Publications by Victor Greiff
89 publications found
Publications 2024
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Systematic evaluation of B-cell clonal family inference approaches
BMC Immunol, 25 (1), 13
DOI 10.1186/s12865-024-00600-8, PubMed 38331731 -
Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability
Commun Biol, 7 (1), 922
DOI 10.1038/s42003-024-06561-3, PubMed 39085379 -
MHC heterozygosity limits T cell receptor variability in CD4 T cells
Sci Immunol, 9 (97), eado5295
DOI 10.1126/sciimmunol.ado5295, PubMed 38996008 -
Author Correction: Insights into next generation sequencing guided antibody selection strategies
Sci Rep, 14 (1), 3090
DOI 10.1038/s41598-024-53751-4, PubMed 38326401 -
Corrigendum: Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence
Front Immunol, 15, 1377041
DOI 10.3389/fimmu.2024.1377041, PubMed 38449865 -
Unlocking protein-based biomarker potential for graft-versus-host disease following allogenic hematopoietic stem cell transplants
Front Immunol, 15, 1327035
DOI 10.3389/fimmu.2024.1327035, PubMed 38433830 -
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling
NPJ Syst Biol Appl, 10 (1), 73
DOI 10.1038/s41540-024-00402-z, PubMed 38997321 -
The dengue-specific immune response and antibody identification with machine learning
NPJ Vaccines, 9 (1), 16
DOI 10.1038/s41541-023-00788-7, PubMed 38245547 -
Author Correction: The dengue-specific immune response and antibody identification with machine learning
NPJ Vaccines, 9 (1), 30
DOI 10.1038/s41541-024-00820-4, PubMed 38351085 -
Assessing AF2's ability to predict structural ensembles of proteins
Structure (in press)
DOI 10.1016/j.str.2024.09.001, PubMed 39332396 -
Predictability of antigen binding based on short motifs in the antibody CDRH3
Brief Bioinform, 25 (6)
DOI 10.1093/bib/bbae537, PubMed 39438077 -
ExpoSeq: simplified analysis of high-throughput sequencing data from antibody discovery campaigns
Bioinform Adv, 4 (1), vbae020
DOI 10.1093/bioadv/vbae020, PubMed 38425781 -
NKG2A discriminates natural killer cells with a suppressed phenotype in pediatric acute leukemia
J Leukoc Biol, 115 (2), 334-343
DOI 10.1093/jleuko/qiad112, PubMed 37738462 -
Linguistics-based formalization of the antibody language as a basis for antibody language models
Nat Comput Sci, 4 (6), 412-422
DOI 10.1038/s43588-024-00642-3, PubMed 38877120 -
Best practices for machine learning in antibody discovery and development
Drug Discov Today, 29 (7), 104025
DOI 10.1016/j.drudis.2024.104025, PubMed 38762089
Publications 2023
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Flow Cytometry of CD5-Positive Hairy Cell Leukemia
Mol Diagn Ther, 27 (5), 593-599
DOI 10.1007/s40291-023-00658-x, PubMed 37291380 -
Pitfalls in patenting academic CAR-T cells therapy
Expert Opin Ther Pat, 33 (5), 339-348
DOI 10.1080/13543776.2023.2220883, PubMed 37254751 -
Application and challenges of TCR and BCR sequencing to investigate T- and B-cell clonality in elastase-induced experimental murine abdominal aortic aneurysm
Front Cardiovasc Med, 10, 1221620
DOI 10.3389/fcvm.2023.1221620, PubMed 38034381 -
Insights into next generation sequencing guided antibody selection strategies
Sci Rep, 13 (1), 18370
DOI 10.1038/s41598-023-45538-w, PubMed 37884618 -
Author Correction: Insights into next generation sequencing guided antibody selection strategies
Sci Rep, 13 (1), 22616
DOI 10.1038/s41598-023-49214-x, PubMed 38114562 -
Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence
Front Immunol, 14, 1265044
DOI 10.3389/fimmu.2023.1265044, PubMed 38045681 -
Assessing developability early in the discovery process for novel biologics
MAbs, 15 (1), 2171248
DOI 10.1080/19420862.2023.2171248, PubMed 36823021 -
Human thymic putative CD8αα precursors exhibit a biased TCR repertoire in single cell AIRR-seq
Sci Rep, 13 (1), 17714
DOI 10.1038/s41598-023-44693-4, PubMed 37853083 -
Toward real-world automated antibody design with combinatorial Bayesian optimization
Cell Rep Methods, 3 (1), 100374
DOI 10.1016/j.crmeth.2022.100374, PubMed 36814835 -
Defining and Studying B Cell Receptor and TCR Interactions
J Immunol, 211 (3), 311-322
DOI 10.4049/jimmunol.2300136, PubMed 37459189 -
Predicting the immune escape of SARS-CoV-2 neutralizing antibodies upon mutation
Biochim Biophys Acta Mol Basis Dis, 1870 (2), 166959
DOI 10.1016/j.bbadis.2023.166959, PubMed 37967796 -
Design and preclinical testing of an anti-CD41 CAR T cell for the treatment of acute megakaryoblastic leukaemia
J Cell Mol Med, 27 (19), 2864-2875
DOI 10.1111/jcmm.17810, PubMed 37667538 -
RNA sequencing suggests that non-coding RNAs play a role in the development of acquired haemophilia
J Cell Mol Med, 27 (13), 1790-1796
DOI 10.1111/jcmm.17741, PubMed 37317065 -
Pathology and Molecular Biology of Melanoma
Curr Issues Mol Biol, 45 (7), 5575-5597
DOI 10.3390/cimb45070352, PubMed 37504268
Publications 2022
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Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies
MAbs, 14 (1), 2008790
DOI 10.1080/19420862.2021.2008790, PubMed 35293269 -
In silico proof of principle of machine learning-based antibody design at unconstrained scale
MAbs, 14 (1), 2031482
DOI 10.1080/19420862.2022.2031482, PubMed 35377271 -
TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences
Brief Bioinform, 23 (2)
DOI 10.1093/bib/bbab566, PubMed 35062022 -
Development of a High-Affinity Antibody against the Tumor-Specific and Hyperactive 611-p95HER2 Isoform
Cancers (Basel), 14 (19)
DOI 10.3390/cancers14194859, PubMed 36230782 -
What are the current driving questions in immune repertoire research?
Cell Syst, 13 (9), 683-686
DOI 10.1016/j.cels.2022.08.006, PubMed 36137509 -
Antibody variable sequences have a pronounced effect on cellular transport and plasma half-life
iScience, 25 (2), 103746
DOI 10.1016/j.isci.2022.103746, PubMed 35118359 -
Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes
Bioinform Adv, 2 (1), vbac062
DOI 10.1093/bioadv/vbac062, PubMed 36699357 -
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases
Gigascience, 12
DOI 10.1093/gigascience/giad032, PubMed 37161965 -
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification
Gigascience, 11
DOI 10.1093/gigascience/giac046, PubMed 35639633 -
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods
Gigascience, 12
DOI 10.1093/gigascience/giad074, PubMed 37848619 -
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis
Methods Mol Biol, 2453, 297-316
DOI 10.1007/978-1-0716-2115-8_17, PubMed 35622333 -
Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells
Cell Rep, 41 (9), 111764
DOI 10.1016/j.celrep.2022.111764, PubMed 36450255 -
The evolutionary and functional significance of germline immunoglobulin gene variation
Trends Immunol, 44 (1), 7-21
DOI 10.1016/j.it.2022.11.001, PubMed 36470826 -
Apyrase-mediated amplification of secretory IgA promotes intestinal homeostasis
Cell Rep, 40 (3), 111112
DOI 10.1016/j.celrep.2022.111112, PubMed 35858559 -
Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction
Nat Comput Sci, 2 (12), 845-865
DOI 10.1038/s43588-022-00372-4, PubMed 38177393 -
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching
Bioinformatics, 38 (17), 4230-4232
DOI 10.1093/bioinformatics/btac505, PubMed 35852318 -
Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking
Bioinformatics, 38 (21), 4994-4996
DOI 10.1093/bioinformatics/btac612, PubMed 36073940 -
Reference-based comparison of adaptive immune receptor repertoires
Cell Rep Methods, 2 (8), 100269
DOI 10.1016/j.crmeth.2022.100269, PubMed 36046619 -
Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery
Brief Bioinform, 23 (4)
DOI 10.1093/bib/bbac267, PubMed 35830864
Publications 2021
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A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
Cell Rep, 34 (11), 108856
DOI 10.1016/j.celrep.2021.108856, PubMed 33730590 -
TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood
EBioMedicine, 68, 103429
DOI 10.1016/j.ebiom.2021.103429, PubMed 34127432 -
Ancestral diversity is limited in published T cell receptor sequencing studies
Immunity, 54 (10), 2177-2179
DOI 10.1016/j.immuni.2021.09.015, PubMed 34644550 -
Animal Immunization, in Vitro Display Technologies, and Machine Learning for Antibody Discovery
Trends Biotechnol, 39 (12), 1263-1273
DOI 10.1016/j.tibtech.2021.03.003, PubMed 33775449 -
Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells
Cell Rep, 35 (12), 109286
DOI 10.1016/j.celrep.2021.109286, PubMed 34161770 -
Extended plasma half-life of albumin-binding domain fused human IgA upon pH-dependent albumin engagement of human FcRn in vitro and in vivo
MAbs, 13 (1), 1893888
DOI 10.1080/19420862.2021.1893888, PubMed 33691596 -
Immunoglobulin germline gene variation and its impact on human disease
Genes Immun, 22 (4), 205-217
DOI 10.1038/s41435-021-00145-5, PubMed 34175903 -
Germline polymorphisms and alternative splicing of human immunoglobulin light chain genes
iScience, 24 (10), 103192
DOI 10.1016/j.isci.2021.103192, PubMed 34693229 -
Profiling the specificity of clonally expanded plasma cells during chronic viral infection by single-cell analysis
Eur J Immunol, 52 (2), 297-311
DOI 10.1002/eji.202149331, PubMed 34727578 -
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
Nat Mach Intell, 3 (11), 936-944
DOI 10.1038/s42256-021-00413-z, PubMed 37396030 -
Diversity in immunogenomics: the value and the challenge
Nat Methods, 18 (6), 588-591
DOI 10.1038/s41592-021-01169-5, PubMed 34002093 -
Modeling the Dynamics of T-Cell Development in the Thymus
Entropy (Basel), 23 (4)
DOI 10.3390/e23040437, PubMed 33918050 -
Individualized VDJ recombination predisposes the available Ig sequence space
Genome Res, 31 (12), 2209-2224
DOI 10.1101/gr.275373.121, PubMed 34815307 -
Progress and challenges in mass spectrometry-based analysis of antibody repertoires
Trends Biotechnol, 40 (4), 463-481
DOI 10.1016/j.tibtech.2021.08.006, PubMed 34535228 -
Dynamic changes in the T cell receptor repertoire during treatment with radiotherapy combined with an immune checkpoint inhibitor
Mol Oncol, 15 (11), 2958-2968
DOI 10.1002/1878-0261.13082, PubMed 34402187
Publications 2020
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The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies
Front Immunol, 11, 559
DOI 10.3389/fimmu.2020.00559, PubMed 32328061 -
Chronic Viral Infection Promotes Efficient Germinal Center B Cell Responses
Cell Rep, 30 (4), 1013-1026.e7
DOI 10.1016/j.celrep.2019.12.023, PubMed 31995746 -
Quantitative and Qualitative Analysis of Humoral Immunity Reveals Continued and Personalized Evolution in Chronic Viral Infection
Cell Rep, 30 (4), 997-1012.e6
DOI 10.1016/j.celrep.2019.12.088, PubMed 31995768 -
Mucosal or systemic microbiota exposures shape the B cell repertoire
Nature, 584 (7820), 274-278
DOI 10.1038/s41586-020-2564-6, PubMed 32760003 -
Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow
Nat Commun, 11 (1), 2570
DOI 10.1038/s41467-020-16464-6, PubMed 32444631 -
Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences
Bioinformatics, 36 (6), 1731-1739
DOI 10.1093/bioinformatics/btz845, PubMed 31873728 -
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
Bioinformatics, 36 (11), 3594-3596
DOI 10.1093/bioinformatics/btaa158, PubMed 32154832 -
Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes
Immunogenetics, 72 (5), 279-294
DOI 10.1007/s00251-020-01164-8, PubMed 32367185 -
IgM Antibody Repertoire Fingerprints in Mice Are Personalized but Robust to Viral Infection Status
Front Cell Infect Microbiol, 10, 254
DOI 10.3389/fcimb.2020.00254, PubMed 32547966
Publications 2019
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Resident memory CD8 T cells persist for years in human small intestine
J Exp Med, 216 (10), 2412-2426
DOI 10.1084/jem.20190414, PubMed 31337737 -
Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires
Mol. Syst. Des. Eng., 4 (4), 701-736
DOI 10.1039/c9me00071b -
Editorial: Methods and Applications of Computational Immunology
Front Immunol, 10, 2818
DOI 10.3389/fimmu.2019.02818, PubMed 31849986 -
Large-scale network analysis reveals the sequence space architecture of antibody repertoires
Nat Commun, 10 (1), 1321
DOI 10.1038/s41467-019-09278-8, PubMed 30899025 -
Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming
Front Immunol, 10, 435
DOI 10.3389/fimmu.2019.00435, PubMed 30936866 -
Persistence of intrathecal oligoclonal B cells and IgG in multiple sclerosis
J Neuroimmunol, 333, 576966
DOI 10.1016/j.jneuroim.2019.576966, PubMed 31153015
Publications 2018
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High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis
Nucleic Acids Res, 46 (14), 7436-7449
DOI 10.1093/nar/gky550, PubMed 29931269 -
Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires
Front Immunol, 9, 224
DOI 10.3389/fimmu.2018.00224, PubMed 29515569
Publications 2017
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Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development
Cell Rep, 19 (7), 1467-1478
DOI 10.1016/j.celrep.2017.04.054, PubMed 28514665 -
Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires
J Immunol, 199 (8), 2985-2997
DOI 10.4049/jimmunol.1700594, PubMed 28924003 -
Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim)
Bioinformatics, 33 (24), 3938-3946
DOI 10.1093/bioinformatics/btx533, PubMed 28968873
Publications 2015
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Influenza vaccine response profiles are affected by vaccine preparation and preexisting immunity, but not HIV infection
Hum Vaccin Immunother, 11 (2), 391-6
DOI 10.1080/21645515.2015.1008930, PubMed 25692740 -
A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status
Genome Med, 7 (1), 49
DOI 10.1186/s13073-015-0169-8, PubMed 26140055 -
Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires
Trends Immunol, 36 (11), 738-749
DOI 10.1016/j.it.2015.09.006, PubMed 26508293
Publications 2014
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Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice
BMC Immunol, 15, 40
DOI 10.1186/s12865-014-0040-5, PubMed 25318652 -
Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing
PLoS One, 9 (5), e96727
DOI 10.1371/journal.pone.0096727, PubMed 24809667
Publications 2012
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A minimal model of peptide binding predicts ensemble properties of serum antibodies
BMC Genomics, 13, 79
DOI 10.1186/1471-2164-13-79, PubMed 22353141