scROSHI: robust supervised hierarchical identification of single cells Article Swipe
Michael Prummer
,
Anne Bertolini
,
Lars Bosshard
,
Florian Barkmann
,
Josephine Yates
,
Valentina Boeva
,
Rudolf Aebersold
,
Melike Ak
,
Faisal Alquaddoomi
,
Jonas Albinus
,
Ilaria Alborelli
,
Sonali Andani
,
Per-Olof Attinger
,
Marina Bacac
,
Daniel Baumhoer
,
Beatrice Beck‐Schimmer
,
Niko Beerenwinkel
,
Christian Beisel
,
Lara Bernasconi
,
Anne Bertolini
,
Bernd Bodenmiller
,
Ximena Bonilla
,
Lars Bosshard
,
Byron Calgua
,
Ruben Casanova
,
Stéphane Chevrier
,
Natalia Chicherova
,
Maya D’Costa
,
Esther Danenberg
,
Natalie J. Davidson
,
Monica-Andreea Drăgan
,
Reinhard Dummer
,
Stefanie Engler
,
Martin Erkens
,
Katja Eschbach
,
Cinzia Esposito
,
André Fedier
,
Pedro Ferreira
,
Joanna Ficek
,
Anja Frei
,
Bruno S. Frey
,
Sandra Goetze
,
Linda Grob
,
Gabriele Gut
,
Detlef Günther
,
Martina Haberecker
,
Pirmin Haeuptle
,
Viola Heinzelmann‐Schwarz
,
Sylvia Herter
,
René Holtackers
,
Tamara Huesser
,
Anja Irmisch
,
Francis Jacob
,
Alice K. Jacobs
,
Tim M. Jaeger
,
Katharina Jahn
,
Alva Rani James
,
Philip Jermann
,
André Kahles
,
Abdullah Kahraman
,
Viktor H. Koelzer
,
Werner Kuebler
,
Jack Kuipers
,
Christian P. Kunze
,
Christian Kurzeder
,
Kjong-Van Lehmann
,
Mitchell Levesque
,
Sebastian Lugert
,
Gerd Maass
,
Markus G. Manz
,
Philipp Markolin
,
Julien Mena
,
Ulrike Menzel
,
Julian M. Metzler
,
Nicola Miglino
,
Emanuela S. Milani
,
Holger Moch
,
Simone Muenst
,
Riccardo Murri
,
Charlotte K.Y. Ng
,
Stefan Nicolet
,
Marta Nowak
,
Patrick G. A. Pedrioli
,
Lucas Pelkmans
,
Salvatore Piscuoglio
,
Michael Prummer
,
Mathilde Ritter
,
Christian Rommel
,
María L. Rosano-González
,
Gunnar Rätsch
,
Natascha Santacroce
,
Jacobo Sarabia del Castillo
,
Ramona Schlenker
,
Petra Schwalie
,
Severin Schwan
,
Tobias Schär
,
Gabriela Senti
,
Franziska Singer
,
Sujana Sivapatham
,
Berend Snijder
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/nargab/lqad058
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/nargab/lqad058
Identifying cell types based on expression profiles is a pillar of single cell analysis. Existing machine-learning methods identify predictive features from annotated training data, which are often not available in early-stage studies. This can lead to overfitting and inferior performance when applied to new data. To address these challenges we present scROSHI, which utilizes previously obtained cell type-specific gene lists and does not require training or the existence of annotated data. By respecting the hierarchical nature of cell type relationships and assigning cells consecutively to more specialized identities, excellent prediction performance is achieved. In a benchmark based on publicly available PBMC data sets, scROSHI outperforms competing methods when training data are limited or the diversity between experiments is large.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nargab/lqad058
- https://academic.oup.com/nargab/article-pdf/5/2/lqad058/50626273/lqad058.pdf
- OA Status
- gold
- Cited By
- 9
- References
- 30
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4380989198
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- OpenAlex ID
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https://openalex.org/W4380989198Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/nargab/lqad058Digital Object Identifier
- Title
-
scROSHI: robust supervised hierarchical identification of single cellsWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
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2022-06-01Full publication date if available
- Authors
-
Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, Rudolf Aebersold, Melike Ak, Faisal Alquaddoomi, Jonas Albinus, Ilaria Alborelli, Sonali Andani, Per-Olof Attinger, Marina Bacac, Daniel Baumhoer, Beatrice Beck‐Schimmer, Niko Beerenwinkel, Christian Beisel, Lara Bernasconi, Anne Bertolini, Bernd Bodenmiller, Ximena Bonilla, Lars Bosshard, Byron Calgua, Ruben Casanova, Stéphane Chevrier, Natalia Chicherova, Maya D’Costa, Esther Danenberg, Natalie J. Davidson, Monica-Andreea Drăgan, Reinhard Dummer, Stefanie Engler, Martin Erkens, Katja Eschbach, Cinzia Esposito, André Fedier, Pedro Ferreira, Joanna Ficek, Anja Frei, Bruno S. Frey, Sandra Goetze, Linda Grob, Gabriele Gut, Detlef Günther, Martina Haberecker, Pirmin Haeuptle, Viola Heinzelmann‐Schwarz, Sylvia Herter, René Holtackers, Tamara Huesser, Anja Irmisch, Francis Jacob, Alice K. Jacobs, Tim M. Jaeger, Katharina Jahn, Alva Rani James, Philip Jermann, André Kahles, Abdullah Kahraman, Viktor H. Koelzer, Werner Kuebler, Jack Kuipers, Christian P. Kunze, Christian Kurzeder, Kjong-Van Lehmann, Mitchell Levesque, Sebastian Lugert, Gerd Maass, Markus G. Manz, Philipp Markolin, Julien Mena, Ulrike Menzel, Julian M. Metzler, Nicola Miglino, Emanuela S. Milani, Holger Moch, Simone Muenst, Riccardo Murri, Charlotte K.Y. Ng, Stefan Nicolet, Marta Nowak, Patrick G. A. Pedrioli, Lucas Pelkmans, Salvatore Piscuoglio, Michael Prummer, Mathilde Ritter, Christian Rommel, María L. Rosano-González, Gunnar Rätsch, Natascha Santacroce, Jacobo Sarabia del Castillo, Ramona Schlenker, Petra Schwalie, Severin Schwan, Tobias Schär, Gabriela Senti, Franziska Singer, Sujana Sivapatham, Berend SnijderList of authors in order
- Landing page
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https://doi.org/10.1093/nargab/lqad058Publisher landing page
- PDF URL
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https://academic.oup.com/nargab/article-pdf/5/2/lqad058/50626273/lqad058.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://academic.oup.com/nargab/article-pdf/5/2/lqad058/50626273/lqad058.pdfDirect OA link when available
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Overfitting, Computer science, Machine learning, Artificial intelligence, Identification (biology), Benchmark (surveying), Training set, Data type, Data mining, Pattern recognition (psychology), Artificial neural network, Biology, Geography, Geodesy, Botany, Programming languageTop concepts (fields/topics) attached by OpenAlex
- Cited by
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9Total citation count in OpenAlex
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2025: 1, 2024: 4, 2023: 2, 2022: 2Per-year citation counts (last 5 years)
- References (count)
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30Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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