Sascha Duttke

dblp:424/4293 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2024
0000-0003-4717-000XORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
comparative genomics
0.812024
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements · Bioinform. 2024
Bioinformatics and computational biology › molecular evolution
evolutionary conservation analysis
0.812024
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements · Bioinform. 2024
Bioinformatics and computational biology › gene regulation
gene regulation analysis
0.812024
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements · Bioinform. 2024
Bioinformatics and computational biology › gene regulation
transcription factor binding site prediction
0.812024
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements · Bioinform. 2024

Methods — techniques the papers use, named apart from their topics

motif scanning · 0.8TSS dataset quality assessment · 0.8
YearPublicationVenuePosition
2024 ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements
abstract
MOTIVATION: Prediction and identification of core promoter elements and transcription factor binding sites is essential for understanding the mechanism of transcription initiation and deciphering the biological activity of a specific locus. Thus, there is a need for an up-to-date tool to detect and curate core promoter elements/motifs in any provided nucleotide sequences. RESULTS: Here, we introduce ElemeNT 2023-a new and enhanced version of the Elements Navigation Tool, which provides novel capabilities for assessing evolutionary conservation and for readily evaluating the quality of high-throughput transcription start site (TSS) datasets, leveraging preferential motif positioning. ElemeNT 2023 is accessible both as a fast web-based tool and via command line (no coding skills are required to run the tool). While this tool is focused on core promoter elements, it can also be used for searching any user-defined motif, including sequence-specific DNA binding sites. Furthermore, ElemeNT's CORE database, which contains predicted core promoter elements around annotated TSSs, is now expanded to cover 10 species, ranging from worms to human. In this applications note, we describe the new workflow and demonstrate a case study using ElemeNT 2023 for core promoter composition analysis of diverse species, revealing motif prevalence and highlighting evolutionary insights. We discuss how this tool facilitates the exploration of uncharted transcriptomic data, appraises TSS quality, and aids in designing synthetic promoters for gene expression optimization. Taken together, ElemeNT 2023 empowers researchers with comprehensive tools for meticulous analysis of sequence elements and gene expression strategies. AVAILABILITY AND IMPLEMENTATION: ElemeNT 2023 is freely available at https://www.juven-gershonlab.org/resources/element-v2023/. The source code and command line version of ElemeNT 2023 are available at https://github.com/OritAdato/ElemeNT. No coding skills are required to run the tool.
Orit Adato, Anna Sloutskin, Hodaya Komemi, Ian Brabb, Sascha Duttke, Philipp Bucher, Ron Unger, Tamar Juven-Gershon
Bioinform.5