Oliver Stegle
Active 2008–2026
- 185
- Papers
- 49,354
- Citations
- 91
- h-index
- 159
- i10-index
Citations
Citation sources
Countries
Institutions
- Harvard University1.2%
- Broad Institute0.8%
- University of Cambridge0.8%
- Stanford University0.7%
- Wellcome Sanger Institute0.6%
- Howard Hughes Medical Institute0.5%
- Other95.4%
Fields
- Biochemistry, Genetics and Molecular Biology66.1%
- Medicine14.3%
- Computer Science4.9%
- Agricultural and Biological Sciences4.4%
- Immunology and Microbiology3.6%
- Neuroscience2%
- Other4.7%
Topics
- Single-cell and spatial transcriptomics9.4%
- Gene expression and cancer classification3.5%
- Epigenetics and DNA Methylation3.1%
- Bioinformatics and Genomic Networks3%
- Genetic Associations and Epidemiology2.7%
- Cell Image Analysis Techniques2.5%
- Other75.8%
Coauthors
- Marc Jan Bonder24
- John C. Marioni16
- Davis J. McCarthy14
- Francesco Paolo Casale13
- Sarah A. Teichmann13
- Christoph Lippert12
- Wolf Reik12
- Karsten M. Borgwardt10
- Britta Velten9
- Daniel D. Seaton8
- Danila Bredikhin8
- Felix Krueger8
- Florian Buettner8
- Leopold Parts8
- Ricard Argelaguet8
- Richard Durbin8
- Damien Arnol7
- Ewan Birney7
- Gavin Kelsey7
- Karsten Borgwardt7
- Minal Patel7
- Moritz Gerstung7
- Stephen J. Clark7
- André Kahles6
All papers
- Cell2location maps fine-grained cell types in spatial transcriptomics
Authors: Vitalii Kleshchevnikov, Artem Shmatko, Emma Dann, Alexander Aivazidis, Hamish W. King, Tong Li, Rasa Elmentaite, Artem Lomakin, Veronika R. Kedlian, Adam Gayoso, Mika Sarkin Jain, Jun Sung Park, Lauma Ramona, Elizabeth Tuck, Anna Arutyunyan, Roser Vento‐Tormo, Moritz Gerstung, Louisa K. James, Oliver Stegle, Omer Ali Bayraktar - Nature Biotechnology 2022 cited by 1,235
- The Human Cell Atlas
Authors: Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed Lein, Sten Linnarsson, Emma Lundberg, Joakim Lundeberg, Partha Majumder, John C Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe'er, Anthony Phillipakis, Chris P Ponting, Stephen Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua Sanes, Rahul Satija, Ton N Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W Shin, Oliver Stegle, Michael Stratton, Michael J T Stubbington, Fabian J Theis, Matthias Uhlen, Alexander van Oudenaarden, Allon Wagner, Fiona Watt, Jonathan Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, Human Cell Atlas Meeting Participants - eLife 2017 cited by 2,352
- Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets
Authors: Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C. Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle - Molecular Systems Biology 2018 cited by 1,459
- MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data
Authors: Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni, Oliver Stegle - Genome biology 2020 cited by 1,007
- Eleven grand challenges in single-cell data science
Authors: David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan‐Otto Attolini, Samuel Aparício, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M. Kiełbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion Măndoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Alicja Rączkowska, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth - Genome biology 2020 cited by 1,429
- SpatialDE: identification of spatially variable genes
Authors: Valentine Svensson, Sarah A. Teichmann, Oliver Stegle - Nature Methods 2018 cited by 797
- Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Authors: Peter Ebert, Peter A. Audano, Qihui Zhu, Bernardo Rodríguez–Martín, David Porubskỳ, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari, Feyza Yilmaz, Xuefang Zhao, PingHsun Hsieh, Joyce Lee, Sushant Kumar, Jiadong Lin, Tobias Rausch, Yu Chen, Jingwen Ren, Martín Santamarina, Wolfram Höps, Hufsah Ashraf, Nelson T. Chuang, Xiaofei Yang, Katherine M. Munson, Alexandra P. Lewis, Susan Fairley, Luke J. Tallon, Wayne E. Clarke, Anna O. Basile, Marta Byrska-Bishop, André Corvelo, Uday S. Evani, Tsung-Yu Lu, Mark Chaisson, Junjie Chen, Chong Li, Harrison Brand, Aaron M. Wenger, Maryam Ghareghani, William T. Harvey, Benjamin Raeder, Patrick Hasenfeld, Allison Regier, Haley Abel, Ira M. Hall, Paul Flicek, Oliver Stegle, Mark Gerstein, José M. C. Tubío, Zepeng Mu, Yang Li, Xinghua Shi, Alex Hastie, Kai Ye, Zechen Chong, Ashley D. Sanders, Michael C. Zody, Michael E. Talkowski, Ryan E. Mills, Scott E. Devine, Charles Lee, Jan O. Korbel, Tobias Marschall, Evan E. Eichler - Science 2021 cited by 816
- An integrated map of structural variation in 2,504 human genomes
Authors: Peter H. Sudmant, Tobias Rausch, Eugene J. Gardner, Robert E. Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz, Miriam K. Konkel, Ankit Malhotra, Adrian M. Stütz, Xinghua Shi, Francesco Paolo Casale, Jieming Chen, Fereydoun Hormozdiari, Gargi Dayama, Ken Chen, Maika Malig, Mark Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y. K. Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter S. Chines, Zechen Chong, Laura Clarke, Elif Dal, Li Ding, Sarah B. Emery, Xian Fan, Madhusudan Gujral, Fatma Kahveci, Jeffrey M. Kidd, Yu Kong, Eric-Wubbo Lameijer, Shane McCarthy, Paul Flicek, Richard A. Gibbs, Gábor Marth, Christopher E. Mason, Androniki Menelaou, Donna M. Muzny, Bradley J. Nelson, Amina Noor, Nicholas F. Parrish, Matthew Pendleton, Andrew Quitadamo, Benjamin Raeder, Eric E. Schadt, Mallory Romanovitch, Andreas Schlattl, Robert Sebra, Andrey A. Shabalin, Andreas Untergasser, Jerilyn A. Walker, Min Wang, Fuli Yu, Chengsheng Zhang, Jing Zhang, Xiangqun Zheng-Bradley, Wanding Zhou, Thomas Zichner, Jonathan Sebat, Mark A. Batzer, Steven A. McCarroll, Ryan E. Mills, Mark Gerstein, Ali Bashir, Oliver Stegle, Scott E. Devine, Charles Lee, Evan E. Eichler, Jan O. Korbel - Nature 2015 cited by 2,695
- Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
Authors: André Kahles, Kjong-Van Lehmann, Nora C. Toussaint, Matthias Hüser, Stefan G. Stark, Timo Sachsenberg, Oliver Stegle, Oliver Kohlbacher, Chris Sander, Rory Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy Defreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila M. Reynolds, Ilya Shmulevich, Vésteinn Thórsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael T. Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Galen F. Gao, Benjamin E. Gross, Zachary Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah Phillips, Ed Reznik, Francisco Sánchez-Vega, Chris Sander, Nikolaus Schultz, Robert E. Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto and 635 more - Cancer Cell 2018 cited by 962
- Computational principles and challenges in single-cell data integration
Authors: Ricard Argelaguet, Anna Cuomo, Oliver Stegle, John C. Marioni - Nature Biotechnology 2021 cited by 489
- Deep learning for computational biology
Authors: Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle - Molecular Systems Biology 2016 cited by 1,530
- The scverse project provides a computational ecosystem for single-cell omics data analysis
Authors: Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Philipp Angerer, Volker Bergen, Pierre Boyeau, Maren Büttner, Gökçen Eraslan, David S. Fischer, Max Frank, Justin Hong, Michal Klein, Marius Lange, Romain Lopez, Mohammad Lotfollahi, Malte D. Luecken, Fidel Ramírez, Jeffrey Regier, Sergei Rybakov, Anna C. Schaar, Valeh Valiollah Pour Amiri, Philipp Weiler, Galen Xing, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, Fabian J. Theis - Nature Biotechnology 2023 cited by 343
- The Polygenic and Monogenic Basis of Blood Traits and Diseases
Authors: Dragana Vuckovic, Erik L. Bao, Parsa Akbari, Caleb A. Lareau, Abdou Mousas, Tao Jiang, Ming‐Huei Chen, Laura M. Raffield, Manuel Tardáguila, Jennifer E. Huffman, Scott C. Ritchie, Karyn Mégy, Hannes Ponstingl, Christopher J. Penkett, Patrick K. Albers, Emilie M. Wigdor, Saori Sakaue, Arden Moscati, Regina Manansala, Ken Sin Lo, Huijun Qian, Masato Akiyama, Traci M. Bartz, Yoav Ben‐Shlomo, Andrew D Beswick, Jette Bork‐Jensen, Erwin P. Böttinger, Jennifer A. Brody, Frank J.A. van Rooij, Kumaraswamy Naidu Chitrala, Peter W.F. Wilson, Hélène Choquet, John Danesh, Emanuele Di Angelantonio, Niki Dimou, Jingzhong Ding, Paul Elliott, Tõnu Esko, Michele K. Evans, Stephan B. Felix, James S. Floyd, Linda Broer, Niels Grarup, Michael H. Guo, Qi Guo, Andreas Greinacher, Jeff Haessler, Torben Hansen, Joanna M. M. Howson, Wei Huang, Eric Jorgenson, Tim Kacprowski, Mika Kähönen, Yoichiro Kamatani, Masahiro Kanai, Savita Karthikeyan, Fotios Koskeridis, Leslie A. Lange, Terho Lehtimäki, Allan Linneberg, Yongmei Liu, Leo‐Pekka Lyytikäinen, Ani Manichaikul, Koichi Matsuda, Karen L. Mohlke, Nina Mononen, Yoshinori Murakami, Girish N. Nadkarni, Kjell Nikus, Nathan Pankratz, Oluf Pedersen, Michael Preuß, Bruce M. Psaty, Olli T. Raitakari, Stephen S. Rich, Blanca Rodríguez, Jonathan D. Rosen, Jerome I. Rotter, Petra Schubert, Cassandra N. Spracklen, Praveen Surendran, Hua Tang, Jean‐Claude Tardif, Mohsen Ghanbari, Uwe Völker, Henry Völzke, Nicholas A. Watkins, Stefan Weiß, Na Cai, Kousik Kundu, Stephen B. Watt, Klaudia Walter, Alan B. Zonderman, Kelly Cho, Yun Li, Ruth J. F. Loos, Julian C. Knight, Michel Georges, Oliver Stegle, Εvangelos Εvangelou and 12 more - Cell 2020 cited by 756
- Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
Authors: Oliver Stegle, Leopold Parts, Matias Piipari, John Winn, Richard Durbin - Nature Protocols 2012 cited by 1,264
- Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
Authors: Sébastien A. Smallwood, Heather Lee, Christof Angermueller, Felix Krueger, Heba Saadeh, Julian R. Peat, Simon Andrews, Oliver Stegle, Wolf Reik, Gavin Kelsey - Nature Methods 2014 cited by 1,205
- Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
Authors: Yuanhua Huang, Davis J. McCarthy, Oliver Stegle - Genome biology 2019 cited by 390
- Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
Authors: Elisabetta Mereu, Atefeh Lafzi, Cátia Moutinho, Christoph Ziegenhain, Davis J. McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Sagar, Dominic Grün, Julia K. Lau, Stéphane C. Boutet, Chad Sanada, Aik T. Ooi, Robert C. Jones, Kelly A. Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Caroline Braeuning, Cornelius Fischer, Sascha Sauer, Timo B. Trefzer, Christian Conrad, Xian Adiconis, Lan Nguyễn, Aviv Regev, Joshua Z. Levin, Swati Parekh, Aleksandar Janjic, Lucas E. Wange, Johannes Bagnoli, Wolfgang Enard, Marta Gut, Rickard Sandberg, Itoshi Nikaido, Marta Gut, Oliver Stegle, Holger Heyn - Nature Biotechnology 2020 cited by 533
- Computational and analytical challenges in single-cell transcriptomics
Authors: Oliver Stegle, Sarah A. Teichmann, John C. Marioni - Nature Reviews Genetics 2015 cited by 1,320
- A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
Authors: Elo Madissoon, Amanda J. Oliver, Vitalii Kleshchevnikov, Anna Wilbrey-Clark, Krzysztof Polański, Nathan Richoz, Ana Elisa Ribeiro Orsi, Lira Mamanova, Liam Bolt, Rasa Elmentaite, J. Patrick Pett, Ni Huang, Chuan Xu, Peng He, Monika Dabrowska, Sophie Pritchard, Elizabeth Tuck, Elena Prigmore, Shani Perera, Andrew Knights, Ágnes Oszlánczi, Adam Hunter, Sara F. Vieira, Minal Patel, Rik G.H. Lindeboom, Lia S. Campos, Kazuhiko Matsuo, Takashi Nakayama, Masahiro Yoshida, Kaylee B. Worlock, Marko Nikolić, Nikitas Georgakopoulos, Krishnaa T. Mahbubani, Kourosh Saeb‐Parsy, Omer Ali Bayraktar, Menna R. Clatworthy, Oliver Stegle, Natsuhiko Kumasaka, Sarah A. Teichmann, Kerstin B. Meyer - Nature Genetics 2022 cited by 220
- Transcriptome and genome sequencing uncovers functional variation in humans
Authors: Tuuli Lappalainen, Michael Sammeth, Marc R. Friedländer, Peter A.C. ’t Hoen, Jean Monlong, Manuel A. Rivas, Mar Gonzàlez-Porta, Natalja Kurbatova, Thasso Griebel, Pedro G. Ferreira, Matthias Barann, Thomas Wieland, Liliana Greger, Maarten van Iterson, Jonas Carlsson Almlöf, Paolo Ribeca, Irina Pulyakhina, Daniela Esser, Thomas Giger, Andrew Tikhonov, Marc Sultan, Gabrielle Bertier, Daniel G. MacArthur, Monkol Lek, Esther Lizano, Henk P.J. Buermans, Ismaël Padioleau, Thomas Schwarzmayr, Olof Karlberg, Halit Ongen, Helena Kilpinen, Sergi Beltrán, Marta Gut, Katja Kahlem, Vyacheslav Amstislavskiy, Oliver Stegle, Matti Pirinen, Stephen B. Montgomery, Peter Donnelly, Mark I. McCarthy, Paul Flicek, Tim M. Strom, Hans Lehrach, Stefan Schreiber, Ralf Sudbrak, Ãngel Carracedo, Stylianos E. Antonarakis, Robert Häsler, Ann‐Christine Syvänen, Gert‐Jan B. van Ommen, Alvis Brāzma, Thomas Meitinger, Philip Rosenstiel, Roderic Guigó, Marta Gut, Xavier Estivill, Emmanouil T. Dermitzakis - Nature 2013 cited by 2,195
- Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
Authors: Florian Buettner, Kedar Nath Natarajan, Francesco Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J. Theis, Sarah A. Teichmann, John C. Marioni, Oliver Stegle - Nature Biotechnology 2015 cited by 1,300
- Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
Authors: Biola M. Javierre, Oliver S. Burren, Steven P. Wilder, Roman Kreuzhuber, Steven M. Hill, Sven Sewitz, Jonathan Cairns, Steven Wingett, Csilla Várnai, Michiel J. Thiecke, Frances Burden, Samantha Farrow, Antony J. Cutler, Karola Rehnström, Kate Downes, Luigi Grassi, Myrto Kostadima, Paula Freire-Pritchett, Fan Wang, Hendrik G. Stunnenberg, John A. Todd, Daniel R. Zerbino, Oliver Stegle, Willem H. Ouwehand, Mattia Frontini, Chris Wallace, Mikhail Spivakov, Peter Fraser, Joost H.A. Martens, Bowon Kim, Nilofar Sharifi, Eva M. Janssen‐Megens, Marie‐Laure Yaspo, Matthias Linser, Alexander Kovacsovics, Laura Clarke, David Richardson, Avik Datta, Paul Flicek - Cell 2016 cited by 1,192
- Spatial multiomics map of trophoblast development in early pregnancy
Authors: Anna Arutyunyan, Kenny Roberts, Kevin Troulé, Frederick C.K. Wong, Megan A. Sheridan, Ilia Kats, Luz García‐Alonso, Britta Velten, Regina Hoo, Elias R. Ruiz-Morales, Carmen Sancho‐Serra, Jarrod Shilts, Louis‐François Handfield, Luca Marconato, Elizabeth Tuck, Lucy Gardner, Cecilia Mazzeo, Qian Li, Iva Kelava, Gavin J. Wright, Elena Prigmore, Sarah A. Teichmann, Omer Ali Bayraktar, Ashley Moffett, Oliver Stegle, Margherita Y. Turco, Roser Vento‐Tormo - Nature 2023 cited by 292
- Multi-omics profiling of mouse gastrulation at single-cell resolution
Authors: Ricard Argelaguet, Stephen J. Clark, Hisham Mohammed, L. Carine Stapel, Christel Krueger, Chantriolnt-Andreas Kapourani, Iván Imaz-Rosshandler, Tim Lohoff, Yunlong Xiang, Courtney W. Hanna, Sébastien A. Smallwood, Ximena Ibarra-Soria, Florian Buettner, Guido Sanguinetti, Wei Xie, Felix Krueger, Berthold Göttgens, Peter J. Rugg‐Gunn, Gavin Kelsey, Wendy Dean, Jennifer Nichols, Oliver Stegle, John C. Marioni, Wolf Reik - Nature 2019 cited by 516
