PhD Student Position in Statistics

Bayesian Methods for Integrated Genomics

The position is now filled!

Our budget is limited, and so we sadly were not able to consider several great candidates with impressive CVs. If you were among them then I do hope you are not too disappointed now, and I would like to thank you once more for your efforts, and I wish you all the best for your future carreer. Please check out http://www.idsia.ch/jobs.html for new job openings.

Ivo Kwee
Marcus Hutter
Francesco Bertoni


IOSI Oncology Institute of Southern Switzerland,
Dep. of Experimental Oncology,
Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland

IDSIA Dalle Molle Institute for Artificial Intelligence,
Galleria 2, CH-6928 Manno (Lugano), Switzerland


Quest. We are offering a fellowship for a PhD student with excellent mathematical skills, interested in Project description. Microarrays allow one to simultaneously measure the expression of tens of thousands of genes in human (cancer) cells, and recently also the copy-number at a hundred-thousand different positions on the genomic DNA. Typically one has to compare microarray data from as few as three, up to hundreds of patients. The data, for instance, contains information on cancer relevant genes and types of cancer. But the enormous amount of data has to be appropriately processed and integrated in order to allow the extraction of the relevant information. Novel statistical methods have to be developed that are able to cope with such complex data, yet small sample sizes. The Bayesian approach is particularly suited for this problem.

Job description. The goal of the PhD project is to develop an integrative Bayesian approach to microarray data analysis, prove its consistency, implement and apply it to the data sets of IOSI, and compare it to other methods. A currently hot topic in Bioinformatics is the reverse engineering of gene regulatory networks. Strong candidates will have the chance to work on this in later stages of their PhD.

Your background. The candidate should In the course of their PhD, the candidates need to familiarize themselves with genomics and microarrays to a certain degree. Not required but a plus would be Appointment. The initial appointment will be for 2 years, starting in summer 2006 (or later) with possibility of prolongation. The goal is to finish the PhD thesis within 3-4 years. The candidate will be supervised by English is the official language at IDSIA and IOSI. The salary is roughly SFr 33'000 per year, low taxes. No teaching is required, etc. - just research for PhD degree. IDSIA is affiliated with the University in Lugano, where the candidate can enroll for his PhD. There is travel funding in case of papers accepted at important conferences. The position is suitable for students no older than 35 years.

References. To get an idea of the research area and the required skills, please have a look at the following publications:
Application. Applicants should submit:

  (i) Detailed curriculum vitae (including grades),
 (ii) List of three references (including their email addresses),
(iii) Statement on how their research interests fit the above topics (1-2 pages).
(iv) Links to their master's thesis or publications.

We would like to fill the position as soon as possible.
Please send all documents at your earliest convenience to:

Marcus Hutter, IDSIA, Galleria 2, 6928 Manno (Lugano), Switzerland.

Applications can also be submitted by email to marcus @ idsia.ch (1MB max!).
WWW pointers to ps/pdf/doc/html files are welcome.
Use Firstname.Lastname.DocDescription.DocType for filename convention.
Please also indicate how you became aware of this announcement.

Thanks for your interest

Ivo Kwee, Senior researcher, IDSIA/IOSI
Marcus Hutter, Senior researcher, IDSIA
Francesco Bertoni, Group leader, IOSI
[Ticino, March 2006]


ABOUT IDSIA. Our research focuses on artificial neural nets, reinforcement learning, complexity and generalization issues, unsupervised learning and information theory, forecasting, artificial ants, combinatorial optimization, evolutionary computation. IDSIA is small but visible, competitive, and influential. IDSIA's algorithms hold the world records for several important operations research benchmarks (see Nature 406(6791):39-42 for an overview of artificial ant algorithms developed at IDSIA). In the "X-Lab Survey" by Business Week magazine, IDSIA was ranked in fourth place in the category "COMPUTER SCIENCE - BIOLOGICALLY INSPIRED" - after the Santa Fe Institute, Stanford University, and EPFL (also in Switzerland). Its comparatively tiny size notwithstanding, IDSIA also ranked among the top ten labs worldwide in the broader category "ARTIFICIAL INTELLIGENCE". Our collaborators at CSCS (the Swiss supercomputing center) are right beneath us; we are also affiliated with the University of Lugano and SUPSI.

ABOUT IOSI. The Laboratory of Experimental Oncology of the Oncology Institute of Southern Switzerland (IOSI) employs a group of scientists working in the area of molecular pharmacology, drug development, cancer genetics and molecular biology. The laboratory is particularly active in the study of the biology and pathogenesis of lymphomas and prostate cancer. These studies promise to shed light into basic mechanisms of tumorigenesis and provide insights for development of novel therapeutic and preventive strategies for cancer. Dr. Catapano is the director of the laboratory, while Dr. Bertoni is responsible of the lymphoma lab projects and functional genomics/unit. This unit currently consists of investigators with expertise in the areas of molecular biology, cytogenetics and microarray analysis. The unit performs gene expression studies, including data mining, in collaborative projects with scientists from the Institute for Research in Biomedicine. The Laboratory of Experimental Oncology is fully equipped to carry out all standard cell biology and molecular biology techniques. Other laboratory personnel assist and complement the unit as needed. All the equipment needed for more advanced genetic and molecular biology-based research is also available, including Affymetrix GeneChip system, Agilent Bioanalyzer, Packard/PE ScanArray Express scanner for spotted microarrays, ABI 7000 Real Time PCR, PALM MicroBeam Laser capture Microdissection System, ABI 310 nucleic acid sequencer. The Oncology Institute of Southern Oncology, directed by Prof. Franco Cavalli is the world leading group for lymphomas and clinical trials for new anti-cancer drugs.

LUGANO and BELLINZONA are located in Ticino (pictures, more), the scenic southernmost province of Switzerland, origin of special relativity and the WWW. Milano, Italy's center of fashion and finance, is 1 hour away, Venice 3 hours. Switzerland boasts the highest citation impact factor, the highest supercomputing capacity pc (per capita), the most Nobel prizes pc (450 % of the US value), and perhaps the best chocolate.

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