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38 Publications visible to you, out of a total of 38
High-Throughput Phenotypic Screening and Machine Learning Methods Enabled the Selection of Broad-Spectrum Low-Toxicity Antitrypanosomatidic Agents.

Abstract (Expand)

Broad-spectrum anti-infective chemotherapy agents with activity against Trypanosomes, Leishmania, and Mycobacterium tuberculosis species were identified from a high-throughput phenotypic screening … program of the 456 compounds belonging to the Ty-Box, an in-house industry database. Compound characterization using machine learning approaches enabled the identification and synthesis of 44 compounds with broad-spectrum antiparasitic activity and minimal toxicity against Trypanosoma brucei, Leishmania Infantum, and Trypanosoma cruzi. In vitro studies confirmed the predictive models identified in compound 40 which emerged as a new lead, featured by an innovative N-(5-pyrimidinyl)benzenesulfonamide scaffold and promising low micromolar activity against two parasites and low toxicity. Given the volume and complexity of data generated by the diverse high-throughput screening assays performed on the compounds of the Ty-Box library, the chemoinformatic and machine learning tools enabled the selection of compounds eligible for further evaluation of their biological and toxicological activities and aided in the decision-making process toward the design and optimization of the identified lead.

Authors: P. Linciano, A. Quotadamo, R. Luciani, M. Santucci, K. M. Zorn, D. H. Foil, T. R. Lane, A. Cordeiro da Silva, N. Santarem, C. B Moraes, L. Freitas-Junior, U. Wittig, W. Mueller, M. Tonelli, S. Ferrari, A. Venturelli, S. Gul, M. Kuzikov, B. Ellinger, J. Reinshagen, S. Ekins, M. P. Costi

Date Published: 3rd Nov 2023

Publication Type: Journal

NFDI4Health Local Data Hubs for Finding and Accessing Health Data

Abstract (Expand)

To support federated data structuring and sharing for sensitive health data from clinical trial, epidemiological and public health studies in the context of the German National Research Data Infrastructure … for Personal Health Data (NFDI4Health), we have developed Local Data Hubs (LDHs) based on the FAIRDOM-SEEK platform. Those LDHs connect to the German Central Health Study Hub (CSH) to make the health data searchable and findable. This decentralised approach supports researchers to make health studies with their data FAIR (Findable, Accessible, Interoperable and Reusable), and at the same time fully preserves data protection for sensitive data.

Authors: Frank Meineke, Martin Golebiewski, Xiaoming Hu, Toralf Kirsten, Matthias Löbe, Sebastian Klammt, Ulrich Sax, Wolfgang Müller

Date Published: 7th Sep 2023

Publication Type: Proceedings

Improved insights into the SABIO-RK database via visualization.

Abstract (Expand)

SABIO-RK is a database for biochemical reactions and their kinetics. Data in SABIO-RK are inherently multidimensional and complex. The complex relationships between the data are often difficult to … follow or even not represented when using standard tabular views. With an increasing number of data points the mismatch between tables and insights becomes more obvious, and getting an overview of the data becomes harder. Such complex data benefit from being presented using specially adapted visual tools. Visualization is a natural and user-friendly way to quickly get an overview of the data and to detect clusters and outliers. Here, we describe the implementation of a variety of visualization concepts into a common interface within the SABIO-RK biochemical reaction kinetics database. For that purpose, we use a heat map, parallel coordinates and scatter plots to allow the interactive visual exploration of general entry-based information of biochemical reactions and specific kinetic parameter values. Database URL https://sabiork.h-its.org/.

Authors: D. Dudas, U. Wittig, M. Rey, A. Weidemann, W. Muller

Date Published: 31st Mar 2023

Publication Type: Journal

ReStoRunT: Simple Recording, Storing, Running and Tracing changes in Spreadsheets

Abstract (Expand)

In addition to the ubiquitous big data, one key challenge indata processing and management in the life sciences is the diversity ofsmall data. Diverse pieces of small data have to be transformed … intostandards-compliant data. Here, the challenge lies not in the difficulty ofsingle steps that need to be performed, but rather in the fact that manytransformation tasks are to be performed once or only a few times. Thislimits the time that can be put into automated approaches, which inturn severely limits the verifiability of such transformations.As much of the data to be processed is stored in spreadsheets, withinthis paper we justify and propose a lightweight recording-based solutionthat works on a wide variety of spreadsheet programs, from MicrosoftExcel to Google Docs.

Authors: Wolfgang Müller, Lukrecia Mertova

Date Published: 23rd Feb 2023

Publication Type: Journal

WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning

Abstract (Expand)

Fine-tuning biomedical pre-trained language models (BioPLMs) such as BioBERT has become a common practice dominating leaderboards across various natural language processing tasks. Despite their success … and wide adoption, prevailing fine-tuning approaches for named entity recognition (NER) naively train BioPLMs on targeted datasets without considering class distributions. This is problematic especially when dealing with imbalanced biomedical gold-standard datasets for NER in which most biomedical entities are underrepresented. In this paper, we address the class imbalance problem and propose WeLT, a cost-sensitive fine-tuning approach based on new re-scaled class weights for the task of biomedical NER. We evaluate WeLT’s fine-tuning performance on mixed-domain and domain-specific BioPLMs using eight biomedical gold-standard datasets. We compare our approach against vanilla fine-tuning and three other existing re-weighting schemes. Our results show the positive impact of handling the class imbalance problem. WeLT outperforms all the vanilla fine-tuned models. Furthermore, our method demonstrates advantages over other existing weighting schemes in most experiments.

Authors: Ghadeer Mobasher, Wolfgang Müller, Olga Krebs, Michael Gertz

Date Published: 2023

Publication Type: Proceedings

More findability, more interoperability for SABIO-RK, the curated database for biochemical reaction kinetics

Abstract (Expand)

SABIO-RK represents a repository for structured, curated, and annotated data on reactions and their kinetics. The data are manually extracted from the scientific literature and stored in a relational … database. The content comprises both naturally occurring and alternatively measured biochemical reactions, and the data are made available to the public via a web-based search interface as well as easy-to-use JSON web services for programmatic access. Data are highly interlinked to external databases, ontologies, and controlled vocabularies. This includes cross-references with eg Uniprot, ChEBI, KEGG, BRENDA, Biomodels, and MetaNetX. In the past year we have worked on improving findability of SABIO-RK data as well as interoperability: SABIO-RK was extended to read the additional annotations in the EnzymeML data exchange format to allow the direct import of enzymology data from EnzymeML documents. SABIO-RK is part of the EnzymeML workflow to support the data transfer between experimental platforms, modelling tools and databases (Range et al. FEBS J 2021). In the BMBF-funded project SABIO-VIS we focused on visualizing SABIORK data for the purpose of interactive search and search refinement.

Authors: Andreas Weidemann, Dorotea Dudas, Maja Rey, Ulrike Wittig, Wolfgang Müller

Date Published: 1st Aug 2022

Publication Type: InCollection

Towards Effortless Navigation of Scientific-Literature Screen Reading for Biocuration

Abstract

Not specified

Authors: Sucheta Ghosh, Wolfgang Müller, Ulrike Wittig, Maja Rey

Date Published: 5th May 2022

Publication Type: InProceedings

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