John C Marioni (John Marioni, J C Marioni)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 80

Top Topics

Acute Myeloid Leukemia

Genome Wide Association

Gene Expression

Top Venues

Nature communications

Nature genetics

Science immunology

This page only lists publications with an associated author ORCID identifier.

Publications

Austin D Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J Kunz, Linsey J Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J Q Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J Gomm, Valerie Speirs, J Louise Jones, John C Marioni, Walid T Khaled
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nature genetics 56 (4) (2024)
Jasper Panten, Tobias Heinen, Christina Ernst, Nils Eling, Rebecca E Wagner, Maja Satorius, John C Marioni, Oliver Stegle, Duncan T Odom
The dynamic genetic determinants of increased transcriptional divergence in spermatids. Nature communications 15 (1) (2024)
Richard J Gilbertson, Sam Behjati, Anna-Lisa Böttcher, Marianne E Bronner, Matthew Burridge, Henrick Clausing, Harry Clifford, Tracey Danaher, Laura K Donovan, Jarno Drost, Alexander M M Eggermont, Chris Emerson, Mona G Flores, Petra Hamerlik, Nada Jabado, Andrew Jones, Henrick Kaessmann, Claudia L Kleinman, Marcel Kool, Lena M Kutscher, Gavin Lindberg, Emily Linnane, John C Marioni, John M Maris, Michelle Monje, Alexandra Macaskill, Steven A Niederer, Paul A Northcott, Elizabeth Peeters, Willemijn Plieger-van Solkema, Liane Preußner, Anne C Rios, Karsten Rippe, Peter Sandford, Nikolaos G Sgourakis, Adam Shlien, Pete Smith, Karin Straathof, Patrick J Sullivan, Mario L Suvà, Michael D Taylor, Emma Thompson, Roser Vento-Tormo, Brandon J Wainwright, Robert J Wechsler-Reya, Frank Westermann, Shannon Winslade, Bissan Al-Lazikani, Stefan M Pfister
The Virtual Child. Cancer discovery 14 (4) (2024)
Luca Peruzzotti-Jametti, C M Willis, G Krzak, R Hamel, L Pirvan, Rosana-Bristena Ionescu, J A Reisz, Hiran A Prag, M E Garcia-Segura, V Wu, Y Xiang, B Barlas, Alva M Casey, A M R van den Bosch, Alexandra M Nicaise, L Roth, G R Bates, H Huang, P Prasad, A E Vincent, Christian Frezza, Carlos Pardo-Hernández, Gabriel Balmus, Zoltán Takáts, John C Marioni, Angelo D'Alessandro, Michael P Murphy, Irina I Mohorianu, Stefano Pluchino
Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature (2024)
Austin D Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J Kunz, Linsey J Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J Q Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J Gomm, Valerie Speirs, J Louise Jones, John C Marioni, Walid T Khaled
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nature genetics 56 (4) (2024)
Luca Peruzzotti-Jametti, C M Willis, G Krzak, R Hamel, L Pirvan, Rosana-Bristena Ionescu, J A Reisz, Hiran A Prag, M E Garcia-Segura, V Wu, Y Xiang, B Barlas, Alva M Casey, A M R van den Bosch, Alexandra M Nicaise, L Roth, G R Bates, H Huang, P Prasad, A E Vincent, Christian Frezza, Carlos Pardo-Hernández, Gabriel Balmus, Zoltán Takáts, John C Marioni, Angelo D'Alessandro, Michael P Murphy, Irina I Mohorianu, Stefano Pluchino
Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature (2024)
Jasper Panten, Tobias Heinen, Christina Ernst, Nils Eling, Rebecca E Wagner, Maja Satorius, John C Marioni, Oliver Stegle, Duncan T Odom
The dynamic genetic determinants of increased transcriptional divergence in spermatids. Nature communications 15 (1) (2024)
Austin D Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J Kunz, Linsey J Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J Q Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J Gomm, Valerie Speirs, J Louise Jones, John C Marioni, Walid T Khaled
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nature genetics 56 (4) (2024)
Alsu Missarova, Emma Dann, Leah Rosen, Rahul Satija, John C Marioni
Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome biology 25 (1) (2024)
Stathis Megas, Valentina Lorenzi, John C Marioni
EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays. Genome biology 25 (1) (2024)
Luca Peruzzotti-Jametti, C M Willis, G Krzak, R Hamel, L Pirvan, Rosana-Bristena Ionescu, J A Reisz, Hiran A Prag, M E Garcia-Segura, V Wu, Y Xiang, B Barlas, Alva M Casey, A M R van den Bosch, Alexandra M Nicaise, L Roth, G R Bates, H Huang, P Prasad, A E Vincent, Christian Frezza, Carlos Pardo-Hernández, Gabriel Balmus, Zoltán Takáts, John C Marioni, Angelo D'Alessandro, Michael P Murphy, Irina I Mohorianu, Stefano Pluchino
Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature 628 (8006) (2024)
Jasper Panten, Tobias Heinen, Christina Ernst, Nils Eling, Rebecca E Wagner, Maja Satorius, John C Marioni, Oliver Stegle, Duncan T Odom
The dynamic genetic determinants of increased transcriptional divergence in spermatids. Nature communications 15 (1) (2024)
Luca Peruzzotti-Jametti, C M Willis, G Krzak, R Hamel, L Pirvan, Rosana-Bristena Ionescu, J A Reisz, Hiran A Prag, M E Garcia-Segura, V Wu, Y Xiang, B Barlas, Alva M Casey, A M R van den Bosch, Alexandra M Nicaise, L Roth, G R Bates, H Huang, P Prasad, A E Vincent, Christian Frezza, Carlos Pardo-Hernández, Gabriel Balmus, Zoltán Takáts, John C Marioni, Angelo D'Alessandro, Michael P Murphy, Irina I Mohorianu, Stefano Pluchino
Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature 628 (8006) (2024)
Austin D Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J Kunz, Linsey J Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J Q Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J Gomm, Valerie Speirs, J Louise Jones, John C Marioni, Walid T Khaled
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nature genetics (2024)
Jasper Panten, Tobias Heinen, Christina Ernst, Nils Eling, Rebecca E Wagner, Maja Satorius, John C Marioni, Oliver Stegle, Duncan T Odom
The dynamic genetic determinants of increased transcriptional divergence in spermatids. Nature communications 15 (1) (2024)
Austin D Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J Kunz, Linsey J Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J Q Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J Gomm, Valerie Speirs, J Louise Jones, John C Marioni, Walid T Khaled
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nature genetics 56 (4) (2024)
Stathis Megas, Valentina Lorenzi, John C Marioni
EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays. Genome biology 25 (1) (2024)
Francesca Nadalin, M J Marzi, M Pirra Piscazzi, Patricio Fuentes-Bravo, Simone Proccacia, M Climent, P Bonetti, C Rubolino, B Giuliani, Irene Papatheodorou, John C Marioni, Francesco Nicassio
Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution. Nature communications 15 (1) (2024)
Austin D Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J Kunz, Linsey J Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J Q Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J Gomm, Valerie Speirs, J Louise Jones, John C Marioni, Walid T Khaled
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nature genetics 56 (4) (2024)
Luca Peruzzotti-Jametti, C M Willis, G Krzak, R Hamel, L Pirvan, Rosana-Bristena Ionescu, J A Reisz, Hiran A Prag, M E Garcia-Segura, V Wu, Y Xiang, B Barlas, Alva M Casey, A M R van den Bosch, Alexandra M Nicaise, L Roth, G R Bates, H Huang, P Prasad, A E Vincent, Christian Frezza, Carlos Pardo-Hernández, Gabriel Balmus, Zoltán Takáts, John C Marioni, Angelo D'Alessandro, Michael P Murphy, Irina I Mohorianu, Stefano Pluchino
Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature 628 (8006) (2024)
Alsu Missarova, Emma Dann, Leah Rosen, Rahul Satija, John C Marioni
Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome biology 25 (1) (2024)
Stathis Megas, Valentina Lorenzi, John C Marioni
EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays. Genome biology 25 (1) (2024)
Issac Goh, Rachel Anne Botting, Antony Rose, Simone Webb, Justin Engelbert, Yorick Gitton, Emily Stephenson, Mariana Quiroga Londoño, Michael Mather, Nicole Mende, Iván Imaz-Rosshandler, Lu Yang, David Horsfall, Daniela Basurto-Lozada, Nana-Jane Chipampe, Victoria Rook, Jimmy Tsz Hang Lee, Mai-Linh Nu Ton, Daniel Keitley, Pavel V Mazin, M S Vijayabaskar, Rebecca Hannah, Laure Gambardella, Kile Green, Stephane Ballereau, Megumi Inoue, Elizabeth Tuck, Valentina Lorenzi, Kwasi Kwakwa, Clara Alsinet, Bayanne Olabi, Mohi Miah, Chloe Admane, Dorin-Mirel Popescu, Meghan Acres, David Dixon, Thomas Ness, Rowen Coulthard, Steven N Lisgo, Deborah J Henderson, Emma Dann, Chenqu Suo, Sarah J Kinston, Jong-Eun Park, Krzysztof Polański, John C Marioni, Stijn van Dongen, Kerstin B Meyer, Marella de Bruijn, James Palis, Sam Behjati, Elisa Laurenti, Nicola K Wilson, Roser Vento-Tormo, Alain Chédotal, Omer Ali Bayraktar, Irene Roberts, Laura Jardine, Berthold Göttgens, Sarah A Teichmann, Muzlifah A Haniffa
Yolk sac cell atlas reveals multiorgan functions during human early development. Science (New York, N.Y.) 381 (6659) (2023)
Bao Zhang, Peng He, John E G Lawrence, Shuaiyu Wang, Elizabeth Tuck, Brian A Williams, Kenny Roberts, Vitalii Kleshchevnikov, Lira Mamanova, Liam Bolt, Krzysztof Polański, Tong Li, Rasa Elmentaite, Eirini S Fasouli, Martin Prete, Xiaoling He, Nadav Yayon, Yixi Fu, Hao Yang, Chen Liang, Hui Zhang, Raphael Blain, Alain Chédotal, David R FitzPatrick, Helen Firth, Andrew Dean, Omer Ali Bayraktar, John C Marioni, Roger A Barker, Mekayla A Storer, Barbara J Wold, Hongbo Zhang, Sarah A Teichmann
A human embryonic limb cell atlas resolved in space and time. Nature (2023)
Emma Dann, Ana-Maria Cujba, Amanda J Oliver, Kerstin B Meyer, Sarah A Teichmann, John C Marioni
Precise identification of cell states altered in disease using healthy single-cell references. Nature genetics (2023)
Ran Wang, Xianfa Yang, Jiehui Chen, Lin Zhang, Jonathan A Griffiths, Guizhong Cui, Yingying Chen, Yun Qian, Guangdun Peng, Jinsong Li, Liantang Wang, John C Marioni, Patrick P L Tam, Naihe Jing
Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation. Nature communications 14 (1) (2023)
Mai-Linh Nu Ton, Daniel Keitley, Bart Theeuwes, Carolina Guibentif, Jonas Ahnfelt-Rønne, Thomas Kjærgaard Andreassen, Fernando J Calero-Nieto, Ivan Imaz-Rosshandler, Blanca Pijuan-Sala, Jennifer Nichols, Èlia Benito-Gutiérrez, John C Marioni, Berthold Göttgens
An atlas of rabbit development as a model for single-cell comparative genomics. Nature cell biology (2023)
Iván Imaz-Rosshandler, Christina Rode, Carolina Guibentif, Luke T G Harland, Mai-Linh Nu Ton, Parashar Dhapola, Daniel Keitley, Ricard Argelaguet, Fernando J Calero-Nieto, Jennifer Nichols, John C Marioni, Marella F T R de Bruijn, Berthold Göttgens
Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale. Development (Cambridge, England) (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Arianne C Richard, Claire Y Ma, John C Marioni, Gillian M Griffiths
Cytotoxic T lymphocytes require transcription for infiltration but not target cell lysis. EMBO reports (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Nadav Yayon, Veronika R Kedlian, Lena Boehme, Chenqu Suo, Brianna Wachter, Rebecca T Beuschel, Oren Amsalem, Krzysztof Polański, Simon Koplev, Elizabeth Tuck, Emma Dann, Jolien Van Hulle, Shani Perera, Tom Putteman, Alexander V Predeus, Monika Dabrowska, Laura Richardson, Catherine Tudor, Alexandra Y Kreins, Justin Engelbert, Emily Stephenson, Vitalii Kleshchevnikov, Fabrizio De Rita, David Crossland, Marita Bosticardo, Francesca Pala, Elena Prigmore, Nana-Jane Chipampe, Martin Prete, Lijiang Fei, Kendrick To, Roger A Barker, Xiaoling He, Filip Van Nieuwerburgh, Omer Bayraktar, Minal Patel, Graham E Davies, Muzlifah A Haniffa, Virginie Uhlmann, Luigi Daniele Notarangelo, Ronald N Germain, Andrea J Radtke, John C Marioni, Tom Taghon, Sarah A Teichmann
A spatial human thymus cell atlas mapped to a continuous tissue axis. bioRxiv : the preprint server for biology (2023)
Shila Ghazanfar, Carolina Guibentif, John C Marioni
Stabilized mosaic single-cell data integration using unshared features. Nature biotechnology (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Josephine L Barnes, Masahiro Yoshida, Peng He, Kaylee B Worlock, Rik G H Lindeboom, Chenqu Suo, Jan Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Krzysztof Polański, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T Herczeg, Romina Arzili, Robert Edward Hynds, Vitor H Teixeira, Muzlifah A Haniffa, Kyungtae Lim, Dawei Sun, Emma L Rawlins, Amanda J Oliver, Paul A Lyons, John C Marioni, Christiana Ruhrberg, Zewen Kelvin Tuong, Menna R Clatworthy, James L Reading, Samuel M Janes, Sarah A Teichmann, Kerstin B Meyer, Marko Z Nikolić
Early human lung immune cell development and its role in epithelial cell fate. Science immunology 8 (90) (2023)
Natushiko Kumasaka, Raghd Rostom, Ni Huang, Krzysztof Polański, Kerstin B Meyer, Sharad Patel, Rachel Boyd, Celine Gomez, Sam N Barnett, Nikolaos I Panousis, Jeremy Schwartzentruber, Maya Ghoussaini, Paul A Lyons, Fernando J Calero-Nieto, Berthold Göttgens, Josephine L Barnes, Kaylee B Worlock, Masahiro Yoshida, Marko Z Nikolić, Emily Stephenson, Gary Reynolds, Muzlifah A Haniffa, John C Marioni, Oliver Stegle, Tzachi Hagai, Sarah A Teichmann
Mapping interindividual dynamics of innate immune response at single-cell resolution. Nature genetics 55 (6) (2023)
Xionghui Lin, Benjamin Swedlund, Mai-Linh Nu Ton, Shila Ghazanfar, Carolina Guibentif, Catherine Paulissen, Elodie Baudelet, Elise Plaindoux, Younes Achouri, Emilie Calonne, Christine Dubois, William Mansfield, Stephane Zaffran, John C Marioni, Francois Fuks, Berthold Göttgens, Fabienne Lescroart, Cédric Blanpain
Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors. Nature cell biology 24 (7) (2022)
Chenqu Suo, Emma Dann, Issac Goh, Laura Jardine, Vitalii Kleshchevnikov, Jong-Eun Park, Rachel Anne Botting, Emily Stephenson, Justin Engelbert, Zewen Kelvin Tuong, Krzysztof Polański, Nadav Yayon, Chuan Xu, Ondrej Suchanek, Rasa Elmentaite, Cecilia Domínguez Conde, Peng He, Sophie Pritchard, Mohi Miah, Corina Moldovan, Alexander S Steemers, Pavel V Mazin, Martin Prete, David Horsfall, John C Marioni, Menna R Clatworthy, Muzlifah A Haniffa, Sarah A Teichmann
Mapping the developing human immune system across organs. Science (New York, N.Y.) 376 (6597) (2022)
Luke T G Harland, Claire S Simon, Anna D Senft, Ita Costello, Lucas Greder, Ivan Imaz-Rosshandler, Berthold Göttgens, John C Marioni, Elizabeth K Bikoff, Catherine Porcher, Marella F T R de Bruijn, Elizabeth J Robertson
The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors. Nature cell biology 23 (1) (2021)
Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael D Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natushiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis C S Gardner, Issac Goh, David Horsfall, Jim McGrath, Simone Webb, Michael William Mather, Rik G H Lindeboom, Emma Dann, Ni Huang, Krzysztof Polański, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Frederica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Samuel M Janes, Claire Mary Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Yu Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, null null, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolić, Christopher J A Duncan, Kenneth G C Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Göttgens, Muzlifah A Haniffa
Single-cell multi-omics analysis of the immune response in COVID-19. Nature medicine 27 (5) (2021)
Alsu Missarova, Jaison Jain, Andrew Butler, Shila Ghazanfar, Tim Stuart, Maigan Brusko, Clive Wasserfall, Harry Nick, Todd Brusko, Mark Atkinson, Rahul Satija, John C Marioni
geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq. Genome biology 22 (1) (2021)
Ricard Argelaguet, Anna S E Cuomo, Oliver Stegle, John C Marioni
Computational principles and challenges in single-cell data integration. Nature biotechnology 39 (10) (2021)
Rasa Elmentaite, Natushiko Kumasaka, Kenny Roberts, Aaron Fleming, Emma Dann, Hamish W King, Vitalii Kleshchevnikov, Monika Dabrowska, Sophie Pritchard, Liam Bolt, Sara F Vieira, Lira Mamanova, Ni Huang, Francesca Perrone, Issac Goh Kai'En, Steven N Lisgo, Matilda Katan, Steven Leonard, Thomas Richard William Oliver, C Elizabeth Hook, Komal Nayak, Lia S Campos, Cecilia Domínguez Conde, Emily Stephenson, Justin Engelbert, Rachel Anne Botting, Krzysztof Polański, Stijn van Dongen, Minal Patel, Michael D Morgan, John C Marioni, Omer Ali Bayraktar, Kerstin B Meyer, Xiaoling He, Roger A Barker, Hans Holm Uhlig, Krishnaa T A Mahbubani, Kourosh Saeb Parsy, Matthias Zilbauer, Menna R Clatworthy, Muzlifah A Haniffa, Kylie Renee James, Sarah A Teichmann
Cells of the human intestinal tract mapped across space and time. Nature 597 (7875) (2021)
Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer, Anja Füllgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti J Kundu, Shengbo Wang, Mathias Walzer, Laura Clarke, David Osumi-Sutherland, Marcela Karey Tello-Ruiz, Sunita Kumari, Doreen Ware, Jana Eliasova, Mark J Arends, Martijn C Nawijn, Kerstin Meyer, Tony Burdett, John C Marioni, Sarah Teichmann, Juan Antonio Vizcaino, Alvis Brazma, Irene Papatheodorou
Expression Atlas update: gene and protein expression in multiple species. Nucleic acids research (2021)
Can Aztekin, Tom W Hiscock, John Gurdon, Jerome Jullien, John C Marioni, Benjamin David Simons
Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs. Development (Cambridge, England) 148 (11) (2021)
T Lohoff, S Ghazanfar, A Missarova, N Koulena, N Pierson, Jonathan A Griffiths, E S Bardot, C-H L Eng, Richard C V Tyser, Ricard Argelaguet, Carolina Guibentif, Shankar Srinivas, James Briscoe, Benjamin David Simons, A-K Hadjantonakis, Berthold Göttgens, Juan I Garaycoechea, J Nichols, Long Cai, John C Marioni
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nature biotechnology (2021)
Anja Füllgrabe, Nancy George, Matthew Green, Parisa Nejad, Bruce J Aronow, Silvie Korena Fexova, Clay Fischer, Mallory Ann Freeberg, Laura Huerta, Norman Morrison, Richard H Scheuermann, Deanne M Taylor, Nicole A Vasilevsky, Laura Clarke, Nils Gehlenborg, Jim Kent, John C Marioni, Sarah A Teichmann, Alvis Brazma, Irene Papatheodorou
Guidelines for reporting single-cell RNA-seq experiments. Nature biotechnology 38 (12) (2021)
Richard C V Tyser, Ximena Ibarra-Soria, Katie McDole, Satish Arcot Jayaram, Jonathan Godwin, Teun A H van den Brand, Antonio M A Miranda, Antonio Scialdone, Philipp J Keller, John C Marioni, Shankar Srinivas
Characterization of a common progenitor pool of the epicardium and myocardium. Science (New York, N.Y.) 371 (6533) (2021)
Karol Nowicki-Osuch, Lizhe Zhuang, Sriganesh Jammula, Christopher W Bleaney, Krishnaa T A Mahbubani, Ginny Devonshire, Annalise Katz-Summercorn, Nils Eling, Anna Wilbrey-Clark, Elo Madissoon, John Gamble, Massimilliano di Pietro, Maria O'Donovan, Kerstin B Meyer, Kourosh Saeb Parsy, Andrew D Sharrocks, Sarah A Teichmann, John C Marioni, Rebecca C Fitzgerald
Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition. Science (New York, N.Y.) 373 (6556) (2021)
Julie Jerber, Daniel D Seaton, Anna S E Cuomo, Natushiko Kumasaka, James Haldane, Juliette Steer, Minal Patel, Daniel Pearce, Malin H L Andersson, Marc Jan Bonder, Ed Mountjoy, Maya Ghoussaini, Madeline A Lancaster, null null, John C Marioni, Florian T Merkle, Daniel J Gaffney, Oliver Stegle
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nature genetics 53 (3) (2021)
Emma Dann, Neil C Henderson, Sarah A Teichmann, Michael D Morgan, John C Marioni
Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nature biotechnology (2021)
Muzlifah A Haniffa, Deanne M Taylor, Sten Linnarsson, Bruce J Aronow, Gary D Baider, Roger A Barker, Pablo G Camara, J Gray Camp, Alain Chédotal, Andrew J Copp, Heather C Etchevers, Paolo Giacobini, Berthold Göttgens, Guoji Guo, Ania Hupalowska, Kylie R James, Emily Kirby, Arnold R Kriegstein, Joakim Lundeberg, John C Marioni, Kerstin B Meyer, Kathy K Niakan, Mats Nilsson, Bayanne Olabi, Dana Pe'er, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Rahul Satija, Sarah A Teichmann, Barbara Treutlein, Roser Vento-Tormo, Simone Webb, null null
A roadmap for the Human Developmental Cell Atlas. Nature 597 (7875) (2021)
Claire Y Ma, John C Marioni, Gillian M Griffiths, Arianne C Richard
Stimulation strength controls the rate of initiation but not the molecular organisation of TCR-induced signalling. eLife 9 (2020)
Nikolaus Rajewsky, Geneviève Almouzni, Stanislaw A Gorski, Stein Aerts, Bjørt K Kragesteen, Michela G Bertero, Christoph Bock, Annelien L Bredenoord, Giacomo Cavalli, Susanna Chiocca, Hans Clevers, Bart De Strooper, Angelika Eggert, Jan Ellenberg, Xosé M Fernández, Marek Figlerowicz, Susan M Gasser, Norbert Hübner, Jørgen Kjems, Jürgen Arthur Knoblich, Grietje Krabbe, Peter Lichter, Sten Linnarsson, Jean-Christophe Marine, John C Marioni, Marc A Marti-Renom, Mihai M Netea, Dörthe Nickel, Marcelo Nollmann, Halina R Novak, Helen Parkinson, Stefano Piccolo, Inês Pinheiro, Ana Pombo, Christian Popp, Juan I Garaycoechea, Sergio Roman-Roman, Philip Rosenstiel, Joachim L Schultze, Oliver Stegle, Amos Tanay, Giuseppe Testa, Dimitris Thanos, Fabian Joachim Theis, Maria-Elena Torres-Padilla, Alfonso Valencia, Céline Vallot, Alexander van Oudernaarden, Marie Vidal, Thierry Voet, null null
LifeTime and improving European healthcare through cell-based interceptive medicine. Nature 587 (7834) (2020)
Shila Ghazanfar, Yingxin Lin, Xian-Bin Su, David Ming Lin, Ellis Patrick, Ze-Guang Han, John C Marioni, Jean Yee Hwa Yang
Investigating higher-order interactions in single-cell data with scHOT. Nature methods 17 (8) (2020)
Michael D Morgan, Etienne Patin, Bernd Jagla, Milena Hasan, Lluis Quintana-Murci, John C Marioni
Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels. PLoS genetics 16 (3) (2020)
Jeanette Baran-Gale, Michael D Morgan, Stefano Maio, Fatima Dhalla, Irene Calvo-Asensio, Mary E Deadman, Adam E Handel, Ashley Maynard, Steven Chen, Foad Green, Rene V Sit, Norma F Neff, Spyros Darmanis, Weilun Tan, Andy P May, John C Marioni, Chris Paul Ponting, Georg A Hollander
Ageing compromises mouse thymus function and remodels epithelial cell differentiation. eLife 9 (2020)
Anna S E Cuomo, Daniel D Seaton, Davis J McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew J Knights, Kedar Nath Natrajan, null null, Ludovic Vallier, John C Marioni, Mariya Chhatriwala, Oliver Stegle
Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nature communications 11 (1) (2020)
Anna S E Cuomo, Daniel D Seaton, Davis J McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew J Knights, Kedar Nath Natrajan, null null, Ludovic Vallier, John C Marioni, Mariya Chhatriwala, Oliver Stegle
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nature communications 11 (1) (2020)
Can Aztekin, Tom W Hiscock, John C Marioni, J B Gurdon, Benjamin David Simons, Jerome Jullien
Identification of a regeneration-organizing cell in the Xenopus tail. Science (New York, N.Y.) 364 (6441) (2019)
Hung-Chang Chen, Nils Eling, Celia Pilar Martinez-Jimenez, Louise McNeill O'Brien, Valentina Carbonaro, John C Marioni, Duncan T Odom, Maike de la Roche
IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response. EMBO reports 20 (8) (2019)
Aaron T L Lun, Samantha Riesenfeld, Tallulah Andrews, The Phuong Dao, Tomas Gomes, null null, John C Marioni
EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome biology 20 (1) (2019)
Christina Ernst, Nils Eling, Celia Pilar Martinez-Jimenez, John C Marioni, Duncan T Odom
Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis. Nature communications 10 (1) (2019)
Nils Eling, Michael D Morgan, John C Marioni
Challenges in measuring and understanding biological noise. Nature reviews. Genetics 20 (9) (2019)
Luís R Saraiva, Fernando Riveros-McKay, Massimo Mezzavilla, Eman H Abou-Moussa, Charles J Arayata, Melanie Makhlouf, Casey Trimmer, Ximena Ibarra-Soria, Mona Khan, Laura Van Gerven, Mark Jorissen, Matthew Gibbs, Ciaran O'Flynn, Scott McGrane, Peter Mombaerts, John C Marioni, Joel D Mainland, Darren W Logan
A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans. Science advances 5 (7) (2019)
Arianne C Richard, Aaron T L Lun, Winnie W Y Lau, Berthold Göttgens, John C Marioni, Gillian M Griffiths
T cell cytolytic capacity is independent of initial stimulation strength. Nature immunology 19 (8) (2018)
Jonathan A Griffiths, Arianne C Richard, Karsten Bach, Aaron T L Lun, John C Marioni
Detection and removal of barcode swapping in single-cell RNA-seq data. Nature communications 9 (1) (2018)
Stephen J Clark, Ricard Argelaguet, Chantriolnt-Andreas Kapourani, Thomas M Stubbs, Heather J Lee, Celia Alda-Catalinas, Felix Krueger, Guido Sanguinetti, Gavin Kelsey, John C Marioni, Oliver Stegle, Wolf Reik
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nature communications 9 (1) (2018)
Christopher E Laumer, Harald Gruber-Vodicka, Michael G Hadfield, Vicki B Pearse, Ana Riesgo, John C Marioni, Gonzalo Giribet
Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias. eLife 7 (2018)
Jonathan A Griffiths, Antonio Scialdone, John C Marioni
Using single-cell genomics to understand developmental processes and cell fate decisions. Molecular systems biology 14 (4) (2018)
Konstantinos Tzelepis, Etienne De Braekeleer, Demetrios Aspris, Isaia Barbieri, M S Vijayabaskar, Wen-Hsin Liu, Malgorzata Gozdecka, Emmanouil Metzakopian, Hamish D Toop, Monika Dudek, Samuel C Robson, Francisco Hermida-Prado, Yu Hsuen Yang, Roya Babaei-Jadidi, Dimitrios A Garyfallos, Hannes Ponstingl, Joao M L Dias, Paolo Gallipoli, Michael Seiler, Silvia Buonamici, Binje Vick, Andrew J Bannister, Roland Rad, Rabinder K Prinjha, John C Marioni, Brian James Patrick Huntly, Jennifer Batson, Jonathan C Morris, Cristina Pina, Allan Bradley, Irmela Jeremias, David O Bates, Kosuke Yusa, Tony Kouzarides, George S Vassiliou
SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4. Nature communications 9 (1) (2018)
Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle
Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Molecular systems biology 14 (6) (2018)
Ximena Ibarra-Soria, Wajid Jawaid, Blanca Pijuan-Sala, Vasileios Ladopoulos, Antonio Scialdone, David J Jörg, Richard C V Tyser, Fernando J Calero-Nieto, Carla Mulas, Jennifer Nichols, Ludovic Vallier, Shankar Srinivas, Benjamin D Simons, Berthold Göttgens, John C Marioni
Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation. Nature cell biology 20 (2) (2018)
Jonathan A Griffiths, Antonio Scialdone, John C Marioni
Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data. BMC genomics 18 (1) (2017)
Kerstin Howe, Philipp H Schiffer, Julia Zielinski, Thomas Wiehe, Gavin K Laird, John C Marioni, Onuralp Soylemez, Fyodor Kondrashov, Maria Leptin
Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open biology 6 (4) (2016)