Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

Autor: Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, Sarah Ouologuem, Kevin Rue-Albrecht, Lilly May, Giulia E. L. Garcia, Lukas Heumos, Tom Thomas, Wojciech Lason, David Sims, Fabian J. Theis, Calliope A. Dendrou

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-20 (2024)

Abstract Single-cell multiomic analysis of the epigenome, transcriptome, and proteome allows for comprehensive characterization of the molecular circuitry that underpins cell identity and state. However, the holistic interpretation of such datasets p

Externí odkaz: https://doaj.org/article/fc8d9ca0247842cda6a85765f6c6baf1

Sfaira accelerates data and model reuse in single cell genomics

Autor: David S. Fischer, Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Lukas Heumos, Sophie Tritschler, Olle Holmberg, Hananeh Aliee, Fabian J. Theis

Publikováno v: Genome Biology, Vol 22, Iss 1, Pp 1-21 (2021)

Abstract Single-cell RNA-seq datasets are often first analyzed independently without harnessing model fits from previous studies, and are then contextualized with public data sets, requiring time-consuming data wrangling. We address these issues with

Externí odkaz: https://doaj.org/article/42d3581d43904bdf861e73681f736824

Probe set selection for targeted spatial transcriptomics

Autor: Louis B. Kuemmerle, Malte D. Luecken, Alexandra B. Firsova, Lisa Barros de Andrade e Sousa, Lena Straßer, Lukas Heumos, Ilhem Isra Mekki, Krishnaa T. Mahbubani, Alexandros Sountoulidis, Tamás Balassa, Ferenc Kovacs, Peter Horvath, Marie Piraud, Ali Ertürk, Christos Samakovlis, Fabian J. Theis

Targeted spatial transcriptomics methods capture the topology of cell types and states in tissues at single cell- and subcellular resolution by measuring the expression of a predefined set of genes. The selection of an optimal set of probed genes is

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1680be11e0f1dc924c379a2c7c630916
https://doi.org/10.1101/2022.08.16.504115

An integrated cell atlas of the human lung in health and disease

Autor: Malte Luecken, Lisa Sikkema, Daniel Strobl, Luke Zappia, Elo Madissoon, Nikolay Markov, Laure-Emmanuelle Zaragosi, Meshal Ansari, Marie-Jeanne Arguel, Leonie Apperloo, Christophe Becavin, Marijn Berg, Evgeny Chichelnitskiy, Mei-i Chung, Antoine Collin, Aurore Gay, Baharak Hooshiar Kashani, Manu Jain, Theodore Kapellos, Tessa Kole, Christoph Mayr, Michael von Papen, Lance Peter, Ciro Ramírez-Suástegui, Janine Schniering, Chase Taylor, Thomas Walzthoeni, Chuan Xu, Linh Bui, Carlo de Donno, Leander Dony, Minzhe Guo, Austin Gutierrez, Lukas Heumos, Ni Huang, Ignacio Ibarra Del Río, Nathan Jackson, Preetish Kadur Lakshminarasimha Murthy, Mohammad Lotfollahi, Tracy Tabib, Carlos Talavera-Lopez, Kyle Travaglini, Anna Wilbrey-Clark, Kaylee Worlock, Masahiro Yoshida, Tushar Desai, Orit Rozenblatt-Rosen, Christine Falk, Naftali Kaminski, Mark Krasnow, Robert Lafyatis, Marko Nikolic, Joseph Powell, Jay Rajagopal, Max Seibold, Dean Sheppard, Douglas Shepherd, Sarah Teichmann, Alexander Tsankov, Jeffrey Whitsett, Yan Xu, Nicholas Banovich, Pascal Barbry, Thu Duong, Kerstin Meyer, Jonathan Kropski, Dana Pe'er, Herbert Schiller, Purushothama Rao Tata, Joachim Schultze, Maarten van den Berge, Yuexin Chen, James Hagood, Ahmed Hassan, Peter Horvath, Joakim Lundeberg, Sylvie Leroy, Charles Marquette, Gloria Pryhuber, Christos Samakovlis, Xin Sun, Lorraine Ware, Kun Zhang, Alexander Misharin, Martijn Nawijn, Fabian Theis

Organ- and body-scale cell atlases have the potential to transform our understanding of human biology. To capture the variability present in the population, these atlases must include diverse demographics such as age and ethnicity from both healthy a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::6c225b8ec842494e3c796c31c793715c
https://doi.org/10.21203/rs.3.rs-1438584/v1

Global analysis of human SARS-CoV-2 infection and host-virus interaction

Autor: Núria Queralt-Rosinach, Andreas Gruber, Alexander Kanitz, Scheila G. Mucha, Olaitan Igbagbo Awe, Meldal B, de Oliveira Ds, Tsagiopoulou M, Neiro J, Mariana Galvão Ferrarini, Georgaki M, Eric T. Dawson, Ben Busby, Itziar Martinez Gonzalez, Aguiar-Pulido, James C, Ruiz-Arenas C, Sarbjit Singh Bedi, Andrea Guarracino, Lukas Heumos, Amit Kumar Lal, Philippe Rocca-Serra, Noushin Nabavi, Rita Rebollo, Brett E. Pickett

As part of the virtual BioHackathon 2020, we formed a working group that focused on the analysis of gene expression in the context of COVID-19. More specifically, we performed transcriptome analyses on published datasets in order to better understand

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::83a3939568fefff6f8212e4b3ec4c400
https://hal.inrae.fr/hal-03514119