[Corpora-List] Biomedical text mining position available at CNIO (Madrid, Spain)

[Martin Krallinger]

Title: Biomedical Text mining Position available (job announcement)


Description:
The candidate will work within a multidisciplinary team involved in the 
development and application of biomedical text mining and natural 
language processing approaches.

The overall aim of this work is to develop and apply text mining and 
natural language processing technologies to biomedical literature, 
covering aspects related to automatic text classification using machine 
learning methods, the detection of entities of biological interest from 
text and the extraction and ranking of biological relations from the 
biomedical literature. A special focus will be given to certain topics 
such as cancer related literature and protein interactions.

Expected outcomes will include fundamental research in biomedical text 
mining, publications in high-impact journals and development of 
biomedical text mining applications and services. The resulting 
strategies will be applied to process article abstracts, full text 
articles as well as clinical records.

Requirements:
Applicants should possess an MSc (preferably a PhD) in biology, computer 
science or related areas with specific knowledge in Computer Science, 
Bioinformatics, Computational Linguistics, Statistics or Machine 
Learning or Text Mining.

1) Candidates should have the following qualifications:
- Competitive software engineering skills (demonstrable knowledge of at 
least two programming languages such as python, C/C++, Java, Perl and 
the development of online web applications).
- A solid background and interest in statistical and machine learning 
methods
- Ability to develop algorithms and software for natural language 
processing/text mining systems
- Good English communication skills
- A strong interest in collaborating with experts from the biomedical, 
molecular biology and bioinformatics domains and text mining.

2) Other desirable skills and selection criteria include:
- Exposure to biomedical texts/domain.
- Familiarity with development of Web Services
- Well organized and have the ability to work in an interdisciplinary team.
- The publication record would be an advantage.
- Familiarity with NLP tasks such as named entity recognition, 
summarization, information extraction, and information retrieval will
be also highly desirable.
- Familiarity with some of the existing software that might be relevant 
to the research topic (like Weka, LibSVM, Lucene, GATE, NLTK, or Mallet).
- Interest in the evaluation of systems performance and community 
challenges.



Organization:
The Spanish National Cancer Centre (CNIO, Madrid, Spain - 
http://www.cnio.es/ing/index.asp) is one of the few European Cancer 
Centers to allocate resources to both basic and applied research in an 
integrated fashion, thus supporting the interaction of basic research 
programmes with those of molecular diagnostics and drug discovery. All 
CNIO programmes benefit from excellent equipment, technology, and 
technical services. The CNIO employs about 500 scientists, it offers 
excellent work conditions including competitive salary, and world-class 
computing infrastructure.
The Structural and Computational Biology Programme at CNIO, leaded by 
Dr. Alfonso Valencia integrates several research groups, including the 
Computational Biology group, a Bioinformatics support unit and the 
central node of the Spanish Bioinformatics Institute, a Genome Spain 
platform. The computational facilities and infrastructure cover all the 
needs of the research in modern text mining and NLP, computational 
biology and provides excellent grounds for the analysis of 
high-throughput genomic data.
The research group contributed significantly to the biomedical text 
mining research over the past years, from initial work related to the 
analysis of protein families, microarray data and protein interactions 
to the development of popular online applications such as the iHOP 
server or PLAN2L. Recent research efforts also promoted the organization 
of the BioCreative text-mining challenges, the development of the 
BioCreative metaserver and the BioCreative II.5 competition. The 
research group has a well-established international network of 
collaborations with other text mining groups, bioinformatics and 
biological database teams and experimental biomedical researches.


Application:
Requests for additional information or formal applications (including 
Application letters, extensive CV and PhD/MA thesis and the names of at 
least two references) can be sent to Martin Krallinger: mkrallinger at cnio.es


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