Publications 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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