PhD Student Position in Computational Pan-Genomics

Computer Science Department of the University of Pisa

fully funded 3 years PhD Student position

on Computational Pan-genomics: Algorithms & Applications

Within the Marie Skodowska-Curie ITN Programme Early Stage Researchers ALPACA.
PhD position title: Matching to and between pan-genomes
Closing date: January 31st February 15th 2021
Positions starts: September 1st, 2021 (indicative)
Interview period: February-March 2021

We seek a talented and motivated PhD student
with a special interest in algorithms and data structures
and their application in bioinformatics (sequence analysis).

To be supervised by: Nadia Pisanti (website), University of Pisa.

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:

Your tasks for the position Matching to and between pan-genomes at the University of Pisa:


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:

Applications that do not meet the eligibility criteria or that are received after the deadline will not be considered.

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. Additional family allowance will be granted upon specific conditions.
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 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:

Incomplete applications will be automatically rejected.

The deadline for applications is Jan 31st, 2021.

For more information about the vacancy, please contact Nadia Pisanti, email:

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:

The selection is assessed by qualifications and an interview. The total rating allowed is 100/100. Qualifications and publications will be assigned up to 60 points, with a required minimum qualification rate of 36/60. The interview will be assigned up to 40 points (minimum qualification threshold rate 24/40). The final ranking list will be compiled summing both ratings.
The interview, reserved only to applicants passing the first qualification rate, will be held at the University of Pisa, Department of Computer Science, Largo B. Pontecorvo 3, Pisa, Italy.
Candidates unable to attend the interview at the University of Pisa will be allowed to be interviewed via web or conference call.
The Selection committee is appointed to establish the duly examination of the candidates and shall acquire the identity card or passport of each candidate.

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.