Alessia PetesciaBC training on modern sequencing technologies, short-term research projectUNIBI collaboration on a research project, soft skills trainingUDUS collaboration on a research project, soft skills training
Daria FrolovaUNIBI Alexander Schönhuth, focusing on learning about machine learning approachesBC for sequencing of informative bacterial strains that have unusual resistance profilesUNIBI Alexander Schönhuth, to evaluate and improve the results so far
Estéban GaboryBC for early practical metagenomics analysis experiencesINRIA Lyon to work in research team ERABLE of M-F. SagotUNIMIB for the phylogenetic part of the project
Francesco AndreaceUDUS Tobias Marschall, for co-supervision of the ESRINRIA Rennes Pierre Peterlongo, for collaboration on WP1DNANEXUS for practical industrial experience on de novo assembly and pan-genome graph creation of a collection of bacterial pan-genomes
Jorge AvilaINRIA Lyon collaboration on research project (representation of pan-genomes by colored dBG)DEINOVE start training on bacterial dataUK BA collaboration on research project (probabilistic methods)WCM development of experimental work on tumor sequencing data
Khodor HannoushUNIBI Jens Stoye, Practical applications of the ESR pan-genomic alignment free approaches to guide the pan-genome graph splitting decisionCEA/GENOSCOPE Olivier Jaillon, Apply and validate pan-genome update approaches to large viral datasetsDEINOVE Pan-genomic update approaches application to large scale bacterial pan-genomes storing and indexing
Konstantinn BonnetIP Rayan Chikhi, for training on de Bruijn graphs in general and on their implementation in the GATB library in particularPENDULUM extensively discuss the inclusion of PacBio dataEMBL to exchange experiences with the Iqbal group, which has developed the related Cortex software
Luca ParmigianiINRIA Rennes align with basic data structure development in WP1GENETON extensively discuss the applicability of the developed methods
Nicola RizzoFRCBS Mikko Arvas, on enhancing HLA-region analysis with a pan-genomic componentIP Rayan Chikhi on studying encodings of paths in the de Bruijn graph of the core-pan-genome developed earlier in the project
Njagi MwanikiNWO-I investigating pattern matching and similarity notions among pan-genomes (degenerate strings) representations (T1.4 of WP1 and T2.1 of WP2)NWO-I investigating inter-pan-genomes variants detection (T2.1 of WP2)UHEL Tailoring the degenerate text approach to hypervariable genomic regions, a setup provided by Mäkinen's project partner (T1.4)DNANEXUS (Elastic)-degenerate text and Pan-genomes real data analyses (T1.2 and T1.5)
Pengfei WangDEINOVE Guillaume Letellier, pan-genome analysis for bacterial diversity, short-term projectUDUS Tobias Marschall, methods for inferring recombination on virus genomes
Pío SierraUHEL Veli Mäkinen, focusing on pan-genome guided haplotyping strategiesUHEL to evaluate and improve the results so farPENDULUM to explore ancestral relations in microbiome data using the tcPBWT data structure
Raghuram Dandinasivara RangaramINRIA Lyon working on microbiomes (WP1)PENDULUM for practical experiencesEMBL for collaboration within WP3UK BA for statistical aspects
Tomáš SládečekUNIBI training in advanced algorithmic and data structure skills for pan-genomes; short-term research projectsEMBL collaboration on a research project related to sequencing of microbial communities (T3.5)UNIMIB algorithm and data-structures optimization, soft skills training