Zobrazeno 1 - 8
of 8
pro vyhledávání: '"Alexander Karollus"'
Autor:
Alexander Karollus, Johannes Hingerl, Dennis Gankin, Martin Grosshauser, Kristian Klemon, Julien Gagneur
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-21 (2024)
Abstract Background The rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conservation to capture regul
Externí odkaz:
https://doaj.org/article/4b05a8916fe6481881a83c500063193b
Autor:
Elisabeth Esser, Eva C. Schulte, Alexander Graf, Alexander Karollus, Nicholas H. Smith, Thomas Michler, Stefan Dvoretskii, Angel Angelov, Michael Sonnabend, Silke Peter, Christina Engesser, Aleksandar Radonic, Andrea Thürmer, Max von Kleist, Friedemann Gebhardt, Clarissa Prazeres da Costa, Dirk H. Busch, Maximilian Muenchhoff, Helmut Blum, Oliver T. Keppler, Julien Gagneur, Ulrike Protzer
Publikováno v:
Scientific Reports, Vol 14, Iss 1, Pp 1-11 (2024)
Abstract The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can cont
Externí odkaz:
https://doaj.org/article/d2e44a1b69c64e72a9c65953950f2384
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-29 (2023)
Abstract Background The largest sequence-based models of transcription control to date are obtained by predicting genome-wide gene regulatory assays across the human genome. This setting is fundamentally correlative, as those models are exposed durin
Externí odkaz:
https://doaj.org/article/4598f522f8c14181a708f441eebc7a85
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 5, p e1008982 (2021)
The 5' untranslated region plays a key role in regulating mRNA translation and consequently protein abundance. Therefore, accurate modeling of 5'UTR regulatory sequences shall provide insights into translational control mechanisms and help interpret
Externí odkaz:
https://doaj.org/article/de07f319f31f466bb7988d7fd7f6a845
The full analysis code for the paper "Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers". See the readme for more information. Github link: https://github.com/Karollus/SequenceModelBenc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::958b6fea6f389afb73ea35b1a9e65430
Autor:
Dennis Gankin, Alexander Karollus, Martin Grosshauser, Kristian Klemon, Johannes Hingerl, Julien Gagneur
MotivationPredicting gene expression from DNA is an open field of research. As in many areas, labeled data is dwarfed by unlabelled data, i.e. species with a sequenced genome but no gene expression assay data. Pretraining on unlabelled data using mas
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::36bd07884e44abd2a3c905e7584399e0
https://doi.org/10.1101/2023.01.26.525670
https://doi.org/10.1101/2023.01.26.525670
Autor:
Dennis Hecker, Fatemeh Behjati Ardakani, Alexander Karollus, Julien Gagneur, Marcel H. Schulz
Publikováno v:
Bioinformatics. 39
MotivationIdentifying regulatory regions in the genome is of great interest for understanding the epigenomic landscape in cells. One fundamental challenge in this context is to find the target genes whose expression is affected by the regulatory regi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b9933a674a1971ae9e1a7e9bb51e4e8a
https://doi.org/10.1093/bioinformatics/btad062
https://doi.org/10.1093/bioinformatics/btad062
Background The largest sequence-based models of transcription control to date are obtained by predicting genome-wide gene regulatory assays across the human genome. This setting is fundamentally correlative, as those models are exposed during trainin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6c67857ba53594dcb011ef0dbc12944b