Article
Chemistry, Multidisciplinary
Hsueh-Fen Juan, Hsuan-Cheng Huang
Summary: The study of multiple omes is widely used in biomedical research to gain a comprehensive perspective on biological systems. The generation of high-dimensional multiomics data through high-throughput techniques is enabled, but the quantitative analysis and integration of different types of omics data pose challenges. This article provides an up-to-date review on the methods used for quantification and integration of omics data, focusing on transcriptomics, proteomics, and batch effects reduction. The potential of network analysis in understanding biological systems and the current trends in extending quantitative omics data analysis to biological networks are also discussed.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Biochemical Research Methods
Raghu Chandramohan, Nipun Kakkar, Angshumoy Roy, D. Williams Parsons
Summary: reconCNV is a tool designed for interactive and dynamic visualization of CNV data from NGS, providing detailed annotations and charts to assist users in viewing and summarizing CNV results. The tool is user-friendly, viewable in a web browser, and compatible with result files from most NGS CNV callers. In addition to displaying relative fold change and copy numbers, reconCNV includes features like an auxiliary variant allele fraction track for a more comprehensive CNV visualization and interpretation experience.
Article
Biochemistry & Molecular Biology
Lorena de la Fuente, Marta Del Pozo-Valero, Irene Perea-Romero, Fiona Blanco-Kelly, Lidia Fernandez-Caballero, Marta Corton, Carmen Ayuso, Pablo Minguez
Summary: Screening for pathogenic variants in rare genetic diseases has become more comprehensive with the use of whole exome and genome sequencing. However, the gene-disease associations are still not fully known. In this study, the researchers compiled functional networks and observed their varying ability to recover genes associated with different genetic diseases. They developed a network-based algorithm, GLOWgenes, which showed promising results in identifying new gene-disease associations, especially for less obvious ones.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Heidi F. Hubbard, Caroline L. Ring, Tao Hong, Cara C. Henning, Daniel A. Vallero, Peter P. Egeghy, Michael-Rock Goldsmith
Summary: Ex Priori is a flexible exposure model based on Excel, used to prioritize potential exposures for chemicals with minimal data. It quickly visualizes exposure rankings from consumer product use and considers the impact of consumer use pattern changes on exposure risk.
Article
Chemistry, Analytical
Gerjen H. Tinnevelt, Kristiaan Wouters, Geert J. Postma, Rita Folcarelli, Jeroen J. Jansen
Summary: White blood cells play a crucial role in protecting the body from diseases, but can also be related to chronic inflammation, auto immune diseases, or leukemia. High-throughput analytical instruments have been developed to measure multiple proteins on millions of single cells to study the identity and function of different white blood cell types. Multivariate statistics are essential for fully extracting the information-rich biochemistry data. The process involves analyzing the study design, formulating a research question, preparing the data, converting single cells into a cellular distribution, and using clustering methods or models for analysis to differentiate cell (sub)types between groups.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemistry & Molecular Biology
Petr V. Nazarov, Stephanie Kreis
Summary: This review focuses on miRNAs as key post-transcriptional regulators, summarizing current computational approaches for miRNA:target gene prediction and new data-driven methods to comprehensively and accurately dissect miRNome-targetome interactions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Computer Science, Software Engineering
Juliane Muller, Laura Garrison, Philipp Ulbrich, Stefanie Schreiber, Stefan Bruckner, Helwig Hauser, Steffen Oeltze-Jafra
Summary: The Dual Analysis framework is a powerful technology for exploring high-dimensional quantitative data, visualizing both quantitative and qualitative dimensions in the same view for natural joint treatment of mixed data. Utilizing various measures for different types of data allows for generating new insights and hypotheses.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Review
Biochemical Research Methods
Zhaoqian Liu, Anjun Ma, Ewy Mathe, Marlena Merling, Qin Ma, Bingqiang Liu
Summary: The relationships between microbes and their hosts or environments are associated with critical diseases and ecological changes. High-throughput Omics technologies offer an opportunity for understanding the structures and functions of microbiome, but data analysis remains challenging. Network analyses provide an efficient way to understand complex microbial communities.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Daniel J. Lawson, Vinesh Solanki, Igor Yanovich, Johannes Dellert, Damian Ruck, Phillip Endicott
Summary: Integrating datasets from different disciplines is challenging due to qualitative differences in data. The CLARITY method quantifies consistency, identifies inconsistencies, and allows comparison of similarity matrices. It is robust to noise, scales, and makes weak assumptions about data generation.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Agriculture, Multidisciplinary
Yu-Syuan Luo, Tsung Hsien Wu
Summary: This study comprehensively characterized and prioritized endocrine-active pesticides using an exposure-activity ratio (EAR) method and toxicological prioritization index (ToxPi), aiming to provide guidance for future in-depth health risk assessments.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Shuangbin Xu, Zehan Dai, Pingfan Guo, Xiaocong Fu, Shanshan Liu, Lang Zhou, Wenli Tang, Tingze Feng, Meijun Chen, Li Zhan, Tianzhi Wu, Erqiang Hu, Yong Jiang, Xiaochen Bo, Guangchuang Yu
Summary: ggtreeExtra is a universal tool for visualizing tree data, supporting various data types and visualization methods. By integrating evolutionary statistics and external data, it extends the applications of phylogenetic trees in different disciplines.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Mario Grassi, Fernando Palluzzi, Barbara Tarantino
Summary: With the advancements in high-throughput sequencing, it has become crucially important to have scalable statistical solutions for modeling complex biological systems. This study combined network analysis and causal inference to develop an automated toolkit that can handle large amounts of heterogeneous biological system data and provide explanations in terms of causal effects.
Article
Biochemistry & Molecular Biology
Ji Yang, Hongchun Li, Fan Wang, Fei Xiao, Wenying Yan, Guang Hu
Summary: This study proposed a computational framework that combines biomolecular network modeling and structural dynamics analysis to facilitate the discovery of new drugs with potential activity in multiple sclerosis. The research suggested that TNF-alpha-induced protein 3 (TNFAIP3) could be a potential therapeutic target for MS.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Computer Science, Software Engineering
Benjamin Karer, Hans Hagen, Dirk J. Lehmann
Summary: The article highlights the imbalance in contemporary data analysis and visualization research, where there is an overemphasis on data-centric findings rather than qualitative aspects and their relation to the investigation domain. It argues for the inclusion of qualitative components to support domain insight and introduces the inside-outside principle as a conceptual basis for the development of visualization systems.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Operations Research & Management Science
Cong Wu, Hongxin Li, Jiajia Ren, K. Marimuthu, Priyan Malarvizhi Kumar
Summary: Data-driven corporate landscape data visualization plays a crucial role in e-commerce. However, the current large-data visualization applications are complex and lack standardized creation methods, making them difficult to reuse and extend. This study proposes an artificial neural network-based high dimensional data visualization technique and applies it to e-commerce product advertising recommendation, achieving high prediction accuracy and customer consistency rates.
ANNALS OF OPERATIONS RESEARCH
(2023)