V. Greiff

发表

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

Cédric R. Weber, Ingrid Hobæk Haff, R. Akbar, 2019, bioRxiv.

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

Geir Kjetil Sandve, Cédric R. Weber, Rahmad Akbar, 2019, bioRxiv.

A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status

V. Greiff, S. Reddy, P. Bhat, 2015, Genome Medicine.

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires.

Enkelejda Miho, V. Greiff, S. Reddy, 2015, Trends in immunology.

High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis

Cédric R. Weber, V. Greiff, S. Reddy, 2018, bioRxiv.

Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development.

Cédric R. Weber, Enkelejda Miho, V. Greiff, 2017, Cell reports.

A minimal model of peptide binding predicts ensemble properties of serum antibodies

V. Greiff, J. Schuchhardt, Atijeh Valai, 2012, BMC Genomics.

Modern Hopfield Networks and Attention for Immune Repertoire Classification

Geir Kjetil Sandve, Sepp Hochreiter, Victor Greiff, 2020, bioRxiv.

In silico proof of principle of machine learning-based antibody design at unconstrained scale

Cédric R. Weber, Ingrid Hobæk Haff, S. Hochreiter, 2021, bioRxiv.

Single cell BCR and transcriptome analysis after respiratory virus infection reveals spatiotemporal dynamics of antigen-specific B cell responses

Jonathan L. Robinson, V. Greiff, J. Yewdell, 2020, bioRxiv.

Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics

G. K. Sandve, V. Greiff, Ghadi S. Al Hajj, 2022, ArXiv.

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice

Victor Greiff, Mark Pogson, Ulrike Haessler, 2014, BMC Immunology.

Comprehensive Evaluation and Optimization of Amplicon Library Preparation Methods for High-Throughput Antibody Sequencing

Sai T. Reddy, Victor Greiff, Mark Pogson, 2014, PloS one.

Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming

Steven H. Kleinstein, Victor Greiff, Nishanth Marthandan, 2019, Front. Immunol..

Resident memory CD8 T cells persist for years in human small intestine

V. Greiff, L. Sollid, S. Qiao, 2019, The Journal of experimental medicine.

Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes

V. Greiff, A. Oxenius, A. Yermanos, 2020, Immunogenetics.

Learning the high-dimensional immunogenomic features that predict public and private antibody repertoires

Cédric R. Weber, Enkelejda Miho, V. Greiff, 2017, bioRxiv.

High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis

Cédric R. Weber, V. Greiff, S. Reddy, 2018, bioRxiv.

The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires

Chakravarthi Kanduri, Geir Kjetil Sandve, Eivind Hovig, 2021, Nature Machine Intelligence.

Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow

V. Greiff, Hyun-Dong Chang, S. Reddy, 2020, Nature Communications.

Quantitative and Qualitative Analysis of Humoral Immunity Reveals Continued and Personalized Evolution in Chronic Viral Infection.

Suzanne P. M. Welten, V. Greiff, A. Oxenius, 2020, Cell reports.

The influence of the phylogenetic inference pipeline on murine antibody repertoire sequencing data following viral infection

V. Greiff, A. Oxenius, A. Yermanos, 2020, bioRxiv.

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

V. Greiff, B. Mazzanti, L. Massacesi, 2020, Frontiers in Immunology.

Diversity in immunogenomics: the value and the challenge

William D. Lees, Khalid Olajide Adekoya, Yana Safonova, 2020, Nature Methods.

Advancing protein language models with linguistics: a roadmap for improved interpretability

R. Akbar, Philippe A. Robert, Dag Trygve Tryslew Haug, 2022, ArXiv.

Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery

V. Greiff, K. Krawczyk, Jędrzej Kaniewski, 2022, Briefings Bioinform..

Apyrase-mediated amplification of secretory IgA promotes intestinal homeostasis.

V. Greiff, C. Donati, A. Macpherson, 2022, Cell reports.

Sexuality in older women.

V. Greiff, A. Mooradian, 1990, Archives of internal medicine.

Risk factors for pneumocystis pneumonia in giant cell arteritis: a single-centre cohort study.

V. Greiff, C. Hess, M. Recher, 2015, Clinical and experimental rheumatology.

AB0653 Prediction of relapses in autoimmune large-vessel vasculitis – towards personalised immunosuppressive treatment stewardship

V. Greiff, M. Aschwanden, D. Staub, 2018, Vasculitis.

Resident memory CD8 T cells persist for years in human small intestine

Dan B. Phung, V. Greiff, L. Sollid, 2019, bioRxiv.

Development of a High-Affinity Antibody against the Tumor-Specific and Hyperactive 611-p95HER2 Isoform

V. Greiff, H. Russnes, Puneet Rawat, 2022, Cancers.

ImmunoLingo: Linguistics-based formalization of the antibody language

R. Akbar, Philippe A. Robert, Dag Trygve Tryslew Haug, 2022, ArXiv.

AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation

Philippe A. Robert, V. Greiff, Jun Wang, 2022, SSRN Electronic Journal.

The evolutionary and functional significance of germline immunoglobulin gene variation.

V. Greiff, O. Rodriguez, C. Watson, 2022, Trends in immunology.

ImmunoLingo: Linguistics-based formalization of the antibody language

R. Akbar, Philippe A. Robert, Dag Trygve Tryslew Haug, 2022, ArXiv.

Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction

Ingrid Hobæk Haff, S. Hochreiter, R. Akbar, 2022, Nat. Comput. Sci..

Hopfield Networks is All You Need

David P. Kreil, S. Hochreiter, G. K. Sandve, 2020, ICLR.

Low immunoglobulin E flags two distinct types of immune dysregulation

V. Greiff, A. Navarini, A. Bircher, 2017, Clinical and experimental immunology.

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice

V. Greiff, M. Pogson, S. Reddy, 2014, BMC Immunology.

Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires

Cédric R. Weber, Enkelejda Miho, V. Greiff, 2017, The Journal of Immunology.

Influenza vaccine response profiles are affected by vaccine preparation and preexisting immunity, but not HIV infection

Victor Greiff, Manuel Battegay, Sai T Reddy, 2015, Human vaccines & immunotherapeutics.

Individualized VDJ recombination predisposes the available Ig sequence space

Cédric R. Weber, Ingrid Hobæk Haff, R. Akbar, 2021, bioRxiv.

Germline polymorphisms and alternative splicing of human immunoglobulin light chain genes

V. Greiff, G. Yaari, L. Sollid, 2021, iScience.

Alternative splice variants and germline polymorphisms in human immunoglobulin light chain genes

V. Greiff, G. Yaari, L. Sollid, 2021, bioRxiv.

The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires

Cédric R. Weber, Ingrid Hobæk Haff, S. Hochreiter, 2021, Nature Machine Intelligence.

Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires

Rahmad Akbar, Igor Snapkov, Victor Greiff, 2019, Molecular Systems Design & Engineering.

Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells

Jonathan L. Robinson, V. Greiff, J. Yewdell, 2021, Cell reports.

Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires

Cédric R. Weber, Alexander Yermanos, Sai T. Reddy, 2017, Front. Immunol..

Immunoglobulin germline gene variation and its impact on human disease

V. Greiff, L. Sollid, Ivana Mikocziova, 2021, Genes & Immunity.

Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes

Cédric R. Weber, V. Greiff, A. Oxenius, 2021, bioRxiv.

Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification

Milena Pavlović, Lonneke Scheffer, G. K. Sandve, 2021, bioRxiv.

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

Cédric R. Weber, Ingrid Hobæk Haff, R. Akbar, 2021, Cell reports.

Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences

Mikhail Shugay, Victor Greiff, Enkelejda Miho, 2019, Bioinform..

Large-scale network analysis reveals the sequence space architecture of antibody repertoires

Victor Greiff, Enkelejda Miho, Rok Roškar, 2019, Nature Communications.

Comparison of methods for phylogenetic B‐cell lineage inference using time‐resolved antibody repertoire simulations (AbSim)

Tanja Stadler, Alexander Yermanos, Sai T. Reddy, 2017, Bioinform..

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

A. H. Laustsen, V. Greiff, S. Muyldermans, 2021, Trends in biotechnology.

Reference-based comparison of adaptive immune receptor repertoires

Cédric R. Weber, R. Akbar, Philippe A. Robert, 2022, bioRxiv.

Chronic Viral Infection Promotes Efficient Germinal Center B Cell Responses

Yi Hao, Victor Greiff, Ulrike Menzel, 2020, Cell reports.

Ancestral diversity is limited in published T cell receptor sequencing studies.

V. Greiff, A. Popejoy, L. Quintana-Murci, 2021, Immunity.

Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow

V. Greiff, Hyun-Dong Chang, S. Reddy, 2019, bioRxiv.

Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies

R. Akbar, Philippe A. Robert, F. Lund-Johansen, 2022, mAbs.

Dynamic changes in the T cell receptor repertoire during treatment with radiotherapy combined with an immune checkpoint inhibitor

V. Greiff, I. Snapkov, Å. Helland, 2021, Molecular oncology.

Assessing developability early in the discovery process for novel biologics

A. H. Laustsen, V. Greiff, H. Kettenberger, 2023, mAbs.

Bridging the neutralization gap for unseen antibodies

Philippe A. Robert, V. Greiff, 2022, Nature Machine Intelligence.

Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking

G. K. Sandve, V. Greiff, 2022, Bioinform..

Modeling the Dynamics of T-Cell Development in the Thymus

Victor Greiff, Andreas Krueger, Philippe A. Robert, 2021, Entropy.

TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences

Lonneke Scheffer, G. K. Sandve, V. Greiff, 2022, Briefings Bioinform..

Mucosal or systemic microbiota exposures shape the B cell repertoire

Victor Greiff, V. Greiff, S. Hapfelmeier, 2020, Nature.

Antibody variable sequences have a pronounced effect on cellular transport and plasma half-life

V. Greiff, J. Andersen, I. Sandlie, 2022, iScience.

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

V. Greiff, J. Andersen, I. Sandlie, 2021, mAbs.

Progress and challenges in mass spectrometry-based analysis of antibody repertoires.

V. Greiff, I. Snapkov, T. Nyman, 2021, Trends in biotechnology.

Toward real-world automated antibody design with combinatorial Bayesian optimization

R. Akbar, Philippe A. Robert, V. Greiff, 2023, Cell reports methods.

Persistence of intrathecal oligoclonal B cells and IgG in multiple sclerosis

V. Greiff, T. Holmøy, F. Vartdal, 2019, Journal of Neuroimmunology.

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

Geir Kjetil Sandve, Yana Safonova, Cédric R. Weber, 2019, bioRxiv.

Linguistically inspired roadmap for building biologically reliable protein language models

R. Akbar, Philippe A. Robert, Dag Trygve Tryslew Haug, 2022, Nature Machine Intelligence.

Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics

G. K. Sandve, V. Greiff, Ghadi S. Al Hajj, 2022, ArXiv.

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

Lindsay G. Cowell, Victor Greiff, Gur Yaari, 2020 .

One billion synthetic 3D-antibody-antigen complexes enable unconstrained machine-learning formalized investigation of antibody specificity prediction

Ingrid Hobæk Haff, S. Hochreiter, R. Akbar, 2021 .

Using TCR and BCR sequencing to unravel the role of T and B cells in abdominal aortic aneurysm

V. Greiff, S. Schmidt, Maria Chernigovskaya, 2022, bioRxiv.

A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data

V. Greiff, A. Conesa, V. Felipo, 2022, ImmunoInformatics.

IgM Antibody Repertoire Fingerprints in Mice Are Personalized but Robust to Viral Infection Status

V. Greiff, A. Oxenius, A. Yermanos, 2020, Frontiers in Cellular and Infection Microbiology.

Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection

V. Greiff, A. Oxenius, A. Yermanos, 2020, bioRxiv.

T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases.

V. Greiff, E. Hovig, S. Lorenz, 2022, GigaScience.

TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood

V. Greiff, L. Massacesi, Maria Chernigovskaya, 2021, EBioMedicine.

Modern Hopfield Networks and Attention for Immune Repertoire Classification

Geir Kjetil Sandve, Sepp Hochreiter, Victor Greiff, 2020, bioRxiv.

Large-scale network analysis reveals the sequence space architecture of antibody repertoires

Enkelejda Miho, V. Greiff, S. Reddy, 2019, Nature Communications.

CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching

Lonneke Scheffer, G. K. Sandve, V. Greiff, 2021, bioRxiv.

A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status

V. Greiff, S. Reddy, P. Bhat, 2015, Genome Medicine.

Pathology and Molecular Biology of Melanoma

V. Greiff, J. Bergthórsson, D. Cenariu, 2023, Current issues in molecular biology.

High-resolution mapping of cell-cycle dynamics during steady-state T-cell development and regeneration in vivo

Philippe A. Robert, V. Greiff, M. Meyer-Hermann, 2023, bioRxiv.

Profiling the specificity of clonally expanded plasma cells during chronic viral infection by single‐cell analysis

V. Greiff, A. Oxenius, A. Yermanos, 2021, European journal of immunology.

Defining and Studying B Cell Receptor and TCR Interactions.

V. Greiff, N. Wu, A. Mayer, 2023, Journal of immunology.

Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for real-world antibody specificity prediction

Ingrid Hobæk Haff, S. Hochreiter, R. Akbar, 2021, bioRxiv.

Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies

V. Greiff, A. Oxenius, A. Yermanos, 2021, bioRxiv.

Atypical memory B cells form a pre-plasmacellular reservoir for steady-state IgD responses to common nasopharyngeal antigens

Andrei Slabodkin, V. Greiff, S. Mehandru, 2023, bioRxiv.

Weakly supervised identification and generation of adaptive immune receptor sequences associated with immune disease status

Philippe A. Robert, Andrei Slabodkin, G. K. Sandve, 2023, bioRxiv.

Flow Cytometry of CD5-Positive Hairy Cell Leukemia

V. Greiff, J. Bergthórsson, D. Cenariu, 2023, Molecular Diagnosis & Therapy.

3 Inter-and intra-species comparison of phylogenetic fingerprints and sequence 4 diversity of immunoglobulin variable genes 5

V. Greiff, A. Oxenius, A. Yermanos, 2021 .

DeepRC: Immune repertoire classiﬁcation with attention-based deep massive multiple instance learning

S. Hochreiter, G. K. Sandve, V. Greiff, 2020 .