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ARCHITECTURE AND TOOLS FOR THE QUERY OF ANTIBODY AND T-CELL RECEPTOR SEQUENCING DATA REPOSITORIES FOR ENABLING IMPROVED PERSONALIZED MEDICINE AND IMMUNOTHERAPY

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Publications

Polyclonal expansion of TCR Vbeta 21.3 + CD4 + and CD8 + T cells is a hallmark of Multisystem Inflammatory Syndrome in Children

Author(s): Marion Moreews, Kenz Le Gouge, Samira Khaldi-Plassart, Rémi Pescarmona, Anne-Laure Mathieu, Christophe Malcus, Sophia Djebali, Alicia Bellomo, Olivier Dauwalder, Magali Perret, Marine Villard, Emilie Chopin, Isabelle Rouvet, Francois Vandenesh, Céline Dupieux, Robin Pouyau, Sonia Teyssedre, Margaux Guerder, Tiphaine Louazon, Anne Moulin-Zinsch, Marie Duperril, Hugues Patural, Lisa Giovannini-Cha
Published in: Science Immunology, Issue 6/59, 2021, Page(s) eabh1516, ISSN 2470-9468
DOI: 10.1126/sciimmunol.abh1516

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Author(s): Pierre Barennes, Valentin Quiniou, Mikhail Shugay, Evgeniy S. Egorov, Alexey N. Davydov, Dmitriy M. Chudakov, Imran Uddin, Mazlina Ismail, Theres Oakes, Benny Chain, Anne Eugster, Karl Kashofer, Peter P. Rainer, Samuel Darko, Amy Ransier, Daniel C. Douek, David Klatzmann, Encarnita Mariotti-Ferrandiz
Published in: Nature Biotechnology, 2020, ISSN 1087-0156
DOI: 10.1038/s41587-020-0656-3

Polymorphisms in human immunoglobulin heavy chain variable genes and their upstream regions

Author(s): Ivana Mikocziova, Moriah Gidoni, Ida Lindeman, Ayelet Peres, Omri Snir, Gur Yaari, Ludvig M Sollid
Published in: Nucleic Acids Research, Issue 48/10, 2020, Page(s) 5499-5510, ISSN 0305-1048
DOI: 10.1093/nar/gkaa310

The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies

Author(s): Roberta Amoriello, Victor Greiff, Alessandra Aldinucci, Elena Bonechi, Alberto Carnasciali, Benedetta Peruzzi, Anna Maria Repice, Alice Mariottini, Riccardo Saccardi, Benedetta Mazzanti, Luca Massacesi, Clara Ballerini
Published in: Frontiers in Immunology, Issue 11, 2020, ISSN 1664-3224
DOI: 10.3389/fimmu.2020.00559

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

Author(s): Cédric R Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlović, Igor Snapkov, Geir K Sandve, Sai T Reddy, Victor Greiff
Published in: Bioinformatics, Issue 36/11, 2020, Page(s) 3594-3596, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btaa158

Diversity in immunogenomics: the value and the challenge

Author(s): Kerui Peng, Yana Safonova, Mikhail Shugay, Alice B. Popejoy, Oscar L. Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van-Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes-Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jönsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei Zhang, Malak S. Abedalthagafi, Khalid
Published in: Nature Methods, Issue 18/6, 2021, Page(s) 588-591, ISSN 1548-7091
DOI: 10.1038/s41592-021-01169-5

Machine Learning Analysis of Naïve B-Cell Receptor Repertoires Stratifies Celiac Disease Patients and Controls

Author(s): Or Shemesh, Pazit Polak, Knut E. A. Lundin, Ludvig M. Sollid, Gur Yaari
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
DOI: 10.3389/fimmu.2021.627813

Animal Immunization, in Vitro Display Technologies, and Machine Learning for Antibody Discovery

Author(s): Andreas H. Laustsen, Victor Greiff, Aneesh Karatt-Vellatt, Serge Muyldermans, Timothy P. Jenkins
Published in: Trends in Biotechnology, 2021, ISSN 0167-7799
DOI: 10.1016/j.tibtech.2021.03.003

Mining adaptive immune receptor repertoires for biological and clinical information using machine learning

Author(s): Victor Greiff, Gur Yaari, Lindsay Cowell
Published in: Current Opinion in Systems Biology, 2020, ISSN 2452-3100
DOI: 10.1016/j.coisb.2020.10.010

Extended plasma half-life of albumin-binding domain fused human IgA upon pH-dependent albumin engagement of human FcRn in vitro and in vivo

Author(s): Simone Mester, Mitchell Evers, Saskia Meyer, Jeannette Nilsen, Victor Greiff, Inger Sandlie, Jeanette Leusen, Jan Terje Andersen
Published in: mAbs, Issue 13/1, 2021, Page(s) 1893888, ISSN 1942-0870
DOI: 10.1080/19420862.2021.1893888

Impaired Activated/Memory Regulatory T Cell Clonal Expansion Instigates Diabetes in NOD Mice

Author(s): Vanessa Mhanna, Gwladys Fourcade, Pierre Barennes, Valentin Quiniou, Hang P. Pham, Paul-Gydeon Ritvo, Faustine Brimaud, Bruno Gouritin, Guillaume Churlaud, Adrien Six, Encarnita Mariotti-Ferrandiz, David Klatzmann
Published in: Diabetes, Issue 70/4, 2021, Page(s) 976-985, ISSN 0012-1797
DOI: 10.2337/db20-0896

Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling

Author(s): Johannes Trück, Anne Eugster, Pierre Barennes, Christopher M Tipton, Eline T Luning Prak, Davide Bagnara, Cinque Soto, Jacob S Sherkow, Aimee S Payne, Marie-Paule Lefranc, Andrew Farmer, Magnolia Bostick, Encarnita Mariotti-Ferrandiz
Published in: eLife, Issue 10, 2021, ISSN 2050-084X
DOI: 10.7554/elife.66274

Mucosal or systemic microbiota exposures shape the B cell repertoire

Author(s): Hai Li, Julien P. Limenitakis, Victor Greiff, Bahtiyar Yilmaz, Olivier Schären, Camilla Urbaniak, Mirjam Zünd, Melissa A. E. Lawson, Ian D. Young, Sandra Rupp, Mathias Heikenwälder, Kathy D. McCoy, Siegfried Hapfelmeier, Stephanie C. Ganal-Vonarburg, Andrew J. Macpherson
Published in: Nature, Issue 584/7820, 2020, Page(s) 274-278, ISSN 0028-0836
DOI: 10.1038/s41586-020-2564-6

RAbHIT: R Antibody Haplotype Inference Tool

Author(s): Ayelet Peres, Moriah Gidoni, Pazit Polak, Gur Yaari
Published in: Bioinformatics, Issue 35/22, 2019, Page(s) 4840-4842, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz481

VDJbase: an adaptive immune receptor genotype and haplotype database.

Author(s): Gur Yaari; William Lees; Adrian Shepherd
Published in: Nucleic Acids Research, Issue 48, 2020, ISSN 0305-1048
DOI: 10.1093/nar/gkz872

Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue

Author(s): Jared Ostmeyer, Scott Christley, Inimary T. Toby, Lindsay G. Cowell
Published in: Cancer Research, Issue 79/7, 2019, Page(s) 1671-1680, ISSN 0008-5472
DOI: 10.1158/0008-5472.can-18-2292

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

Author(s): Rahmad Akbar, Philippe A. Robert, Milena Pavlović, Jeliazko R. Jeliazkov, Igor Snapkov, Andrei Slabodkin, Cédric R. Weber, Lonneke Scheffer, Enkelejda Miho, Ingrid Hobæk Haff, Dag Trygve Tryslew Haug, Fridtjof Lund-Johansen, Yana Safonova, Geir K. Sandve, Victor Greiff
Published in: Cell Reports, Issue 34/11, 2021, Page(s) 108856, ISSN 2211-1247
DOI: 10.1016/j.celrep.2021.108856

Modeling the Dynamics of T-Cell Development in the Thymus

Author(s): Philippe A. Robert, Heike Kunze-Schumacher, Victor Greiff, Andreas Krueger
Published in: Entropy, Issue 23/4, 2021, Page(s) 437, ISSN 1099-4300
DOI: 10.3390/e23040437

Modern Hopfield Networks and Attention for Immune Repertoire Classification.

Author(s): Michael Widrich; Bernhard Schäfl; Hubert Ramsauer; Milena Pavlović; Lukas Gruber; Markus Holzleitner; Johannes Brandstetter; Geir Kjetil Sandve; Victor Greiff; Sepp Hochreiter; Günter Klambauer
Published in: NeurIPS, Issue 8, 2020
DOI: 10.1101/2020.04.12.038158