Article
Computer Science, Information Systems
Rihem Nasfi, Antoon Bronselaer, Guy De Tre
Summary: Data integration is crucial for enriching databases with external information, and the lack of syntactic interoperability can be challenging. This paper presents a method to evaluate and enhance syntactic interoperability, with the aim of helping data integrators make informed decisions regarding data integration.
INFORMATION PROCESSING & MANAGEMENT
(2023)
Review
Biochemical Research Methods
Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Stefano Ceri
Summary: With thousands of new experimental datasets being generated daily within large cooperative efforts, data integration becomes crucial but faces challenges due to heterogeneity. This paper outlines a technological pipeline for data production to integration, introduces a taxonomy of genomic data players, and focuses on addressing issues in genomic data integration.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Computer Science, Information Systems
Mikko Koho, Toby Burrows, Eero Hyvonen, Esko Ikkala, Kevin Page, Lynn Ransom, Jouni Tuominen, Doug Emery, Mitch Fraas, Benjamin Heller, David Lewis, Andrew Morrison, Guillaume Porte, Emma Thomson, Athanasios Velios, Hanno Wijsman
Summary: Manuscripts are crucial for research into premodern European history and culture, but comprehensive study across platforms has been challenging due to incompatible data models. Mapping Manuscript Migrations (MMM) successfully integrates distinct manuscript datasets into a shared platform, showcasing the potential for future expansion. Collaboration between manuscript scholars and computer scientists is crucial for shaping digital platforms and enabling more sophisticated research questions to be asked of aggregated data.
JOURNAL OF THE ASSOCIATION FOR INFORMATION SCIENCE AND TECHNOLOGY
(2022)
Review
Biochemical Research Methods
Vasundra Toure, Asmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper
Summary: Causal molecular interactions are crucial for computational modeling and predicting biological behaviors. Different biological interests have led to various ways of describing and annotating these interactions, making it challenging to efficiently explore and utilize the data. Understanding the variety of data formats, biological process representations, and exchange procedures is important in extracting and downloading causal interaction data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agriculture, Multidisciplinary
Imma Subirats-Coll, Kristin Kolshus, Andrea Turbati, Armando Stellato, Esther Mietzsch, Daniel Martini, Marcia Zeng
Summary: This chapter describes the current status of AGROVOC thesaurus and how it has become the Linked Data Concept Hub for food and agriculture.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2022)
Article
Computer Science, Information Systems
Pengxu Tian, Cheng Guo, Kim-Kwang Raymond Choo, Xinyu Tang, Lin Yao
Summary: This article presents a hybrid searchable encryption scheme for efficient, secure, and accurate range searches over encrypted medical IoT data. The designed graph structure filters out most false data, and batch processing on ciphertexts accelerates the removal of irrelevant data. The proposed random index and probabilistic fixed-length trapdoor enhance security and efficiency in range searches.
IEEE INTERNET OF THINGS JOURNAL
(2023)
Article
Construction & Building Technology
Shushan Hu, Jiale Wang, Cathal Hoare, Yehong Li, Pieter Pauwels, James O'Donnell
Summary: This paper introduces a method to infer implicit knowledge using the semantic web technology for building energy performance assessment. The approach can reduce burdensome intervention from building managers and improve energy efficiency.
AUTOMATION IN CONSTRUCTION
(2021)
Article
Oncology
Shin-Ruen Yang, Kuo-Feng Hua, Akiko Takahata, Chung-Yao Wu, Chih-Yu Hsieh, Hsiao-Wen Chiu, Cheng-Hsu Chen, Debabrata Mukhopadhyay, Yusuke Suzuki, Shuk-Man Ka, Hsu-Shan Huang, Ann Chen
Summary: The study identified a novel compound, LCC18, that can treat IgA nephropathy (IgAN) by targeting the NLRP3 inflammasome and activating autophagy, resulting in significantly improved renal function in mice with IgAN.
JOURNAL OF PATHOLOGY
(2021)
Article
Chemistry, Medicinal
Thomas Liphardt, Thomas Sander
Summary: We propose an efficient algorithm for substructure search in combinatorial libraries defined by synthons. Our method improves on existing approaches by introducing powerful heuristics and fast fingerprint screening. With this, we achieve quick response times for searches in large combinatorial libraries. We have also made the Java source code available under the BSD license and implemented tools for substructure search in custom combinatorial libraries.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Statistics & Probability
N. Salvati, E. Fabrizi, M. G. Ranalli, R. L. Chambers
Summary: In this paper, small area estimators based on linear mixed models and M-quantile models are developed to accommodate linked data containing a mix of outliers. The properties of these estimators and their mean squared error are illustrated through simulation experiments. The methodology is further applied to linked data from European Survey on Income and Living Conditions and Italian integrated archive of economic and demographic micro data to obtain estimates for average equivalised income in central Italy's labour market areas.
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY
(2021)
Article
Computer Science, Information Systems
Eduardo Magalhaes de Lacerda Filho, Geraldo P. Pereira Rocha Filho, Rafael Timoteo de Sousa Jr, Vinicius P. Goncalves
Summary: This paper proposes a probabilistic scheme to encrypt biometric database indexes and a novel approach to interoperability among systems interchanging biometric characteristics, thus enhancing the security, privacy, and interoperability of the IEEE Biometric Open Protocol Standard (BOPS). The proposed scheme ensures semantic security evidence and imposes high complexity barriers for attackers. It also introduces new integrity and control procedures to improve system reliability and maintain anonymity of individuals.
Article
Computer Science, Artificial Intelligence
Hiteshwar Kumar Azad, Akshay Deepak, Amisha Azad
Summary: In recent years, there has been significant growth in the amount of data published in RDF and adoption of Linked Data principles. However, traditional search engines are unable to perform searches on Linked Data due to its interlinked structure. To address this challenge, a novel LOD search engine has been introduced, which searches on Semantic Web documents and outperforms other semantic search engines in terms of precision, recall, and F-Measure.
JOURNAL OF INTELLIGENT INFORMATION SYSTEMS
(2022)
Article
Pharmacology & Pharmacy
Chen-Fu Lo, Tai-Yu Chiu, Yu-Tzu Liu, Li-Rung Huang, Teng-Kuang Yeh, Kuan-Hsun Huang, Kuan-Liang Liu, Chia-Yu Hsu, Ming-Yu Fang, Yu-Chen Huang, Tsu-An Hsu, Chiung-Tong Chen, Lun Kelvin Tsou
Summary: Ligand-targeting drug conjugates are a type of biopharmaceutical drugs that combine cytotoxic drugs with disease antigen targeting ligands, providing a mechanism for selective accumulation and engagement with the disease antigen. This study explores the utility of a new linker-drug structure in the small molecule drug conjugate system, demonstrating its effectiveness in tumor regression and antitumor growth in breast cancer and liver cancer models. This work suggests the potential of antibody- or small molecule-based targeting ligands for generating new ligand-targeting drug conjugates in the era of omics.
Article
Computer Science, Interdisciplinary Applications
Justine Flore Tchouanguem Djuedja, Fonbeyin Henry Abanda, Bernard Kamsu-Foguem, Pieter Pauwels, Camille Magniont, Mohamed Hedi Karray
Summary: This study proposes an approach that can provide environmental data for buildings, relying on Semantic Web technologies and BIM technology, with a focus on enhancing information exchange for sustainable building assessment.
ADVANCES IN ENGINEERING SOFTWARE
(2021)
Article
Computer Science, Information Systems
Chang Xu, Ruijuan Wang, Liehuang Zhu, Chuan Zhang, Rongxing Lu, Kashif Sharif
Summary: Searchable symmetric encryption (SSE) allows keyword search on encrypted data. Dynamic searchable symmetric encryption (DSSE) enables data updating. Existing DSSE schemes suffer from keyword pair result pattern (KPRP) leakage. We propose the first DSSE scheme that achieves strong privacy-preserving conjunctive keyword search.
IEEE TRANSACTIONS ON BIG DATA
(2023)
Article
Biochemical Research Methods
Miroslav Kratochvil, David Bednarek, Tomas Sieger, Karel Fiser, Jiri Vondrasek
Correction
Chemistry, Multidisciplinary
Miroslav Kratochvil, Jiri Vondrasek, Jakub Galgonek
JOURNAL OF CHEMINFORMATICS
(2020)
Article
Chemistry, Physical
David Jakubec, Jiri Vondrasek
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Biochemistry & Molecular Biology
Kristyna Bousova, Lucie Bednarova, Monika Zouharova, Veronika Vetyskova, Klara Postulkova, Katerina Hofbauerova, Olivia Petrvalska, Ondrej Vanek, Konstantinos Tripsianes, Jiri Vondrasek
Summary: Research indicates that domains extracted from proteins may retain their original structure and function in artificial fusion proteins, shedding light on communication rules between internal and external domains. Biophysical analysis of two fusion proteins reveals their distinct structural and denaturation properties.
Article
Chemistry, Multidisciplinary
Jakub Galgonek, Jiri Vondrasek
Summary: The integration of RDF and SPARQL enhances data interoperability and usability, with many biological and chemical databases presenting data in RDF and supporting SPARQL querying. Our project aims to build the Integrated Database of Small Molecules (IDSM) to integrate multiple datasets and improve mutual interoperability between them.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Biochemical Research Methods
Miroslav Kratochvil, Laurent Heirendt, St Elmo Wilken, Taneli Pusa, Sylvain Arreckx, Alberto Noronha, Marvin van Aalst, Venkata P. Satagopam, Oliver Ebenhoh, Reinhard Schneider, Christophe Trefois, Wei Gu
Summary: COBREXA.jl is a Julia package that enables scalable and high-performance constraint-based reconstruction and analysis of very large-scale biological models. The package is designed to integrate modern high performance computing environments with the processing and analysis of complex metabolic models. The authors report on the architecture of the package and demonstrate its scalability in several use-cases involving multi-organism community models.
Article
Computer Science, Hardware & Architecture
Luca Rossetto, Ralph Gasser, Silvan Heller, Mahnaz Parian-Scherb, Loris Sauter, Florian Spiess, Heiko Schuldt, Ladislav Peska, Tomas Soucek, Miroslav Kratochvil, Frantisek Mejzlik, Patrik Vesely, Jakub Lokoc
Summary: In the research on video retrieval systems, dedicated retrieval competitions offer valuable insights into system performance, but are limited by set-up costs, logistics, and organization complexity. A proposed remote evaluation methodology provides statistically robust results and increases experiment replicability, making a significant contribution to open science in interactive retrieval benchmarks. Additionally, detailed evaluation reports provide new observations on previously inaccessible aspects of video retrieval.
Article
Biochemistry & Molecular Biology
Kristyna Bousova, Monika Zouharova, Petr Herman, Jiri Vymetal, Veronika Vetyskova, Katerina Jiraskova, Jiri Vondrasek
Summary: In this study, we found that the N-terminus of TRPM5 interacts with calcium-binding proteins CaM and S100A1, and these binding regions possess unique basic residues.
Article
Biology
Adriano Rutz, Maria Sorokina, Jakub Galgonek, Daniel Mietchen, Egon Willighagen, Arnaud Gaudry, James G. Graham, Ralf Stephan, Roderic Page, Jiri Vondrasek, Christoph Steinbeck, Guido F. Pauli, Jean-Luc Wolfender, Jonathan Bisson, Pierre-Marie Allard
Summary: Contemporary bioinformatic and chemoinformatic capabilities have the potential to reshape knowledge management, analysis, and interpretation in natural products research. However, the reliance on disparate and specialized databases poses challenges for data access and integration. The LOTUS initiative aims to address these challenges by consolidating and sharing referenced structure-organism pairs on an open platform, promoting collaboration and transformative research.
Article
Biochemistry & Molecular Biology
Jiri Vymetal, Katerina Mertova, Kristyna Bousova, Josef Sulc, Konstantinos Tripsianes, Jiri Vondrasek
Summary: Proteins can be naturally formed by domains with specific functional and structural properties. Artificial fusion multidomain proteins with unique combinations of functions can be constructed. The challenges in designing new proteins lie in structure/function prediction and its context dependency. Predicting the structure of fusion proteins is complex and nontrivial, even with the use of advanced computational methods.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Chemistry, Medicinal
Jiri Vymetal, Jiri Vondrasek
Summary: This article proposes an efficient resampling protocol for computer simulations of biomolecules, which utilizes the ILBUS method to resample the conformational space using collected off-equilibrium trajectories, and reconstructs static equilibrium properties using the MBAR method. The ILBUS protocol does not require additional variables or dimension-reduction techniques, and only needs a set of reference conformations. Additionally, the ILBUS protocol can optimize the force constant used in the umbrella sampling simulation.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biotechnology & Applied Microbiology
St Elmo Wilken, Mathieu Besancon, Miroslav Kratochvil, Chilperic Armel Foko Kuate, Christophe Trefois, Wei Gu, Oliver Ebenhoh
Summary: In this paper, the sensitivity analysis of constraint-based metabolic models is studied, and several applications of this technique are demonstrated. By calculating the sensitivity of reaction fluxes and enzyme concentrations to parameters, rate limiting enzymes can be identified and parameter estimation can be improved. Furthermore, this technique can be expanded to study complex models and validated against experimental data.
METABOLIC ENGINEERING
(2022)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Carlos Vega, Miroslav Kratochvil, Venkata Satagopam, Reinhard Schneider
Summary: The increasing use of artificial intelligence in biomedical sciences requires closer interdisciplinary collaborations between life scientists and computer science researchers. The use of AI-based solutions in clinical and laboratory settings has proven problematic due to differences in data interpretation and mismatched result quality metrics. Overcoming these translational challenges can be guided by explicit interpretable inference reporting.
BIOINFORMATICS AND BIOMEDICAL ENGINEERING, PT II
(2022)
Proceedings Paper
Computer Science, Theory & Methods
Adam Smelko, Miroslav Kratochvil, Martin Krulis, Tomas Sieger
Summary: Hierarchical clustering is a widely used tool for simplification, exploration, and analysis of datasets in various research areas. A specific variant of this clustering method, Mahalanobis-average linkage, has been shown to outperform common linkages in flow cytometry data. The authors introduce an optimized, GPU-accelerated open-source implementation that significantly improves algorithm performance, making it suitable for large datasets.
EURO-PAR 2021: PARALLEL PROCESSING
(2021)
Article
Biology
Miroslav Kratochvil, Oliver Hunewald, Laurent Heirendt, Vasco Verissimo, Jiri Vondrasek, Venkata P. Satagopam, Reinhard Schneider, Christophe Trefois, Markus Ollert
