Publications by Victor Greiff

91 publications found

Publications 2024

1. Balashova D, van Schaik BDC, Stratigopoulou M, Guikema JEJ, Caniels TG, Claireaux M, van Gils MJ, Musters A, Anang DC, de Vries N, Greiff V, van Kampen AHC (2024)
   Systematic evaluation of B-cell clonal family inference approaches
   BMC Immunol, 25 (1), 13
   DOI 10.1186/s12865-024-00600-8, PubMed 38331731
2. Bashour H, Smorodina E, Pariset M, Zhong J, Akbar R, Chernigovskaya M, Lê Quý K, Snapkow I, Rawat P, Krawczyk K, Sandve GK, Gutierrez-Marcos J, Gutierrez DN, Andersen JT, Greiff V (2024)
   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
3. Brown AJ, White J, Shaw L, Gross J, Slabodkin A, Kushner E, Greiff V, Matsuda J, Gapin L, Scott-Browne J, Kappler J, Marrack P (2024)
   MHC heterozygosity limits T cell receptor variability in CD4 T cells
   Sci Immunol, 9 (97), eado5295
   DOI 10.1126/sciimmunol.ado5295, PubMed 38996008
4. Erasmus MF, Ferrara F, D'Angelo S, Spector L, Leal-Lopes C, Teixeira AA, Sørensen J, Nagpal S, Perea-Schmittle K, Choudhary A, Honnen W, Calianese D, Antonio Rodriguez Carnero L, Cocklin S, Greiff V, Pinter A, Bradbury ARM (2024)
   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
5. Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T, Munthe LA (2024)
   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
6. Iacobescu M, Pop C, Uifălean A, Mogoşan C, Cenariu D, Zdrenghea M, Tănase A, Bergthorsson JT, Greiff V, Cenariu M, Iuga CA, Tomuleasa C, Tătaru D (2024)
   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
7. Lê Quý K, Chernigovskaya M, Stensland M, Singh S, Leem J, Revale S, Yadin DA, Nice FL, Povall C, Minns DH, Galson JD, Nyman TA, Snapkow I, Greiff V (2024)
   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
8. Natali EN, Horst A, Meier P, Greiff V, Nuvolone M, Babrak LM, Fink K, Miho E (2024)
   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
9. Natali EN, Horst A, Meier P, Greiff V, Nuvolone M, Babrak LM, Fink K, Miho E (2024)
   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
10. Natali EN, Horst A, Meier P, Greiff V, Nuvolone M, Babrak LM, Fink K, Miho E (2024)
    Publisher Correction: The dengue-specific immune response and antibody identification with machine learning
    NPJ Vaccines, 9 (1), 242
    DOI 10.1038/s41541-024-01027-3, PubMed 39653698
11. O'Donnell TJ, Kanduri C, Isacchini G, Limenitakis JP, Brachman RA, Alvarez RA, Haff IH, Sandve GK, Greiff V (2024)
    Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning
    Cell Syst, 15 (12), 1168-1189
    DOI 10.1016/j.cels.2024.11.006, PubMed 39701034
12. Riccabona JR, Spoendlin FC, Fischer AM, Loeffler JR, Quoika PK, Jenkins TP, Ferguson JA, Smorodina E, Laustsen AH, Greiff V, Forli S, Ward AB, Deane CM, Fernández-Quintero ML (2024)
    Assessing AF2's ability to predict structural ensembles of proteins
    Structure, 32 (11), 2147-2159.e2
    DOI 10.1016/j.str.2024.09.001, PubMed 39332396
13. Scheffer L, Reber EE, Mehta BB, Pavlović M, Chernigovskaya M, Richardson E, Akbar R, Lund-Johansen F, Greiff V, Haff IH, Sandve GK (2024)
    Predictability of antigen binding based on short motifs in the antibody CDRH3
    Brief Bioinform, 25 (6)
    DOI 10.1093/bib/bbae537, PubMed 39438077
14. Sørensen CV, Hofmann N, Rawat P, Sørensen FV, Ljungars A, Greiff V, Laustsen AH, Jenkins TP (2024)
    ExpoSeq: simplified analysis of high-throughput sequencing data from antibody discovery campaigns
    Bioinform Adv, 4 (1), vbae020
    DOI 10.1093/bioadv/vbae020, PubMed 38425781
15. Ulvmoen A, Greiff V, Bechensteen AG, Inngjerdingen M (2024)
    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
16. Vu MH, Robert PA, Akbar R, Swiatczak B, Sandve GK, Haug DTT, Greiff V (2024)
    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
17. Wossnig L, Furtmann N, Buchanan A, Kumar S, Greiff V (2024)
    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

1. Cenariu D, Rus I, Bergthorsson JT, Grewal R, Cenariu M, Greiff V, Tigu AB, Dima D, Selicean C, Petrushev B, Zdrenghea M, Fromm J, Aanei CM, Tomuleasa C (2023)
   Flow Cytometry of CD5-Positive Hairy Cell Leukemia
   Mol Diagn Ther, 27 (5), 593-599
   DOI 10.1007/s40291-023-00658-x, PubMed 37291380
2. Constantinescu C, Constantinescu R, Bergthorsson JT, Greiff V, Tanase A, Colita A, Gulei D, Tomuleasa C (2023)
   Pitfalls in patenting academic CAR-T cells therapy
   Expert Opin Ther Pat, 33 (5), 339-348
   DOI 10.1080/13543776.2023.2220883, PubMed 37254751
3. Elster C, Ommer-Bläsius M, Lang A, Vajen T, Pfeiler S, Feige M, Yau Pang T, Böttenberg M, Verheyen S, Lê Quý K, Chernigovskaya M, Kelm M, Winkels H, Schmidt SV, Greiff V, Gerdes N (2023)
   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
4. Erasmus MF, Ferrara F, D'Angelo S, Spector L, Leal-Lopes C, Teixeira AA, Sørensen J, Nagpal S, Perea-Schmittle K, Choudhary A, Honnen W, Calianese D, Antonio Rodriguez Carnero L, Cocklin S, Greiff V, Pinter A, Bradbury ARM (2023)
   Insights into next generation sequencing guided antibody selection strategies
   Sci Rep, 13 (1), 18370
   DOI 10.1038/s41598-023-45538-w, PubMed 37884618
5. Erasmus MF, Ferrara F, D'Angelo S, Spector L, Leal-Lopes C, Teixeira AA, Sørensen J, Nagpal S, Perea-Schmittle K, Choudhary A, Honnen W, Calianese D, Antonio Rodriguez Carnero L, Cocklin S, Greiff V, Pinter A, Bradbury ARM (2023)
   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
6. Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T, Munthe LA (2023)
   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
7. Fernández-Quintero ML, Ljungars A, Waibl F, Greiff V, Andersen JT, Gjølberg TT, Jenkins TP, Voldborg BG, Grav LM, Kumar S, Georges G, Kettenberger H, Liedl KR, Tessier PM, McCafferty J, Laustsen AH (2023)
   Assessing developability early in the discovery process for novel biologics
   MAbs, 15 (1), 2171248
   DOI 10.1080/19420862.2023.2171248, PubMed 36823021
8. Heimli M, Tennebø Flåm S, Sagsveen Hjorthaug H, Bjørnstad PM, Chernigovskaya M, Le QK, Tekpli X, Greiff V, Lie BA (2023)
   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
9. Khan A, Cowen-Rivers AI, Grosnit A, Deik DG, Robert PA, Greiff V, Smorodina E, Rawat P, Akbar R, Dreczkowski K, Tutunov R, Bou-Ammar D, Wang J, Storkey A, Bou-Ammar H (2023)
   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
10. Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ (2023)
    Defining and Studying B Cell Receptor and TCR Interactions
    J Immunol, 211 (3), 311-322
    DOI 10.4049/jimmunol.2300136, PubMed 37459189
11. Sharma D, Rawat P, Greiff V, Janakiraman V, Gromiha MM (2023)
    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
12. Tigu AB, Constantinescu CS, Teodorescu P, Kegyes D, Munteanu R, Feder R, Peters M, Pralea I, Iuga C, Cenariu D, Marcu A, Tanase A, Colita A, Drula R, Bergthorsson JT, Greiff V, Dima D, Selicean C, Rus I, Zdrenghea M, Gulei D, Ghiaur G, Tomuleasa C (2023)
    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
13. Tigu AB, Hotea I, Drula R, Zimta AA, Dirzu N, Santa M, Constantinescu C, Dima D, Bergthorsson JT, Greiff V, Gulei D, Coriu D, Serban M, Mahlangu J, Tomuleasa C (2023)
    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
14. Timis T, Bergthorsson JT, Greiff V, Cenariu M, Cenariu D (2023)
    Pathology and Molecular Biology of Melanoma
    Curr Issues Mol Biol, 45 (7), 5575-5597
    DOI 10.3390/cimb45070352, PubMed 37504268

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. Dorraji E, Borgen E, Segura-Peña D, Rawat P, Smorodina E, Dunn C, Greiff V, Sekulić N, Russnes H, Kyte JA (2022)
   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
5. 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
6. 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
7. Han J, Masserey S, Shlesinger D, Kuhn R, Papadopoulou C, Agrafiotis A, Kreiner V, Dizerens R, Hong KL, Weber C, Greiff V, Oxenius A, Reddy ST, Yermanos A (2022)
   Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes
   Bioinform Adv, 2 (1), vbac062
   DOI 10.1093/bioadv/vbac062, PubMed 36699357
8. Høye E, Dagenborg VJ, Torgunrud A, Lund-Andersen C, Fretland ÅA, Lorenz S, Edwin B, Hovig E, Fromm B, Inderberg EM, Greiff V, Ree AH, Flatmark K (2022)
   T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases
   Gigascience, 12
   DOI 10.1093/gigascience/giad032, PubMed 37161965
9. 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
10. Kanduri C, Scheffer L, Pavlović M, Rand KD, Chernigovskaya M, Pirvandy O, Yaari G, Greiff V, Sandve GK (2022)
    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
11. 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
12. 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 (2022)
    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
13. Pennell M, Rodriguez OL, Watson CT, Greiff V (2022)
    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
14. 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
15. Robert PA, Akbar R, Frank R, Pavlović M, Widrich M, Snapkov I, Slabodkin A, Chernigovskaya M, Scheffer L, Smorodina E, Rawat P, Mehta BB, Vu MH, Mathisen IF, Prósz A, Abram K, Olar A, Miho E, Haug DTT, Lund-Johansen F, Hochreiter S, Haff IH, Klambauer G, Sandve GK, Greiff V (2022)
    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
16. 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, 38 (17), 4230-4232
    DOI 10.1093/bioinformatics/btac505, PubMed 35852318
17. 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, 38 (21), 4994-4996
    DOI 10.1093/bioinformatics/btac612, PubMed 36073940
18. 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
19. 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. Pavlović 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), 936-944
    DOI 10.1038/s42256-021-00413-z, PubMed 37396030
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, 31 (12), 2209-2224
    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