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Friday, 3 July 2015

Using bioinformatics to untangle second-most widespread parasitic disease

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Sitting humbly in his silence, gathering dozens of pages of data, New Mexico State University student Cesar Montelongo is tucked away in a biology lab eager to make his mark on society. Montelongo is a biology master’s graduate with a unique past, inspiring story and bright future.

  • He is part of a team of researchers using live snail tissue and bioinformatics to identify immune factors in the Biomphalaria glabrata snail. The research, shared and reachable worldwide, sequences and annotates the B. glabrata genome. Information gained from the snail is helping scientists determine how humans become infected with schistomiasis, the second-most widespread parasitic disease in tropical and sub-tropical areas, next to malaria.
  • The disease is acquired when people come into contact with fresh water that has been infested with the larval form of schistosomes. When these microscopic parasites become adults, they embed themselves into a person’s veins, draining the urinary tract and intestines. Eggs laid by these worms become trapped in the body’s tissue and trouble arises when the body begins to respond, by fighting off the attacker and the body.
  • By controlling the snail vectors and browsing specific genomes, scientists and researchers are able to hypothesize how the snails may resist becoming infected themselves by the parasite.

Bioinformatics is the process in which scientists and doctors manage biological information. It is the area where Montelongo believes he can make a difference in patients’ lives.
“I have a hope that bioinformatics will make a difference in how patients are treated, and overall how the medical field works,” he said. “My father became very sick in Ciudad Juarez, Mexico, and for the longest time we had no idea what was wrong with him. With my father incapacitated and all the violence throughout the city, that made a huge impression on me. It was in that moment I decided I wanted to become the kind of person who could prevent that.”

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Lyda Hill donates $25 million to establish Department of Bioinformatics

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UT Southwestern Medical Center announced today that it has received an exceptional $25 million gift from Lyda Hill, funding the establishment of the Lyda Hill Department of Bioinformatics to bridge research and clinical care.

The new Department, recently approved by the UT System Board of Regents, is dedicated to developing UT Southwestern’s capability in bioinformatics, a discipline that provides tools for managing and analyzing the extremely large data sets that are increasingly key to addressing the most important scientific and medical challenges. Finding the patterns in these data sets has become an essential component of biomedical discovery and is crucial to developing new therapeutic strategies and to understanding the foundations of life and the defects that cause disease.

  • With this commitment, Miss Hill has now contributed more than $37.5 million to UT Southwestern, supporting research ranging from systems biology to the development of a genetic mutations database.
  • “We are deeply grateful for this transformative gift from Lyda Hill, which underscores her role in supporting and promoting Dallas’ reputation as a growing center for biotechnology and medical innovation,” said Dr. Daniel K. Podolsky, President of UT Southwestern. “By establishing the Lyda Hill Department of Bioinformatics, UT Southwestern will significantly expand our existing expertise in this critical field,” noted Dr. Podolsky, who holds the Philip O’Bryan Montgomery Jr., M.D., Distinguished Presidential Chair in Academic Administration, and the Doris and Bryan Wildenthal Distinguished Chair in Medical Science.

Miss Hill added, “Over the long term, I believe bioinformatics will prove indispensable in bridging the outstanding research activity at UT Southwestern with the most promising clinical applications. My hope is that our investment will help overcome the technological barriers in managing and analyzing data, enabling patients to benefit from research breakthroughs.”

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Wednesday, 1 July 2015

The Vienna Biocenter PhD Programme in Life Sciences

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The Vienna Biocenter (VBC) PhD Programme in Life Sciences has been running since 1993, providing students from all over the world with excellent training. As a student at the Vienna Biocenter you will be supervised by a top scientist and have full access to state-of-the-art facilities, thus giving you the opportunity to start a strong scientific career.
The VBC campus is highly multidisciplinary with research areas ranging from molecules to populations: RNA biology, gene regulation and epigenetics; Biochemistry, structural and cell biology; Stem cells and developmental biology; Molecular medicine; Neurosciences; Plant biology; Bioengineering and computational biology; and Evolutionary and population biology.

IMP Vienna PhD Programme

  • Importantly the scientific environment is extremely dynamic and collaborative, you will have numerous opportunities to meet, talk, listen and collaborate with fellow scientists. The VBC PhD Programme offers a flexible curriculum structure with an initial training course, lectures on scientific topics as well as technical and complementary skills training. Moreover, students contribute to the management of the institutes, through representatives, and organize events that promote networking and career development, such as an annual retreat and a symposium.
  • Not only will you be in one of Europe’s best institutes, you will also have the opportunity to live in Vienna, which is rated as one of the top cities in the world for quality of life. Vienna is a fun, young city embedded in beautiful old buildings, an international metropolis in the heart of Central Europe.
To find out more about the programme please visit our website: www.vbcphdprogramme.at
You can also find us in Facebook: https://www.facebook.com/VBCPhdProgramme
  • Applications are accepted each year for the Winter call from 15 September to 15 November and for the Summer call from 1 March to 30 April.
  • To apply you must hold a Master's degree or equivalent from a university in a related topic (or you will complete a master's degree within six months of the application deadline). Successful applicants will be hired on a full employment contract with a competitive salary.
The VBC PhD Programme (www.vbcphd.at) is organized jointly by the Research Institute of Molecular Pathology (IMP – http://www.imp.ac.at), the Max F. Perutz Laboratories (MFPL – http://www.mfpl.ac.at), the Institute of Molecular Biotechnology (IMBA – http://www.imba.oeaw.ac.at) and the Gregor Mendel Institute (GMI – www.gmi.oeaw.ac.at). Degrees are awarded by the Vienna University or the Medical University of Vienna.

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Sunday, 28 June 2015

Biomedical Research PhD Scholarships

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The Department of Biomedical Sciences is an integral part of Macquarie University’s Health Science Centre and is committed to improving patient health through world-class fundamental and translational medical research. We are currently offering three-year PhD scholarships to outstanding candidates wishing to undertake research training in the following core disciplines:
  • Anatomy
  • Biomedical engineering
  • Cancer biology
  • Neurobiology
  • Pathology
  • Pharmacology
  • Physiology

Why should I study at Macquarie University?


  • Our department offers a dynamic training environment, focused on a cross-disciplinary collaborative approach that integrates cutting edge proteomic, genomic and cell biology methods with unique animal models and human tissue analysis.

Prospective students can apply for a PhD in one of the following research programs within our department:

  • Motor Neuron Disease and Neurodegeneration
  • Melanoma Cell Biology
  • Cancer Proteomics
  • Neuropharmacology
  • Bacterial biofilms in medicine
  • Neurobiology of vital systems
  • Biomedical Engineering
  • Biomechanical Engineering
  • Pulsatile function of the cardiovascular system
Please visit our PhD information web page for more information on the available projects. http://www.mq.edu.au/about_us/

We are looking for international and domestic candidates who have:

  • Completed a Master of Research (MRes) degree (or equivalent) and achieved excellent results
  • Achieved all requirements for direct PhD entry (including English requirements) and are competitive for scholarship
  • A high level of motivation and a keen interest in medical science
  • Excellent communication, teamwork and project management skills
  • Demonstrated aptitude for undertaking laboratory work
To find out more about projects and our research, please visit our website and PhD information page:www.medicine.mq.edu.au

Prospective PhD applicants should refer to the Higher Degree Research Office webpage for information on:

Program eligibility criteria
How to submit an application

Before you apply, please ensure you first make contact with a researcher listed against the project you are interested in applying for.

For international and domestic scholarship opportunities visit here
http://www.hdr.mq.edu.au/information_about
  • Some applications close 31 August 2015 for 2015 and 2016 enrollments.
  • Please contact the Faculty HDR office for general enquires: fmhs.hdr@mq.edu.au

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Saturday, 27 June 2015

PHD IN COMPUTATIONAL SYSTEMS BIOLOGY

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Construction of a biochemical reaction network model to predict the chemical patterns arising from complex processing steps in cocoa

Jacobs University Bremen is a private, state-recognized, English-language research university, offering Bachelor, Master or PhD programs in the focus areas Health, Mobility and Diversity. The guiding principles are first class research and teaching, international diversity and transdisciplinary cooperation. Jacobs University’s goal is to prepare young talents from all around the world to take on the new challenges in today’s globalized workplace. Currently, more than 1,300 students from over 100 nations live and study on the residential campus.

Imagine a Special Place in Germany


Subject

  • The collaborative project COMETA (COcoa METAbolism) analyzes the precise chemical composition of cocoa beans from various origins. The overarching goal is to develop new rapid quality tests for cocoa classification, processing, and planning requirements for raw material. This project bridges cutting edge research areas, including Microbiology, Analytical Chemistry, and Systems Biology, with direct industrial applications in a unique, highly interdisciplinary framework.
  • The aim of the PhD project is the elucidation of chemical and metabolic reactions of industrial processing steps, such as fermentation and roasting to determine quality indicators for flavor and other relevant chocolate characteristics. Solely considering intermediates of the cocoa metabolism is insufficient as these processing steps are performed under non-physiological conditions, e.g., high temperature. Within this PhD project, a metabolic model of the cocoa bean will be reconstructed and interfaced with chemical databases, in order to predict the chemical scope of the system under diverse conditions. Mapping the identified quality indicators back to the assembled cocoa processing model allows an a priori assessment of the chocolate quality, for instance for a quality test directly on the plantation.

Tasks and responsibilities

  • Statistical analysis of various high-throughput data sets for predicting quality indicators
  • Development of software tools for data integration and management
  • Identification of processing step-specific chemical and metabolic markers
  • Reconstruction of a processing model including the relevant chemical and metabolic reactions for the quality indicators starting from the identified markers

Qualifications

  • MSc degree (or equivalent) in Bioinformatics, Applied Mathematics, Computer Science or a similar field
  • Solid knowledge of biochemistry and molecular biology
  • Strong programming skills including Python and R
  • Experience in mathematical modeling
  • Experience in handling high-throughput data
  • Knowledge of analytical chemistry and structure elucidation would be beneficial
  • Ability to work in an interdisciplinary environment and good communication skills including fluent in spoken and written English
  • Willingness to travel

What we offer

  • We offer an innovative, multidisciplinary, and dynamic research environment with a strong international profile and close connections to industry partners. The PhD position is available for a period of three years.

How to apply

Letters of application must be received by August 31st, 2015, for consideration. Interested candidates are encouraged to submit a CV, contact details of two references and a short letter of motivation electronically to: Prof. Dr. Marc-Thorsten Hütt (m.huett@jacobs-university.de) and Dr. Sergio Grimbs (s.grimbs@jacobs-university.de). Please, feel free to contact us for informal inquiries and additional information.

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Thursday, 25 June 2015

PhD @ University of Southern Denmark

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Phosphorus (P) is a non-renewable resource essential as fertilizer to ensure sufficient food production. Phosphorus in Danish waste water is estimated to cover 15-25% of the Danish demand and consequently constitutes an important source for recycling of P.
We are looking for a motivated candidate to study recovery of P from waste water. The candidate should have a strong background in both biology and chemistry. Experience with analytical chemistry and characterization of materials by e.g. NMR spectroscopy and X-ray diffraction will be preferred. The candidate should be independent and able to communicate fluently in English, have good writing skills as well as possess good interpersonal skills.
The PhD scholarship is within the area of biogeochemistry and analytical chemistry and will be linked to the research at the Freshwater Ecology Group at the Department of Biology and the Inorganic Chemistry Group at the Department of Physics, Chemistry and Pharmacy, University of Southern Denmark.

University of Southern Denmark - Presentation – 2013

  • The PhD candidate will be appointed to the Department of Biology, University of Southern Denmark with a main supervisor Kasper Reitzel (reitzel@biology.sdu.dk) and a co-supervisor Ulla Gro Nielsen (ugn@sdu.dk) from the Department of Physics, Chemistry and Pharmacy.
  • The starting date is 30 September 2015. Application deadline is 15 August 2015.
  • For further information please contact Associate Professor Kasper Reitzel, tel.: +45 6550 2774, e-mail: reitzel@biology.sdu.dk.

Application, salary etc.

  • Appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.
  • The successful applicant will be employed in accordance with the agreement of 1 July 2013 on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations).
  • The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).
  • The university encourages all persons interested in the position to apply, regardless of their age, gender, religious affiliation or ethnic background.

Application must be made in the form of a Declaration of Interest including the following:

  1. A research proposal/description of your approach to the above project (max one page excluding references)
  2. A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form")
  3. Detailed CV, including personal contact information
  4. Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes
  5. At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: anc@sdu.dk mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.
  • Further information about the PhD-study can be found at the homepage of the University.
  • Applications must be submitted electronically using the link below.
  • Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb.
  • Please read How to apply before you apply.
  • Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.
  • Further information for international applicants about entering and working in Denmark.

Apply Online

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Monday, 15 June 2015

17 Early Stage Research PhD training positions

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Marie Curie PhD Training Network

This network, bringing together 7 European Universities and 5 collaborating academic and commercial partners, offers 17 Early Stage Research (ESR) PhD training positions for 36 months.  The PhD projects will be based around genomics/transcriptomics but with strong immunology, statistics and bioinformatics.
  • The MELGEN European Training Network (ETN) will create a co-operative environment for research and training in melanoma research, with the ultimate aim of improving precision medicine for patients with this disease. In recent years remarkable progress has been made in melanoma research, which has led to the introduction of the first treatments to prolong life in patients with advanced disease: both targeted treatments and immune therapies.

University of Leeds open days - come and find your place


  • Although genomics has yielded a wealth of information on the genomic alterations in melanoma, further characterisation is urgently needed in order to predict responses to combinations of targeted therapies and MELGEN will address this need. The dramatic responses seen in melanoma patients to immunotherapies indicate that immune responses to melanoma are crucial, and we need to better understand what predicts response in order to improve treatment strategies, particularly in the adjuvant setting.
  • MELGEN will explore host/tumour interactions and detect biomarkers of response to treatment. The academic centres and several commercial partners of this network will address these research questions using unique samples and data sets and the most sophisticated technologies, including genomic and transcriptomic analyses, functional genetic screens, CRISPR genome editing, iPS cell-based disease models, liquid biopsy technology, developmental statistics and bioinformatics.
All students will be expected to have a good level of English as the basic language of the network is English. Please take good note of the rules for ETN training networks. They are designed to encourage movement within Europe and therefore applicants may only have lived for 12 months in the previous 3 years in the country of supervision. There are a total of 17 posts available in this call.

Projects available:

University of Leeds, UK

Lund University, Sweden

The Wellcome Trust Sanger Institute, UK

Leiden University Medical Center, Netherlands

University of Oslo, Norway

Universitätsklinikum Essen, Germany

University of Zürich Hospital, Switzerland

Key benefits:

  • Generous salary and additional allowances to cover living costs and travel, including a contribution to some family related expenses and the cost of annual travel back to the home country.
  • Opportunities for international collaboration and travel to world class academic and industrial partners.
  • Participation in the GenoMEL melanoma genetics consortium scientific meetings (www.genomel.org)
  • Training in a range of state-of-the-art scientific skills, complimentary skills, intellectual property, and project management skills.
  • Training will include a 2 week introductory course on genomics, statistics and bioinformatics at Leiden University Medical Center, and a statistics and bioinformatics course in year two.
  • There will be training in the use of social media and other technologies in communicating science to scientists and to the general public, and students will take part actively in this throughout their training
  • Secondment placements between network partners including Universities across the network and genomics, bioinformatics, and biomarker development commercial companies
  • Committed supervision from academic units with integration between groups and commercial partners

How to apply

Within the details of each research project listed above are details of contact email addresses for those who seek further information.  Applicants may apply for up to three of the projects and must prioritise these as 1 (most preferred) to 3. Applicants will be asked to submit the following information to the Faculty of Medicine and Health Graduate School at the University of Leeds -fmhgrad@leeds.ac.uk:
  1. Personal Statement of application
  2. CV including details of 3 academic referees
  3. Degree Transcripts and Certificates
  4. Certificates of English Language Qualifications
The closing date for application will be 26 June 2015.  Recruitment to these posts will involve a two round process: shortlisted candidates will undertake an initial interview via Skype or teleconference in the week beginning 6 July 2015; successful candidates from the first round will then be asked to attend a two-day interview event held at Leiden University Medical Center in Leiden, The Netherlands on 4 and 5 August 2015 alongside candidates for all 17 ESRs funded by the MELGEN ETN.  Final round applicants who are unsuccessful in being appointed for their chosen ESR may be considered for other MELGEN ESR positions if they wish, subject to meeting the eligibility criteria of the hosting institution.
  • Candidates must be available to start the position by 1 January 2016.

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