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Publications

Polypheme® Publications

Validation of KIR3DL1 alleles assigned by next generation sequencing, Paganini J, Pedini P, Rijkers M, Chiaroni J, Di Cristofaro J. HLA. 2024

An HERV-W ENV transcription in atypical memory B cells linked to COVID-19 evolution and risk for long COVID can express the encoded protein from a ribosome readthrough of mRNA from chromosome X, Brunel J, Paganini J, Galloux M, Charvet B, Perron H (2024) medRxiv

Validation of tag SNPs for multiple sclerosis HLA risk alleles across the 1000 genomes panel, Anne Boullerne, Benjamin Goudey, Julien Paganini, Michael Erlichster, Sujata Gaitonde, Douglas L Feinstein, Human Immunology (2024)

HLA-F and LILRB1 Genetic Polymorphisms Associated with Alloimmunisation in Sickle Cell Disease. Emmanuelle Bernit, Estelle Jean, Bastien Marlot, Laurine Laget, Caroline Izard, Isabelle Dettori, Sophie Beley, Isabelle Gautier, Imane Agouti, Coralie Frassati, Pascal Pedini, Christophe Picard, Julien Paganini, Jacques Chiaroni, Julie Di Cristofaro, Int. J. Mol. Sci. (2023)

HLA-F transcriptional and protein differential expression according to its genetic polymorphisms, Julien Paganini, Pierre Faux, Sophie Beley, Christophe Picard, Jacques Chiaroni, Julie Di Cristofaro, HLA (2023)

Mobilisation of HLA-F on the Surface of Bronchial Epithelial Cells and Platelets in Asthmatic Patients. Sabrina Fiouane, Mohamad Chebbo, Sophie Beley, Julien Paganini, Christophe Picard, Xavier-Benoît D’Journo, Pascal-Alexandre Thomas, Jacques Chiaroni, Pascal Chanez, Delphine Gras, Julie Di Cristofaro. HLA (2022)

HLA-H*02:07 Is a Membrane-Bound Ligand of Denisovan Origin That Protects against Lysis by Activated Immune Effectors, Lucas Hubert, Julien Paganini, Christophe Picard, Jacques Chiaroni, Laurent Abi-Rached, Pierre Pontarotti and Julie Di Cristofaro. The journal of Immunology(2021)

Validation of new HLA-J alleles assigned by Next Generation Sequencing. Paganini J, Picard C, Gouret P, Chiaroni J, Di Cristofaro J. HLA. (2021)

HLA-H : transcriptional activity and HLA-E mobilization. Jordier,F., Gras, D., Degrandis,M., D’Journo, X.B, Thomas,P., Chanez,P., Picard,C., Chiaroni, J., Paganini,J., Di Cristofaro,J. Front. Immunol (2020).

Complete genetic sequence of new HLA-H alleles. Julien Paganini, Peter Dallas, Jacques Chiaroni, David Sayer, Julie Di Cristofaro. HLA (2020).

Blood group typing from whole-genome sequencing data. Paganini, J., Nagy, P. L., Rouse, N., Gouret, P., Chiaroni, J., Picard, C., & Di Cristofaro, J. PloS one (2020).

Identification of eleven novel HLA‐A,‐B,‐C,‐DRB1 and‐DQB1 alleles in the 1000 Genomes Project panel. Di Cristofaro, J., Gouret, P., Chiaroni, J., Abi‐Rached, L., & Paganini, J. HLA (2020).

HLAIb worldwide genetic diversity: new HLA-H alleles and haplotype structure description. Julien Paganini, Laurent Abi-Rached, Philippe Gouret, Pierre Pontarotti, Jacques Chiaroni, Julie Di Cristofaro Molecular immunology (2019).

HLA-G haplotypes are differentially associated with asthmatic features. Camille Ribeyre, Federico Carlini, Céline René, François Jordier, Christophe Picard, Jacques Chiaroni, Laurent Abi-Rached, Philippe Gouret, Grégory Marin, Nicolas Molinari, Pascal Chanez, Julien Paganini, Delphine Gras, Julie Di Cristofaro. Front. Immunol (2018).

Immune diversity sheds light on missing variation in worldwide genetic diversity panels. Abi-Rached, L., Gouret, P., Yeh, J. H., Di Cristofaro, J., Pontarotti, P., Picard, C., & Paganini, J Plos (2018).

Validation of new HLA‐F alleles assigned by next‐generation sequencing. Paganini, J., Ramdane, A., Gouret, P., Chiaroni, J., & Di Cristofaro, J. HLA (2018).

Maternal HLA-G* 01: 01: 01: 04 protects from anti-HLA-class II immunization in pregnant women. Slimane, M., Picard, C., Chiaroni, J., Loundou, A., Paganini, J., Tiberghien, P., Di Cristofaro, J. Human immunology (2018).

Concept

Integration of the immune memory into the pathogen-driven MHC polymorphism hypothesis, Jacek Radwan, Chirine Kohi, Maciej Ejsmond, Julien Paganini, Pierre Pontarotti, HLA (2023)

COVID-19 Pandemic: Escape of Pathogenic Variants and MHC Evolution, Pontarotti P, Paganini J International Journal of Molecular Sciences (2022)

Search for MHC/TCR-like systems in living organisms. Julien Paganini, Pierre Pontarotti Front. Immunol (2021).

Origins of the RAG Transposome and the MHC. Tsakou L, Paganini J, Kaufman J, Pontarotti P, Trends in Immunology (2020).

Self-Peptidome Variation Shapes Individual Immune Responses. Pontarotti P, Abi-Rached L, Yeh JH, Paganini J, Trends in Genetics (2020).

Convergent evolution of the adaptive immune response in jawed vertebrates and cyclostomes: An evolutionary biology approach based study. Poole J. R. M, Paganini J, Pontarotti P. Developmental & Comparative Immunology (2017)

Genomic resources and their influence on the detection of the signal of positive selection in genome scans. Manel, S., Perrier, C., Pratlong, M., Abi‐Rached, L., Paganini, J., Pontarotti, P., & Aurelle, D. Molecular ecology (2016).

Xegen thanked

Customized Analysis

Transposon molecular domestication and the evolution of the RAG recombinase. Zhang Yuhang et al. Nature (2019).

Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree?. Pratlong Marine et al. Zoologica Scripta (2017).

Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum. Pinos Sandrine et al. BMC evolutionary biology (2017).

Metagenomics

Successful fecal microbiota transplantation in a patient suffering from irritable bowel syndrome and recurrent urinary tract infections. Hocquart Marie et al. Open forum infectious diseases. (2019)

Blastocystis colonization is associated with increased diversity and altered gut bacterial communities in healthy Malian children. Kodio Aly et al. Microorganisms (2019).

Bacterial Genomics

Xegen is thanked in many bacterial genomes publication : Publications list

Top publications

Self-Peptidome Variation Shapes Individual Immune Responses. Pontarotti P, Abi-Rached L, Yeh JH, Paganini J, Trends in Genetics (2020).

Identification of eleven novel HLA‐A,‐B,‐C,‐DRB1 and‐DQB1 alleles in the 1000 Genomes Project panel. Di Cristofaro, J., Gouret, P., Chiaroni, J., Abi‐Rached, L., & Paganini, J. HLA (2021).

Immune diversity sheds light on missing variation in worldwide genetic diversity panels. Abi-Rached, L., Gouret, P., Yeh, J. H., Di Cristofaro, J., Pontarotti, P., Picard, C., & Paganini, J Plos (2018).

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