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Computational biology and Systems Immunology (CoSI)

Aridaman Pandit

Pic_AridamanPandit.jpg

Assistant Professor and Group Leader

Room: KC.01.063.0, WKZ Building,

Radstake's Group, Laboratory of Translational Immunology,

University Medical Center Utrecht (UMCU),

Utrecht, The Netherlands

Google Scholar Profile

ORCID Profile

Research | Members | Publications | Tools | Contact us

Research

Immune cell subset profiling using multi-omic data: with the acquisition of ever-more big data, bioinformatic analysis is becoming a challenge. We are working on several approaches based on graph theory and machine learning to integrate multi-omic data generated from different immune cells to study how immune system is dysregulated in autoimmunity.

T cell repertoire dynamics: it is crucial to understand this for personalized medicine and therapeutics of cancer, autoimmunity and infectious diseases. Every T cell carries a T cell receptor (TCR) that is used to sense the presence of foreign antigens infecting our cells. From only 65 TCR genes, our body uses random mutations and new combinations to produce >10E8 TCR receptors. Thus, nearly every T cell that circulates in our blood could carry a unique TCR molecule that can theoretically recognize a unique antigen. Due to the enormous diversity, every individual can mount a very personalized immune response against the same pathogen.

HIV Haplotyping: a major problem in finding a cure for HIV is that the virus develops extreme diversity within a patient in order to evolve resistance and escape the immune response. With next-generation sequencing, we typically generate short reads, so we cannot capture the entire spectrum of co-evolving mutations that take place throughout HIV genome. We have been developing bioinformatic methods to extract HIV haplotypes (co-evolving HIV variants) from a single NGS sample.

Group members

Current PhD students

  • Abhinandan Devaprasad
  • Nila Servaas
  • Rianne Rijken
  • Jingwen Deng
  • Terry Huisman

Current Postdocs

  • Bram Gerritsen

Current Staff members

  • Laura S Guerrero
  • Hidde M Smits

Former group members

  • Bram Gerritsen (Graduated in January 2018; Postdoctoral Researcher in Yale University 2018-2021)
  • Sandra C. Silva-Cardoso (Graduated in December 2019; Currently running her own business in Portugal)
  • Weiyang Tao (Graduated in March 2021; Currently pursuing Postdoctoral research in China)

Masters students

Current Masters Students

  • Zora R Sinay
  • Joeri Tersteeg
  • Carlotta Schieler
  • Charles Meijer

Former Masters students

  • Nandhini Kanagasabesan
  • Ligia Monne
  • Gijs Schröder
  • Divyae Prasad
  • Wannisa Ritmahan
  • Terry Huisman
  • Eduardo Lucio de Esesarte
  • Rianne Rijken
  • Giovanni Palla
  • Emre Küçükköse

Publications

Google Scholar Profile

ORCID Profile

* indicates corresponding author

2021

Judith Prado, Remco HS Westerink, Jelena Popov-Celeketic, Cristine Steen-Louws, Aridaman Pandit, Sabine Versteeg, Wouter van de Worp, Deon HAJ Kanters, Kris A Reedquist, Leo Koenderman, Erik Hack, Niels Eijkelkamp. Cytokine receptor clustering in sensory neurons with an engineered cytokine fusion protein triggers unique pain resolution pathways, 118(11): e2009647118. https://www.pnas.org/content/118/11/e2009647118.short

Weiyang Tao, Timothy RDJ Radstake, Aridaman Pandit*. Personalized TNFi therapy for RA: Response to the comment by Cohen et al., Arthritis & Rheumatology, https://onlinelibrary.wiley.com/doi/abs/10.1002/art.41711.https://onlinelibrary.wiley.com/doi/abs/10.1002/art.41711

Nila Servaas, Fatiha Zaaraoui-Boutahar, Rina Kommer-Wichers, Andrea Ottria, Eleni Chouri, Alsya Affandi, Sandra Silva-Cardoso, Maarten van der Kroef, Tiago Ferreira-Carvalheiro, Femke van Wijk, Timothy Radstake, Arno Andeweg, Aridaman Pandit*. Longitudinal analysis of T-cell receptor repertoires reveals persistence of antigen-driven CD4+ and CD8+ T-cell clusters in Systemic Sclerosis, Journal of Autoimmunity, 117: 102574. https://www.sciencedirect.com/science/article/pii/S0896841120302079

Weiyang Tao, Arno N Concepcion, Marieke Vianen, Anne CA Marijnissen, Floris PGJ Lafeber, Timothy RDJ Radstake, Aridaman Pandit*. Multi‐omics and machine learning accurately predicts clinical response to Adalimumab and Etanercept therapy in patients with rheumatoid arthritis, Arthritis & Rheumatology, 73(2):212-222. https://onlinelibrary.wiley.com/doi/abs/10.1002/art.41516

Emmerik Leijten, Weiyang Tao, Juliette Pouw, Tessa van Kempen, Michel Olde Nordkamp, Deepak Balak, J Tekstra, Ernesto Muñoz-Elías, Samuel DePrimo, Julia Drylewicz, Aridaman Pandit, Marianne Boes, Timothy Radstake. Broad proteomic screen reveals shared serum proteomic signature in patients with psoriatic arthritis and psoriasis without arthritis, Rheumatology, 60(2):751-761. https://academic.oup.com/rheumatology/article-abstract/60/2/751/5892431

Roy Spijkerman, Nikita KN Jorritsma, Suzanne H Bongers, Bas JJ Bindels, Bernard N Jukema, Lillian Hesselink, Falco Hietbrink, Luke PH Leenen, Harriët MR van Goor, Nienke Vrisekoop, Karin AH Kaasjager, Leo Koenderman, COVPACH study group, Feike Stiphout, Thomas MP Nijdam, Nils LM van de Ven, Remi Verhaegh, Judith S Spanjaard, Benjamin W Verboeket, Duco Laane, Karlijn van Wessem, Daan EJ van spengler, Wiebe Buitenwerf, Giulio Giustarini, Eva Mulder, Harry Heijerman, Amely Daza Zabaleta, Frederique van den bos, Emma Rademaker, Meri RJ Varkila, Nikki de Mul, Olaf L Cremer, Arjen Slooter, Eveline M Delemarre, Stefan Nierkens, Maarten Limper, Femke van Wijk, Aridaman Pandit, Helen Leavis, Chantal C Clark, Arjan D Barendrecht, Cor W Seinen, Sandra Drost‐Verhoef, Simone Smits, Naomi MJ Parr, Sylvie AE Sebastian, Arnold C Koekman, Annet C van Wesel, Erhard van der Vries, Coen Maas, Steven de Maat, Saskia Haitjema, Imo E Hoefer. An increase in CD62Ldim neutrophils precedes the development of pulmonary embolisms in COVID‐19 patients, Scandinavian Journal of Immunology, e13023. https://onlinelibrary.wiley.com/doi/abs/10.1111/sji.13023

Eleni Chouri, Maojie Wang, Maarten R Hillen, Chiara Angiolilli, Sandra C Silva-Cardoso, Catharina GK Wichers, Maarten van der Kroef, Cornelis PJ Bekker, Marta Cossu, Lenny van Bon, Alsya J Affandi, Tiago Carvalheiro, Aridaman Pandit, Joel AG van Roon, Lorenzo Beretta, Boudewijn MT Burgering, Timothy RDJ Radstake, Marzia Rossato. Implication of miR-126 and miR-139-5p in Plasmacytoid Dendritic Cell Dysregulation in Systemic Sclerosis, Journal of Clinical Medicine, 10(3):491. https://www.mdpi.com/980212

Weiyang Tao, Timothy RDJ Radstake, Aridaman Pandit*. RegEnrich: An R package for gene regulator enrichment analysis reveals key role of ETS transcription factor family in interferon signaling, bioRxiv, https://doi.org/10.1101/2021.01.24.428029. https://doi.org/10.1101/2021.01.24.428029

Aridaman Pandit*, Rob J de Boer. Delayed Differentiation Makes Many Models Compatible with Data for CD8+ T Cell Differentiation, Mathematical, Computational and Experimental T Cell Immunology, Book pages:121-132. https://link.springer.com/chapter/10.1007/978-3-030-57204-4_8

2020

Sandra C Silva‐Cardoso, Weiyang Tao, Beatriz Malvar Fernández, Marianne Boes, Timothy RDJ Radstake, Aridaman Pandit*. CXCL4 suppresses tolerogenic immune signature of monocyte‐derived dendritic cells, European Journal of Immunology, 50(10):1598. https://onlinelibrary.wiley.com/doi/full/10.1002/eji.201948341

Nila H Servaas, Julia Spierings, Aridaman Pandit, Jacob M van Laar. The role of innate immune cells in systemic sclerosis in the context of autologous hematopoietic stem cell transplantation, Clinical & Experimental Immunology, 201(1):34-39. https://onlinelibrary.wiley.com/doi/full/10.1111/cei.13419

Maarten R Hillen, Katia Urso, Emma Koppe, Ana Pinheiro Lopes, Sofie LM Blokland, Aridaman Pandit, Tom Slocombe, André van Maurik, Joel AG van Roon, Timothy RDJ Radstake. Autoantigen TRIM21/Ro52 is expressed on the surface of antigen-presenting cells and its enhanced expression in Sjögren’s syndrome is associated with B cell hyperactivity and type I interferon activity, RMD Open, 6(2):e001184. https://rmdopen.bmj.com/content/6/2/e001184

Kamil G Laban, Rianne Rijken, Sanne Hiddingh, Jorre S Mertens, Rob LP van der Veen, Christine AE Eenhorst, Aridaman Pandit, Timothy RDJ Radstake, Joke H de Boer, Rachel Kalmann, Jonas JW Kuiper. cDC2 and plasmacytoid dendritic cells diminish from tissues of patients with non‐Hodgkin orbital lymphoma and idiopathic orbital inflammation, European Journal of Immunology, 50(4):548-557. https://onlinelibrary.wiley.com/doi/full/10.1002/eji.201948370

Eefje Hanna Martine van der Heijden, Sofie Liny Marie Blokland, Maarten Reinier Hillen, Ana Paula Pinheiro Lopes, Fréderique Marie van Vliet-Moret, Antoine Johan Wilhelm Peter Rosenberg, Nard Gabriëlle Janssen, Paco Mattheus Jacobus Welsing, Valentina Iannizzotto, Weiyang Tao, Aridaman Pandit, Francesca Barone, Aike Albert Kruize, Timothy Ruben Dirk Jan Radstake, Joel Adrianus Gijsbert van Roon. Leflunomide–hydroxychloroquine combination therapy in patients with primary Sjögren's syndrome (RepurpSS-I): a placebo-controlled, double-blinded, randomised clinical trial, The Lancet Rheumatology, 2(5):e260-e269. https://www.sciencedirect.com/science/article/pii/S2665991320300576

Aridaman Pandit*, Timothy RDJ Radstake. Machine learning in rheumatology approaches the clinic, Nature Reviews Rheumatology, 16:69–70. https://www.nature.com/articles/s41584-019-0361-0

Sofie LM Blokland, Fréderique M van Vliet-Moret, Maarten R Hillen, Aridaman Pandit, Roel Goldschmeding, Aike A Kruize, Gerben Bouma, André van Maurik, Sven Olek, Ulrich Hoffmueller, Joel AG van Roon, Timothy RDJ Radstake. 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, 59(2):335-343. https://academic.oup.com/rheumatology/article/59/2/335/5536354

Gerdien Mijnheer, Lisanne Lutter, Michal Mokry, Marlot van der Wal, Veerle Fleskens, Rianne Scholman, Aridaman Pandit, Weiyang Tao, Mark Wekking, Stephin Vervoort, Ceri Roberts, Alissandra Petrelli, Janneke Peeters, Marthe Knijff, Sytze de Roock, Sebastiaan Vastert, Leonie Taams, Jorg van Loosdregt, Femke van Wijk. Conserved human effector Treg signature is reflected in transcriptomic and epigenetic landscape, BioRxiv, https://doi.org/10.1101/2020.09.30.319962. https://www.biorxiv.org/content/10.1101/2020.09.30.319962v1

Sandra C Silva-Cardoso, Weiyang Tao, Chiara Angiolilli, Ana P Lopes, Cornelis Bekker, Abhinandan Devaprasad, Barbara Giovannone, Jaap Van Laar, Marta Cossu, Wioleta Marut, Erik Hack, Rob J De Boer, Marianne Boes, Timothy RDJ Radstake, Aridaman Pandit*. CXCL4 links inflammation and fibrosis by reprogramming monocyte-derived dendritic cells in vitro, Frontiers in Immunology, 11:2149. https://www.frontiersin.org/articles/10.3389/fimmu.2020.02149/full

Roos AW Wennink, Aridaman Pandit (shared first), Anne-Mieke JW Haasnoot, Sanne Hiddingh, Viera Kalinina Ayuso, Nico M Wulffraat, Bas J Vastert, Timothy RDJ Radstake, Joke H de Boer, Jonas JW Kuiper. Whole transcriptome analysis reveals heterogeneity in B cell memory populations in patients with juvenile idiopathic arthritis-associated uveitis, Frontiers in Immunology, 11:2170. https://www.frontiersin.org/articles/10.3389/fimmu.2020.02170/full

Bram Gerritsen, Aridaman Pandit, Fatiha Zaaraoui-Boutahar, Mirjam CGN van den Hout, Wilfred FJ van IJcken, Rob J de Boer, Arno C Andeweg. Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis, Immunogenetics, 72, 101–108. https://link.springer.com/article/10.1007/s00251-019-01142-9

Laure Gossec, Joanna Kedra, Hervé Servy, Aridaman Pandit, Simon Stones, Francis Berenbaum, Axel Finckh, Xenofon Baraliakos, Tanja A Stamm, David Gomez-Cabrero, Christian Pristipino, Remy Choquet, Gerd R Burmester, Timothy RDJ Radstake. EULAR points to consider for the use of big data in rheumatic and musculoskeletal diseases, Annals of the Rheumatic Diseases, 79(1):69-76. https://ard.bmj.com/content/early/2019/06/22/annrheumdis-2019-215694

2019

Abhinandan Devaprasad, Timothy RDJ Radstake, Aridaman Pandit*. Integration of immunome with disease gene network reveals pleiotropy and novel drug repurposing targets, BioRxiv, 10.1101/2019.12.12.874321. https://www.biorxiv.org/content/10.1101/2019.12.12.874321v1

Sandra C Silva-Cardoso, Weiyang Tao, Chiara Angiolilli, Ana P Lopes, Cornelis PJ Bekker, Abhinandan Devaprasad, Barbara Giovannone, Jaap Van Laar, Marta Cossu, Wioleta Marut, Erik Hack, Rob J De Boer, Marianne Boes, Timothy RDJ Radstake, Aridaman Pandit*. CXCL4 links inflammation and fibrosis through transcriptional and epigenetic reprogramming of monocyte-derived cells, BioRxiv, 10.1101/807230. https://www.biorxiv.org/content/10.1101/807230v1

Weiyang Tao, Timothy RDJ Radstake, Aridaman Pandit*. Machine learning to molecularly classify systemic sclerosis patients, Arthritis & Rheumatology, 71(10):1595-1598. https://doi.org/10.1002/art.40902.

Maarten R Hillen, Aridaman Pandit (shared first), Sofie LM Blokland, Sarita Ay Hartgring, Cornelis PJ Bekker, Eefje HM van der Heijden, Nila H Servaas, Marzia Rossato, Aike A Kruize, Joel AG van Roon, Timothy RDJ Radstake. Plasmacytoid DCs from patients with Sjögren’s syndrome are transcriptionally primed for enhanced pro-inflammatory cytokine production, Frontiers in Immunology, 10:2096. https://www.frontiersin.org/articles/10.3389/fimmu.2019.02096/full

Joanna Kedra, Timothy Radstake, Aridaman Pandit, Xenofon Baraliakos, Francis Berenbaum, Axel Finckh, Bruno Fautrel, Tanja A Stamm, David Gomez-Cabrero, Christian Pristipino, Remy Choquet, Hervé Servy, Simon Stones, Gerd Burmester, Laure Gossec. Current status of use of big data and artificial intelligence in RMDs: a systematic literature review informing EULAR recommendations, RMD open, 5(2):e001004.
https://rmdopen.bmj.com/content/5/2/e001004

Kamil G Laban, Rianne Rijken, Sanne Hiddingh, Jorre S Mertens, Rob LP van der Veen, Christine AE Eenhorst, Aridaman Pandit, Timothy RDJ Radstake, Joke H de Boer, Rachel Kalmann, Jonas JW Kuiper. cDC2 and plasmacytoid dendritic cells diminish from tissues of patients with non‐Hodgkin orbital lymphoma and idiopathic orbital inflammation, European Journal of Immunology. doi:10.1002/eji.201948370. https://onlinelibrary.wiley.com/doi/full/10.1002/eji.201948370

Alsya J Affandi, Tiago Carvalheiro, Andrea Ottria, Jasper CA Broen, Lara Bossini-Castillo, Ralph G Tieland, Lenny van Bon, Eleni Chouri, Marzia Rossato, Jorre S Mertens, Samuel Garcia, Aridaman Pandit, Laurie MG de Kroon, Romy B Christmann, Javier Martin, Joel AG van Roon, Timothy RDJ Radstake, Wioleta Marut. Low RUNX3 expression alters dendritic cell function in patients with systemic sclerosis and contributes to enhanced fibrosis, Annals of the Rheumatic Diseases, 78:1249-1259. https://ard.bmj.com/content/early/2019/05/23/annrheumdis-2018-214991.

Aridaman Pandit*, Rob J de Boer. Stochastic Inheritance of Division and Death Times Determines the Size and Phenotype of CD8+ T Cell Families, Frontiers in Immunology, 10:436. https://www.frontiersin.org/articles/10.3389/fimmu.2019.00436/full

Silvia De Alessandris, G. John Ferguson, Alison J. Dodd, Jatinder K. Juss, Abhinandan Devaprasad, Siân Piper, Owen Wyatt, Helen Killick, Dominic J. Corkill, E. Suzanne Cohen, Aridaman Pandit, Timothy R.D.J. Radstake, Rosalind Simmonds, Alison M. Condliffe, Matthew A. Sleeman, Andrew S. Cowburn, Donna K. Finch, Edwin R. Chilvers. Neutrophil GM‐CSF receptor dynamics in acute lung injury, Journal of Leukocyte Biology, 105:1183–1194. https://doi.org/10.1002/JLB.3MA0918-347R

Sofie LM Blokland, Maarten R Hillen, Fréderique M van Vliet-Moret, Angela Bikker, Wilco de Jager, Aridaman Pandit, Aike A Kruize, Timothy RDJ Radstake, Joel AG van Roon. Salivary gland secretome: a novel tool towards molecular stratification of patients with primary Sjögren’s syndrome and non-autoimmune sicca, RMD Open, 5(1):e000772. https://rmdopen.bmj.com/content/5/1/e000772

2018

Alessandra Petrelli, Gerdien Mijnheer, David P Hoytema van Konijnenburg, Maria M van der Wal, Barbara Giovannone, Enric Mocholi, Nadia Vazirpanah, Jasper C Broen, Dirkjan Hijnen, Bas Oldenburg, Paul J Coffer, Sebastian J Vastert, Berent J Prakken, Eric Spierings, Aridaman Pandit, Michal Mokry, Femke van Wijk. PD-1+CD8+ T cells are clonally expanding effectors in human chronic inflammation, The Journal of Clinical Investigation, 128(10):4669–4681. https://www.jci.org/articles/view/96107

Lucas L van den Hoogen, Joël AG van Roon, Jorre S Mertens, Judith Wienke, Ana Pinheiro Lopes, Wilco de Jager, Marzia Rossato, Aridaman Pandit, Catharina GK Wichers, Femke van Wijk, Ruth DE Fritsch-Stork, Timothy RDJ Radstake. Galectin-9 is an easy to measure biomarker for the interferon signature in systemic lupus erythematosus and antiphospholipid syndrome, Annals of the rheumatic diseases, doi: 10.1136/annrheumdis-2018-213497. https://ard.bmj.com/content/early/2018/09/05/annrheumdis-2018-213497?int_source=trendmd&int_medium=trendmd&int_campaign=trendmd

Lucas L van den Hoogen, Marzia Rossato, Ana P Lopes, Aridaman Pandit, Cornelis PJ Bekker, Ruth DE Fritsch-Stork, Joel AG van Roon, Timothy RDJ Radstake. microRNA downregulation in plasmacytoid dendritic cells in interferon-positive systemic lupus erythematosus and antiphospholipid syndrome, Rheumatology, 57(9):1669–1674. https://academic.oup.com/rheumatology/article-abstract/57/9/1669/5032988?redirectedFrom=fulltext

Fleurieke H. Verhagen, Cornelis P. J. Bekker, Marzia Rossato, Sanne Hiddingh, Lieuwe de Vries, Abhinandan Devaprasad, Aridaman Pandit, Jeannette Ossewaarde-van Norel, Ninette ten Dam, Maartje C. A. Moret-Pot, Saskia M. Imhof, Joke H. de Boer, Timothy R. D. J. Radstake, Jonas J. W. Kuiper. A Disease-Associated MicroRNA Cluster Links Inflammatory Pathways and an Altered Composition of Leukocyte Subsets to Noninfectious Uveitis, Investigative Ophthalmology & Visual Science, 59(2):878-888. https://iovs.arvojournals.org/article.aspx?articleid=2672887

Fleurieke H Verhagen, Sanne Hiddingh, Rianne Rijken, Aridaman Pandit, Emmerik Leijten, Michel Olde-Nordkamp, Ninette H ten Dam-van Loon, Stefan Nierkens, Saskia M Imhof, Joke H de Boer, Timothy RDJ Radstake, Jonas JW Kuiper. High-dimensional profiling reveals heterogeneity of the Th17 subset and its association with systemic immunomodulatory treatment in non-infectious uveitis, Frontiers in Immunology, 9:2519. https://www.frontiersin.org/articles/10.3389/fimmu.2018.02519/abstract

2017

Jorre S Mertens, EMGJ de Jong, Aridaman Pandit, MMB Seyger, EPAH Hoppenreijs, RM Thurlings, MC Vonk, Judith Wienke, Femke van Wijk, A van Royen-Kerkhof, Wiola Marut, Timothy RDJ Radstake. Regarding “Transcriptional and cytokine profiles identify CXCL9 as a biomarker of disease activity in morphea", Journal of Investigative Dermatology, 138:1212-1215. https://www.jidonline.org/article/S0022-202X(17)33265-7/fulltext

Aridaman Pandit, Linde Meyaard, Timothy RDJ Radstake. Is sex bias orchestrated in the skin?, Nature Immunology, 18:142-143. https://www.nature.com/articles/ni.3658

2016

Bram Gerritsen, Aridaman Pandit, Arno C Andeweg, Rob J de Boer. RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data, Bioinformatics, 32(20):3098-3106. https://academic.oup.com/bioinformatics/article/32/20/3098/2196383

Sakshi Singh, Ashish Singh, Raja Rajkumar, Katakam Sampath Kumar, Subburaj Kadarkarai Samy, Sheikh Nizamuddin, Amita Singh, Shahnawaz Ahmed Sheikh, Vidya Peddada, Vinee Khanna, Pandichelvam Veeraiah, Aridaman Pandit, Gyaneshwer Chaubey, Lalji Singh, Kumarasamy Thangaraj. Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup, Scientific Reports, 5:19157. https://www.nature.com/articles/srep19157

2015

Bram Gerritsen, Aridaman Pandit*. The memory of a killer T cell: Models of CD8+ T cell differentiation, Immunology and Cell Biology, 94(3):236-241. https://onlinelibrary.wiley.com/doi/abs/10.1038/icb.2015.118

Aridaman Pandit*, Rob J de Boer. HIV-1 CCR5 gene therapy will fail unless it is combined with a suicide gene, Scientific reports, 5:18088. https://www.nature.com/articles/srep18088

2014

Aridaman Pandit*, Rob J de Boer. Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants, Retrovirology, 11:56. https://retrovirology.biomedcentral.com/articles/10.1186/1742-4690-11-56

2013

Aridaman Pandit, Jyothirmayi Vadlamudi, Somdatta Sinha. Analysis of dinucleotide signatures in HIV-1 subtype B genomes, Journal of Genetics, 92(3):403-412. https://link.springer.com/article/10.1007/s12041-013-0281-8

2012

Aridaman Pandit, Anil Kumar Dasanna, Somdatta Sinha. Multifractal analysis of HIV-1 genomes, Molecular Phylogenetics and Evolution, 62(2):756-763. https://www.sciencedirect.com/science/article/pii/S105579031100488X

2011

Aridaman Pandit, Somdatta Sinha. Differential Trends in the Codon Usage Patterns in HIV-1 Genes, PLoS ONE, 6(12):e28889. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028889

2010

Aridaman Pandit, Somdatta Sinha. Using genomic signatures for HIV-1 sub-typing, BMC bioinformatics, 11(1):S26. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-S1-S26

Aditi Gupta, Aridaman Pandit, Somdatta Sinha. VAMA: A Versatile Web-Based Tool for Variability Analysis in Multiply-Aligned Amino Acid Sequences, IEEE Proceedings of 2010 4th International Conference on Bioinformatics and Biomedical Engineering, doi: 10.1109/ICBBE.2010.5515824. https://ieeexplore.ieee.org/abstract/document/5515824/

Tools

RTCR

Recover T Cell Receptor (RTCR) is a pipeline for complete and accurate recovery of TCR repertoires from high throughput sequencing data.

https://github.com/uubram/RTCR

RegEnrich

RegEnrich is an open source R package that generates data-driven gene regulatory networks and performs enrichment analysis to rank the key regulators. RegEnrich produces a refined regulator-regulator network consisting of key regulatorys involved in the biological processes of interest to the user.

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("RegEnrich")

https://bioconductor.org/packages/release/bioc/html/RegEnrich.html

Tcell Fate

After antigen stimulation cognate naive CD8+ T cells undergo rapid proliferation and ultimately their progeny differentiates into short-lived effectors and longer-lived memory T cells. Although the expansion of individual cells is very heterogeneous, the kinetics are reproducible at the level of the total population of cognate cells. After the expansion phase, the population contracts, and if antigen is cleared, a population of memory T cells remains behind. Different markers like CD62L, CD27, and KLRG1 have been used to define several T cell subsets (or cell fates) developing from individual naive CD8+ T cells during the expansion phase. Growing evidence from high-throughput experiments, like single cell RNA sequencing, epigenetic profiling and lineage tracing, highlights the need to model this differentiation process at the level of single cells.

We model CD8+ T cell proliferation and differentiation as a competitive process between the division and death probabilities of individual cells (like in the Cyton model). We use an extended form of the Cyton model in which daughter cells inherit the division and death times from their mother cell in a stochastic manner (using lognormal distributions). We show that this stochastic model reproduces the dynamics of CD8+ T cells both at the population and at the single cell level. Modeling the expression of the CD62L, CD27, and KLRG1 markers of each individual cell, we find agreement with the changing phenotypic distributions of these markers in single cell RNA sequencing data. Retrospectively re-defining conventional T-cell subsets by gating on these markers, we find agreement with published population data, without having to assume that these subsets have different properties, i.e., correspond to different fates.

https://bitbucket.org/aridaman/tcellfate

DIME: Disease-gene IMmune cell Expression network

DIME is a R Shinyapp, that can be used to assess the impact of disease genes on immune cells. It uses non-negative matrix factorization (NMF) technique to identify clusters/network of disease associated cells (DAC) that express the disease associated genes (DAG). The DIME network in this tool has been implemented on two disease networks, the DisGeNet and the EBI GWAS network. It can also be used on custom set of genes to assess the impact of these genes on the immune cells.

https://bitbucket.org/systemsimmunology/dime/src/master

Contact us

A(dot)Pandit (at) umcutrecht(dot)nl

Updated