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Parameter optimization for stable clustering using FlowSOM: a case study from CyTOF.
Published in:
Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1414400
By:
- Tao, Weiyang;
- Sinha, Anirban;
- Raddassi, Khadir;
- Pandit, Aridaman
Publication type:
Article
CXCL4 suppresses tolerogenic immune signature of monocyte‐derived dendritic cells.
Published in:
European Journal of Immunology, 2020, v. 50, n. 10, p. 1598, doi. 10.1002/eji.201948341
By:
- Silva‐Cardoso, Sandra C.;
- Tao, Weiyang;
- Fernández, Beatriz Malvar;
- Boes, Marianne;
- Radstake, Timothy R.D.J.;
- Pandit, Aridaman
Publication type:
Article
cDC2 and plasmacytoid dendritic cells diminish from tissues of patients with non‐Hodgkin orbital lymphoma and idiopathic orbital inflammation.
Published in:
European Journal of Immunology, 2020, v. 50, n. 4, p. 548, doi. 10.1002/eji.201948370
By:
- Laban, Kamil G.;
- Rijken, Rianne;
- Hiddingh, Sanne;
- Mertens, Jorre S.;
- der Veen, Rob L. P.;
- Eenhorst, Christine A.E.;
- Pandit, Aridaman;
- Radstake, Timothy R.D.J.;
- Boer, Joke H.;
- Kalmann, Rachel;
- Kuiper, Jonas J. W.
Publication type:
Article
Analysis of dinucleotide signatures in HIV-1 subtype B genomes.
Published in:
Journal of Genetics, 2013, v. 92, n. 3, p. 403, doi. 10.1007/s12041-013-0281-8
By:
- PANDIT, ARIDAMAN;
- VADLAMUDI, JYOTHIRMAYI;
- SINHA, SOMDATTA
Publication type:
Article
Characterization of Long Non-Coding RNAs in Systemic Sclerosis Monocytes: A Potential Role for PSMB8-AS1 in Altered Cytokine Secretion.
Published in:
International Journal of Molecular Sciences, 2021, v. 22, n. 9, p. 4365, doi. 10.3390/ijms22094365
By:
- Servaas, Nila H.;
- Mariotti, Barbara;
- van der Kroef, Maarten;
- Wichers, Catharina G. K.;
- Pandit, Aridaman;
- Bazzoni, Flavia;
- Radstake, Timothy R. D. J.;
- Rossato, Marzia;
- Crea, Francesco
Publication type:
Article
RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling.
Published in:
Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-021-02991-5
By:
- Tao, Weiyang;
- Radstake, Timothy R. D. J.;
- Pandit, Aridaman
Publication type:
Article
Implication of miR-126 and miR-139-5p in Plasmacytoid Dendritic Cell Dysregulation in Systemic Sclerosis.
Published in:
Journal of Clinical Medicine, 2021, v. 10, n. 3, p. 491, doi. 10.3390/jcm10030491
By:
- Chouri, Eleni;
- Wang, Maojie;
- Hillen, Maarten R.;
- Angiolilli, Chiara;
- Silva-Cardoso, Sandra C.;
- Wichers, Catharina G. K.;
- van der Kroef, Maarten;
- Bekker, Cornelis P. J.;
- Cossu, Marta;
- van Bon, Lenny;
- Affandi, Alsya J.;
- Carvalheiro, Tiago;
- Pandit, Aridaman;
- van Roon, Joel A. G.;
- Beretta, Lorenzo;
- Burgering, Boudewijn M. T.;
- Radstake, Timothy R. D. J.;
- Rossato, Marzia;
- Sato, Shinichi
Publication type:
Article
Finding Gene Regulatory Networks in Psoriasis: Application of a Tree-Based Machine Learning Approach.
Published in:
Frontiers in Immunology, 2022, v. 13, p. 1, doi. 10.3389/fimmu.2022.921408
By:
- Jingwen Deng;
- Schieler, Carlotta;
- Borghans, José A. M.;
- Chuanjian Lu;
- Pandit, Aridaman
Publication type:
Article
Conserved human effector Treg cell transcriptomic and epigenetic signature in arthritic joint inflammation.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22975-7
By:
- Mijnheer, Gerdien;
- Lutter, Lisanne;
- Mokry, Michal;
- van der Wal, Marlot;
- Scholman, Rianne;
- Fleskens, Veerle;
- Pandit, Aridaman;
- Tao, Weiyang;
- Wekking, Mark;
- Vervoort, Stephin;
- Roberts, Ceri;
- Petrelli, Alessandra;
- Peeters, Janneke G. C.;
- Knijff, Marthe;
- de Roock, Sytze;
- Vastert, Sebastiaan;
- Taams, Leonie S.;
- van Loosdregt, Jorg;
- van Wijk, Femke
Publication type:
Article
Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup.
Published in:
Scientific Reports, 2016, p. 19157, doi. 10.1038/srep19157
By:
- Singh, Sakshi;
- Singh, Ashish;
- Rajkumar, Raja;
- Sampath Kumar, Katakam;
- Kadarkarai Samy, Subburaj;
- Nizamuddin, Sheikh;
- Singh, Amita;
- Ahmed Sheikh, Shahnawaz;
- Peddada, Vidya;
- Khanna, Vinee;
- Veeraiah, Pandichelvam;
- Pandit, Aridaman;
- Chaubey, Gyaneshwer;
- Singh, Lalji;
- Thangaraj, Kumarasamy
Publication type:
Article
HIV-1 CCR5 gene therapy will fail unless it is combined with a suicide gene.
Published in:
Scientific Reports, 2015, p. 18088, doi. 10.1038/srep18088
By:
- Pandit, Aridaman;
- de Boer, Rob J.
Publication type:
Article
High-Dimensional Profiling Reveals Heterogeneity of the Th17 Subset and Its Association With Systemic Immunomodulatory Treatment in Non-infectious Uveitis.
Published in:
Frontiers in Immunology, 2018, p. 1, doi. 10.3389/fimmu.2018.02519
By:
- Verhagen, Fleurieke H.;
- Hiddingh, Sanne;
- Rijken, Rianne;
- Pandit, Aridaman;
- Leijten, Emmerik;
- Nordkamp, Michel Olde;
- Loon, Ninette H. ten Dam-van;
- Nierkens, Stefan;
- Imhof, Saskia M.;
- de Boer, Joke H.;
- Radstake, Timothy R. D. J.;
- Kuiper, Jonas J. W.
Publication type:
Article
Differential Trends in the Codon Usage Patterns in HIV-1 Genes.
Published in:
PLoS ONE, 2011, v. 6, n. 12, p. 1, doi. 10.1371/journal.pone.0028889
By:
- Pandit, Aridaman;
- Sinha, Somdatta
Publication type:
Article
Plasmacytoid DCs From Patients With Sjögren's Syndrome Are Transcriptionally Primed for Enhanced Pro-inflammatory Cytokine Production.
Published in:
Frontiers in Immunology, 2019, p. 1, doi. 10.3389/fimmu.2019.02096
By:
- Hillen, Maarten R.;
- Pandit, Aridaman;
- Blokland, Sofie L. M.;
- Hartgring, Sarita A. Y.;
- Bekker, Cornelis P. J.;
- van der Heijden, Eefje H. M.;
- Servaas, Nila H.;
- Rossato, Marzia;
- Kruize, Aike A.;
- van Roon, Joel A. G.;
- Radstake, Timothy R. D. J.
Publication type:
Article
Stochastic Inheritance of Division and Death Times Determines the Size and Phenotype of CD8<sup>+</sup> T Cell Families.
Published in:
Frontiers in Immunology, 2019, p. N.PAG, doi. 10.3389/fimmu.2019.00436
By:
- Pandit, Aridaman;
- De Boer, Rob J.
Publication type:
Article
Using genomic signatures for HIV-1 sub-typing.
Published in:
BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-S1-S26
By:
- Pandit, Aridaman;
- Sinha, Somdatta
Publication type:
Article
Multi‐omics integration reveals a core network involved in host defence and hyperkeratinization in psoriasis.
Published in:
Clinical & Translational Medicine, 2022, v. 12, n. 12, p. 1, doi. 10.1002/ctm2.976
By:
- Deng, Jingwen;
- Leijten, Emmerik;
- Nordkamp, Michel Olde;
- Zheng, Guangjuan;
- Pouw, Juliëtte;
- Tao, Weiyang;
- Hartgring, Sarita;
- Balak, Deepak;
- Rijken, Rianne;
- Huang, Runyue;
- Radstake, Timothy;
- Lu, Chuanjian;
- Pandit, Aridaman
Publication type:
Article
PD-1+CD8+ T cells are clonally expanding effectors in human chronic inflammation.
Published in:
2018
By:
- Petrelli, Alessandra;
- Mijnheer, Gerdien;
- Hoytema van Konijnenburg, David P.;
- van der Wal, Maria M.;
- Giovannone, Barbara;
- Mocholi, Enric;
- Vazirpanah, Nadia;
- Broen, Jasper C.;
- Hijnen, Dirkjan;
- Oldenburg, Bas;
- Coffer, Paul J.;
- Vastert, Sebastian J.;
- Prakken, Berent J.;
- Spierings, Eric;
- Pandit, Aridaman;
- Mokry, Michal;
- van Wijk, Femke;
- van Konijnenburg, David P Hoytema
Publication type:
journal article
Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis.
Published in:
Immunogenetics, 2020, v. 72, n. 1/2, p. 101, doi. 10.1007/s00251-019-01142-9
By:
- Gerritsen, Bram;
- Pandit, Aridaman;
- Zaaraoui-Boutahar, Fatiha;
- van den Hout, Mirjam C. G. N.;
- van IJcken, Wilfred F. J.;
- de Boer, Rob J.;
- Andeweg, Arno C.
Publication type:
Article
The Transcriptomic Profile of Monocytes from Patients With Sjögren's Syndrome Is Associated With Inflammatory Parameters and Is Mimicked by Circulating Mediators.
Published in:
Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.701656
By:
- Lopes, Ana P.;
- Bekker, Cornelis P. J.;
- Hillen, Maarten R.;
- Blokland, Sofie L. M.;
- Hinrichs, Anneline C.;
- Pandit, Aridaman;
- Kruize, Aike A.;
- Radstake, Timothy R. D. J.;
- van Roon, Joel A. G.
Publication type:
Article
Transcriptome Analysis of CCR9+ T Helper Cells From Primary Sjögren's Syndrome Patients Identifies CCL5 as a Novel Effector Molecule.
Published in:
Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.702733
By:
- Hinrichs, Anneline C.;
- Blokland, Sofie L. M.;
- Lopes, Ana P.;
- Wichers, Catharina G. K.;
- Kruize, Aike A.;
- Pandit, Aridaman;
- Radstake, Timothy R. D. J.;
- van Roon, Joel A. G.
Publication type:
Article
Integration of Immunome With Disease-Gene Network Reveals Common Cellular Mechanisms Between IMIDs and Drug Repurposing Strategies.
Published in:
Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.669400
By:
- Devaprasad, Abhinandan;
- Radstake, Timothy R. D. J.;
- Pandit, Aridaman
Publication type:
Article
Whole Transcriptome Analysis Reveals Heterogeneity in B Cell Memory Populations in Patients With Juvenile Idiopathic Arthritis-Associated Uveitis.
Published in:
Frontiers in Immunology, 2020, v. 11, p. N.PAG, doi. 10.3389/fimmu.2020.02170
By:
- Wennink, Roos A. W.;
- Pandit, Aridaman;
- Haasnoot, Anne-Mieke J. W.;
- Hiddingh, Sanne;
- Kalinina Ayuso, Viera;
- Wulffraat, Nico M.;
- Vastert, Bas J.;
- Radstake, Timothy R. D. J.;
- de Boer, Joke H.;
- Kuiper, Jonas J. W.
Publication type:
Article
CXCL4 Links Inflammation and Fibrosis by Reprogramming Monocyte-Derived Dendritic Cells in vitro.
Published in:
Frontiers in Immunology, 2020, v. 11, p. N.PAG, doi. 10.3389/fimmu.2020.02149
By:
- Silva-Cardoso, Sandra C.;
- Tao, Weiyang;
- Angiolilli, Chiara;
- Lopes, Ana P.;
- Bekker, Cornelis P. J.;
- Devaprasad, Abhinandan;
- Giovannone, Barbara;
- van Laar, Jaap;
- Cossu, Marta;
- Marut, Wioleta;
- Hack, Erik;
- de Boer, Rob J.;
- Boes, Marianne;
- Radstake, Timothy R. D. J.;
- Pandit, Aridaman
Publication type:
Article
Broad proteomic screen reveals shared serum proteomic signature in patients with psoriatic arthritis and psoriasis without arthritis.
Published in:
Rheumatology, 2021, v. 60, n. 2, p. 751, doi. 10.1093/rheumatology/keaa405
By:
- Leijten, Emmerik;
- Tao, Weiyang;
- Pouw, Juliette;
- Kempen, Tessa van;
- Nordkamp, Michel Olde;
- Balak, Deepak;
- Tekstra, J;
- Muñoz-Elías, Ernesto;
- DePrimo, Samuel;
- Drylewicz, Julia;
- Pandit, Aridaman;
- Boes, Marianne;
- Radstake, Timothy
Publication type:
Article
Epigenetically quantified immune cells in salivary glands of Sjögren's syndrome patients: a novel tool that detects robust correlations of T follicular helper cells with immunopathology.
Published in:
Rheumatology, 2020, v. 59, n. 2, p. 335, doi. 10.1093/rheumatology/kez268
By:
- Blokland, Sofie L M;
- Vliet-Moret, Fréderique M van;
- Hillen, Maarten R;
- Pandit, Aridaman;
- Goldschmeding, Roel;
- Kruize, Aike A;
- Bouma, Gerben;
- Maurik, André van;
- Olek, Sven;
- Hoffmueller, Ulrich;
- Roon, Joel A G van;
- Radstake, Timothy R D J
Publication type:
Article
microRNA downregulation in plasmacytoid dendritic cells in interferon-positive systemic lupus erythematosus and antiphospholipid syndrome.
Published in:
Rheumatology, 2018, v. 57, n. 9, p. 1669, doi. 10.1093/rheumatology/key159
By:
- Hoogen, Lucas L van den;
- Rossato, Marzia;
- Lopes, Ana P;
- Pandit, Aridaman;
- Bekker, Cornelis P J;
- Fritsch-Stork, Ruth D E;
- Roon, Joel A G van;
- Radstake, Timothy R D J
Publication type:
Article
Enrichment of SARS-CoV-2 Entry Factors and Interacting Intracellular Genes in Tissue and Circulating Immune Cells.
Published in:
Viruses (1999-4915), 2021, v. 13, n. 9, p. 1757, doi. 10.3390/v13091757
By:
- Devaprasad, Abhinandan;
- Pandit, Aridaman
Publication type:
Article
Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis.
Published in:
eLife, 2023, p. 1, doi. 10.7554/eLife.74913
By:
- Hiddingh, Sanne;
- Pandit, Aridaman;
- Verhagen, Fleurieke;
- Rijken, Rianne;
- Servaas, Nila Hendrika;
- Wichers, Rina C. G. K.;
- ten Dam-van Loon, Ninette H.;
- Imhof, Saskia M.;
- Radstake, Timothy R. D. J.;
- de Boer, Joke H.;
- Kuiper, Jonas J. W.
Publication type:
Article
Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis.
Published in:
eLife, 2023, p. 1, doi. 10.7554/eLife.79016
By:
- Mijnheer, Gerdien;
- Servaas, Nila Hendrika;
- Jing Yao Leong;
- Boltjes, Arjan;
- Spierings, Eric;
- Chen, Phyllis;
- Liyun Lai;
- Petrelli, Alessandra;
- Vastert, Sebastiaan;
- de Boer, Rob J.;
- Albani, Salvatore;
- Pandit, Aridaman;
- van Wijk, Femke
Publication type:
Article
Neutrophil GM‐CSF receptor dynamics in acute lung injury.
Published in:
Journal of Leukocyte Biology, 2019, v. 105, n. 6, p. 1183, doi. 10.1002/JLB.3MA0918-347R
By:
- Alessandris, Silvia;
- Juss, Jatinder K.;
- Simmonds, Rosalind;
- Condliffe, Alison M.;
- Cowburn, Andrew S.;
- Chilvers, Edwin R.;
- Ferguson, G. John;
- Dodd, Alison J.;
- Piper, Siân;
- Wyatt, Owen;
- Killick, Helen;
- Corkill, Dominic J.;
- Cohen, E. Suzanne;
- Sleeman, Matthew A.;
- Finch, Donna K.;
- Devaprasad, Abhinandan;
- Pandit, Aridaman;
- Radstake, Timothy R.D.J.
Publication type:
Article
Reply.
Published in:
2021
By:
- Tao, Weiyang;
- Radstake, Timothy R. D. J.;
- Pandit, Aridaman
Publication type:
Letter to the Editor
Tissue‐Resident Memory CD8+ T Cells From Skin Differentiate Psoriatic Arthritis From Psoriasis.
Published in:
Arthritis & Rheumatology, 2021, v. 73, n. 7, p. 1220, doi. 10.1002/art.41652
By:
- Leijten, Emmerik F.;
- Kempen, Tessa S.;
- Olde Nordkamp, Michel A.;
- Pouw, Juliette N.;
- Kleinrensink, Nienke J.;
- Vincken, Nanette L.;
- Mertens, Jorre;
- Balak, Deepak M. W.;
- Verhagen, Fleurieke H.;
- Hartgring, Sarita A.;
- Lubberts, Erik;
- Tekstra, Janneke;
- Pandit, Aridaman;
- Radstake, Timothy R.;
- Boes, Marianne
Publication type:
Article
Multiomics and Machine Learning Accurately Predict Clinical Response to Adalimumab and Etanercept Therapy in Patients With Rheumatoid Arthritis.
Published in:
Arthritis & Rheumatology, 2021, v. 73, n. 2, p. 212, doi. 10.1002/art.41516
By:
- Tao, Weiyang;
- Concepcion, Arno N.;
- Vianen, Marieke;
- Marijnissen, Anne C. A.;
- Lafeber, Floris P. G. J.;
- Radstake, Timothy R. D. J.;
- Pandit, Aridaman
Publication type:
Article
Using Machine Learning to Molecularly Classify Systemic Sclerosis Patients.
Published in:
2019
By:
- Tao, Weiyang;
- Radstake, Timothy R. D. J.;
- Pandit, Aridaman
Publication type:
Editorial
The memory of a killer T cell: models of CD8<sup>+</sup> T cell differentiation.
Published in:
Immunology & Cell Biology, 2016, v. 94, n. 3, p. 236, doi. 10.1038/icb.2015.118
By:
- Gerritsen, Bram;
- Pandit, Aridaman
Publication type:
Article
Parameter optimization for stable clustering using FlowSOM: a case study from CyTOF.
Published in:
Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1414400
By:
- Weiyang Tao;
- Sinha, Anirban;
- Raddassi, Khadir;
- Pandit, Aridaman
Publication type:
Article
Unraveling IFN-I response dynamics and TNF crosstalk in the pathophysiology of systemic lupus erythematosus.
Published in:
Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1322814
By:
- Van Eyndhoven, Laura C.;
- Chouri, Eleni;
- Matos, Catarina I.;
- Pandit, Aridaman;
- Radstake, Timothy R. D. J.;
- Broen, Jasper C. A.;
- Singh, Abhyudai;
- Tel, Jurjen
Publication type:
Article
RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data.
Published in:
Bioinformatics, 2016, v. 32, n. 20, p. 3098, doi. 10.1093/bioinformatics/btw339
By:
- Gerritsen, Bram;
- Pandit, Aridaman;
- Andeweg, Arno C.;
- de Boer, Rob J.
Publication type:
Article
Nuclear Receptor Subfamily 4A Signaling as a Key Disease Pathway of CD1c+ Dendritic Cell Dysregulation in Systemic Sclerosis.
Published in:
Arthritis & Rheumatology, 2023, v. 75, n. 2, p. 279, doi. 10.1002/art.42319
By:
- Servaas, Nila H.;
- Hiddingh, Sanne;
- Chouri, Eleni;
- Wichers, Catharina G. K.;
- Affandi, Alsya J.;
- Ottria, Andrea;
- Bekker, Cornelis P. J.;
- Cossu, Marta;
- Silva‐Cardoso, Sandra C.;
- van der Kroef, Maarten;
- Hinrichs, Anneline C.;
- Carvalheiro, Tiago;
- Vazirpanah, Nadia;
- Beretta, Lorenzo;
- Rossato, Marzia;
- Bonte‐Mineur, Femke;
- Radstake, Timothy R. D. J.;
- Kuiper, Jonas J. W.;
- Boes, Marianne;
- Pandit, Aridaman
Publication type:
Article
Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants.
Published in:
Retrovirology, 2014, v. 11, n. 1, p. 56, doi. 10.1186/1742-4690-11-56
By:
- Pandit, Aridaman;
- de Boer, Rob J.
Publication type:
Article

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