PhD Position F/M Novel computational methods for phylogenetic compression of data structures
Contract type : Fixed-term contract
Level of qualifications required : Graduate degree or equivalent
Fonction : PhD Position
About the research centre or Inria department
The Inria Centre at Rennes University is one of Inria's eight centres and has more than thirty research teams. The Inria Centre is a major and recognized player in the field of digital sciences. It is at the heart of a rich R&D and innovation ecosystem: highly innovative PMEs, large industrial groups, competitiveness clusters, research and higher education players, laboratories of excellence, technological research institute, etc.
The emergence of modern DNA sequencing technologies has revolutionized the life sciences. However, the exponential growth of sequencing data outpaces the expansion of computational capacities, making traditional search methods such as Basic Local Alignment Search Tool (BLAST)  and its successors increasingly less effective. To keep up with the volumes of sequencing data being generated, we need novel sublinear approaches that could store and analyze data directly in the compressed domain. However, while it has been shown that genomic data have particular geometrical properties that guarantee the existence of such efficient algorithms , , the compression of exponentially growing genome collections in a scalable manner remains an unsolved challenge.
A novel approach, called phylogenetic compression, has recently been proposed to address this challenge . The technique builds upon the insight that the redundancies in genomic data have, in fact, a highly predictable structure, mirroring the underlying evolutionary processes. As the evolutionary history of genomes can be rapidly estimated, this history can be embedded directly into the compression and search algorithms to increase their efficiency and scalability. The preliminary results demonstrated remarkable improvements over the state-of-the-art compression methods and suggested its applicability to many diverse data structures across bioinformatics .
 S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” J. Mol. Biol., vol. 215, no. 3, pp. 403–410, Oct. 1990.
 P.-R. Loh, M. Baym, and B. Berger, “Compressive genomics,” Nat. Biotechnol., vol. 30, no. 7, pp. 627–630, Jul. 2012.
 Y. W. Yu, N. M. Daniels, D. C. Danko, and B. Berger, “Entropy-scaling search of massive biological data,” Cell Syst, vol. 1, no. 2, pp. 130–140, Aug. 2015.
 K. Břinda et al., “Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression,” bioRxiv, Apr. 2023, doi: 10.1101/2023.04.15.536996.
The objective of this PhD thesis is to develop novel computational techniques and mathematical frameworks for the phylogenetic compression of data structures. The candidate will combine skills in algorithm design and analysis, discrete mathematics, and probability, with a taste for programming and experimenting with big genomic data. One focus of the thesis will be the development of a mathematical framework for formalizing phylogenetic compression as an optimization problem, with the use of data structure modeling based on evolutionary models. Another direction will focus on the development of phylogenetically compressed variants of modern indexing structures, such as those based on de Bruijn graphs, Bloom filters, and sketches. An important aspect of the thesis will be the efficient implementations of the proposed algorithms and experimental evaluations on high-performance computing clusters with large genomic databases. The thesis is expected to provide novel computational solutions to the current challenges and its results may have a direct impact on a range of applications, from search engines for sequence data to infectious disease diagnostics in remote locations.
- Subsidized meals
- Partial reimbursement of public transport costs
- Possibility of teleworking (90 days per year) and flexible organization of working hours
- Partial payment of insurance costs
Monthly gross salary amounting to 2100 euros for the first and second years and 2200 euros for the third year
- Theme/Domain : Computational Biology
- Town/city : Rennes
- Inria Center : Centre Inria de l'Université de Rennes
- Starting date : 2024-09-01
- Duration of contract : 3 years
- Deadline to apply : 2024-04-05
Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed.
Instruction to apply
Please submit online : your resume, cover letter and letters of recommendation eventually.
Recruitment on September 1, 2024 conditional on financing agreement.
Defence Security :
This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment.
Recruitment Policy :
As part of its diversity policy, all Inria positions are accessible to people with disabilities.
Inria is the French national research institute dedicated to digital science and technology. It employs 2,600 people. Its 200 agile project teams, generally run jointly with academic partners, include more than 3,500 scientists and engineers working to meet the challenges of digital technology, often at the interface with other disciplines. The Institute also employs numerous talents in over forty different professions. 900 research support staff contribute to the preparation and development of scientific and entrepreneurial projects that have a worldwide impact.