 24, 1596–1599 (2007).
Rank: 57 Citations: 15,993
Maximum likelihood from incomplete data via EM algorithm.
Dempster, A. P., Laird, N. M. & Rubin, D. B.
J. R. Stat. Soc., B 39, 1–38 (1977).
Rank: 71 Citations: 14,462
PROCHECK:
a program to check the stereochemical quality of protein structures. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M.
J. Appl. Crystallogr. 26, 283–291 (1993).
Rank: 76 Citations: 14,099
MODELTEST:
Testing the model of DNA. Posada, D. & Crandall, K. A.
Bioinformatics 14, 817–818 (1998).
Rank: 82 Citations: 13,496
MOLSCRIPT:
a program to produce both detailed and schematic plots of protein structures. Kraulis, P. J.
J. Appl. Crystallogr. 24, 946–950 (1991).
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Crystallography

George Sheldrick, a chemist at the University of Göttingen in Germany, began to write software to help solve crystal structures in the 1970s. In those days, he says, “you couldn’t get grant money for that kind of project. My job was to teach chemistry, and I wrote the programs as a hobby in my spare time.” But over 40 years, his work gave rise to the regularly updated SHELX suite of computer programs, which has become one of the most popular tools for analysing the scattering patterns of X-rays that are shot through a crystal — thereby revealing the atomic structure.
  • The extent of that popularity became apparent after 2008, when Sheldrick published a review paper24 about the history of the system, and noted that it might serve as a general literature citation whenever any of the SHELX programs were used. Readers followed his advice. In the past 6 years, that review paper has amassed almost 38,000 citations, catapulting it to number 13 and making it the highest-ranked paper published in the past two decades.
  • The top-100 list is scattered with other tools essential to crystallography and structural biology. These include papers describing the HKL suite25 (number 23) for analysing X-ray diffraction data; the PROCHECK programs26 (number 71) used to analyse whether a proposed protein structure seems geometrically normal or outlandish; and two programs27, 28 used to sketch molecular structures (numbers 82 and 95). These tools are the “bricks and mortar” for determining crystal structures, says Philip Bourne, associate director for data science at the US National Institutes of Health in Bethesda, Maryland.
  • An unusual entry, appearing at number 22, is a 1976 paper29 from Robert Shannon — a researcher at the giant chemical firm DuPont in Wilmington, Delaware, who compiled a comprehensive list of the radii of ions in a series of different materials. Robin Grimes, a materials scientist at Imperial College London, says that physicists, chemists and theorists still cite this paper when they look up values of ionic size, which often correlate neatly with other properties of a substance. This has made it the highest formally-cited database of all time.
“We often cite these kinds of papers almost without thinking about it,” says Paul Fossati, one of Grimes’s research colleagues. The same could be said for many of the methods and databases in the top 100. The list reveals just how powerfully research has been affected by computation and the analysis of large data sets. But it also serves as a reminder that the position of any particular methods paper or database at the top of the citation charts is also down to luck and circumstance.
Still, there is one powerful lesson for researchers, notes Peter Moore, a chemist at Yale University in New Haven, Connecticut. “If citations are what you want,” he says, “devising a method that makes it possible for people to do the experiments they want at all, or more easily, will get you a lot further than, say, discovering the secret of the Universe”.

Read Full Article @ nature.com

Wednesday, 29 October 2014

JRF(Bioinformatics) @ University College of Medical Sciences

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Subject : Adhoc appointment of Staff under time-bound Research Project, sponsored by Department of Biotechnology( DBT), Govt. of India, New Delhi
Applications are invited by post or in person at the above mentioned address, up to 04.11.2014[Tuesday,4th November,2014] for Ad-hoc appointment of one Junior Research Fellow under time-bound Research Project entitled “"Transcriptome analysis for identification of novel biomarker for disease progression in Dengue patients”, a collaborative project of Translational Health Science, Technology Institute, Gurgaon, School of Tropical Medicine, Kolkata, & University College of Medical Sciences[ University of Delhi], sponsored by Department of Biotechnology, Govt. of India, for a period of three years, depending on the progress of the work and approval of the funding agency
  • Name of the Post: Junior Research Fellow
  • Number of Posts : ONE
  • Rs. 16,000/- + HRA For 1st & 2nd year and Rs.18, 000/- + HRA for 3rd year for NET-JRF Qualified.
  • Rs.12000/- + HRA For 1st & 2nd year and Rs.14000/- + HRA for the 3rd year for NET – LS qualified.

Essential Qualifications

  • Post-graduate in Life Sciences/Basic Sciences/Bioinformatics or any related field including Research in Basic Sciences with or without NET qualification.

Desirable:

  • Candidates with experience in any of the following areas will be preferred:
  1. Bioinformatics analysis, Perl/Python etc.
  2. Molecular Biology techniques
  3. Immunological techniques
  4. Microbiology

GENERAL TERMS & CONDITIONS:

  • The probation period for this position will be will be six months. The probation may be extended at the discretion of the competent authority.
  • The above appointment is purely contractual in nature and those appointed to this post will not have any claim for regularization of their employment.
  • All educational, professional and technical qualification should be from a recognized Board/University.
  • The experience requirement specified shall be experience acquired after obtaining the minimum educational qualifications required for the post.
  • The age limit, qualification, experience and other requirements for the post is relaxable at the discretion of the competent authority, in case of candidates otherwise well qualified.
  • Incomplete applications will stand summarily rejected.
  • In case a large number of applications are received for the post, screening will be done to limit the number of candidates to those possessing higher/relevant qualification.
  • Only shortlisted candidates will be called for interview.
  • Canvassing in any form will be a disqualification.
  • Applications with details of qualifications and work experience may be submitted on-line at proj.den@gmail.com
  • Selected candidates shall have the opportunity to enroll for PhD degree as per the rules of Faculty of Medical Sciences, University of Delhi.
  • No accommodation/medical benefits etc. will be applicable and no TA/DA would be paid for attending the interview.
  • Contact telephone number and E-Mail Id must be mentioned in the application form submitted for the post.
Short listed candidates will be informed by email or telephonically to appear before Staff Selection Committee for appointment at Virology Laboratory, Room No. 311, 3rd floor, Department of Microbiology, UCMS & GTB Hospital, Dilshad Garden, Delhi – 110095. Kindly bring all your original certificates/testimonials along with one set of photocopies. The post is purely temporary, on ad-hoc basis for the period of one year and may be extended based on satisfactory performance and approval of funding agency for the subsequent period.
  • CLOSING DATE FOR RECEIPT OF APPLICATIONS: 04.11.2014

NOTICE FOR CIRCULATION

Read More

Tuesday, 28 October 2014

RESEARCH INTERN(Bioinformatics) AWARDS @ NISCAIR

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Applications are invited for 16 Research Intern Awards from Indian nationals, who are creative and have passion and desire to pursue S&T as a career. CSIR Diamond Jubilee Research Intern Awards scheme is meant to be a preparatory phase for young interns imbibing the spirit of enquiry and learning the tools and techniques of research through participation and doing. The scheme thus seeks for young interns to gain from the knowledge and experience of accomplished scientists by working with them and to take up S&T as a career.

About NISCAIR:

  • National Institute of Science Communication And Information Resource (NISCAIR) is devoted to science communication and dissemination and S&T information. Broadly the core activity of NISCAIR is to collect/ store, publish and disseminate S&T information which benefits different segments of society. The Institute offers wide range of information services ranging from literature search to production and printing of S&T publications. The Institute has strong Human Resource Development Programme for training personnel in library & information science, documentation, science communication, IPR and herbarium techniques. NISCAIR also undertakes projects on turnkey basis for other organizations.

Eligibility:

  • Only the Candidates whose final results have been declared, as on date of interview may apply
Post
Code
Qualification DIV./JOU./
PRO.
No. of
positions
Date of
Interview
2 First class M.Sc. Chemistry (preferably Organic Chemistry)/Bioinformatics OR
equivalent GPA
LRF- Proj.
(TKJ)
01 20th November 2014
5 First class B. Tech./ M. Sc. Or equivalent GPA in Botany/ Life Science.
Desirable: Flair for translation from Hindi to English and vice versa,
proficiency in reading and writing Hindi Language
BKS,CSIR-Samachar 01 20th November 2014
6 First Class M.Sc. OR Equivalent GPA in Botany/ Life Science.
Desirable: 1.Specialization in Ethnobotany or Ethnobotany's one
subject/ paper at PG level.
2. Working knowledge of editing on computer.
IJTK 01 20th November 2014
8 First Class M. Sc. in Biochemistry/ Biotechnology/ Life Science OR
equivalent GPA
IJBB 01 20th November 2014
9** First Class M. Sc. OR Equivalent GPA in Life Science/ Bioscience IJEB 01 20th November 2014
* The total number is tentative and may vary as per subsequent requirements.
The applicant should be well conversant with the use of Computers/ must possess writing skills in their specific areas of specialization/ able to conduct search through internet/ able to do routine correspondence/ management of library activities/ editing / compilation/ data management/ experience in data entry pertaining to NISCAIR activities.
  • Age Limit : Not more than 25 yrs. as on the date of interview which is relaxable up to 5 years in case of SC/ ST/OBC/ Physically Handicapped and female candidates.
  • Stipend: Rs.15000/- per month consolidated. No other allowance is admissible.
  • Leave: The interns shall be entitled 30 days leave in a year and shall avail leave with the permission of the competent authority (i.e. 2.5 day leave after completion of each month)
  • Tenure: Maximum period of 02 yrs not extendable under any circumstances and subject to satisfactory performance to be evaluated every 06 months. The interns shall have no claim for further extension, absorption or regularization in CSIR after the expiry / termination of the internship.
  • Mode of Selection: Candidates must report at the NISCAIR reception desk at 9.00 A.M. (Candidates will not be entertained after 9.30 A.M.). The selection of the RIs would be based on (a) academic records, and/ or (b) performance in the test and (c) interview. In case the number of candidates is large the Selection Committee may adopt higher cut offpercentage of academic records, as a measure to short list candidates for interview.

How to Apply :

The prescribed application form can be downloaded from NISCAIR website and duly filled in forms may be submitted at the time of interview. The application forms should be accompanied by attested photograph and copies of testimonials/ certificates in support of age, educational qualifications, experience and caste / tribe etc. mentioned in the application. The applicant must also bring all original certificates/ testimonials at the time of test/ interview for verification.
  • ** For Post Code-11 candidates may possess any of the specialization- " Agriculture including interdisciplinary fields suchas Biochemistry, Biotechnology, Bioinformatics, Microbiology and allied fields, Genetics and allied fields, Physiology, Nanoscience, Nanotechnology, Toxicology, Neuroscience, Bioengineering, Food Technology, Food Science, Nutrition, Pharmacology or B. Tech in Biotechnology/Bioinformatics/Agriculture Or BS-MS (integrated) in Biological Sciences

Venue for Walk-in-Interview(20th November 2014)

NISCAIR, Dr. K. S. Krishnan Marg,
Near Rajendra Nagar Metro Station,
Pusa Gate, New Delhi – 110012

Application form

Read More

Monday, 27 October 2014

4 year PhD Scholars Programme @ The Radcliffe Department of Medicine

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The Radcliffe Department of Medicine at the University of Oxford is a large multi-disciplinary Department that links high quality basic biological science with medical applications. RDM scientists were rated at the highest level in both basic science and clinical research across a wide range of fields in the last UK Research Assessment Exercise (RAE).
The department has internationally renowned programmes in a broad spectrum of sciences related to medicine, including:
  • Cardiovascular Medicine
  • Diabetes, Endocrinology & Metabolism
  • Genes, Genetics & Genomics
  • Haematology & Pathology
  • Immunology
  • Regenerative Medicine & Stem Cells
  • Acute Stroke

Oxford in Your Day

  • These themes span the translational research spectrum, from basic biological research through to clinical application.
We are committed to training the next generation of scientists in biological and clinical sciences through our graduate programme at the University of Oxford. Our PhD Scholars Programme is open to outstanding candidates of any nationality. It provides fully-funded awards for students wishing to undertake a 4-year DPhil in Medical Sciences or Cardiovascular Medicine.
  • Students are full members of the University of Oxford, have their College and University fees paid (home/EU or overseas) and receive a generous stipend of £18,000/annum. These awards allow students to carry out research in a single laboratory for the full 4 years.
  • Further details on the application process and the wide range of projects are available on the RDM website. Individual supervisors can also be contacted by email about their projects.
  • The closing date for applications is 12 noon (midday) on 9th January 2015
  • Interviews will take place on 28th & 29th January 2015
  • Offers will be made in early February 2015

The Radcliffe Department of Medicine actively promotes a family friendly working environment.

DPhil Projects List

The majority of applicants to the DPhil in Medical Sciences and the DPhil in Cardiovascular Medicine apply to work with a specific PI on a predefined project. The project list below shows projects available for entry in October 2015. The list can be resorted by supervisor or research theme or filtered by research theme.
  • We encourage applicants to contact their prospective supervisors to discuss projects and their suitability to carry out research in advance of application. In any particular year, some Principal Investigators choose not to advertise any projects. If you are particularly interested in working with a specific PI and no project is listed, please contact them directly to enquire as to whether they will be offering projects or accepting students in October 2015.
  • If you are applying for a project and are seeking funding, please see our funding overview for further information.
  • Please note that all projects are provisional and may be revised before you start or during the period of research owing to developments in the field and refinement of research topics.
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Bioinformatics, Statistics & Computational Biology Project Overview

Risk stratification and personalised management support in heart failure

The provision of evidence-based care to heart failure patients is a growing challenge to health systems worldwide. It has been suggested that IT- supported systems of care that enable patients and their caregivers to monitor and manage their own health may improve patient outcomes and increase the capacity of health systems to provide chronic care more efficiently.
  • The SUPPORT-HF (Seamless User-centred Proactive Provision Of Risk-stratified Treatment for Heart Failure) is a study of IT-supported home monitoring and management in heart failure. The system is based on a tablet PC which is wirelessly connected to several sensors. These are used to measure blood pressure, heart rate, weight, blood oxygen level, drug adherence, activity patterns as well as patient reported outcomes. The home monitoring data is also being linked to patient’s records to retrieve additional information about test results and treatment plans.
  • We have now completed the first stage of the study, which has established a high standard of usability and strong patient adherence of the tele- health platform. We are now starting the second phase of the study as a randomized trial of about 200 patients to test the feasibility and safety of remote drug management in this patient population.
  • A DPhil student is sought to derive and validate an adaptive early risk prediction and clinical decision support algorithm, which is to enhance the SUPPORT-HF tele-health system. This work will use multiple data sources from both observational datasets (e.g. Clinical Practice Research Datalink (CPRD)) as well as interventional studies (SUPPORT-HF 2 randomized trial),  to detect patterns of variation that correlate with health and adverse clinical outcomes. Where appropriate, evidence-based treatment recommendations are to be enhanced by information about intervention costs and patient preferences. As part of a background research, a review of existing clinical decision support systems as well as the personalisation of care with the use of  ICT  is to be performed.

Training Opportunities

  • This is an interdisciplinary project with involvement of researchers across several departments of the University. The learning opportunities available are wide-ranging and may involve learning and applying advanced statistical methods, as well as learning about complex intervention trials, implementation research and cardiovascular medicine.
  • The George Institute provides an exceptional educational environment with expert individual supervision and support from several of experienced and enthusiastic researchers with backgrounds in clinical medicine, statistics, epidemiology and engineering.

Theme

  • Bioinformatics, Statistics & Computational Biology and Evidence-based Practice, Epidemiology & Health

Admissions

Project reference number: 573

Information for Applicants

The Radcliffe Department of Medicine (RDM) is a large multi-disciplinary department with research interests that span the translational spectrum, from basic biological research through to clinical application. We are able to offer research degrees in a broad range of sciences related to medicine, ranging from cardiovascular, diabetes, endocrinology, and stroke research, to molecular medicine, immunology, haematology and pathology, including programmes in stem cell & regenerative medicine.
  • We offer two DPhil (Doctor of Philosophy) degrees, which are the University of Oxford equivalent of a PhD. The DPhil in Medical Sciences covers all areas of RDM research. Complementing this, our DPhil in Cardiovascular Medicine covers the entire spectrum of cardiovascular research. In keeping with our focus on translational research, applications are welcomed from both basic scientists and clinicians for either programme.
A DPhil typically lasts 3-4 years, depending on the project and the student. We have considerable experience supervising clinicians who hold 3-year fellowships and tailor research projects for such students accordingly. Students are admitted to work on a specified research project in a single laboratory, with close supervision from one or more of our PIs and their team.

DPhil Projects

  • The majority of our applicants apply to undertake a project advertised on our DPhil Project List, which is refreshed in September each year. The projects listed span the research that is being done in RDM. Please be aware that it is usual for projects to be modified during the early stages of research. We actively encourage DPhil students' input in refining the parameters of their research.
  • A small number of applicants have their own plans for a research project or develop a research project in collaboration with a proposed supervisor which is not on the DPhil project list. (This is sometimes called a 'direct application'.) In such cases, you must contact your proposed supervisor in advance of application in order to discuss whether the project is viable within their laboratory and whether available funding will be sufficient to cover research costs. Your initial email should contain your curriculum vitae and names and addresses of referees. If your prospective supervisor indicates that he/she is able to supervise your project then you should apply online in the usual way. Your application will go through the standard Departmental selection process; your supervisor's acceptance does not constitute acceptance onto the programme.
  • Eligibility for funding is unaffected by which type of application you make.

Fees and Living Costs

  • Before being admitted to the University, students must demonstrate their ability to cover their fees and living costs. You will be asked to complete a financial declaration to show that you understand the costs involved and that you have plans in place to finance yourself through your studies.

Funding

  • Most of our students, whether basic scientists or clinical fellows, are fully funded. The Department is able to offer full funding at a generous level for basic scientists and our PIs have considerable experience in supporting clinicians in their applications for Clinical Research Fellowships (CRF).
  • In order to be considered for Departmental funding schemes your application must be received by the January deadline each year. We are able to consider applications from applicants with external funding at other times of the year.

Making an Application

You must submit your application online using the University's application form. If you are applying for a funded place you must submit your application, including all supporting materials and references, by the deadline in early January. You can find more information on making an application on our how to apply page.
  • If you are an international student, you may need to provide evidence of your English language abilities in order to secure a place.
  • All students are also members of a college. You do not need to specify a college preference, but you are welcome to do so. Please be aware that an offer of a place on the DPhil programme will not constitute a guarantee that you will be offered a place in your first choice college.

Read More /Apply

Saturday, 25 October 2014

Bioinformatics Insight

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Introduction to bioinformatics with Dr. Steve Jones, Head, Bioinformatics, Genome Sciences Centre, BC Cancer Agency
In 2005 Steven Jones was identified as one of Canada's top 40 professionals under 40 by Caldwell Partners International as well as by Business in Vancouver. He also received the Spencer Award for IT innovation as well as the 2007 Medical Genetics teaching award for UBC. Further contributions include his involvement as the founding director of the CIHR/MSFHR Bioinformatics Training Program as well as director of the University of British Columbia Bioinformatics Graduate Program. In 2011 he was inducted as a Fellow of the Royal Society of Canada for his contributions to Genomics and Bioinformatics. In 2012, Dr Jones was a recipient of the prestigious UBC Killam teaching prize in recognition of his contributions to graduate bioinformatic education.

Dr. Steven Jones, PhD

Head of Bioinformatics and Associate Director, Michael Smith Genome Sciences Centre, BC Cancer Agency
Professor, Molecular Biology & Biochemistry, Simon Fraser University
Professor, Medical Genetics, University of British Columbia
Read More
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Friday, 24 October 2014

PhD Fellowships in Bioinformatics & Bioscience @ QBM,Munich, Germany

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Welcome to the Graduate School of Quantitative Biosciences Munich (QBM). This newly established School is designed to prepare young life scientists for the emerging era of quantitative, systems-oriented bioscience. It provides an innovative, integrated PhD training program that is international in outlook and brings together a range of diverse disciplines, from biochemistry and medicine to bioinformatics, experimental and theoretical (bio-)physics, and applied mathematics. Both student research projects and classroom teaching are highly interdisciplinary, with a thematic focus on the problem of gene regulation in all its facets. The School is a joint initiative by leading scientists from the Ludwig-Maximilians-University (LMU) Munich as well as from the Max-Planck Institute of Biochemistry and the Helmholtz Center Munich.

PhD Program

QBM offers an integrated interdisciplinary PhD program that consists of three main components:

  1. An interdisciplinary research project jointly supervised by two PIs from different fields.
  2. A substantial program of formal course work with a general and an individual component, centered around an interdisciplinary core course that covers key problems in bioscience from multiple perspectives.
  3. Further activities to enhance students’ communication and other transferable skills.
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Key components of the PhD program and course of study

Beyond the formal curriculum, QBM offers its students a multi-facetted mentoring and support structure to help them grow into independent scientists. Aside from their research advisors and lab colleagues, they are able to call upon assistance and advice from their thesis advisory committee. The QBM central staff, in particular the two lecturers (one from an experimental, one from a theoretical discipline) are available to informally advise and coach students as they navigate the complex demands of interdisciplinary research and communication. The administrative staff assists students with all matters relating to relocation and living and working in Germany. QBM students will also have many opportunities to interact with one another, in their courses and through attendance of lecture series, annual retreats and other events.
  • The QBM doctoral program is fully Bologna compatible and leads to a PhD degree. Students submit their written thesis to a thesis evaluation committee, composed of their TAC (thesis advisory committee) and one external reviewer. The PhD defense consists of a public presentation and an examination in closed session with the committee.
  • QBM students receive an attractive compensation package that is competitive with other top graduate schools in the life sciences in Europe. The comprehensive financial support includes a fellowship package totaling 1700 €/month in take-home pay. In addition, the School provides financial support for educational and scientific activities such as conference travel, as well as relocation and child care expenses. The School does not charge tuition or other fees.

Research

The aim of an integrated quantitative analysis of biological systems is to accurately describe the outcome of a multitude of molecular interactions and to forecast system behavior under various internal and external perturbations. To achieve this goal, it is necessary on the one hand to measure the status and behavior of all participating components as precisely as possible, ideally at high resolution, time-resolved, and at genome-scale. This requires new technologies and experimental methods: many types of approaches, such as biochemical or in vivo binding and kinetic assays, have yet to be made sufficiently quantitative or scaled to permit high-throughput testing.
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  • On the other hand, the complex data sets resulting from such experiments need to be evaluated and integrated, posing profound challenges for statistical data analysis, mathematical modeling and theory. Genome-scale experiments (microarrays, deep sequencing, mass spectrometry, high throughput assays, high content microscopy) often produce noisy data, and the dynamic range, error, and limitations of the different methods vary significantly, making comparisons difficult. New inference methods need to be developed for the intelligent analysis of such data sets, to extract information about the underlying biochemical networks.
  • More demanding still is the next step: integrating the data to create predictive quantitative models that realistically capture the underlying biochemical and biological processes; the conceptual and mathematical approaches for this task are only beginning to be developed. To make progress in these areas, established disciplines are no longer able to function autonomously; rather, scientists from diverse fields such as biochemistry/structural biology, molecular and organismal genetics, biophysics and physical chemistry, statistics, bioinformatics, theoretical physics and mathematics have to interact and collaborate.

Requirements

We invite MSc graduates from any relevant discipline (biochemistry, biophysics, (physical) chemistry, theoretical physics, mathematics, statistics, (bio)informatics) and any country who are interested in interdisciplinary research to apply; we particularly encourage the application of women.
  • Please note that you need to have completed your Master's degree by the time you start the QBM program, but not necessarily at the time of application.

Applicants have to submit:

  • academic record (high school, Bachelor and Master’s transcripts)
  • 2 letters of recommendation
  • 2 brief essays – one describing the student’s prior research experience, the other describing the reasons for their interest in the QBM program and research goals
  • an indication of their specific research interests
Highly promising students who do not have a Master’s degree will be offered the option of qualifying by passing an entrance exam.
  • The Application Tool is now open (application window for the class starting in September/October 2015).
  1. Application deadline is January 5, 2015 (12pm CET).
  2. Deadline for references is January 10, 2015 (12pm CET).
  3. Candidates will be notified by January 30, 2015.
  4. The Interview week in Munich is scheduled for February 23-27, 2015.

How to apply:

Requirements

For detailed information about our application requirements see:http://www.qbm.lmu.de/requirements/
Please note that you need to have completed a Master's degree or equivalent in a relevant field prior to starting the PhD program.  In exceptional circumstances, highly promising students with a Bachelor’s degree can qualify by passing an entrance exam; please contact us directly by email.

Registration

  • In order to apply for the program, you need to register first. You will have to enter your name and choose a username and password. You will then immediately receive a confirmation email with an activation link that will give you access to our online application tool.

PhD research

  • In your application, please select up to four research groups you are interested in. You can find details about research areas and participating research groups on our webpage: http://www.qbm.lmu.de/research/

Letters of recommendation

To process your application, we need at least two letters of recommendation from scientists familiar with you and your work (e.g. Master or Bachelor advisor) . A third letter of recommendation is optional. You will be asked to provide email addresses of your referees, they will then be invited to submit a letter of recommendation on your behalf. You can monitor receipt of the letter within the online application tool; it is your responsibility to make sure that the referees submit their letters by the application deadline.

Please take note of the following rules:

  • You have to apply using our online application tool; applications submitted by mail or email will not be considered
  • You have to submit your application in English
  • Incomplete applications will not be considered
  • Please remember to formally submit your application by clicking the “Submit” button once your application is complete. Applications that are not submitted will not be considered
  • We do not charge application fees
  • The maximum file size per uploaded document is limited to 5 MB
Applications will be independently reviewed by multiple QBM members. The most promising candidates will be selected for personal interviews in Munich, based on academic qualification, research experience, motivation, scientific background and the letters of recommendation .

Selection Procedure

Based on their written application, selected candidates will be invited for a one week visit to Munich to explore the mutual interest. The week consists of brief scientific presentations by the PIs of QBM, 4 interviews of each candidate with PIs whose research they expressed interest in, subsequent visits to the labs and further discussion of potential projects with PI and appropriate co-PI. At the end of the week, both candidates and PIs have to declare their prioritized interests; candidates who have met our criteria and are matched with an interdisciplinary PI/co-PI pair will be invited to join the program. We expect to admit 25 students per year on average.
Travel expenses and accommodation for the interview week will be covered by QBM.

Contact

  • For further information or questions do not hesitate to contact us!

Professor Dr. Ulrike Gaul (speaker of QBM)
Alexander von Humboldt-Professor
Gene Center of the LMU
Department of Biochemistry
Feodor-Lynen-Strasse 25
81377 Munich
Germany
phone: +49.(0)89.2180.76878
fax: +49.(0)89.2180.76704
gaul@genzentrum.lmu.de
Professor Dr. Erwin Frey (co-speaker of QBM)
Faculty of Physics
Theresienstr. 37
80333 Munich
Germany
phone: +49.(0)89.2180.4538
fax: +49.(0)89.2180.4154
erwin.frey@physik.lmu.de
Dr. Michael Mende (Administrative Coordinator)
Gene Center of the LMU
Department of Biochemistry
Feodor-Lynen-Strasse 25
81377 Munich
Germany
phone: +49.(0)89.2180.76841
fax: +49.(0)89.2180.76799
mende-qbm@genzentrum.lmu.de

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Bioinformatics Jobs @ NEHU,Shillong,India

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North-Eastern Hill University was set up by an Act of Parliament and notified on 19th July 1973.
The objectives of the University, as laid down in the act, are "to disseminate and advance knowledge by providing instructional and research facilities in such branches of learning as it may deem fit; to pay special attention to the improvement of the social and economic conditions and welfare of the people of the hill areas of the North-eastern region, and in particular, the intellectual, academic and cultural advancement".

#1:JRF(3 nos.) & Project Assistant (1)

Applications with complete bio-data from candidates possessing the required qualifications are invited for the posts of Junior Research Fellow (3) and Project Assistant (1) in DBT, GOI-funded research project “Next Generation Sequencing (NGS)- based de novo assembly of expressed transcripts and genome information of Orchids in North-East India” in DBT’s Twinning programme for NE, sanctioned for a period of 3 years.

(i) Posts: JRF (3 nos.)

  • @ Rs. 16,000/- plus 10% HRA p.m. for the 1st and 2nd year and SRF @ Rs.18,000/- plus 10% HRA for the 3rd year - applicable only if JRF/SRF is NET/GATE/BET/BINC qualified, otherwise it shall be @ Rs. 12,000 + 10% HRA p.m. for the 1st two years and Rs.14,000 plus 10% HRA for the 3rd year for SRF.
  • Qualifications: M.Tech/M.Sc in Life Sciences/ Botany/ Zoology/ Biochemistry/ Biotechnology/ Bioinformatics.
  • Desirable: Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis

(ii) Project Assistant (1) @ Rs. 8,000/- p.m.

  • Qualifications: The candidate must be a graduate in science.
  • Desirable: Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.
The applications through email bicnehu@gmail.com or post must reach the undersigned within 15 days from the date of publication of this advertisement. The advertised posts are purely temporary for the duration of the project and subject to availability of the funds from DBT. The appointment does not confer any entitlement or right over the posts for absorption in the University service.

#2:Senior Research Fellow

Advertisement for the post of a Senior Research Fellow in a DST-SERB funded Research Project Applications are invited for the post of One Senior Research Fellow to be appointed in a DST-funded major research project entitled “Biochemical and functional properties of Synechocystis Glutathione S-transferase(s)” sanctioned to Dr. Timir Tripathi, Molecular and Structural Biophysics Laboratory, Department of Biochemistry, NEHU, Shillong.
  • Stipend: Rs. 18,000/- + 20% HRA per month.
  • Essential Qualifications: M.Sc. or equivalent with a good academic record and 2 years research experience is a prerequisite. Student should have atleast 2 publications in journals of national/international repute.
  • Strong experience in bioinformatics/computational biology is essential.
Interested students can email their detailed bio-data including mobile number and recent photograph to msb.biochem@gmail.com, latest by 03.11.14. The hard copy of the application is not required at this stage. The date of interview will be informed after primary scrutiny of the applications. No TA/DA will be paid if called for interview.

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Wednesday, 22 October 2014

JRF in Bioinformatics @ IIT,Delhi

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Candidates of Indian nationality are invited to appear for the Walk-in test / interview for project appointments under the following project. Appointment shall be on contractual basis on consolidated pay renewable yearly or upto the duration of the project, whichever is earlier.
Title of the Project
Next Generation Sequencing (NGS) – Based De Novo Assembly of Expressed Transcripts and Genome Information in North-East India (RP02943)
Funding Agency
Department of Biotechnology (DBT)
Name of the Project
Investigator
Prof. D. Sundar
Deptt/.Centre
Department of Biochemical Engineering & Biotechnology
Duration of the Project
Upto:06.08.2017
Post (s) Consolidated Pay-slab Qualifications
Jr. Research Fellow Rs.16,000/- p.m. plus HRA @ 30%
          Or
Rs.12,000/- p.m. plus HRA @ 30% (without NET/GATE qualified candidates)
Essential: Candidates having first class B. Tech. /
M.Sc. Degree or equivalent in Bioinformatics / Biotechnology / Life Sciences / Molecular Biology      or any other related field with NET/GATE qualification.
Desirable: Candidates having computer skills
(Linux, Perl, Java, MySQL) and / or experience in advanced Molecular Biology, next generation sequencing data analysis, MD Simulations will be preferred.
Walk In Test / Date of Interview      Time of Interview             Venue
11/11/2014 03.00 p.m.
Committee Room No. 230, Block-I, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016.
Ph: 011-26591061
The candidates who fulfill the above qualifications/experience should appear for the interview. Kindly bring your formal application on Form No. IRD/REC-4, which can be downloaded from IRD Website (http://ird.iitd.ac.in/rec) through proper channel along with complete information regarding educational qualifications indicating percentage of marks of each examination passed, details of work experience and a recent passport size photograph, along with original certificates (both academic & professional) for verification on the date of interview. No candidate, who is already employed at the Institute / IRD shall be interviewed unless his/her application has been duly forwarded by their concerned establishment/sections. 5% relaxation of marks may be granted to the SC/ST Candidates. In case of selection of a retired/superannuated government employee, his/her salary will be fixed as per prevailing IRD norms.
  • In case any clarification is required on eligibility regarding the above post, the candidate may contact Prof. D. Sundar at his e-mail id: sundar@dbeb.iitd.ac.in

Application Form for Selection under IRD Sponsored Projects/Consultancies


Jr. Research Fellow @ INDIAN INSTITUTE OF TECHNOLOGY DELHI


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