Cited by

This page lists scientific publications that have cited core publications of the Immcantation framework in their research. Citations are collected from PubMed and updated regularly. Citing papers are counted only once, even if they cite multiple Immcantation core publications.

Total citations: 2031 | Unique citations: 1080 | Last updated: June 05, 2026

• Zeglinski Kathleen et al. Alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing.. mAbs. 2026. PMID:41631412

• Jena Kautilya K et al. A glycan-based adjuvant expands the breadth and duration of protection of mRNA-based vaccines.. Nature immunology. 2026. PMID:42174265

• Pinto Juliana Edelvacy Lima et al. Identification of gene conversion events in horse IGHV suggests preferential hotspots for diversification.. Immunogenetics. 2026. PMID:42151624

• Dehghannasiri Roozbeh et al. Reference-free discovery with barcoded single-cell sequencing.. Nature biotechnology. 2026. PMID:42020848

• Demela Pietro et al. Competing gene regulatory networks drive naive and memory B cell differentiation.. Molecular systems biology. 2026. PMID:41991769

• Vasilenko Nicole et al. Extensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugs.. Journal of neuroinflammation. 2026. PMID:41981407

• Zost Seth J et al. Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants.. Nature microbiology. 2026. PMID:41820555

• Officer Aengus et al. Immunoglobulin gene polymorphisms shape the naïve B-cell receptor repertoire; relevance to celiac disease.. Genes and immunity. 2026. PMID:41748905

• Zhang Wuji et al. IFN-gene signatures in B cells following influenza A and B virus infection and influenza vaccination.. EMBO molecular medicine. 2026. PMID:41803327

• Benavides Sara et al. Increased VH4+JH6+ antibody heavy chain use in plasmablasts from asymptomatic multiple sclerosis patients.. Genes and immunity. 2026. PMID:41857375

• Hayashi Fumie et al. Antigen specificity of clonally enriched CD8+ T cells in multiple sclerosis.. Nature immunology. 2026. PMID:41644766

• Yu Xinjie et al. Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.. Journal of translational medicine. 2026. PMID:41689101

• Jiang Shaowen et al. A temporal and spatial atlas of adaptive immune responses in the lymph node following viral infection.. Proceedings of the National Academy of Sciences of the United States of America. 2026. PMID:41587309

• Vatovec Taja et al. Somatic deficiency of the human E3 ubiquitin ligase CBL in leukocytes impairs B cell but not T cell development and function.. Nature immunology. 2026. PMID:41540267

• Huang Shulun et al. Porcine B cell receptor repertoire uncovers balanced recognition of antigenic structures on serotype Asia1 foot-and-mouth disease virus.. PLoS pathogens. 2026. PMID:41650013

• Wu Qingqin et al. Refined phenotyping of vaccine responses reveals transcriptomic determinants of neutralizing antibody heterogeneity.. NPJ vaccines. 2026. PMID:41617721

• Thörnqvist Linnea et al. Allergen-specific human IgE isolated through an allergen-agnostic pipeline-understanding immune response and allergen recognition.. Communications biology. 2026. PMID:41606257

• Mathews Joseph et al. Computing the inducibility of broadly neutralizing antibodies under a context-dependent model of affinity maturation: applications to sequential vaccine design.. Journal of immunology (Baltimore, Md. : 1950). 2026. PMID:40971634

• Zhou Pingjing et al. Targeting senescent EGR1+ B cells enhances immunotherapy efficacy in esophageal squamous cell carcinoma.. Cell reports. Medicine. 2026. PMID:41483805

• Song Shengli et al. Profiling Allogeneic HLA-specific B-cell Responses Utilizing a 64-plex Single-HLA Reporter Cell Panel.. bioRxiv : the preprint server for biology. 2026. PMID:41659507

• Al-Khatib Hebah A et al. Dynamics of B-cell response in MERS-CoV patients and survivors with hybrid immunity.. mBio. 2026. PMID:41400350

• Song Shengli et al. Functional Convergence of Genetically Diverse B-Cell Receptors in Simian-HIV Infected Rhesus Macaques.. bioRxiv : the preprint server for biology. 2026. PMID:41648506

• Wiatr Marie et al. Memory B cell development in response to mRNA SARS-CoV-2 and nanoparticle immunization in mice.. Proceedings of the National Academy of Sciences of the United States of America. 2026. PMID:41481458

• Lees William D et al. The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase.. Nucleic acids research. 2026. PMID:41206474

• Muir Luke et al. Multifaceted B cell response to transient HIV viremia in elite controllers.. PLoS pathogens. 2026. PMID:41544177

• Naouar Ikbel et al. Lymphotoxin-dependent elevated meningeal CXCL13:BAFF ratios drive gray matter injury.. Nature immunology. 2026. PMID:41482555

• Giff Alexis Elena et al. Deep cervical lymph node analysis in central nervous system inflammatory disease.. Frontiers in immunology. 2026. PMID:41668753

• Gridley John et al. iHALT unlocks liver functionality as a surrogate secondary lymphoid organ.. Nature. 2026. PMID:41299178

• Wetzel Nora Sandrine et al. Patient-Derived Monoclonal Myelin Oligodendrocyte Glycoprotein Autoantibodies Mediate Cytotoxicity.. Neurology(R) neuroimmunology & neuroinflammation. 2026. PMID:41406408

• Guo Dongjun et al. ImmunoMatch learns and predicts cognate pairing of heavy and light immunoglobulin chains.. Nature methods. 2026. PMID:41254366

• Miglierina Emma et al. DIS3 licenses B cells for plasma cell differentiation in humans.. Cellular & molecular immunology. 2026. PMID:41286079

• Li Qi et al. B cell targeted CAR-T therapy for autoimmune diseases.. Frontiers of medicine. 2025. PMID:41452401

• Zhang Lei et al. Distinct immune cell dynamics associated with immune-related adverse events during combined chemoradiation and immune checkpoint inhibitor therapy.. Nature communications. 2025. PMID:41430079

• Reers Ashley B et al. Immunoglobulin germline reference sequences enable investigations and reveal insights into bat-specific immunity.. iScience. 2025. PMID:41321632

• Yasumizu Yoshiaki et al. Host Genetic Architecture between Epstein-Barr Virus Activity and Multiple Sclerosis Reveals Shared Pathways.. medRxiv : the preprint server for health sciences. 2025. PMID:41445616

• Siniscalco Emily R et al. Sequential class switching generates antigen-specific gut IgA from IgG1 B cells.. Immunity. 2025. PMID:41253159

• Marina-Zárate Ester et al. Highly functional and prolonged germinal center T follicular helper cell responses are associated with enhanced neutralizing antibody development.. Immunity. 2025. PMID:41205611

• Kim Jeong Yeon et al. B cell-reactive neoantigens boost antitumor immunity.. Science advances. 2025. PMID:41337574

• Li Haibo et al. Reading of human acute immune dynamics in omicron SARS-CoV-2 breakthrough infection.. Emerging microbes & infections. 2025. PMID:40231451

• Johnson Mackenzie M et al. Nucleotide context models outperform protein language models for predicting antibody affinity maturation.. PLoS computational biology. 2025. PMID:41325480

• Engelbrecht Eric et al. Germline polymorphisms in the immunoglobulin kappa and lambda loci underpinning antibody light chain repertoire variability.. Nature communications. 2025. PMID:41315391

• Chen Xiaomei et al. Challenges and strategies in clinical applications of CAR-T therapy for autoimmune diseases.. Journal of hematology & oncology. 2025. PMID:41316450

• Lin Xinqing et al. Uncovering the immune mechanisms underlying the emergence of immunotherapy-induced pneumonitis in lung cancer patients.. Nature communications. 2025. PMID:41298513

• Sigorskikh A I et al. Fastq-dupaway: a fast and memory-efficient tool for deduplication of single- and paired-end NGS data.. Scientific reports. 2025. PMID:41290940

• Johnson Mackenzie M et al. Nucleotide context models outperform protein language models for predicting antibody affinity maturation.. bioRxiv : the preprint server for biology. 2025. PMID:40666976

• Çakan Elif et al. CTLA-4 blockade shifts the B cell repertoire toward autoimmunity.. The Journal of clinical investigation. 2025. PMID:41026527

• Younis Shady et al. Epstein-Barr virus reprograms autoreactive B cells as antigen-presenting cells in systemic lupus erythematosus.. Science translational medicine. 2025. PMID:41223250

• Wei Yulong et al. Transcription factor BACH2 shapes tissue-resident memory T cell programs to promote HIV-1 persistence.. Immunity. 2025. PMID:40845842

• Dang Van Duc et al. Distinct autoreactive CD19- plasma cell subsets accumulate in lupus-prone mice.. Nature communications. 2025. PMID:41213970

• McEnany John et al. Dynamics of local B cell migration during affinity maturation in the human tonsil.. bioRxiv : the preprint server for biology. 2025. PMID:41279088

• Chernyshev Mark et al. Detection of PCR chimeras in adaptive immune receptor repertoire sequences.. Bioinformatics (Oxford, England). 2025. PMID:41124049

• Kwon Taeyong et al. Pigs lacking Natural Killer T cells have altered cellular responses to influenza.. bioRxiv : the preprint server for biology. 2025. PMID:41279250

• Fielding Jessie J et al. TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.. bioRxiv : the preprint server for biology. 2025. PMID:41279821

• Matsen Frederick A et al. Separating selection from mutation in antibody language models.. bioRxiv : the preprint server for biology. 2025. PMID:41279420

• Grabauskas Titas et al. CMV-specific clonal expansion of Th1, GZMK+ CD8+, and TEMRA T cells revealed by human PBMC single cell profiling.. bioRxiv : the preprint server for biology. 2025. PMID:40666903

• Sutton Henry J et al. Simultaneous induction of multiple classes of broadly neutralizing antibody precursors by combination germline-targeting immunization in nonhuman primates.. Science immunology. 2025. PMID:41105754

• Sarkkinen Joona et al. Intranodal expansion of follicular T helper cells in patients with multiple sclerosis.. JCI insight. 2025. PMID:41059568

• van Ginneken Daphne et al. Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.. Bioinformatics (Oxford, England). 2025. PMID:41065461

• Cheung Michelle W et al. Reduced vaccine-induced germinal center outputs in patients with inflammatory bowel disease treated with anti-TNF biologics.. The Journal of clinical investigation. 2025. PMID:40728886

• Inamo Jun et al. Comparative single-cell and spatial profiling of anti-SSA-positive and anti-centromere-positive Sjögren’s disease reveals common and distinct immune activation and fibroblast-mediated inflammation.. Nature communications. 2025. PMID:40983612

• Knox James J et al. B-Cell Subset Representation Predicts SARS-CoV-2 Vaccine Response in Solid Organ Transplant Recipients.. The Journal of infectious diseases. 2025. PMID:40459569

• Manthiram Kalpana et al. SARS-CoV-2 infection and vaccination elicit distinct pharyngeal mucosal B cell responses in children.. Research square. 2025. PMID:40964019

• Montiel-Armendariz Andrea et al. B cell αv integrin regulates tissue specialization and clonal expansion of lung germinal center and memory B cells after viral infection.. bioRxiv : the preprint server for biology. 2025. PMID:39386536

• Jung Jaeyong et al. Commensal Bacteria Drive B-cell Lymphomagenesis in the Setting of Innate Immunodeficiency.. Blood cancer discovery. 2025. PMID:40608826

• Ford Michael K B et al. Genotyping of selected germline adaptive immune system loci using short-read sequencing data.. Genome research. 2025. PMID:40764056

• Golabi Sahar et al. Omega-3 Fatty Acids Supplementation and Neuroprotection, Inflammation, Fatigue, and Physical Activity in Multiple Sclerosis: A Randomized Controlled Trial.. Food science & nutrition. 2025. PMID:40905016

• Wells Steven B et al. Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age.. Nature immunology. 2025. PMID:40804529

• MohammadiPeyhani Homa et al. deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning.. Bioinformatics (Oxford, England). 2025. PMID:40796135

• Richardson Eve et al. Is the vaccination-induced B cell receptor repertoire predictable?. Immunoinformatics (Amsterdam, Netherlands). 2025. PMID:41311460

• Iyer Lakshmi Rani et al. Current insight into HIV-1 persistence from single-cell transcriptome profiling in acutely treated cohorts of infection.. Current opinion in HIV and AIDS. 2025. PMID:40638066

• Ping Pengyao et al. How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads.. Quantitative biology (Beijing, China). 2025. PMID:41675965

• Sung Kevin et al. Thrifty wide-context models of B cell receptor somatic hypermutation.. eLife. 2025. PMID:40879331

• Rao Vishal N et al. Clonotype-enriched somatic hypermutations drive affinity maturation of a public human antibody targeting an occluded sarbecovirus epitope.. Cell reports. 2025. PMID:40803328

• Schneider-Hohendorf Tilman et al. B- and T cell receptor sequencing elucidates characteristics of lymphocyte depletion by ocrelizumab.. iScience. 2025. PMID:40727939

• Ralph Duncan K et al. Inference of germinal center evolutionary dynamics via simulation-based deep learning.. ArXiv. 2025. PMID:40832049

• Brodsky Nina N et al. Early-life human CD8+ T cells exhibit rapid, short-lived effector responses and a unique transcription factor landscape.. Proceedings of the National Academy of Sciences of the United States of America. 2025. PMID:40720649

• Lv Kexin et al. Broad neuraminidase antibodies confer protection against seasonal and avian influenza viruses.. Nature communications. 2025. PMID:40753167

• Vit Filippo et al. Measurement of Immunoglobulin Intraclonal diversification refines the clinical impact of IGHV mutational status in chronic lymphocytic leukemia.. Leukemia. 2025. PMID:40533497

• Edahiro Ryuya et al. Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution.. Nature genetics. 2025. PMID:40721531

• Bagnara Davide et al. Chronic lymphocytic leukemia often arises by a multiclonal selection process.. Haematologica. 2025. PMID:39973373

• Caniels Tom G et al. Precise targeting of HIV broadly neutralizing antibody precursors in humans.. Science (New York, N.Y.). 2025. PMID:40373114

• Matsen Frederick A et al. A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer-Encoder.. Molecular biology and evolution. 2025. PMID:40794593

• Parks K Rachael et al. Vaccination with mRNA-encoded membrane-anchored HIV envelope trimers elicited tier 2 neutralizing antibodies in a phase 1 clinical trial.. Science translational medicine. 2025. PMID:40737434

• Ramezani-Rad Parham et al. Vaccination with an mRNA-encoded membrane-bound HIV envelope trimer induces neutralizing antibodies in animal models.. Science translational medicine. 2025. PMID:40737430

• Conter Laura et al. BLIMP1 controls GC B cell expansion and exit through regulating cell cycle progression and key transcription factors BCL6 and IRF4.. Cell reports. 2025. PMID:40650910

• Bukhari Ameera M et al. IgM+IgD- B cells in human gut-associated lymphoid tissue have memory features and give rise to IgM+ and IgA+ antibody-secreting cells.. Scientific reports. 2025. PMID:40695977

• Engelbrecht Eric et al. Germline polymorphisms in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire.. Research square. 2025. PMID:40709274

• Kos Justin T et al. Characterization of extensive diversity in immunoglobulin light chain variable germline genes across biomedically important mouse strains.. ImmunoHorizons. 2025. PMID:40682361

• Engelbrecht Eric et al. Germline polymorphisms in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire.. bioRxiv : the preprint server for biology. 2025. PMID:40501977

• Konstantinovsky Thomas et al. Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning.. Nucleic acids research. 2025. PMID:40650972

• Risley Christopher A et al. Transcription factor T-bet regulates the maintenance and differentiation potential of lymph node and lung effector memory B cell subsets.. Immunity. 2025. PMID:40543512

• van Ginneken Daphne et al. Protein language model pseudolikelihoods capture features of in vivo B cell selection and evolution.. Briefings in bioinformatics. 2025. PMID:40825239

• Martins Christina A et al. Profile of the B cell receptor repertoire and antibody responses upon 17DD-YF vaccine boosting.. bioRxiv : the preprint server for biology. 2025. PMID:40631227

• Varano Gabriele et al. B-cell Receptor Silencing Reveals the Origin and Dependencies of High-Grade B-cell Lymphomas with MYC and BCL2 Rearrangements.. Blood cancer discovery. 2025. PMID:40402557

• Ventura Lucas Haniel A et al. Immunosenescence Profile Is Associated With Increased Susceptibility to Severe COVID-19.. Aging cell. 2025. PMID:40388115

• Luo Jiaqi et al. AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees.. Bioinformatics (Oxford, England). 2025. PMID:40674579

• Da Vià Matteo Claudio et al. Aberrant single-cell phenotype and clinical implications of genotypically defined polyclonal plasma cells in myeloma.. Blood. 2025. PMID:40009503

• Rodrigues Kristen A et al. Vaccines combining slow release and follicle targeting of antigens increase germinal center B cell diversity and clonal expansion.. Science translational medicine. 2025. PMID:40531969

• Aron Edel et al. Single cell immunophenotyping identifies CD8+ GZMK+ IFNG+ T cells as a key immune population in cutaneous Lyme disease.. bioRxiv : the preprint server for biology. 2025. PMID:40661371

• Zuo Teng et al. Somatic hypermutation generates antibody specificities beyond the primary repertoire.. Immunity. 2025. PMID:40339575

• DeWitt William S et al. Replaying germinal center evolution on a quantified affinity landscape.. bioRxiv : the preprint server for biology. 2025. PMID:40661619

• Madsen Anders et al. Identification of a seasonal influenza vaccine-induced broadly protective neuraminidase antibody.. The Journal of experimental medicine. 2025. PMID:40178595

• Morgan Gareth J et al. An updated AL-base reveals ranked enrichment of immunoglobulin light chain variable genes in AL amyloidosis.. Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis. 2025. PMID:39641756

• Rodriguez Oscar L et al. Human genetic variation shapes the antibody repertoire across B cell development.. bioRxiv : the preprint server for biology. 2025. PMID:40475565

• Mizumaki Hiroki et al. In depth transcriptomic profiling defines a landscape of dysfunctional immune responses in patients with VEXAS syndrome.. Nature communications. 2025. PMID:40394087

• Sung Kevin et al. Thrifty wide-context models of B cell receptor somatic hypermutation.. bioRxiv : the preprint server for biology. 2025. PMID:39651125

• Dizon Brian L P et al. Human naïve B cells show evidence of anergy and clonal redemption following vaccination.. NPJ vaccines. 2025. PMID:40368926

• Yang Evan et al. In situ profiling of plasma cell clonality with image-based single-cell transcriptomics.. bioRxiv : the preprint server for biology. 2025. PMID:40463110

• Rahimi Rod A et al. Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthma.. bioRxiv : the preprint server for biology. 2025. PMID:40462898

• Li Hao et al. Mature tertiary lymphoid structures evoke intra-tumoral T and B cell responses via progenitor exhausted CD4+ T cells in head and neck cancer.. Nature communications. 2025. PMID:40335494

• Mantus Grace E et al. Distinct binding modes drive the broad neutralization profile of two persistent influenza hemagglutinin stem-specific antibody lineages.. Structure (London, England : 1993). 2025. PMID:40112805

• Waury Katharina et al. Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data.. PLoS computational biology. 2025. PMID:40445971

• Terroba-Navajas Paula et al. Single-Cell Transcriptomics Identifies a Prominent Role for the MIF-CD74 Axis in Myasthenia Gravis Thymus.. Neurology(R) neuroimmunology & neuroinflammation. 2025. PMID:40117520

• Calôba Carolina et al. Systemic 4-1BB stimulation augments extrafollicular memory B cell formation and recall responses during Plasmodium infection.. Cell reports. 2025. PMID:40215168

• Nicholas Catherine A et al. Activated polyreactive B cells are clonally expanded in autoantibody positive and patients with recent-onset type 1 diabetes.. Cell reports. 2025. PMID:40117290

• Perugino Cory A et al. Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection.. Cell reports. 2025. PMID:40173042

• Kotagiri Prasanti et al. Disease-specific B cell clones are shared between patients with Crohn’s disease.. Nature communications. 2025. PMID:40246842

• Ramezani-Rad Parham et al. The saponin monophosphoryl lipid A nanoparticle adjuvant induces dose-dependent HIV vaccine responses in nonhuman primates.. The Journal of clinical investigation. 2025. PMID:40036068

• Beaulaurier John et al. De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies.. Genome research. 2025. PMID:40118521

• Madden Patrick J et al. Diverse priming outcomes under conditions of very rare precursor B cells.. Immunity. 2025. PMID:40168992

• Nelson Alexander J et al. Lung-resident memory B cells maintain allergic IgE responses in the respiratory tract.. Immunity. 2025. PMID:40139187

• França Renato Kaylan Alves de Oliveira et al. Naive and Memory B Cell BCR Repertoires in Individuals Immunized with an Inactivated SARS-CoV-2 Vaccine.. Vaccines. 2025. PMID:40333337

• Guillaume Stephane M et al. Lung B cells in ectopic germinal centers undergo affinity maturation.. Proceedings of the National Academy of Sciences of the United States of America. 2025. PMID:40168127

• Lai Cong et al. Myeloid-Driven Immune Suppression Subverts Neutralizing Antibodies and T Cell Immunity in Severe COVID-19.. Journal of medical virology. 2025. PMID:40183283

• Lee Adrian Ys et al. Self-reactive B cells are increased in all major stages of peripheral development in Sjögren’s disease.. Immunology and cell biology. 2025. PMID:39957579

• Gailleton Romain et al. Ectopic germinal centers in the nasal turbinates contribute to B cell immunity to intranasal viral infection and vaccination.. Proceedings of the National Academy of Sciences of the United States of America. 2025. PMID:40112112

• Okoye G Donald et al. Single-cell map of innate-like lymphocyte response to Francisella tularensis infection reveals interleukin-17-dependent protection by MAIT cells.. iScience. 2025. PMID:40160424

• Abdullah Leena et al. The endogenous antigen-specific CD8+ T cell repertoire is composed of unbiased and biased clonotypes with differential fate commitments.. Immunity. 2025. PMID:40020673

• Spangler Abby et al. Early influenza virus exposure shapes the B cell response to influenza vaccination in individuals 50 years later.. Immunity. 2025. PMID:40023164

• Rao Vishal et al. Convergent and clonotype-enriched mutations in the light chain drive affinity maturation of a public antibody.. bioRxiv : the preprint server for biology. 2025. PMID:40161664

• Fujio Keishi et al. The role of polyreactive memory B cells in systemic lupus erythematosus.. International immunology. 2025. PMID:39514642

• Wang Meng et al. Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction.. PLoS computational biology. 2025. PMID:40163503

• van Lieverloo G G A et al. Unique Nerve Tissue-Restricted T-Cell Clones in Chronic Inflammatory Demyelinating Polyneuropathy.. Journal of the peripheral nervous system : JPNS. 2025. PMID:39967321

• Zhu Airu et al. Robust mucosal SARS-CoV-2-specific T cells effectively combat COVID-19 and establish polyfunctional resident memory in patient lungs.. Nature immunology. 2025. PMID:39875584

• Bréart Béatrice et al. IL-27 elicits a cytotoxic CD8+ T cell program to enforce tumour control.. Nature. 2025. PMID:39910298

• Chernyshev Mark et al. Detection of PCR chimeras in adaptive immune receptor repertoire sequencing using hidden Markov models.. bioRxiv : the preprint server for biology. 2025. PMID:40060431

• Seo Kayoung et al. Comprehensive Analysis of TCR and BCR Repertoires: Insights into Methodologies, Challenges, and Applications.. Genomics & informatics. 2025. PMID:39994831

• Zhou Yun et al. Biomarker expression level changes within rectal gut-associated lymphoid tissues in spinal cord-injured rats.. ImmunoHorizons. 2025. PMID:40048710

• Dumm Will et al. Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 2025. PMID:39976415

• Zhu Wen et al. Prothrombotic antibodies targeting the spike protein’s receptor-binding domain in severe COVID-19.. Blood. 2025. PMID:39576992

• Ma Yao et al. Impact of influenza immune imprinting on immune responses to subsequent vaccinations in mice.. Vaccine. 2025. PMID:39731808

• Jiang Shaowen et al. A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection.. bioRxiv : the preprint server for biology. 2025. PMID:39975238

• Rosenfeld Ronit et al. Efficient Identification of Monoclonal Antibodies Against Rift Valley Fever Virus Using High-Throughput Single Lymphocyte Transcriptomics of Immunized Mice.. Antibodies (Basel, Switzerland). 2025. PMID:39982227

• Amisaki Masataka et al. IL-33-activated ILC2s induce tertiary lymphoid structures in pancreatic cancer.. Nature. 2025. PMID:39814891

• Wilbrink Rick et al. B Cell Receptor Repertoire Analysis of the CD21lo B Cell Compartment in Healthy Individuals, Patients With Sjögren’s Disease, and Patients With Radiographic Axial Spondyloarthritis.. European journal of immunology. 2025. PMID:39707660

• Zuckerbrot-Schuldenfrei Miriam et al. The compositional behavior of the human T cell receptor repertoire in ovarian cancer compared to healthy donors.. Scientific data. 2025. PMID:39880820

• Ramezani-Rad Parham et al. Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models.. bioRxiv : the preprint server for biology. 2025. PMID:39896562

• Chernigovskaya Maria et al. Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.. Nucleic acids research. 2025. PMID:39873270

• Jacobs Benjamin M et al. Single-cell analysis of cerebrospinal fluid reveals common features of neuroinflammation.. Cell reports. Medicine. 2025. PMID:39708811

• Krasik Sofia V et al. Systematic evaluation of intratumoral and peripheral BCR repertoires in three cancers.. eLife. 2025. PMID:39831798

• McGrath Joshua J C et al. Mutability and hypermutation antagonize immunoglobulin codon optimality.. Molecular cell. 2025. PMID:39708804

• Thouvenel Christopher D et al. Hypomorphic RAG2 Deficiency Promotes Selection of Self-Reactive B Cells.. Journal of clinical immunology. 2025. PMID:39812873

• Kliushnikova Dariia et al. Intrathecal Immunoglobulin A Synthesis in Multiple Sclerosis: From Biological Aspects to Clinical Relevance.. Biomolecules. 2025. PMID:39858502

• Merder Alexander K et al. Plasma cells in and around the central nervous system.. Frontiers in immunology. 2025. PMID:41583430

• Konopka Emily N et al. Nucleic acid vaccines: innovations, efficacy, and applications in at-risk populations.. Frontiers in immunology. 2025. PMID:40438110

• Holmes Antony B et al. Single-Cell Transcriptomic Analysis of Normal and Malignant B Cells.. Methods in molecular biology (Clifton, N.J.). 2025. PMID:39424732

• Coffey David G et al. Machine learning reveals distinct T-cell receptor clusters in plasma cell dyscrasias compared to healthy controls.. PloS one. 2025. PMID:41144424

• Kim Hyo Jae et al. B cell receptor repertoire reconstitution in patients with neuromyelitis optica spectrum disorder receiving B-cell depletion therapy.. Frontiers in immunology. 2025. PMID:41246297

• Jian Fanchong et al. Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1.. Nature. 2025. PMID:39510125

• Tran Hoc et al. Evaluating machine learning approaches for host prediction using H3 influenza genomic data.. PloS one. 2025. PMID:41191716

• Ryback Audrey A et al. Deep sequencing of BCR heavy chain repertoires in myalgic encephalomyelitis/chronic fatigue syndrome.. Frontiers in immunology. 2025. PMID:40034707

• Hanna Stephanie J et al. The Type 1 Diabetes T Cell Receptor and B Cell Receptor Repository in the AIRR Data Commons: a practical guide for access, use and contributions through the Type 1 Diabetes AIRR Consortium.. Diabetologia. 2025. PMID:39467874

• Gutierrez Andres H et al. Regulatory T cell epitope content in human antibodies decreases during maturation.. Frontiers in immunology. 2025. PMID:40313951

• Lele Nikhil et al. Deep cervical lymph node volume decreases following B-cell depletion therapy.. Multiple sclerosis journal - experimental, translational and clinical. 2025. PMID:40873659

• Rasche Kamille M et al. B cell phenotypes and antibody signatures associate with interpatient variation in the lung adenocarcinoma tumor microenvironment.. Frontiers in immunology. 2025. PMID:41684542

• Rao Kaihua et al. YiQiWenShen formula ameliorates myasthenia gravis through T follicular helper cells/T follicular regulatory cells immune rebalancing.. American journal of translational research. 2025. PMID:40950289

• Quan Moyuan et al. Neutrophils, NETs and multiple sclerosis: a mini review.. Frontiers in immunology. 2025. PMID:39935468

• Krickeberg Naomi et al. Promiscuous class II-binding SARS-CoV-2-nuc derived vaccine-peptide induced extensive conventional, innate and unconventional T cell responses.. Frontiers in immunology. 2025. PMID:41306962

• Peres Ayelet et al. Towards a sustainable, comprehensive and community-accepted nomenclature and naming standard of antibody and T cell receptor germline genes and alleles.. Frontiers in immunology. 2025. PMID:41368638

• Nakarin Fahsai et al. A paradigm shift in simulating affinity maturation to elicit broadly neutralizing antibodies.. Frontiers in immunology. 2025. PMID:40666529

• Jeon Bong Chan et al. Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.. Cellular & molecular immunology. 2025. PMID:39627609

• Dehghannasiri Roozbeh et al. sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing.. bioRxiv : the preprint server for biology. 2024. PMID:39763839

• Mikelov Artem et al. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.. Genome research. 2024. PMID:39433438

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• Gadala-Maria Daniel et al. Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.. Proceedings of the National Academy of Sciences of the United States of America. 2015. PMID:25675496

• Loeffler M et al. Genomic and epigenomic co-evolution in follicular lymphomas.. Leukemia. 2015. PMID:25027518

• Zinöcker Severin et al. The V gene repertoires of classical and atypical memory B cells in malaria-susceptible West African children.. Journal of immunology (Baltimore, Md. : 1950). 2015. PMID:25556245

• Lees William D et al. Utilities for High-Throughput Analysis of B-Cell Clonal Lineages.. Journal of immunology research. 2015. PMID:26527585

• Willis Simon N et al. Investigating the Antigen Specificity of Multiple Sclerosis Central Nervous System-Derived Immunoglobulins.. Frontiers in immunology. 2015. PMID:26648933

• Galson Jacob D et al. In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire.. Frontiers in immunology. 2015. PMID:26528292

• Sankowski Roman et al. Systemic inflammation and the brain: novel roles of genetic, molecular, and environmental cues as drivers of neurodegeneration.. Frontiers in cellular neuroscience. 2015. PMID:25698933

• von Büdingen H-Christian et al. Update on the autoimmune pathology of multiple sclerosis: B-cells as disease-drivers and therapeutic targets.. European neurology. 2015. PMID:25824054

• Dang Amy K et al. Meningeal Infiltration of the Spinal Cord by Non-Classically Activated B Cells is Associated with Chronic Disease Course in a Spontaneous B Cell-Dependent Model of CNS Autoimmune Disease.. Frontiers in immunology. 2015. PMID:26441975

• Schnoor Michael et al. Crossing the Vascular Wall: Common and Unique Mechanisms Exploited by Different Leukocyte Subsets during Extravasation.. Mediators of inflammation. 2015. PMID:26568666

• Blauth Kevin et al. The Ins and Outs of B Cells in Multiple Sclerosis.. Frontiers in immunology. 2015. PMID:26594215

• Keener Amanda B et al. A sense of immunity: scientists are detailing the immune system as never before.. Nature medicine. 2015. PMID:25569540

• Hauser Stephen L et al. The Charcot Lecture | beating MS: a story of B cells, with twists and turns.. Multiple sclerosis (Houndmills, Basingstoke, England). 2015. PMID:25480864

• Claes Nele et al. B Cells Are Multifunctional Players in Multiple Sclerosis Pathogenesis: Insights from Therapeutic Interventions.. Frontiers in immunology. 2015. PMID:26734009

• Li Rui et al. Cytokine-Defined B Cell Responses as Therapeutic Targets in Multiple Sclerosis.. Frontiers in immunology. 2015. PMID:26779181

• Pikor Natalia B et al. Meningeal Tertiary Lymphoid Tissues and Multiple Sclerosis: A Gathering Place for Diverse Types of Immune Cells during CNS Autoimmunity.. Frontiers in immunology. 2015. PMID:26793195

• Michel Laure et al. B Cells in the Multiple Sclerosis Central Nervous System: Trafficking and Contribution to CNS-Compartmentalized Inflammation.. Frontiers in immunology. 2015. PMID:26732544

• Calis Jorg J A et al. Characterizing immune repertoires by high throughput sequencing: strategies and applications.. Trends in immunology. 2014. PMID:25306219

• Wu Yu-Chang B et al. Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis.. The Journal of allergy and clinical immunology. 2014. PMID:25171866

• Stern Joel N H et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.. Science translational medicine. 2014. PMID:25100741

• Vander Heiden Jason A et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.. Bioinformatics (Oxford, England). 2014. PMID:24618469

• Cho Michael Jeffrey et al. Shared VH1-46 gene usage by pemphigus vulgaris autoantibodies indicates common humoral immune responses among patients.. Nature communications. 2014. PMID:24942562

• Laserson Uri et al. High-resolution antibody dynamics of vaccine-induced immune responses.. Proceedings of the National Academy of Sciences of the United States of America. 2014. PMID:24639495

• Hershberg Uri et al. Persistence and selection of an expanded B-cell clone in the setting of rituximab therapy for Sjögren’s syndrome.. Arthritis research & therapy. 2014. PMID:24517398

• Georgiou George et al. The promise and challenge of high-throughput sequencing of the antibody repertoire.. Nature biotechnology. 2014. PMID:24441474

• Uduman Mohamed et al. Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences.. Journal of immunology (Baltimore, Md. : 1950). 2014. PMID:24376267

• Goenka Radhika et al. Local BLyS production by T follicular cells mediates retention of high affinity B cells during affinity maturation.. The Journal of experimental medicine. 2014. PMID:24367004

• Mehr Ramit et al. Immune system modeling and analysis.. Frontiers in immunology. 2014. PMID:25566257

• Six Adrien et al. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis.. Frontiers in immunology. 2013. PMID:24348479

• Fang Liangjuan et al. The immune cell infiltrate populating meningiomas is composed of mature, antigen-experienced T and B cells.. Neuro-oncology. 2013. PMID:23978377

• Yaari Gur et al. Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.. Nucleic acids research. 2013. PMID:23921631

• Zhu Daxing et al. Biased immunoglobulin light chain use in the Chlamydophila psittaci negative ocular adnexal marginal zone lymphomas.. American journal of hematology. 2013. PMID:23418012

• Yaari Gur et al. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data.. Frontiers in immunology. 2013. PMID:24298272

Immcantation Publications

The following Immcantation core publications were used to identify citing papers:

• Gabernet G et al. nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. PLoS Comput Biol. 2024. PMID:39058741

• Jensen CG et al. Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser. J Immunol. 2024. PMID:38557795

• Hoehn KB et al. Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLoS Comput Biol. 2022. PMID:35468128

• Hoehn KB et al. Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving. Elife. 2021. PMID:34787567

• Nouri N et al. Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. PLoS Comput Biol. 2020. PMID:32574157

• Hoehn KB et al. Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. Proc Natl Acad Sci U S A. 2019. PMID:31636219

• Gadala-Maria D et al. Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data. Front Immunol. 2019. PMID:30814994

• Nouri N et al. Optimized Threshold Inference for Partitioning of Clones From High-Throughput B Cell Repertoire Sequencing Data. Front Immunol. 2018. PMID:30093903

• Nouri N et al. A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. Bioinformatics. 2018. PMID:29949968

• Hoehn KB et al. A Phylogenetic Codon Substitution Model for Antibody Lineages. Genetics. 2017. PMID:28315836

• Gupta NT et al. Hierarchical clustering can identify B cell clones with high confidence in Ig repertoire sequencing data. J Immunol. 2017. PMID:28179494

• Cui A et al. A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data. J Immunol. 2016. PMID:27707999

• Gupta NT et al. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics. 2015. PMID:26069265

• Gadala-Maria D et al. Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proc Natl Acad Sci U S A. 2015. PMID:25675496

• Stern JN et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 2014. PMID:25100741

• Vander Heiden JA et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014. PMID:24618469

• Yaari G et al. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data. Front Immunol. 2013. PMID:24298272

• Yaari G et al. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012. PMID:22641856