PhD Student Position in Computational Pan-Genomics

The ALPACA Project

The Algorithms for PAngenome (ALPACA) project (website) of the European Commission is an Horizon 2020 Marie Sklodowska-Curie ITN Programme.
Modern genomics has been a witness to an unprecedented data revolution in the last decade. Tens of thousands of sequencing machines worldwide sequence genomes at low cost, having generating exabyte-scale genome fragment data in remarkably short time. This development was coined the DNA Data Deluge already in 2013. Still, this has just been the beginning. Significant sequencing technology shifts continue to routinely hit the market, every time skyrocketing sequence data volumes yet again.
Only now, it has become possible to analyze organisms at population scale, which finally sheds light on several topics of urgent interest. Also, the ultra-large data volumes bring about an overwhelming Increase in statistical power, important for genome-wide association studies (GWAS). With genome data rapidly amassing, the urgent need for a shift in computational paradigms, from ordinary sequence-based to graph based representations of genome collections is no longer deniable. Computational pan-genomics recently emerged as a computer science-centric area of genomics and genetics.
ALPACA will train a cohort of 12 ESRs (Early-Stage Researchers) to foster a new generation of researchers who are ready to face the arguably most pressing challenge in computer science relating to the genetic foundations of life.

How you will work

Each ESR will work in an individual research project in a different host institution and will participate in academic and inter-sectoral secondments at the premises of other ALPACA members. The position is offered full-time for three years (36 months). As a successful candidate, you will:

• Conduct research at the Department of Computer Science of the University of Pisa in the context of the ALPACA project.
• Engage in the ALPACA research activities and actively collaborate within the consortium.
• Actively participate in the training programme offered by the ALPACA ITN.
• Engage with researchers at ALPACA partner organizations across the EU.
• Conduct research visits and secondments according to the individual career development plan.

• Objectives: In the specific case of a set of very closely related genomes, a pan-genome can be represented by a so-called (elastic)-degenerate text that actually corresponds to the .vcf file format or, alternatively for slightly less closely related genomes, pan-genomes need to be represented with graphs such as coloured de Bruijn graphs. Several problems can be addressed on such data: pattern matching with a pattern being a simple sequence or another degenerate string or a graph, finding regularities or other structural properties, decompositions into palindromes or other constrained features, finding local similarities among pan- genomes and more in general define similarity notions, detecting inter- pan-genomes variants, etc. Variations of such tasks can be conceived: (i) using weights associated to variants according to frequency or confidence; (ii) designing on-line methods rather than off-line ones such as indexing; (iii) approximate problem version taking into account sequencing errors; (iv) using multiple patterns or texts to extend the range of applications. While being seconded at the University of Helsinki, you will be tailoring the degenerate text approach to hypervariable genomic regions with a setup provided by Makinen’s project partner. While being seconded at CWI Amsterdam you will investigate matching and similarity notions among pan-genomes and inter-pan-genomes variants. While being seconded to DNANEXUS, you will investigate actual conservation and variants distributions properties of real (elastic)-degenerate strings obtained from different kind and size of real pan-genomic data. Moreover, index structures of raw reads pan-genomic data will be investigated with the purposes of seeking new assembly-free representation investigation of pan-genomic data.
• Expected Results: New Algorithms and Tools to investigate and compare a set of closely related genomes.

Requirements

Candidates are required to have a Master degree in Computer Science, Mathematics or a related discipline, and a specialization in Algorithms, Combinatorics, Combinatorial Optimization or related fields. Preferable qualifications for candidates include proven research talent in a Master Degree project, an excellent command of English, and good academic writing and presentation skills.

To be eligible, the applicant must satisfy the mobility requirements of Marie Skłodowska-Curie actions.
At the time of recruitment, the potential candidate:

• "must not have resided or carried out their main activity (work, studies, etc.) in the country of the recruiting beneficiary for more than 12 months in the 3 years immediately before the recruitment date. Compulsory national service, short stays such as holidays, and time spent as part of a procedure for obtaining refugee status under the Geneva Convention are not taken into account”, and
• "be in the first four years (full-time equivalent research experience) of their research careers and have not been awarded a doctoral degree".

Terms and conditions

The selected candidate will be appointed a temporary contract for 36 months, salary will be in line with the funding schemes of MSCA action, and in accordance with Italian rules and regulations, as stated in the Grant Agreement and MSCA Guide for Applicants.
Monthly salary (living allowance + mobility allowance) will be of approx. 3.000 euros net (after taxes) allocated following Italian specific contract conditions for MSCA candidates.
The initial contract will be for a period of 18 months. After a positive evaluation, this will be extended by 18 months.

Information and application

In order to apply, candidates should send an email to nadia.pisanti@unipi.it with subject APPLICATION FOR PHD POSITION.
A single application can be possibly split into several emails, should this turn out to be convenient to reduce the maximum size of attachments per mail.
Should you not be acknowledged receipt of the mail within two working days, please send a second mail without attachments.

All applications should include:

• A detailed CV in English, highlighting your achievements and fit to the applied position;
• Scanned copies of BSc and MSc transcripts, with certified translation in English (if the degree qualification is not in English or in Italian);
• A motivation letter in English, highlighting why you will be a good fit for the position and why you want to be an ALPACA ESR to carry out of a PhD;
• Contact details or recommendation letters of two referees in English or in certified translation;
• Scanned copy of valid identification document and, if applicable, of the Italian fiscal code;
• A copy of the applicant's scientific publications relevant for this selection;
• The list of scientific publications and skill qualifications of the applicant, dated and signed.
• For residents outside the EER-area, a Toefl English language test might be required.

The deadline for applications is Jan 31st, 2021.

For more information about the vacancy, please contact Nadia Pisanti, email: nadia.pisanti@unipi.it.

Diversity code

We encourage a diverse workforce: we endeavour to develop talent and creativity by bringing people from different backgrounds and cultures together. We recruit and select based on capabilities and talent, and therefore we strongly encourage everyone with the appropriate qualifications to apply for the position regardless of age, gender, origin, sexual orientation or physical abilities.

About the University of Pisa and the CS Department

The University of Pisa is one of the earliest in Europe formally founded in 1343. Today it is a large research-oriented university with 1,500 permanent scientists covering all fields, and ranking first at national level in math and computer science disciplines. With less than 90k residents and over 50k students, Pisa city center is actually a campus offering students and scholars a unique learning and research experience.
Pisa has a pioneering role in the international ICT scene since here one of the first computers was real- ized, and in 1968 the first italian degree program in computer science started. The Computer Science (CS) Department has now a faculty of over 60 permanent researchers. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterised by respect and academic freedom tempered by responsibility.

For more information about the Computer Science Department, please visit this website.
For more information about the University of Pisa please visit here or watch our video about working at the University of Pisa.
You may also want to visit our welcome office.

Selection Process

Applications will be processed according to the rules of the University of Pisa and in compliance with the general rules for projects in the H2020 MSCA programmes.
For the selection procedure, the ALPACA consortium has appointed a Committee, consisting of three members:

• Professor Nadia Pisanti, University of Pisa
• Professor Solon Pissis, CWI Amsterdam
• Professor Giovanna Rosone, University of Pisa

Approval and Enrollment in the PhD programme

The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in the PhD programme at the Department of Computer Science of University of Pisa.