Publications by Victor Greiff

53 publications found

Publications 2022

  1. Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V (2022)
    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
  2. Akbar R, Robert PA, Weber CR, Widrich M, Frank R, Pavlović M, Scheffer L, Chernigovskaya M, Snapkov I, Slabodkin A, Mehta BB, Miho E, Lund-Johansen F, Andersen JT, Hochreiter S, Hobæk Haff I, Klambauer G, Sandve GK, Greiff V (2022)
    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
  3. Dahal-Koirala S, Balaban G, Neumann RS, Scheffer L, Lundin KEA, Greiff V, Sollid LM, Qiao SW, Sandve GK (2022)
    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
  4. Greiff V, Luning Prak ET, O'Donnell T, Finotello F, Reddy ST, Walczak A, Mora T (2022)
    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
  5. Grevys A, Frick R, Mester S, Flem-Karlsen K, Nilsen J, Foss S, Sand KMK, Emrich T, Fischer JAA, Greiff V, Sandlie I, Schlothauer T, Andersen JT (2022)
    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
  6. Kanduri C, Pavlović M, Scheffer L, Motwani K, Chernigovskaya M, Greiff V, Sandve GK (2022)
    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
  7. Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U, AIRR Community (2022)
    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
  8. Perruzza L, Strati F, Raneri M, Li H, Gargari G, Rezzonico-Jost T, Palatella M, Kwee I, Morone D, Seehusen F, Sonego P, Donati C, Franceschi P, Macpherson AJ, Guglielmetti S, Greiff V, Grassi F (2022)
    Apyrase-mediated amplification of secretory IgA promotes intestinal homeostasis
    Cell Rep, 40 (3), 111112
    DOI 10.1016/j.celrep.2022.111112, PubMed 35858559
  9. Rognes T, Scheffer L, Greiff V, Sandve GK (2022)
    CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching
    Bioinformatics (in press)
    DOI 10.1093/bioinformatics/btac505, PubMed 35852318
  10. Sandve GK, Greiff V (2022)
    Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking
    Bioinformatics (in press)
    DOI 10.1093/bioinformatics/btac612, PubMed 36073940
  11. Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V (2022)
    Reference-based comparison of adaptive immune receptor repertoires
    Cell Rep Methods, 2 (8), 100269
    DOI 10.1016/j.crmeth.2022.100269, PubMed 36046619
  12. Wilman W, Wróbel S, Bielska W, Deszynski P, Dudzic P, Jaszczyszyn I, Kaniewski J, Młokosiewicz J, Rouyan A, Satława T, Kumar S, Greiff V, Krawczyk K (2022)
    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

  1. Akbar R, Robert PA, Pavlović M, Jeliazkov JR, Snapkov I, Slabodkin A, Weber CR, Scheffer L, Miho E, Haff IH, Haug DTT, Lund-Johansen F, Safonova Y, Sandve GK, Greiff V (2021)
    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
  2. Amoriello R, Chernigovskaya M, Greiff V, Carnasciali A, Massacesi L, Barilaro A, Repice AM, Biagioli T, Aldinucci A, Muraro PA, Laplaud DA, Lossius A, Ballerini C (2021)
    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
  3. Huang YN, Peng K, Popejoy AB, Hu J, Nowicki TS, Gold SM, Quintana-Murci L, Fuentes-Guajardo M, Shugay M, Greiff V, Burkhardt AM, Alachkar H, Mangul S (2021)
    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
  4. Laustsen AH, Greiff V, Karatt-Vellatt A, Muyldermans S, Jenkins TP (2021)
    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
  5. Mathew NR, Jayanthan JK, Smirnov IV, Robinson JL, Axelsson H, Nakka SS, Emmanouilidi A, Czarnewski P, Yewdell WT, Schön K, Lebrero-Fernández C, Bernasconi V, Rodin W, Harandi AM, Lycke N, Borcherding N, Yewdell JW, Greiff V, Bemark M, Angeletti D (2021)
    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
  6. Mester S, Evers M, Meyer S, Nilsen J, Greiff V, Sandlie I, Leusen J, Andersen JT (2021)
    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
  7. Mikocziova I, Greiff V, Sollid LM (2021)
    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
  8. Mikocziova I, Peres A, Gidoni M, Greiff V, Yaari G, Sollid LM (2021)
    Germline polymorphisms and alternative splicing of human immunoglobulin light chain genes
    iScience, 24 (10), 103192
    DOI 10.1016/j.isci.2021.103192, PubMed 34693229
  9. Neumeier D, Pedrioli A, Genovese A, Sandu I, Ehling R, Hong KL, Papadopoulou C, Agrafiotis A, Kuhn R, Shlesinger D, Robbiani D, Han J, Hauri L, Csepregi L, Greiff V, Merkler D, Reddy ST, Oxenius A, Yermanos A (2021)
    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
  10. Pavlovic M, Scheffer L, Motwani K, Kanduri C, Kompova R, Vazov N, Waagan K, Bernal FLM, Costa AA, Corrie B, Akbar R, Al Hajj GS, Balaban G, Brusko TM, Chernigovskaya M, Christley S, Cowell LG, Frank R, Grytten I, Gundersen S, Haff IH, Hovig E, Hsieh PH, Klambauer G, Kuijjer ML et al. (2021)
    The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
    Nat. Mach. Intell., 3 (11), 936-+
    DOI 10.1038/s42256-021-00413-z
  11. Peng K, Safonova Y, Shugay M, Popejoy AB, Rodriguez OL, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau VM, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, Jönsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Abedalthagafi MS, Adekoya KO, Ahmed RA et al. (2021)
    Diversity in immunogenomics: the value and the challenge
    Nat Methods, 18 (6), 588-591
    DOI 10.1038/s41592-021-01169-5, PubMed 34002093
  12. Robert PA, Kunze-Schumacher H, Greiff V, Krueger A (2021)
    Modeling the Dynamics of T-Cell Development in the Thymus
    Entropy (Basel), 23 (4)
    DOI 10.3390/e23040437, PubMed 33918050
  13. Slabodkin A, Chernigovskaya M, Mikocziova I, Akbar R, Scheffer L, Pavlović M, Bashour H, Snapkov I, Mehta BB, Weber CR, Gutierrez-Marcos J, Sollid LM, Haff IH, Sandve GK, Robert PA, Greiff V (2021)
    Individualized VDJ recombination predisposes the available Ig sequence space
    Genome Res (in press)
    DOI 10.1101/gr.275373.121, PubMed 34815307
  14. Snapkov I, Chernigovskaya M, Sinitcyn P, Lê Quý K, Nyman TA, Greiff V (2021)
    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
  15. Öjlert ÅK, Nebdal D, Snapkov I, Olsen V, Kidman J, Greiff V, Chee J, Helland Å (2021)
    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

  1. Amoriello R, Greiff V, Aldinucci A, Bonechi E, Carnasciali A, Peruzzi B, Repice AM, Mariottini A, Saccardi R, Mazzanti B, Massacesi L, Ballerini C (2020)
    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
  2. Fallet B, Hao Y, Florova M, Cornille K, de Los Aires AV, Girelli Zubani G, Ertuna YI, Greiff V, Menzel U, Hammad K, Merkler D, Reddy ST, Weill JC, Reynaud CA, Pinschewer DD (2020)
    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
  3. Kräutler NJ, Yermanos A, Pedrioli A, Welten SPM, Lorgé D, Greczmiel U, Bartsch I, Scheuermann J, Kiefer JD, Eyer K, Menzel U, Greiff V, Neri D, Stadler T, Reddy ST, Oxenius A (2020)
    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
  4. Li H, Limenitakis JP, Greiff V, Yilmaz B, Schären O, Urbaniak C, Zünd M, Lawson MAE, Young ID, Rupp S, Heikenwälder M, McCoy KD, Hapfelmeier S, Ganal-Vonarburg SC, Macpherson AJ (2020)
    Mucosal or systemic microbiota exposures shape the B cell repertoire
    Nature, 584 (7820), 274-278
    DOI 10.1038/s41586-020-2564-6, PubMed 32760003
  5. Riedel R, Addo R, Ferreira-Gomes M, Heinz GA, Heinrich F, Kummer J, Greiff V, Schulz D, Klaeden C, Cornelis R, Menzel U, Kröger S, Stervbo U, Köhler R, Haftmann C, Kühnel S, Lehmann K, Maschmeyer P, McGrath M, Naundorf S, Hahne S, Sercan-Alp Ö, Siracusa F, Stefanowski J, Weber M et al. (2020)
    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
  6. Smakaj E, Babrak L, Ohlin M, Shugay M, Briney B, Tosoni D, Galli C, Grobelsek V, D'Angelo I, Olson B, Reddy S, Greiff V, Trück J, Marquez S, Lees W, Miho E (2020)
    Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences
    Bioinformatics, 36 (6), 1731-1739
    DOI 10.1093/bioinformatics/btz845, PubMed 31873728
  7. Weber CR, Akbar R, Yermanos A, Pavlović M, Snapkov I, Sandve GK, Reddy ST, Greiff V (2020)
    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
  8. Yermanos A, Dounas A, Greiff V, Stadler T, Oxenius A, Reddy ST (2020)
    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
  9. Yermanos A, Kräutler NJ, Pedrioli A, Menzel U, Greiff V, Stadler T, Oxenius A, Reddy ST (2020)
    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

  1. Bartolomé-Casado R, Landsverk OJB, Chauhan SK, Richter L, Phung D, Greiff V, Risnes LF, Yao Y, Neumann RS, Yaqub S, Øyen O, Horneland R, Aandahl EM, Paulsen V, Sollid LM, Qiao SW, Baekkevold ES, Jahnsen FL (2019)
    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
  2. Brown AJ, Snapkov I, Akbar R, Pavlovic M, Miho E, Sandve GK, Greiff V (2019)
    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
  3. Chain B, Greiff V, Textor J, Yaari G (2019)
    Editorial: Methods and Applications of Computational Immunology
    Front Immunol, 10, 2818
    DOI 10.3389/fimmu.2019.02818, PubMed 31849986
  4. Miho E, Roškar R, Greiff V, Reddy ST (2019)
    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
  5. Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen Iv FA, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM (2019)
    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
  6. Tomescu-Baciu A, Johansen JN, Holmøy T, Greiff V, Stensland M, de Souza GA, Vartdal F, Lossius A (2019)
    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

  1. Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST (2018)
    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
  2. Miho E, Yermanos A, Weber CR, Berger CT, Reddy ST, Greiff V (2018)
    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

  1. Greiff V, Menzel U, Miho E, Weber C, Riedel R, Cook S, Valai A, Lopes T, Radbruch A, Winkler TH, Reddy ST (2017)
    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
  2. Greiff V, Weber CR, Palme J, Bodenhofer U, Miho E, Menzel U, Reddy ST (2017)
    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
  3. Yermanos A, Greiff V, Krautler NJ, Menzel U, Dounas A, Miho E, Oxenius A, Stadler T, Reddy ST (2017)
    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

  1. Berger CT, Greiff V, Mehling M, Fritz S, Meier MA, Hoenger G, Conen A, Recher M, Battegay M, Reddy ST, Hess C (2015)
    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
  2. Greiff V, Bhat P, Cook SC, Menzel U, Kang W, Reddy ST (2015)
    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
  3. Greiff V, Miho E, Menzel U, Reddy ST (2015)
    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

  1. Greiff V, Menzel U, Haessler U, Cook SC, Friedensohn S, Khan TA, Pogson M, Hellmann I, Reddy ST (2014)
    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
  2. Menzel U, Greiff V, Khan TA, Haessler U, Hellmann I, Friedensohn S, Cook SC, Pogson M, Reddy ST (2014)
    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

  1. Greiff V, Redestig H, Lück J, Bruni N, Valai A, Hartmann S, Rausch S, Schuchhardt J, Or-Guil M (2012)
    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

 
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