ePlatypus: an ecosystem for computational analysis of immunogenomics data

Tudor-Stefan Cotet; Andreas Agrafiotis; Victor Kreiner; Raphael Kuhn; Danielle Shlesinger; Marcos Manero-Carranza; Keywan Khodaverdi; Evgenios Kladis; Aurora Desideri Perea; Dylan Maassen-Veeters; Wiona Glänzer; Solène Massery; Lorenzo Guerci; Kai-Lin Hong; Jiami Han; Kostas Stiklioraitis; Vittoria Martinolli D'Arcy; Raphael Dizerens; Samuel Kilchenmann; Lucas Stalder; Leon Nissen; Basil Vogelsanger; Stine Anzböck; Daria Laslo; Sophie Bakker; Melinda Kondorosy; Marco Venerito; Alejandro Sanz García; Isabelle Feller; Annette Oxenius; Sai T Reddy; Alexander Yermanos

doi:10.1093/bioinformatics/btad553

ePlatypus: an ecosystem for computational analysis of immunogenomics data

Tudor-Stefan Cotet, Andreas Agrafiotis, Victor Kreiner, Raphael Kuhn, Danielle Shlesinger, Marcos Manero-Carranza, Keywan Khodaverdi, Evgenios Kladis, Aurora Desideri Perea, Dylan Maassen-Veeters, Wiona Glänzer, Solène Massery, Lorenzo Guerci, Kai-Lin Hong, Jiami Han, Kostas Stiklioraitis, Vittoria Martinolli D'Arcy, Raphael Dizerens, Samuel Kilchenmann, Lucas StalderLeon Nissen, Basil Vogelsanger, Stine Anzböck, Daria Laslo, Sophie Bakker, Melinda Kondorosy, Marco Venerito, Alejandro Sanz García, Isabelle Feller, Annette Oxenius, Sai T Reddy, Alexander Yermanos^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Motivation: The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. Results: Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand–receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science.

Original language	English
Article number	btad553
Journal	Bioinformatics (Oxford, England)
Volume	39
Issue number	9
DOIs	https://doi.org/10.1093/bioinformatics/btad553
Publication status	Published - 2 Sept 2023

Keywords

Animals
Computational Biology/methods
Ecosystem
Machine Learning
Phylogeny
Platypus
Software

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btad553Final published version, 2.59 MBLicence: CC BY

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Cotet, T.-S., Agrafiotis, A., Kreiner, V., Kuhn, R., Shlesinger, D., Manero-Carranza, M., Khodaverdi, K., Kladis, E., Desideri Perea, A., Maassen-Veeters, D., Glänzer, W., Massery, S., Guerci, L., Hong, K.-L., Han, J., Stiklioraitis, K., D'Arcy, V. M., Dizerens, R., Kilchenmann, S., ... Yermanos, A. (2023). ePlatypus: an ecosystem for computational analysis of immunogenomics data. Bioinformatics (Oxford, England), 39(9), Article btad553. https://doi.org/10.1093/bioinformatics/btad553

@article{c35174f9a1da441fa40235d423716328,

title = "ePlatypus: an ecosystem for computational analysis of immunogenomics data",

abstract = "Motivation: The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. Results: Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand–receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science.",

keywords = "Animals, Computational Biology/methods, Ecosystem, Machine Learning, Phylogeny, Platypus, Software",

author = "Tudor-Stefan Cotet and Andreas Agrafiotis and Victor Kreiner and Raphael Kuhn and Danielle Shlesinger and Marcos Manero-Carranza and Keywan Khodaverdi and Evgenios Kladis and {Desideri Perea}, Aurora and Dylan Maassen-Veeters and Wiona Gl{\"a}nzer and Sol{\`e}ne Massery and Lorenzo Guerci and Kai-Lin Hong and Jiami Han and Kostas Stiklioraitis and D'Arcy, {Vittoria Martinolli} and Raphael Dizerens and Samuel Kilchenmann and Lucas Stalder and Leon Nissen and Basil Vogelsanger and Stine Anzb{\"o}ck and Daria Laslo and Sophie Bakker and Melinda Kondorosy and Marco Venerito and {Sanz Garc{\'i}a}, Alejandro and Isabelle Feller and Annette Oxenius and Reddy, {Sai T} and Alexander Yermanos",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2023. Published by Oxford University Press.",

year = "2023",

month = sep,

day = "2",

doi = "10.1093/bioinformatics/btad553",

language = "English",

volume = "39",

journal = "Bioinformatics (Oxford, England)",

issn = "1367-4803",

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Cotet, T-S, Agrafiotis, A, Kreiner, V, Kuhn, R, Shlesinger, D, Manero-Carranza, M, Khodaverdi, K, Kladis, E, Desideri Perea, A, Maassen-Veeters, D, Glänzer, W, Massery, S, Guerci, L, Hong, K-L, Han, J, Stiklioraitis, K, D'Arcy, VM, Dizerens, R, Kilchenmann, S, Stalder, L, Nissen, L, Vogelsanger, B, Anzböck, S, Laslo, D, Bakker, S, Kondorosy, M, Venerito, M, Sanz García, A, Feller, I, Oxenius, A, Reddy, ST & Yermanos, A 2023, 'ePlatypus: an ecosystem for computational analysis of immunogenomics data', Bioinformatics (Oxford, England), vol. 39, no. 9, btad553. https://doi.org/10.1093/bioinformatics/btad553

TY - JOUR

T1 - ePlatypus

T2 - an ecosystem for computational analysis of immunogenomics data

AU - Cotet, Tudor-Stefan

AU - Agrafiotis, Andreas

AU - Kreiner, Victor

AU - Kuhn, Raphael

AU - Shlesinger, Danielle

AU - Manero-Carranza, Marcos

AU - Khodaverdi, Keywan

AU - Kladis, Evgenios

AU - Desideri Perea, Aurora

AU - Maassen-Veeters, Dylan

AU - Glänzer, Wiona

AU - Massery, Solène

AU - Guerci, Lorenzo

AU - Hong, Kai-Lin

AU - Han, Jiami

AU - Stiklioraitis, Kostas

AU - D'Arcy, Vittoria Martinolli

AU - Dizerens, Raphael

AU - Kilchenmann, Samuel

AU - Stalder, Lucas

AU - Nissen, Leon

AU - Vogelsanger, Basil

AU - Anzböck, Stine

AU - Laslo, Daria

AU - Bakker, Sophie

AU - Kondorosy, Melinda

AU - Venerito, Marco

AU - Sanz García, Alejandro

AU - Feller, Isabelle

AU - Oxenius, Annette

AU - Reddy, Sai T

AU - Yermanos, Alexander

PY - 2023/9/2

Y1 - 2023/9/2

N2 - Motivation: The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. Results: Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand–receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science.

AB - Motivation: The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. Results: Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand–receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science.

KW - Animals

KW - Computational Biology/methods

KW - Ecosystem

KW - Machine Learning

KW - Phylogeny

KW - Platypus

KW - Software

U2 - 10.1093/bioinformatics/btad553

DO - 10.1093/bioinformatics/btad553

M3 - Article

C2 - 37682115

SN - 1367-4803

VL - 39

JO - Bioinformatics (Oxford, England)

JF - Bioinformatics (Oxford, England)

IS - 9

M1 - btad553

ER -

ePlatypus: an ecosystem for computational analysis of immunogenomics data

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