DISSECT: deep semi-supervised consistency regularization for accurate cell type fraction and gene expression estimation

by Robin Khatri, Pierre Machart, Stefan Bonn
Published 2024-04-01

Performance comparison of TCR-pMHC prediction tools reveals a strong data dependency

by Lihua Deng, Cedric Ly, Sina Abdollahi, Yu Zhao, Immo Prinz, Stefan Bonn
Published 2023-04-01

Pathogen detection in RNA-seq data with Pathonoia

by Anna-Maria Liebhoff, Kevin Menden, Alena Laschtowitz, Andre Franke, Christoph Schramm, Stefan Bonn
Published 2023-02-01

Testosterone affects type I/type II interferon response of neutrophils during hepatic amebiasis

by Marco Er-Lukowiak, Sonja Hänzelmann, Sonja Hänzelmann, Sonja Hänzelmann, Moritz Rothe, David T. Moamenpour, Fabian Hausmann, Fabian Hausmann, Robin Khatri, Robin Khatri, Charlotte Hansen, Jennifer Boldt, Valentin A. Bärreiter, Barbara Honecker, Annika Bea, Marie Groneberg, Helena Fehling, Claudia Marggraff, Dániel Cadar, Stefan Bonn, Stefan Bonn, Stefan Bonn, Julie Sellau, Hanna Lotter
Published 2023-12-01

Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks

by Mohamed Marouf, Pierre Machart, Vikas Bansal, Christoph Kilian, Daniel S. Magruder, Christian F. Krebs, Stefan Bonn
Published 2020-01-01

Determination of allele frequency in pooled DNA: comparison of three PCR-based methods

by Stefan Wilkening, Kari Hemminki, Ranjit Kumar Thirumaran, Justo Lorenzo Bermejo, Stefan Bonn, Asta Försti, Rajiv Kumar
Published 2005-12-01

DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection

by Fabian Hausmann, Can Ergen, Robin Khatri, Mohamed Marouf, Sonja Hänzelmann, Nicola Gagliani, Samuel Huber, Pierre Machart, Stefan Bonn
Published 2023-09-01

Oasis 2: improved online analysis of small RNA-seq data

by Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn
Published 2018-02-01

Upregulation of miR-370 and miR-543 is associated with reduced expression of heat shock protein 40 in spinocerebellar ataxia type 3.

by Bernd O Evert, Rohit Nalavade, Johannes Jungverdorben, Frank Matthes, Stephanie Weber, Ashish Rajput, Stefan Bonn, Oliver Brüstle, Michael Peitz, Sybille Krauß
Published 2018-01-01

Tagger-A Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice.

by Lech Kaczmarczyk, Vikas Bansal, Ashish Rajput, Raza-Ur Rahman, Wiesław Krzyżak, Joachim Degen, Stefanie Poll, Martin Fuhrmann, Stefan Bonn, Walker Scot Jackson
Published 2019-08-01

Distinct translatome changes in specific neural populations precede electroencephalographic changes in prion-infected mice.

by Lech Kaczmarczyk, Melvin Schleif, Lars Dittrich, Rhiannan H Williams, Maruša Koderman, Vikas Bansal, Ashish Rajput, Theresa Schulte, Maria Jonson, Clemens Krost, Fabio J Testaquadra, Stefan Bonn, Walker S Jackson
Published 2022-08-01

Endophilin-A Deficiency Induces the Foxo3a-Fbxo32 Network in the Brain and Causes Dysregulation of Autophagy and the Ubiquitin-Proteasome System

by John D. Murdoch, Christine M. Rostosky, Sindhuja Gowrisankaran, Amandeep S. Arora, Sandra-Fausia Soukup, Ramon Vidal, Vincenzo Capece, Siona Freytag, Andre Fischer, Patrik Verstreken, Stefan Bonn, Nuno Raimundo, Ira Milosevic
Published 2016-10-01

ERR2 and ERR3 promote the development of gamma motor neuron functional properties required for proprioceptive movement control.

by Mudassar N Khan, Pitchaiah Cherukuri, Francesco Negro, Ashish Rajput, Piotr Fabrowski, Vikas Bansal, Camille Lancelin, Tsung-I Lee, Yehan Bian, William P Mayer, Turgay Akay, Daniel Müller, Stefan Bonn, Dario Farina, Till Marquardt
Published 2022-12-01

Chromatin Remodeling BAF155 Subunit Regulates the Genesis of Basal Progenitors in Developing Cortex

by Ramanathan Narayanan, Linh Pham, Cemil Kerimoglu, Takashi Watanabe, Ricardo Castro Hernandez, Godwin Sokpor, Pauline Antonie Ulmke, Kamila A. Kiszka, Anton B. Tonchev, Joachim Rosenbusch, Rho H. Seong, Ulrike Teichmann, Jens Frahm, Andre Fischer, Stefan Bonn, Anastassia Stoykova, Jochen F. Staiger, Tran Tuoc
Published 2018-06-01

Deep learning–based molecular morphometrics for kidney biopsies

by Marina Zimmermann, Martin Klaus, Milagros N. Wong, Ann-Katrin Thebille, Lukas Gernhold, Christoph Kuppe, Maurice Halder, Jennifer Kranz, Nicola Wanner, Fabian Braun, Sonia Wulf, Thorsten Wiech, Ulf Panzer, Christian F. Krebs, Elion Hoxha, Rafael Kramann, Tobias B. Huber, Stefan Bonn, Victor G. Puelles
Published 2021-04-01

A multi-omics dataset for the analysis of frontotemporal dementia genetic subtypes

by Kevin Menden, Margherita Francescatto, Tenzin Nyima, Cornelis Blauwendraat, Ashutosh Dhingra, Melissa Castillo-Lizardo, Noémia Fernandes, Lalit Kaurani, Deborah Kronenberg-Versteeg, Burcu Atasu, Eldem Sadikoglou, Barbara Borroni, Salvador Rodriguez-Nieto, Javier Simon-Sanchez, Andre Fischer, David Wesley Craig, Manuela Neumann, Stefan Bonn, Patrizia Rizzu, Peter Heutink
Published 2023-12-01

Reduction of IFN-I responses by plasmacytoid dendritic cells in a longitudinal trans men cohort

by Benjamin Grünhagel, Malte Borggrewe, Sven Hendrik Hagen, Susanne M. Ziegler, Florian Henseling, Laura Glau, Rebecca-Jo Thiele, Maria Pujantell, Varshi Sivayoganathan, Benedetta Padoan, Janna M. Claussen, Arne Düsedau, Jana Hennesen, Madeleine J. Bunders, Stefan Bonn, Eva Tolosa, Christian F. Krebs, Christoph Dorn, Marcus Altfeld
Published 2023-11-01

A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae

by Oriol Gallego, Matthew J Betts, Jelena Gvozdenovic‐Jeremic, Kenji Maeda, Christian Matetzki, Carmen Aguilar‐Gurrieri, Pedro Beltran‐Alvarez, Stefan Bonn, Carlos Fernández‐Tornero, Lars Juhl Jensen, Michael Kuhn, Jamie Trott, Vladimir Rybin, Christoph W Müller, Peer Bork, Marko Kaksonen, Robert B Russell, Anne‐Claude Gavin
Published 2010-01-01

Regional and subtype-dependent miRNA signatures in sporadic Creutzfeldt-Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis.

by Franc Llorens, Katrin Thüne, Eulàlia Martí, Eirini Kanata, Dimitra Dafou, Daniela Díaz-Lucena, Ana Vivancos, Orr Shomroni, Saima Zafar, Matthias Schmitz, Uwe Michel, Natalia Fernández-Borges, Olivier Andréoletti, José Antonio Del Río, Juana Díez, Andre Fischer, Stefan Bonn, Theodoros Sklaviadis, Juan Maria Torres, Isidre Ferrer, Inga Zerr
Published 2018-01-01

Altered Ca2+ homeostasis induces Calpain-Cathepsin axis activation in sporadic Creutzfeldt-Jakob disease

by Franc Llorens, Katrin Thüne, Beata Sikorska, Matthias Schmitz, Waqas Tahir, Natalia Fernández-Borges, Maria Cramm, Nadine Gotzmann, Margarita Carmona, Nathalie Streichenberger, Uwe Michel, Saima Zafar, Anna-Lena Schuetz, Ashish Rajput, Olivier Andréoletti, Stefan Bonn, Andre Fischer, Pawel P. Liberski, Juan Maria Torres, Isidre Ferrer, Inga Zerr
Published 2017-04-01