Download three post-doctoral researchers four PhD students data mining

Job openings in Belgium for
three post-doctoral researchers
and
four PhD students
in
data mining, machine learning, bioinformatics,
and computational proteomics
These positions are available at:
• Ghent University and VIB, Computational Omics and Systems Biology
Group
• KU Leuven, Machine Learning Group
• University of Antwerp, Department of Mathematics and Computer
Science
• The Flemish Institute for Technological Research (VITO).
The job openings have been created in the context of the IWT-SBO project ‘inspector:
an integrated informatics platform for mass spectrometry-based protein assays’. The
goal of this project is to increase the efficiency of targeted proteomics methods such
as selected reaction monitoring (SRM), enable high-throughput and semi-automatic
quality control of proteomics experiments, and provide more sensitive detection of
peptides carrying complex or unexpected post-translational modifications.
Please see the individual job adverts of the respective groups below for
full function descriptions, profiles, and application details.
Job opening: (junior) postdoc position in computational
proteomics
Job description
The group of Prof. Dr. Lennart Martens, located in Ghent, Belgium, focuses on the
analysis and integration of omics data. In light of a recently granted IWT SBO project
‘inspector: an integrated informatics platform for mass spectrometry-based protein
assays’ the group is now looking for a (junior) postdoc to work on computational
proteomics, specifically with regard to the development and implementation of
novel algorithms and tools to support targeted proteomics approaches.
The goal of this project is to increase the efficiency of targeted proteomics methods
such as Selected Reaction Monitoring (SRM) through ab initio computational
determination of optimal target peptides and transitions.
Starting date will be 1 March 2013 or earlier, based on availability.
We offer an initial 2-year contract that can be extended based on performance, and
competitive remuneration. The group has an international character, is highly
productive and offers a dynamic and open atmosphere in which collaborations and
initiative are welcomed.
Links:
http://www.vib.be/en/research/scientists/Pages/Lennart-Martens%20Lab.aspx
http://www.compomics.com
Profile
The successful candidate will have obtained or submitted a PhD in a relevant field
and will have experience in bioinformatics and/or data mining, along with a proven
track record in research. Experience in proteomics informatics and/or software
development is considered an advantage.
Contact
Please submit a cover letter, a full c.v., and a list of at least 2 contact persons (with
name, email, address, phone number) for letters of reference to: Lennart Martens,
A. Baertsoenkaai 3, B-9000 Gent, BELGIUM, or via email:
[email protected].
Job openings: PhD student position in computational
proteomics
Job description
The group of Prof. Dr. Lennart Martens, located in Ghent, Belgium, focuses on the
analysis and integration of high-throughput omics data. In light of a recently
granted IWT SBO project ‘inspector: an integrated informatics platform for mass
spectrometry-based protein assays’ the group is now looking for a PhD student to
work on computational proteomics, specifically with regard to the development and
implementation of novel algorithms and tools to support targeted proteomics
approaches.
The group of Prof. Martens is very internationally oriented, and has a very strong
publication record. The group offers an open, highly dynamic, and challenging
working environment, in which team work, initiative and originality are stimulated.
The position is available from 1st of March 2013 or earlier, based on availability.
Links:
http://www.vib.be/en/research/scientists/Pages/Lennart-Martens%20Lab.aspx
http://www.compomics.com
Profile
The successful candidate will have obtained or will soon obtain a Master’s degree in
a relevant field (sciences, informatics, statistics, mathematics, (bio-) engineering)
and will have a keen interest in bioinformatics and/or data mining. Experience in
proteomics informatics and/or software development is considered an advantage.
Contact
Please submit a cover letter, a full c.v., and a list of at least 2 contact persons (with
name, email, address, phone number) for letters of reference to
[email protected], or: Lennart Martens, A. Baertsoenkaai 3, B-9000 Gent,
BELGIUM.
Vacancy
The machine learning group at KU Leuven has the following vacancy:
Doctoral student and/or postdoctoral researcher in relational data
mining for proteomics
Research Context
The machine learning group focuses on relational machine learning, graph mining and
probabilistic reasoning.
The successful applicant will collaborate with groups in Ghent,
Antwerp and VITO contributing proteomics domain knowledge and additional statistical
expertise.
Mission
The research will be situated in the context of the IWT-SBO project “inspector: an integrated
informatics platform for mass spectrometry-based protein assays” starting in March 2013 and
running projects on graph mining and probabilistic modelling such as ERC-StG “MiGraNT:
Mining Graphs and Networks, a theory-based approach”. The successful candidate will conduct
research on probabilistic logical mining and inference methods with applications in
computational biology. The developed algorithms will be applied in the design and analysis of
peptide centric mass-spectrometry experiments as specified in the work description of the
project(s).
The starting date and duration is negotiable.
Work description
• You will be in charge of developing and applying novel data mining, machine
learning, inference and search algorithms based on challenges inspired by experimental
computational biology problems.
• You will analyze the performance of these techniques both theoretically and
experimentally.
• You will both publish scientific results and maintain a repository of open source
software.
• You will closely interact and collaborate with the consortium partners of the IWT-SBO
Inspector project and other scientists.
Profile
The ideal candidate will possess the following skills and attitudes:
•
A master degree in computer science, mathematics, or a closely related discipline.
•
A strong background in computer science (e.g. algorithmics, databases, graphs, logic,
...) and mathematics (e.g. linear algebra, statistics, calculus, …)
•
A scientific attitude and the ability to reason through problems; A pro-active and
independent attitude as well as the ability to function well in a team environment; The ability
to communicate written and orally in English or Dutch in a clear and precise manner.
•
Excellent programming skills, including C++, scripting (python) and matlab (or R,
octave)
•
A strong interest in machine learning and data mining and their applications in
computational biology
Further information
• dr. ir. Jan Ramon, [email protected]
• http://people.cs.kuleuven.be/~jan.ramon/jobs/inspector_sep2012.html
Application
Applicants must send to [email protected] with reference Inspector-Sep12
• A short letter of motivation
• A CV.
• An official transcript listing classes taken and grades received (if not in English, Dutch,
French or German, add an English translation)
• A copy of your most recent thesis. If it is not written in English, Dutch, French or German
please include an English translation of the abstract.
• Any published and relevant research papers (in English, preferably PDF format). If you
have several papers, please indicate which ones you consider the three most important
ones.
• A list of previous software development achievements (if any) with a description of the
nature and main challenges
• A list of references.
The Faculty of Sciences of the University of Antwerp, in collaboration with the Flemish
Institute for Technological Research (VITO), is seeking to fill the following full-time
vacancy in the Department of Mathematics and Computer Science.
Post-doctoral researcher in the field of data mining for proteomics.
The research will be conducted within the Advanced Database Research and Modelling
(ADReM) lab of the UA department of Mathematics and Computer Science, and within the
UA/Vito Center for Proteomics. ADReM is a leading group in European data mining
research. The Center for Proteomics (CFP) is a joint research center funded and operated
by VITO and the University of Antwerp. CFP incorporates academic research based on
mass spectrometry and related techniques, as well as applications in a wide range of
biomedical areas. This position is situated in the context of the IWT-SBO project
“inspector: an integrated informatics platform for mass spectrometry-based protein
assays”. The candidate will conduct research to develop new data mining and machine
learning algorithms supporting “mass-spectrometry based proteomics (MS proteomics)”.
MS proteomics is a powerful and promising domain for biotechnology and hospital, but
the enormous complexity of its data requires novel, robust data processing techniques.
Job description
You will perform research on the development of novel data mining and machine learning
techniques, with a focus on translating the challenges of MS proteomics data processing
into novel algorithms and data processing workflows. You will work closely with domain
experts to understand the data and its particular problems, and you will supervise their
applicability in a real laboratory setting. In collaboration with bioinformaticians these
newly developed methods will be embedded in a user-friendly software environment and
application-programming interface. You co-supervise PhD students working in this and
related projects. You collaborate with researchers in different disciplines (from
computational sciences to life sciences) within the consortium (UA, VIB-UGent, Vito and
KULeuven) and with (mainly biotech) companies of the project user committee.
Profile and requirements
• You have a doctoral degree in (applied) data mining, bioinformatics or
chemoinformatics with an excellent publication track record;
• You are strong in interdisciplinary English communication, quality-oriented and
creative, and eager to emerge in new scientific disciplines. Proven people and project
management skills and ability to attract research funds are a plus;
• Previous experience in protein bioinformatics, mass spectrometry or other ‘omics
techniques is an advantage;
We offer
• A postdoctoral research position for a period of two years, with the possibility of
renewal after positive evaluation. The default start date of the position is March 1st
2013;
• A salary commensurate with your experience and academic qualifications;
• A dynamic, stimulating and multinational work environment.
Interested?
Candidates are invited to send a motivation letter, a detailed CV (including courses,
grades, previous work, publications) and contact info of at least two references (including
email addresses and phone numbers) to Prof. Kris Laukens ([email protected]) and
Prof. Dirk Valkenborg ([email protected]). Don’t hesitate to contact us in advance
for more information.
The Faculty of Sciences is seeking to fill the following full-time vacancy in the
Department of Mathematics and Computer Science.
Doctoral researcher in the field of data mining for proteomics.
The Advanced Database Research and Modelling (ADReM) research group of the
department of Mathematics and Computer Science is a leading group in both Belgian and
European data mining. It is one of the founding members of Biomina (biomedical
informatics research center Antwerp), a new interdisciplinary research unit for biomedical
informatics established by the University of Antwerp and the Antwerp University Hospital
that aims to address the growing needs of biomedical data processing and to enable new
interdisciplinary cross-fertilization. This position is situated in the context the IWT-SBO
project “inspector: an integrated informatics platform for mass spectrometry-based
protein assays”. The candidate will conduct research to develop new data mining and
machine learning algorithms supporting “mass-spectrometry based proteomics (MS
proteomics)”. MS proteomics is a powerful and promising domain for biotechnology and
hospital, but the enormous complexity of its data requires novel, robust data processing
techniques.
Job description
Your focus will be on algorithm development, performance evaluation and software
prototyping. In collaboration with bioinformaticians your newly developed methods will
be embedded in a user-friendly software environment and application-programming
interface. You prepare a doctoral thesis in data mining. You collaborate with researchers
in different disciplines (from computational sciences to life sciences) within the
consortium (UA, VIB-UGent, Vito and KULeuven) and with (mainly biotech) companies of
the project user committee.
Profile and requirements
• You have a master degree in Computer Sciences, Mathematics, Physics, (software)
engineering or equivalent, with outstanding study results;
• Profound programming skills (C++, Java, Python) and familiarity with relational
databases (MySQL) are required. Experience with statistical / mathematical software
(R, Matlab) is a plus. You have a strong quantitative background.
• You are strong in interdisciplinary English communication, quality-oriented and
creative, and eager to emerge in new scientific disciplines;
• Previous experience in data mining, protein bioinformatics, mass spectrometry or
other ‘omics techniques is a plus;
We offer
• An exciting research opportunity to complete a PhD;
• A doctoral scholarship for a period of two years, with the possibility of renewal for a
further two-year period after positive evaluation. The default start date of the
scholarship will be March 1st 2013;
• A dynamic, stimulating and multinational work environment.
Interested?
Applications are invited to send a motivation letter, a detailed CV (including courses,
grades, previous work, publications) and contact info of at least two references (including
email addresses and phone numbers) to Prof. Kris Laukens ([email protected]).
Don’t hesitate to contact us in advance for more information.
Verspreiding: General
Ghent University, in collaboration with the Flemish Institute for Technological Research (VITO), announces
the following position (m/f):
Researcher doctoral student in protein informatics and mass spectrometry.
The appointment takes effect from 01.03.2013 for a period of 2 years, extendable to a total period of 4 years.
The candidate will be simultaneously appointed at Ghent University, and at the Center for Proteomics of UAVITO.
Research context
The Center for Proteomics (CFP) is a joint research center funded and operated by VITO and the
University of Antwerp. CFP incorporates academic research based on mass spectrometry and related
techniques, as well as applications in a wide range of areas including protein analysis, post translational
modifications, quantitative proteomics, biomarker research, metabolomics, data handling and bioinformatics
which address questions in human biology.
The Computational Omics and Systems Biology group at Ghent University focuses on the analysis
and integration of high-throughput omics data. The group is very internationally oriented, and has a very
strong publication record. The group offers an open, highly dynamic, and challenging working environment,
in which team work, initiative and originality are stimulated.
The research will be situated in the context of the IWT-SBO project “inspector: an integrated
informatics platform for mass spectrometry-based protein assays”.
Work description
The candidate will be mainly active at the CFP, but also partly at Ghent University. You will be in
charge of developing and applying novel data mining and machine learning techniques on mass
spectrometry-based proteomics experiments. You explore how complicated algorithmic concepts can be
embedded in a user-friendly software environment and application programming interfaces. You will develop
data warehouses and create peripherical software to extract and store data in the most convenient and
efficient manner.
Profile of the successful candidate
You have a licentiate, master, or equivalent diploma in bioinformatics, mathematics, computer
science, physics, chemometrics, computational biology, (bio)engineering, or related fields. Experience in the
use of the listed software packages are considered an advantage: statistical/mathematical software (R,
Matlab), scripting language (Phyton), Front-end graphical interface programming (Java), Scientific computing
(C++), Database systems (mySQL). You have a strong quantitative background and an interest in developing
new methods for data analysis. You have excellent communication and writing skills in English; you can
swiftly integrate in international laboratories and can clearly communicate scientific results to co-workers
and other scientists from different disciplines.
Further information
Prof. dr. Lennart Martens, +32 9 264 93 58, [email protected]
Prof. dr. ir. Dirk Valkenborg, +32 3 265 33 87, [email protected]
Application
Please submit a motivation letter, a full c.v., and a list of at least 2 contact persons (with name, email,
address, phone number) for letters of reference to [email protected], or: Lennart Martens, A.
Baertsoenkaai 3, B-9000 Gent, BELGIUM and [email protected], or: Dirk Valkenborg, Boeretang 200,
B-2400 VITO, BELGIUM.
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