PhD Student on high-performance algorithms for processing genomic data

Organization: 
CNAG - Centro Nacional de Análisis Genómico
Job Location: 
Barcelona, Spain
Job Description: 

The Ph.D. will take place within the Algorithm Development team, whose mission is to design and deploy practical methods to process the hundreds of gigabases of DNA sequencing data produced daily by the Center. A recent publication that illustrates some of the activities of the group is: Marco-Sola S, Sammeth M, Guigó R and Ribeca P. The GEM mapper: fast, accurate and versatile alignment by filtration. Nat. Methods. Epub 2012 Oct 28.

Responsibilities:
The CNAG seeks a talented student who is expected to establish, under the supervision of Dr. Ribeca, a research line focused on the development of high-performance algorithms for the processing of genomic data, with particular emphasis on their implementation and deployment on FPGA-based hardware architectures.

Conditions:
Non-permanent contract. This post is funded by a RD-Connect, an FP7 EU Research Project.

Requirements: 

- Solid theoretical background in computer science, with particular emphasis on algorithmics (data structures, programming languages, theory of parsing and formal languages), string manipulation algorithms (indexing, compression, pattern matching, searches) and program optimization. Detailed knowledge of FPGA hardware architectures, and previous experience with FPGA programming, will be considered a plus.

- Previous practical programming experience in medium-scale software projects (~10 Klines of code). Mastery of the C/C++ programming languages, with particular reference to advanced programming techniques, is required. Some proficiency in the Java programming language will be considered a plus.

- Previous exposure to biology and bioinformatics (in particular, theoretical and practical knowledge of sequence alignment tools).

- In general, enthusiasm, rigor and motivation along with scientific curiosity and good team spirit will be appreciated. The candidate should also show a marked propensity to find original solutions to problems and to “think big”.

Contact Information: 

Interested candidates may submit a CV and a brief statement of experience and interests before September 30th 2013 to the following email address, indicating the offer reference (PhD_Algorithm) in the message subject: borsadetreball@pcb.ub.cat

About Our Organization: 

The CNAG started operating in March 2010 and is aimed to carry out large-scale DNA sequence analysis projects in human and other species in collaboration with researchers in Catalonia, Spain and internationally. The CNAG operates 13 second generations DNA sequencers and has a dedicated 13 Tflop compute cluster with a 2 petabyte disk storage array, becoming one of the major Genome Sequencing Centers in Europe.