Contents

Scientific structure

The PANGAIA project is structured into five work packages.

WP1 and WP5 deal with management, education, and dissemination, while the research objectives are are split between WP2, WP3, and WP4.

WP1: Management and Coordination: building future collaborations to ensure self-sustainability

The goal of this WP is to guarantee that all planned secondments will be executed as expected and that all information will be distributed among all interested parties. This WP is devoted to monitoring the secondments and guaranteeing that all network events are organized following the schedule.

WP2: Representation of Pan-genomes: graph-based algorithms and data structures

The goal of this WP is to to rethink the main essential data structures and algorithms that are components of basic genome analysis pipelines under the paradigm shift from sequences to graphs.

This WP includes four tasks:

Task 2.1: Constructing a pan-genome

The goal of this task is to develop a suitable representations of a pangenome that reflects the genetic variation of a population that will act as a reference system for pangenome based applications.

Task 2.2: Dynamic update of a pan-genome

This task will face the problem of developing efficient dynamic update procedures for the pangenome representations developed in Task 2.1.

Task 2.3: Alignment to graph pan-genomes

The goal of this task is to design algorithms for the aligning sequences to the various pan-genome representations developed in Task 2.1.

Task 2.4: Software development of tools for pan-genome construction and indexing

This task is focused on the implementation and validation of software prototypes related to the functionalities designed in the previous tasks.

WP3: Comparative and Evolutionary Pan-Genomics

The goal of this WP is to developed new algorithmic tools to answer questions related to the comparison of genomes to detect significant genomic variants.

This WP includes three tasks:

Task 3.1: Measures of similarities in pan-genomes

The goal of this task is to develop measures of similarities and dissimilarities between two graph structures that can be used in classical clustering algorithms dealing with data representing graphs.

Task 3.2: Statistical differential analysis in pan-genomes

The goal of this task is to study the differential analysis of pangenome graphs to: (1) discover statistically significant patterns, and (2) perform a comparative analysis in situations of sequencing data with high error rate or low coverage.

Task 3.3: Evolution in pan-genomes

The goal of this task is to develop methods for inferring a
common evolution from the comparative analysis of graph pangenomes.

WP4: Translational pan-genomics data integration and clinical applications

The goal of this WP is to transform the data strctures and algorithmic methods developed in WP2 and WP3 into graph-based pangenomics tools for biomedical and clinical application.

This WP includes two tasks:

Task 4.1: Machine learning approaches to predict disease-related features

The goal of this task is to use machine (deep) learning techniques for predicting disease-related features in individual genomes, exploiting the results developed in WP3.

Task 4.2: Association discover in microbiome pan-genomics

The goal of this task is to develop methods to detect features from bacterial pangenomes that associate with the resistance of antibiotics.

WP5: Communication and Dissemination

The goals of this WP are to disseminate the results obtained by the project to the scientific community and to communicate those results to the general public.

WP6: Ethics requirements

The goal of this WP is to evaluate all ethical aspects of the project, most notably data privacy and informed consent of all individuals involved. Since the project will only use anonymized data, the main task is to guaranteed that data that no personally-identifiable data is used.

Management structure

The coordinator is Paola Bonizzoni (Univ. Milano – Bicocca).

Supervisory Board

The supervisory board monitors the progress of the project and approves the setting-up and execution of network-wide events. Its members are:

• Paola Bonizzoni (Univ. Milano – Bicocca, chair)
• Alexander Schönhuth (Univ. Bielefeld)
• Tomas Szemes (Geneton)
• Tomas Vinar (Comenius Univ.)
• Anthony J Cox (Illumina UK) (until June 2023)
• Ole Schulz-Trieglaff (Illumina UK) (since July 2023)
• Leen Stougie (Centrum Wiskunde & Informatica)
• Rayan Chikhi (Institut Pasteur)
• Nadia Pisanti (Univ. Pisa)
• Jozef Hritz (Masaryk University)
• Iman Hajirasouliha (Weill-Cornell Medical College, non-voting member)
• Cedric Chauve (Simon Fraser Univ., non-voting member)
• Paul Medvedev (Penn State Univ., non-voting member)
• Kunihiko Sadakane (The Univ. of Tokyo, non-voting member)
• Benedict Paten (UC Santa Cruz, non-voting member)

Executive Committee

The Executive Committee carries out the actions decided by the Supervisory Board and it verifies the quality of deliverables, monitors dissemination activities and exploitation of results. Its members are:

• Brona Brejova (Comenius Univ., chair, leader of WP3)
• Yuri Pirola (Univ. Milano – Bicocca, Administrative Manager)
• Paola Bonizzoni (Univ. Milano – Bicocca, leader of WP1)
• Rayan Chikhi (Institut Pasteur, leader of WP2)
• Solon P. Pissis (Centrum Wiskunde & Informatica, leader of WP4)
• Gianluca Della Vedova (Univ. Milano – Bicocca, leader of WP5)
• Jens Stoye (Univ. Bielefeld, leader of WP6)

Advisory Board

The Advisory Board is an independent body that advises on the project’s strategy, including scientific matters, industrial relevance, gender issues, and career development. Its members are:

• Daniel Gusfield (UC Davis)
• Teresa Przytycka (NCBI, NLM, NIH)
• Gabriel Valiente (Technical University of Catalonia)

Administrative Manager

The current Administrative Manager is Yuri Pirola.
From the beginning of project to Nov. 3, 2020 the Administrative Manager has been Marco Previtali.

Secondments

From Geneton

• Marcel Kucharik seconded to University of Milano-Bicocca from 15/11/2021 to 15/12/2021
• Ondrej Pos seconded to University of Milano-Bicocca from 15/11/2021 to 15/12/2021
• Zuzana Pos seconded to University of Milano-Bicocca from 15/11/2021 to 15/12/2021
• Jakub Styk seconded to University of Milano-Bicocca from 02/04/2022 to 03/05/2022
• Rastislav Hekel seconded to University of Milano-Bicocca from 02/04/2022 to 03/06/2022
• Diana Rusnakova seconded to University of Milano-Bicocca from 03/05/2022 to 03/06/2022
• Werner Krampl seconded to The University of Tokyo from 07/11/2022 to 09/01/2023
• Andrea Zatkova seconded to University of Milano-Bicocca from 01/05/2023 to 26/07/2023
• Tomas Szemes seconded to The Regents Of The University Of California from 26/07/2023 to 28/08/2023
• Pavol Misenko seconded to CWI from 23/08/2023 to 22/09/2023
• Juraj Gazdarica seconded to University of Milano-Bicocca from 25/09/2023 to 25/11/2023
• Andrea Zatkova seconded to University of Milano-Bicocca from 12/10/2023 to 18/10/2023
• Andrea Zatkova seconded to University of Milano-Bicocca from 23/02/2024 to 25/03/2024
• Zuzana Hanzlikova seconded to University of Milano-Bicocca from 23/02/2024 to 25/03/2024
• Jozef Martis seconded to University of Milano-Bicocca from 23/02/2024 to 25/03/2024
• Juraj Gazdarica seconded to Institut Pasteur from 05/04/2024 to 04/05/2024

From Institut Pasteur

• Rayan Chikhi seconded to The University of Tokyo from 08/02/2023 to 10/03/2023
• Yoshihiro Shibuya seconded to The University of Tokyo from 20/02/2023 to 10/03/2023
• Yoann Dufresne seconded to The Pennsylvania State University from 25/04/2023 to 04/06/2023
• Rayan Chikhi seconded to The Pennsylvania State University from 25/06/2023 to 11/07/2023
• Rayan Chikhi seconded to The University of Tokyo from 06/04/2024 to 05/05/2024

From CWI

• Solon Pissis seconded to Illumina from 07/05/2022 to 05/06/2022
• Solon Pissis seconded to Geneton from 14/01/2023 to 12/02/2023
• Michelle Sweering seconded to Geneton from 01/02/2023 to 04/03/2023
• Michelle Sweering seconded to The University of Tokyo from 01/06/2023 to 30/06/2023
• Hilde Verbeek seconded to Cornell University from 09/09/2023 to 19/10/2023
• Michelle Sweering seconded to Cornell University from 12/09/2023 to 19/10/2023
• Solon Pissis seconded to Geneton from 29/01/2024 to 28/03/2024
• Wiktor Zuba seconded to The University of Tokyo from 04/06/2024 to 03/07/2024

From University of Milano-Bicocca

• Simone Ciccolella seconded to Geneton from 15/10/2020 to 14/12/2020
• Simone Ciccolella seconded to Geneton from 04/09/2021 to 04/10/2021
• Paola Bonizzoni seconded to Cornell University from 09/05/2022 to 30/05/2022
• Luca Denti seconded to Geneton from 04/08/2022 to 04/12/2022
• Gianluca Della Vedova seconded to Cornell University from 15/08/2022 to 30/08/2022
• Paola Bonizzoni seconded to Cornell University from 16/08/2022 to 29/08/2022
• Simone Ciccolella seconded to Geneton from 18/09/2022 to 18/10/2022
• Luca Denti seconded to The University of Tokyo from 18/02/2023 to 05/03/2023
• Paola Bonizzoni seconded to The University of Tokyo from 18/02/2023 to 05/03/2023
• Simone Ciccolella seconded to The University of Tokyo from 18/02/2023 to 05/03/2023
• Luca Denti seconded to Geneton from 23/05/2023 to 01/06/2023
• Simone Ciccolella seconded to Geneton from 08/08/2023 to 08/10/2023
• Mattia Sgrò seconded to Simon Fraser University from 17/08/2023 to 24/10/2023
• Paola Bonizzoni seconded to Simon Fraser University from 18/08/2023 to 09/09/2023
• Luca Denti seconded to Geneton from 23/08/2023 to 15/01/2024
• Davide Cozzi seconded to The University of Tokyo from 25/01/2024 to 22/04/2024
• Brian Riccardi seconded to The University of Tokyo from 25/01/2024 to 23/04/2024
• Alex Graudenzi seconded to Cornell University from 02/02/2024 to 17/03/2024
• Paola Bonizzoni seconded to The University of Tokyo from 28/03/2024 to 15/04/2024
• Gianluca Della Vedova seconded to Cornell University from 04/08/2024 to 19/08/2024

From Bielefeld University

• Marília Dias Vieira Braga seconded to Simon Fraser University from 29/02/2020 to 30/03/2020
• Andreas Rempel seconded to The Pennsylvania State University from 01/10/2021 to 31/03/2022
• Katharina Sielemann seconded to Simon Fraser University from 24/01/2022 to 10/06/2022
• Janik Sielemann seconded to Simon Fraser University from 24/01/2022 to 10/06/2022
• Tizian Schulz seconded to The Pennsylvania State University from 24/04/2022 to 01/09/2022
• Xiongbin Kang seconded to The Regents Of The University Of California from 26/04/2022 to 25/08/2022
• Xiongbin Kang seconded to Hunan University from 24/06/2023 to 25/09/2023
• Lucas Robidou seconded to Simon Fraser University from 06/05/2024 to 05/06/2024
• Leonard Bohnenkämper seconded to The University of Tokyo from 01/07/2024 to 29/09/2024
• Lucas Robidou seconded to The University of Tokyo from 30/08/2024 to 29/09/2024
• Andreas Rempel seconded to Simon Fraser University from 01/10/2024 to 31/03/2025

From Comenius University

• Askar Gafurov seconded to The Pennsylvania State University from 12/10/2021 to 23/02/2022
• Tomas Vinar seconded to Simon Fraser University from 23/02/2022 to 11/08/2022
• Bronislava Brejova seconded to Simon Fraser University from 23/02/2022 to 11/08/2022
• Peter Peresini seconded to The University of Tokyo from 02/02/2023 to 30/04/2023
• Tomas Vinar seconded to Simon Fraser University from 06/07/2023 to 07/09/2023
• Bronislava Brejova seconded to Simon Fraser University from 06/07/2023 to 07/09/2023