Uwe Ohler

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 31

Top Topics

Embryonic Stem Cells

Transcription Factor

Top Venues

Nature communications

Science immunology

Nucleic acids research

Nature structural & molecular biology

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

Publications

Pia Rautenstrauch, Uwe Ohler
Liam tackles complex multimodal single-cell data integration challenges. Nucleic acids research 52 (12) (2024)
Ioanna Tiniakou, Pei-Feng Hsu, Lorena S Lopez-Zepeda, Görkem Garipler, Eduardo Esteva, Nicholas M Adams, Geunhyo Jang, Chetna Soni, Colleen M Lau, Fan Liu, Alireza Khodadadi-Jamayran, Tori C Rodrick, Drew R Jones, Aristotelis Tsirigos, Uwe Ohler, Mark T Bedford, Stephen D Nimer, Vesa Kaartinen, Esteban Orlando Mazzoni, Boris Reizis
Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Science immunology 9 (94) (2024)
Ioanna Tiniakou, Pei-Feng Hsu, Lorena S Lopez-Zepeda, Görkem Garipler, Eduardo Esteva, Nicholas M Adams, Geunhyo Jang, Chetna Soni, Colleen M Lau, Fan Liu, Alireza Khodadadi-Jamayran, Tori C Rodrick, Drew R Jones, Aristotelis Tsirigos, Uwe Ohler, Mark T Bedford, Stephen D Nimer, Vesa Kaartinen, Esteban Orlando Mazzoni, Boris Reizis
Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Science immunology 9 (94) (2024)
Pia Rautenstrauch, Uwe Ohler
Liam tackles complex multimodal single-cell data integration challenges. Nucleic acids research (2024)
Ioanna Tiniakou, Pei-Feng Hsu, Lorena S Lopez-Zepeda, Görkem Garipler, Eduardo Esteva, Nicholas M Adams, Geunhyo Jang, Chetna Soni, Colleen M Lau, Fan Liu, Alireza Khodadadi-Jamayran, Tori C Rodrick, Drew R Jones, Aristotelis Tsirigos, Uwe Ohler, Mark T Bedford, Stephen D Nimer, Vesa Kaartinen, Esteban Orlando Mazzoni, Boris Reizis
Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Science immunology 9 (94) (2024)
Ioanna Tiniakou, Pei-Feng Hsu, Lorena S Lopez-Zepeda, Görkem Garipler, Eduardo Esteva, Nicholas M Adams, Geunhyo Jang, Chetna Soni, Colleen M Lau, Fan Liu, Alireza Khodadadi-Jamayran, Tori C Rodrick, Drew R Jones, Aristotelis Tsirigos, Uwe Ohler, Mark T Bedford, Stephen D Nimer, Vesa Kaartinen, Esteban Orlando Mazzoni, Boris Reizis
Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Science immunology 9 (94) (2024)
Pia Rautenstrauch, Uwe Ohler
Liam tackles complex multimodal single-cell data integration challenges. Nucleic acids research 52 (12) (2024)
Ioanna Tiniakou, Pei-Feng Hsu, Lorena S Lopez-Zepeda, Görkem Garipler, Eduardo Esteva, Nicholas M Adams, Geunhyo Jang, Chetna Soni, Colleen M Lau, Fan Liu, Alireza Khodadadi-Jamayran, Tori C Rodrick, Drew R Jones, Aristotelis Tsirigos, Uwe Ohler, Mark T Bedford, Stephen D Nimer, Vesa Kaartinen, Esteban Orlando Mazzoni, Boris Reizis
Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Science immunology 9 (94) (2024)
Pia Rautenstrauch, Uwe Ohler
Liam tackles complex multimodal single-cell data integration challenges. Nucleic acids research 52 (12) (2024)
Ioanna Tiniakou, Pei-Feng Hsu, Lorena S Lopez-Zepeda, Görkem Garipler, Eduardo Esteva, Nicholas M Adams, Geunhyo Jang, Chetna Soni, Colleen M Lau, Fan Liu, Alireza Khodadadi-Jamayran, Tori C Rodrick, Drew R Jones, Aristotelis Tsirigos, Uwe Ohler, Mark T Bedford, Stephen D Nimer, Vesa Kaartinen, Esteban Orlando Mazzoni, Boris Reizis
Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Science immunology 9 (94) (2024)
Ioanna Tiniakou, Pei-Feng Hsu, Lorena S Lopez-Zepeda, Görkem Garipler, Eduardo Esteva, Nicholas M Adams, Geunhyo Jang, Chetna Soni, Colleen M Lau, Fan Liu, Alireza Khodadadi-Jamayran, Tori C Rodrick, Drew R Jones, Aristotelis Tsirigos, Uwe Ohler, Mark T Bedford, Stephen D Nimer, Vesa Kaartinen, Esteban Orlando Mazzoni, Boris Reizis
Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Science immunology 9 (94) (2024)
Trevor M Nolan, Nemanja Vukašinović, Che-Wei Hsu, Jingyuan Zhang, Isabelle Vanhoutte, Rachel Shahan, Isaiah W Taylor, Laura Greenstreet, Matthieu Heitz, Anton Afanassiev, Ping Wang, Pablo Szekely, Aiden Brosnan, Yanhai Yin, Geoffrey Schiebinger, Uwe Ohler, Eugenia Russinova, Philip N Benfey
Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root. Science (New York, N.Y.) 379 (6639) (2023)
Trevor M Nolan, Nemanja Vukašinović, Che-Wei Hsu, Jingyuan Zhang, Isabelle Vanhoutte, Rachel Shahan, Isaiah W Taylor, Laura Greenstreet, Matthieu Heitz, Anton Afanassiev, Ping Wang, Pablo Szekely, Aiden Brosnan, Yanhai Yin, Geoffrey Schiebinger, Uwe Ohler, Eugenia Russinova, Philip N Benfey
Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root. Science (New York, N.Y.) 379 (6639) (2023)
Hsu-Min Sung, Johanna Schott, Philipp Drewe-Boss, Janina A Lehmann, Marius Roland Hardt, Doris Lindner, Joris Messens, Ivan Bogeski, Uwe Ohler, Georg Stoecklin
Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing. The Journal of cell biology 222 (12) (2023)
Anna Hendrika Cornelia Vlot, Setareh Maghsudi, Uwe Ohler
Cluster-independent marker feature identification from single-cell omics data using SEMITONES. Nucleic acids research 50 (18) (2022)
Jonathan M Mudge, Jorge Ruiz-Orera, John R Prensner, Marie A Brunet, Ferriol Calvet, Irwin Jungreis, Jose Manuel Gonzalez, Michele Magrane, Cholsoon Jang, Jana Felicitas Schulz, Yucheng T Yang, M Mar Albà, Julie L Aspden, Pavel V Baranov, Ariel Alejandro Bazzini, Elspeth A Bruford, Maria Jesus Martin, Lorenzo Calviello, Anne-Ruxandra Carvunis, Jin Chen, Juan Pablo Couso, Eric W Deutsch, Paul Flicek, Adam Frankish, Mark Gerstein, Norbert Hübner, Nicholas T Ingolia, Manolis Kellis, Gerben Menschaert, Robert L Moritz, Uwe Ohler, Xavier Roucou, Alan Saghatelian, Jonathan S Weissman, Sebastiaan van Heesch
Standardized annotation of translated open reading frames. Nature biotechnology 40 (7) (2022)
Dermot Harnett, Mateusz C Ambrozkiewicz, Ulrike Zinnall, Alexandra Rusanova, Ekaterina Borisova, Amelie N Drescher, Marta Couce-Iglesias, Gabriel Villamil, Rike Dannenberg, Koshi Imami, Agnieszka Münster-Wandowski, Beatrix Fauler, Thorsten Mielke, Matthias Selbach, Markus Landthaler, Christian M T Spahn, Victor Tarabykin, Uwe Ohler, Matthew L Kraushar
A critical period of translational control during brain development at codon resolution. Nature structural & molecular biology (2022)
Damir Baranasic, Matthias Hörtenhuber, Piotr J Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez Gonzalez, Nan Li, Joseph Wragg, Fabio M D'Orazio, Dorde Relic, Mikhail Pachkov, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus Stoiber, Michael X Dong, Irene Stevens, Samuel E Ross, Anne Eagle, Ryan Martin, Oluwapelumi Obasaju, Sepand Rastegar, Alison C McGarvey, Wolfgang Kopp, Emily V Chambers, Dennis Wang, Hyejeong R Kim, Rafael D Acemel, Silvia Naranjo, Maciej Łapiński, Vanessa Chong-Morrison, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carnici, Uwe Ohler, Scott Allen Lacadie, Jason W Sinclair, Cecilia Lanny Winata, Fredericus J M van Eeden, Juan M Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Erik van Nimwegen, Monte Westerfield, Fiona C Wardle, Carsten O Daub, Boris Lenhard, Ferenc Müller
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature genetics 54 (7) (2022)
Remo Monti, Pia Rautenstrauch, Mahsa Ghanbari, Alva Rani James, Matthias Kirchler, Uwe Ohler, Stefan Konigorski, Christoph Lippert
Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes. Nature communications 13 (1) (2022)
Karoline Holler, Anika Neuschulz, Philipp Drewe-Boß, Janita Mintcheva, Bastiaan Spanjaard, Roberto Arsiè, Uwe Ohler, Markus Landthaler, Jan Philipp Junker
Spatio-temporal mRNA tracking in the early zebrafish embryo. Nature communications 12 (1) (2021)
Henriette Miko, Yunjiang Qiu, Bjoern Gaertner, Maike Sander, Uwe Ohler
Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data. BMC genomics 22 (1) (2021)
Lina Worpenberg, Chiara Paolantoni, Sara Longhi, Miriam M Mulorz, Tina Lence, Hans-Hermann Wessels, Erik Dassi, Giuseppe Aiello, F X Reymond Sutandy, Marion Scheibe, Raghu R Edupuganti, Anke Busch, Martin M Möckel, Michiel Vermeulen, Falk Butter, Julian König, Michela Notarangelo, Uwe Ohler, Christoph Dieterich, Alessandro Quattrone, Alessia Soldano, Jean-Yves Roignant
Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. The EMBO journal 40 (4) (2021)
Chloe Chong, Markus Müller, HuiSong Pak, Dermot Harnett, Florian Huber, Delphine Grun, Marion Leleu, Aymeric Auger, Marion Arnaud, Brian J Stevenson, Justine Michaux, Ilija Bilic, Antje Hirsekorn, Lorenzo Calviello, Laia Simó-Riudalbas, Evarist Planet, Jan Lubiński, Marta Bryśkiewicz, Maciej Wiznerowicz, Ioannis Xenarios, Lin Zhang, Didier Trono, Alexandre Harari, Uwe Ohler, Sergio A Quezada, Michal Bassani-Sternberg
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Nature communications 11 (1) (2020)
Wolfgang Kopp, Remo Monti, Annalaura Tamburrini, Uwe Ohler, Altuna Akalin
Deep learning for genomics using Janggu. Nature communications 11 (1) (2020)
Lorenzo Calviello, Antje Hirsekorn, Uwe Ohler
Quantification of translation uncovers the functions of the alternative transcriptome. Nature structural & molecular biology 27 (8) (2020)
Hans-Hermann Wessels, Svetlana Lebedeva, Antje Hirsekorn, Ricardo Wurmus, Altuna Akalin, Neelanjan Mukherjee, Uwe Ohler
Global identification of functional microRNA-mRNA interactions in Drosophila. Nature communications 10 (1) (2019)
Erika C Urdaneta, Carlos H Vieira-Vieira, Timon Hick, Hans-Herrmann Wessels, Davide Figini, Rebecca Moschall, Jan Medenbach, Uwe Ohler, Sander Granneman, Matthias Selbach, Benedikt M Beckmann
Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nature communications 10 (1) (2019)
Aslıhan Karabacak Calviello, Antje Hirsekorn, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler
Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling. Genome biology 20 (1) (2019)
Mahmoud M Ibrahim, Aslihan Karabacak, Alexander Glahs, Ena Kolundzic, Antje Hirsekorn, Alexa Carda, Baris Tursun, Robert P Zinzen, Scott A Lacadie, Uwe Ohler
Determinants of promoter and enhancer transcription directionality in metazoans. Nature communications 9 (1) (2018)
Alessandra Zappulo, David van den Bruck, Camilla Ciolli Mattioli, Vedran Franke, Koshi Imami, Erik McShane, Mireia Moreno-Estelles, Lorenzo Calviello, Andrei Filipchyk, Esteban Peguero-Sanchez, Thomas Müller, Andrew Woehler, Carmen Birchmeier, Enrique Merino, Nikolaus Rajewsky, Uwe Ohler, Esteban O Mazzoni, Matthias Selbach, Altuna Akalin, Marina Chekulaeva
RNA localization is a key determinant of neurite-enriched proteome. Nature communications 8 (1) (2017)
Neelanjan Mukherjee, Lorenzo Calviello, Antje Hirsekorn, Stefano de Pretis, Mattia Pelizzola, Uwe Ohler
Integrative classification of human coding and noncoding genes through RNA metabolism profiles. Nature structural & molecular biology 24 (1) (2016)