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ArticlesPeer ReviewedFull Text
Deep learning for genomics using Janggu
Author / Creator:Kopp, Wolfgang ; Monti, Remo ; Tamburrini, Annalaura ; Ohler, Uwe ; Akalin, Altuna
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-07, Vol.11 (1), p.3488-3488, Article 3488
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Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells
Author / Creator:Kim, Minchul ; Franke, Vedran ; Brandt, Bettina ; Lowenstein, Elijah D. ; Schöwel, Verena ; Spuler, Simone ; Akalin, Altuna ; Birchmeier, Carmen
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-12, Vol.11 (1), p.6375-14, Article 6375
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netSmooth: Network-smoothing based imputation for single cell RNA-seq
Author / Creator:Ronen, Jonathan ; Akalin, Altuna
Publisher:London: Faculty of 1000 Ltd
Journal title:F1000 research, 2018-01, Vol.7, p.8-8
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Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation
Author / Creator:Baubec, Tuncay ; Colombo, Daniele F. ; Wirbelauer, Christiane ; Schmidt, Juliane ; Burger, Lukas ; Krebs, Arnaud R. ; Akalin, Altuna ; Schübeler, Dirk
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2015-04, Vol.520 (7546), p.243-247
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Identifying tumor cells at the single-cell level using machine learning
Author / Creator:Dohmen, Jan ; Baranovskii, Artem ; Ronen, Jonathan ; Uyar, Bora ; Franke, Vedran ; Akalin, Altuna
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2022-05, Vol.23 (1), p.123-123, Article 123
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scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data
Author / Creator:Jeong, Yunhee ; Ronen, Jonathan ; Kopp, Wolfgang ; Lutsik, Pavlo ; Akalin, Altuna
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2024-08, Vol.25 (1), p.257-22, Article 257
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Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program
Author / Creator:Wyler, Emanuel ; Franke, Vedran ; Menegatti, Jennifer ; Kocks, Christine ; Boltengagen, Anastasiya ; Praktiknjo, Samantha ; Walch-Rückheim, Barbara ; Bosse, Jens ; Rajewsky, Nikolaus ; Grässer, Friedrich ; Akalin, Altuna ; Landthaler, Markus
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-10, Vol.10 (1), p.4878-14, Article 4878
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Global identification of functional microRNA-mRNA interactions in Drosophila
Author / Creator:Wessels, Hans-Hermann ; Lebedeva, Svetlana ; Hirsekorn, Antje ; Wurmus, Ricardo ; Akalin, Altuna ; Mukherjee, Neelanjan ; Ohler, Uwe
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-04, Vol.10 (1), p.1626-1626, Article 1626
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Leveraging large language models for data analysis automation
Author / Creator:Jansen, Jacqueline A ; Manukyan, Artür ; Al Khoury, Nour ; Akalin, Altuna
Publisher:United States: Public Library of Science
Journal title:PloS one, 2025-02, Vol.20 (2), p.e0317084
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Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning
Author / Creator:Kopp, Wolfgang ; Akalin, Altuna ; Ohler, Uwe
Publisher:London: Nature Publishing Group UK
Journal title:Nature machine intelligence, 2022-02, Vol.4 (2), p.162-168
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PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC
Author / Creator:Appel, Lisa-Marie ; Franke, Vedran ; Bruno, Melania ; Grishkovskaya, Irina ; Kasiliauskaite, Aiste ; Kaufmann, Tanja ; Schoeberl, Ursula E. ; Puchinger, Martin G. ; Kostrhon, Sebastian ; Ebenwaldner, Carmen ; Sebesta, Marek ; Beltzung, Etienne ; Mechtler, Karl ; Lin, Gen ; Vlasova, Anna ; Leeb, Martin ; Pavri, Rushad ; Stark, Alexander ; Akalin, Altuna ; Stefl, Richard ; Bernecky, Carrie ; Djinovic-Carugo, Kristina ; Slade, Dea
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-10, Vol.12 (1), p.6078-24, Article 6078
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RNA localization is a key determinant of neurite-enriched proteome
Author / Creator:Zappulo, Alessandra ; van den Bruck, David ; Ciolli Mattioli, Camilla ; Franke, Vedran ; Imami, Koshi ; McShane, Erik ; Moreno-Estelles, Mireia ; Calviello, Lorenzo ; Filipchyk, Andrei ; Peguero-Sanchez, Esteban ; Müller, Thomas ; Woehler, Andrew ; Birchmeier, Carmen ; Merino, Enrique ; Rajewsky, Nikolaus ; Ohler, Uwe ; Mazzoni, Esteban O. ; Selbach, Matthias ; Akalin, Altuna ; Chekulaeva, Marina
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2017-09, Vol.8 (1), p.583-13, Article 583
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Pathogenic mutations of human phosphorylation sites affect protein–protein interactions
Author / Creator:Rrustemi, Trendelina ; Meyer, Katrina ; Roske, Yvette ; Uyar, Bora ; Akalin, Altuna ; Imami, Koshi ; Ishihama, Yasushi ; Daumke, Oliver ; Selbach, Matthias
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-04, Vol.15 (1), p.3146-3146, Article 3146
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Predicting lethal courses in critically ill COVID-19 patients using a machine learning model trained on patients with non-COVID-19 viral pneumonia
Author / Creator:Lichtner, Gregor ; Balzer, Felix ; Haufe, Stefan ; Giesa, Niklas ; Schiefenhövel, Fridtjof ; Schmieding, Malte ; Jurth, Carlo ; Kopp, Wolfgang ; Akalin, Altuna ; Schaller, Stefan J. ; Weber-Carstens, Steffen ; Spies, Claudia ; von Dincklage, Falk
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2021-06, Vol.11 (1), p.13205-13205, Article 13205
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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
Author / Creator:Akalin, Altuna ; Kormaksson, Matthias ; Li, Sheng ; Garrett-Bakelman, Francine E ; Figueroa, Maria E ; Melnick, Ari ; Mason, Christopher E
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology (Online Edition), 2012-10, Vol.13 (10), p.R87-R87, Article R87
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The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators
Author / Creator:Appel, Lisa-Marie ; Franke, Vedran ; Benedum, Johannes ; Grishkovskaya, Irina ; Strobl, Xué ; Polyansky, Anton ; Ammann, Gregor ; Platzer, Sebastian ; Neudolt, Andrea ; Wunder, Anna ; Walch, Lena ; Kaiser, Stefanie ; Zagrovic, Bojan ; Djinovic-Carugo, Kristina ; Akalin, Altuna ; Slade, Dea
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-01, Vol.14 (1), p.166-22, Article 166
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The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation
Author / Creator:Benedum, Johannes ; Franke, Vedran ; Appel, Lisa-Marie ; Walch, Lena ; Bruno, Melania ; Schneeweiss, Rebecca ; Gruber, Juliane ; Oberndorfer, Helena ; Frank, Emma ; Strobl, Xué ; Polyansky, Anton ; Zagrovic, Bojan ; Akalin, Altuna ; Slade, Dea
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-11, Vol.14 (1), p.7912-7912, Article 7912
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Two independent transcription initiation codes overlap on vertebrate core promoters
Author / Creator:Haberle, Vanja ; Li, Nan ; Hadzhiev, Yavor ; Plessy, Charles ; Previti, Christopher ; Nepal, Chirag ; Gehrig, Jochen ; Dong, Xianjun ; Akalin, Altuna ; Suzuki, Ana Maria ; van IJcken, Wilfred F. J. ; Armant, Olivier ; Ferg, Marco ; Strähle, Uwe ; Carninci, Piero ; Müller, Ferenc ; Lenhard, Boris
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2014-03, Vol.507 (7492), p.381-385
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Herpesviruses mimic zygotic genome activation to promote viral replication
Author / Creator:Neugebauer, Eva ; Walter, Stephanie ; Tan, Jiang ; Drayman, Nir ; Franke, Vedran ; van Gent, Michiel ; Pennisi, Sandra ; Veratti, Pia ; Stein, Karla S. ; Welker, Isabelle ; Tay, Savaş ; Verjans, Georges M. G. M. ; Timmers, H. T. Marc ; Akalin, Altuna ; Landthaler, Markus ; Ensser, Armin ; Wyler, Emanuel ; Full, Florian
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-01, Vol.16 (1), p.710-15, Article 710
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Publisher Correction: Herpesviruses mimic zygotic genome activation to promote viral replication
Author / Creator:Neugebauer, Eva ; Walter, Stephanie ; Tan, Jiang ; Drayman, Nir ; Franke, Vedran ; van Gent, Michiel ; Pennisi, Sandra ; Veratti, Pia ; Stein, Karla S. ; Welker, Isabelle ; Tay, Savaş ; Verjans, Georges M. G. M. ; Timmers, H. T. Marc ; Akalin, Altuna ; Landthaler, Markus ; Ensser, Armin ; Wyler, Emanuel ; Full, Florian
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-03, Vol.16 (1), p.2211-1, Article 2211
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Showing 1 to 20 of 65 results

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Deep learning for genomics using Janggu

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Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells

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netSmooth: Network-smoothing based imputation for single cell RNA-seq

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Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

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Identifying tumor cells at the single-cell level using machine learning

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scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data

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Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program

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Global identification of functional microRNA-mRNA interactions in Drosophila

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Leveraging large language models for data analysis automation

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Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning

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PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC

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RNA localization is a key determinant of neurite-enriched proteome

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Pathogenic mutations of human phosphorylation sites affect protein–protein interactions

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Predicting lethal courses in critically ill COVID-19 patients using a machine learning model trained on patients with non-COVID-19 viral pneumonia

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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

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The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators

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The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation

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Two independent transcription initiation codes overlap on vertebrate core promoters

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Herpesviruses mimic zygotic genome activation to promote viral replication

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Publisher Correction: Herpesviruses mimic zygotic genome activation to promote viral replication

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