Article
Biochemistry & Molecular Biology
Chen Cao, Mengting Shao, Chunman Zuo, Devin Kwok, Lin Liu, Yuli Ge, Zilong Zhang, Feifei Cui, Mingshuai Chen, Rui Fan, Yijie Ding, Hangjin Jiang, Guishen Wang, Quan Zou
Summary: Rare variants are important for genetic causes of complex traits, but there is currently no systematic collection of these associations. This study presents the Rare Variant Association Repository (RAVAR), which collects a large number of rare variant associations and provides an interactive interface with search functionality.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jingjing Jin, Peng Lu, Yalong Xu, Jiemeng Tao, Zefeng Li, Shuaibin Wang, Shizhou Yu, Chen Wang, Xiaodong Xie, Junping Gao, Qiansi Chen, Lin Wang, Wenxuan Pu, Peijian Cao
Summary: The emergence of single-cell sequencing has revolutionized transcriptomic and genomic research. The lack of a comprehensive database of cell markers for plant research community has been addressed by the development of PCMDB, providing a valuable resource for researchers to annotate cell types and predict the biological function of individual cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Daniel Falster, Rachael Gallagher, Elizabeth H. Wenk, Ian J. Wright, Dony Indiarto, Samuel C. Andrew, Caitlan Baxter, James Lawson, Stuart Allen, Anne Fuchs, Anna Monro, Fonti Kar, Mark A. Adams, Collin W. Ahrens, Matthew Alfonzetti, Tara Angevin, Deborah M. G. Apgaua, Stefan Arndt, Owen K. Atkin, Joe Atkinson, Tony Auld, Andrew Baker, Maria von Balthazar, Anthony Bean, Chris J. Blackman, Keith Bloomfeld, David M. J. S. Bowman, Jason Bragg, Timothy J. Brodribb, Genevieve Buckton, Geof Burrows, Elizabeth Caldwell, James Camac, Raymond Carpenter, JaneA Catford, Gregory R. Cawthray, Lucas A. Cernusak, Gregory Chandler, Alex R. Chapman, David Cheal, Alexander W. Cheesman, Si-Chong Chen, Brendan Choat, Brook Clinton, Peta L. Clode, Helen Coleman, William K. Cornwell, Meredith Cosgrove, Michael Crisp, Erika Cross, Kristine Y. Crous, Saul Cunningham, Timothy Curran, Ellen Curtis, Matthew Daws, Jane L. DeGabriel, Matthew D. Denton, Ning Dong, Pengzhen Du, Honglang Duan, David H. Duncan, Richard P. Duncan, Marco Duretto, John M. Dwyer, Cheryl Edwards, Manuel Esperon-Rodriguez, John R. Evans, Susan E. Everingham, Claire Farrell, Jennifer Firn, Carlos Roberto Fonseca, Ben J. French, Doug Frood, Jennifer L. Funk, Sonya R. Geange, Oula Ghannoum, Sean M. Gleason, Carl R. Gosper, Emma Gray, Philip K. Groom, Saskia Grootemaat, Caroline Gross, Greg Guerin, Lydia Guja, Amy K. Hahs, Matthew Tom Harrison, Patrick E. Hayes, Martin Henery, Dieter Hochuli, Jocelyn Howell, Guomin Huang, Lesley Hughes, John Huisman, Jugoslav Ilic, Ashika Jagdish, Daniel Jin, Gregory Jordan, Enrique Jurado, John Kanowski, Sabine Kasel, Jurgen Kellermann, Belinda Kenny, Michele Kohout, Robert M. Kooyman, Martyna M. Kotowska, Hao Ran Lai, Etienne Laliberte, Hans Lambers, Byron B. Lamont, Robert Lanfear, Frank van Langevelde, Daniel C. Laughlin, Bree-Anne Laugier-kitchener, Susan Laurance, Caroline E. R. Lehmann, Andrea Leigh, Michelle R. Leishman, Tanja Lenz, Brendan Lepschi, James D. Lewis, Felix Lim, Udayangani Liu, Janice Lord, Christopher H. Lusk, Cate Macinnis-Ng, Hannah McPherson, Susana Magallon, Anthony Manea, Andrea Lopez-Martinez, Margaret Mayfeld, James K. McCarthy, Trevor Meers, Marlien van der Merwe, Daniel J. Metcalfe, Per Milberg, Karel Mokany, Angela T. Moles, Ben D. Moore, Nicholas Moore, John W. Morgan, William Morris, Annette Muir, Samantha Munroe, Aine Nicholson, Dean Nicolle, Adrienne B. Nicotra, Ulo Niinemets, Tom North, Andrew O'Reilly-Nugent, Odhran S. O'Sullivan, Brad Oberle, Yusuke Onoda, Mark K. J. Ooi, Colin P. Osborne, Grazyna Paczkowska, Burak Pekin, Caio Guilherme Pereira, Catherine Pickering, Melinda Pickup, Laura J. Pollock, Pieter Poot, Jef R. Powell, SallyA Power, Iain Colin Prentice, Lynda Prior, Suzanne M. Prober, Jennifer Read, Victoria Reynolds, Anna E. Richards, Ben Richardson, Michael L. Roderick, Julieta A. Rosell, Maurizio Rossetto, Barbara Rye, Paul D. Rymer, MichaelA Sams, Gordon Sanson, Herve Sauquet, Susanne Schmidt, Juerg Schoenenberger, Ernst-Detlef Schulze, Kerrie Sendall, Steve Sinclair, Benjamin Smith, Renee Smith, Fiona Soper, Ben Sparrow, Rachel J. Standish, Timothy L. Staples, Ruby Stephens, Christopher Szota, Guy Taseski, Elizabeth Tasker, Freya Thomas, David T. Tissue, Mark G. Tjoelker, David Yue Phin Tng, Felix de Tombeur, Kyle Tomlinson, Neil C. Turner, Erik J. Veneklaas, Susanna Venn, Peter Vesk, Carolyn Vlasveld, Maria S. Vorontsova, Charles A. Warren, Nigel Warwick, Lasantha K. Weerasinghe, Jessie Wells, Mark Westoby, Matthew White, Nicholas S. G. Williams, Jarrah Wills, Peter G. Wilson, Colin Yates, Amy E. Zanne, Graham Zemunik, Kasia Zieminska
Summary: AusTraits is a database compiling values of plant traits for taxa in the Australian flora, encompassing data from various sources and traits ranging from physiological to morphological aspects. It provides curated data and contextual information, serving as a template for similar initiatives globally.
Article
Multidisciplinary Sciences
Daniel Roush, Ana Giraldo-Silva, Ferran Garcia-Pichel
Summary: Cydrasil 3 is a curated 16S rRNA gene reference package, database, and web application designed to provide a full phylogenetic perspective for cyanobacterial systematics and routine identification.
Article
Biochemistry & Molecular Biology
Wei Su, Meng-Lu Liu, Yu-He Yang, Jia-Shu Wang, Shi-Hao Li, Hao Lv, Fu-Ying Dao, Hui Yang, Hao Lin
Summary: This study established a Prokaryotic Promoter Database (PPD) which manually extracted 129,148 experimentally validated promoters across 63 prokaryotic species from published papers, providing users with a user-friendly interface for browsing, searching, visualizing, submitting, and downloading data.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Corinne Biderre-Petit, Jean-Christophe Charvy, Gisele Bronner, Marina Chauvet, Didier Debroas, Helene Gardon, Claire Hennequin, Isabelle Jouan-Dufournel, Anne Mone, Arthur Monjot, Viviane Ravet, Agnes Vellet, Cecile Lepere
Summary: Freshwater is vital for human survival but facing threats from human activities and climate change. To understand the roles of microbial communities in freshwater ecosystems, researchers have developed a comprehensive database containing information on various microbial taxa from freshwater ecosystems worldwide.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Zbyslaw Sondka, Nidhi Bindal Dhir, Denise Carvalho-Silva, Steven Jupe, Karen Mclaren, Mike Starkey, Sari Ward, Jennifer Wilding, Madiha Ahmed, Joanna Argasinska, David Beare, Manpreet Singh Chawla, Stephen Duke, Ilaria Fasanella, Avirup Guha Neogi, Susan Haller, Balazs Hetenyi, Leonie Hodges, Alex Holmes, Rachel Lyne, Thomas Maurel, Sumodh Nair, Helder Pedro, Amaia Sangrador-Vegas, Helen Schuilenburg, Zoe Sheard, Siew Yit Yong, Jon Teague
Summary: COSMIC is an expert-curated knowledgebase that provides data on somatic variants in cancer, supported by a comprehensive suite of tools for interpreting genomic data and facilitating translational research. It is widely used by cancer researchers and clinicians to access information from a large pool of curated data. In recent years, COSMIC has expanded its utility by adding new resources and improving data accessibility and interoperability.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Tianyi Zhao, Shuxuan Lyu, Guilin Lu, Liran Juan, Xi Zeng, Zhongyu Wei, Jianye Hao, Jiajie Peng
Summary: SC2disease is a manually curated database aiming to provide a comprehensive and accurate resource of gene expression profiles in various cell types for different diseases. It documents comparisons of differentially expressed genes between different cell types, tissues, and disease-related health status, offering new possibilities to address biological and medical questions. The database also reanalyzes gene expression matrix by a unified pipeline to improve comparability between different studies and compares cell-type-specific genes with corresponding genes of lead SNPs identified in GWAS for trait specificity implications.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Toxicology
Judy Strickland, Jaleh Abedini, David G. Allen, John Gordon, Victoria Hull, Nicole C. Kleinstreuer, Hon-Sum Ko, Joanna Matheson, Hermann-Josef Thierse, James Truax, Jens T. Vanselow, Matthias Herzler
Summary: Reference data is critical for evaluating the relevance of non-animal tests. Human reference data have the advantage of not accounting for interspecies variability and are crucial for protecting human health. This study collected data from 2277 human predictive patch tests for skin sensitization, developed a scoring system for reliability evaluation, and created a public database for further evaluation and development of alternative methods for skin sensitization assessments.
ARCHIVES OF TOXICOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jiri Damborsky, Stanislav Mazurenko, David Bednar
Summary: A majority of natural proteins have evolved to function in mild conditions inside organisms, causing challenges in their stability under extreme conditions. Predictors for stabilizing mutations are often used in biotechnological applications, with their accuracy relying on the quality and quantity of data used for training and testing. FireProt(DB) is a new database of experimental thermostability data for single-point mutants designed to address this issue.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Qingqing Huang, Zhengtang Tan, Yanjing Li, Wenzhu Wang, Mei Lang, Changying Li, Zhiyun Guo
Summary: TFcancer is a database that collects experimentally supported associations between transcription factors and 33 TCGA cancers, providing valuable information on TF expression, molecular alterations, regulatory relationships, biological processes, and signaling pathways in cancers. It is a useful resource for researchers seeking to understand the functions and molecular mechanisms of TFs involved in human cancers.
Article
Biochemistry & Molecular Biology
Mingming Lu, Yadong Zhang, Fengchun Yang, Jialin Mai, Qianwen Gao, Xiaowei Xu, Hongyu Kang, Li Hou, Yunfei Shang, Qiheng Qain, Jie Liu, Meiye Jiang, Hao Zhang, Congfan Bu, Jinyue Wang, Zhewen Zhang, Zaichao Zhang, Jingyao Zeng, Jiao Li, Jingfa Xiao
Summary: Transcriptome-wide association studies have led to a better understanding of genetic variants in regulating diseases and traits. However, there is a lack of databases curating public TWAS information. To fill this gap, TWAS Atlas is introduced as an integrated knowledgebase with 401,266 gene-trait associations from 200 publications, providing a user-friendly web interface for browsing, searching, and downloading relevant information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Puneet Rawat, Divya Sharma, R. Prabakaran, Fathima Ridha, Mugdha Mohkhedkar, Vani Janakiraman, M. Michael Gromiha
Summary: Ab-CoV is a database containing manually curated experimental interaction profiles of 1780 coronavirus-related neutralizing antibodies. It provides comprehensive data including IC50, EC50, and K-D, as well as predicted changes in stability and affinity of point mutations of interface residues.
Article
Biochemistry & Molecular Biology
Yan Huang, Jing Wang, Yue Zhao, Huafeng Wang, Tianyuan Liu, Yuhe Li, Tianyu Cui, Weiyi Li, Yige Feng, Jiaxin Luo, Jiaqi Gong, Lin Ning, Yong Zhang, Dong Wang, Yang Zhang
Summary: The article discusses the study of RNA with both protein-coding and noncoding functions, introduces the cncRNAdb database developed to provide a resource for manipulation, browsing, and analysis of cncRNAs. The database contains over 2000 RNAs from various species.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Cari Martini, Ying Frances Liu, Hui Gong, Nicole Sayers, German Segura, Jennifer Fostel
Summary: CEBS is a database containing toxicology study results and metadata, providing public access to high quality curated datasets by integrating growing internal data repositories. Users can access data and related information through the CEBS homepage, guided search applications, FTP, and APIs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yu-Hsin Tang, Po-Liang Lu, Ho-Yin Huang, Ying-Chi Lin
Summary: The study found that in hospitalized diabetic patients with UTIs, beta-lactams were more effective than fluoroquinolones, especially when the resistance rate to fluoroquinolones was higher.
Article
Environmental Sciences
Run-Hsin Lin, Chia-Chi Wang, Chun-Wei Tung
Summary: This study developed blood-sample gene biomarkers to predict stable MCI patients using feature selection and machine learning algorithms. Utilizing datasets from the Alzheimer's Disease Neuroimaging Initiative (ADNI), 29 gene biomarkers (31 probes) were identified for predicting stable MCI patients. A random forest-based classifier showed good performance with AUC values of 0.841 and 0.775 for cross-validation and test datasets, respectively, and achieved 97% concordance for patients with prediction score > 0.9.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Biodiversity Conservation
Guan-Fu Chen, Ying-Chi Lin, Yuan-Chung Lin, Chia-Chi Wang, Wei-Hsiang Chen
Summary: This study estimated the cancer risks posed by PAH emissions during diesel combustion in an industrialized city in southern Taiwan using two different approaches. The results showed that the vapor-phase risk dominated over the total risk and the PM2.5-bound risk was influenced by the mixture effect of particulate pollutants.
HUMAN AND ECOLOGICAL RISK ASSESSMENT
(2022)
Article
Toxicology
Hung-Lin Kan, Chun-Wei Tung, Shao-En Chang, Ying-Chi Lin
Summary: Exposure to neurotoxicants has been associated with Parkinson's disease, but the identification of these neurotoxicants relies on animal models due to the clinical variation and slow progression of the disease. In this study, an innovative in silico model was proposed for predicting parkinsonian neurotoxicants. The model showed high specificity in ruling out non-neurotoxic chemicals and successfully predicted several chemicals related to parkinsonian motor deficits, providing a potential tool for prioritizing chemicals for further evaluations on Parkinson's disease potential.
ARCHIVES OF TOXICOLOGY
(2022)
Article
Medicine, Research & Experimental
Wen-Jane Lee, Keng-Hung Lin, Jun-Sing Wang, Wayne Huey-Herng Sheu, Chin-Chang Shen, Cheng-Ning Yang, Sheng-Mao Wu, Li-Wei Shen, Shu-Hua Lee, De-Wei Lai, Keng-Li Lan, Chun-Wei Tung, Shing-Hwa Liu, Meei-Ling Sheu
Summary: This study investigated the role of aryl hydrocarbon receptor (AhR) in diabetic retinopathy (DR) and found that the downregulation of AhR is associated with the progression of DR. The use of AhR agonists could reverse this downregulation and potentially maintain retinal vascular homeostasis, delaying the development of DR.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biochemical Research Methods
Che-Yu Chou, Pinpin Lin, Jongwoon Kim, Shan-Shan Wang, Chia-Chi Wang, Chun-Wei Tung
Summary: In this study, a valid prediction model for ex vivo human placental barrier permeability was developed, which can be used for assessing the toxic effects of chemicals on the fetus.
BMC BIOINFORMATICS
(2022)
Article
Medicine, Legal
Hui-Lun Lin, Yu-Wen Chiu, Chia-Chi Wang, Chun-Wei Tung
Summary: This study presents the development of a computational model for predicting in vitro pulmonary permeability of chemicals. By integrating multiple algorithms and applying applicability domain adjustment, the model achieved good performance in both cross-validation and independent testing.
REGULATORY TOXICOLOGY AND PHARMACOLOGY
(2022)
Article
Environmental Sciences
Shan-Shan Wang, Chia-Chi Wang, Chun-Wei Tung
Summary: Skin sensitization is an important endpoint associated with allergic contact dermatitis. Several alternative methods based on adverse outcome pathway (AOP) were developed to replace animal testing for evaluating skin sensitizers. An integrated testing strategy (ITS) that combines laboratory data and in silico methods has been proposed as a promising approach for hazard and potency assessment.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Entomology
Chia-Chi Wang, Shan-Shan Wang, Chun-Lin Liao, Wei-Ren Tsai, Chun-Wei Tung
Summary: Adverse outcome pathway (AOP)-based computational models are promising alternatives to animal testing, but their applicability in the field of pesticides needs further investigation. This study identified a consensus chemical space by comparing the predicted results with animal testing data, aiming to reduce animal testing for pesticides.
JOURNAL OF PESTICIDE SCIENCE
(2022)
Article
Food Science & Technology
Shan -Shan Wang, Pinpin Lin, Chia-Chi Wang, Ying-Chi Lin, Chun-Wei Tung
Summary: This study developed a nonlinear machine learning method to predict the migration of chemicals from packaging materials to food, taking into account chemical properties, material type, food type, and temperature. The ensemble model leveraging multiple algorithms provides better performance compared to previous linear regression models. These prediction models can accelerate the assessment of migration of food contact chemicals from package to foods.
FOOD AND CHEMICAL TOXICOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Wan-Chi Hsiao, Guang-Hao Niu, Chen-Fu Lo, Jing-Ya Wang, Ya-Hui Chi, Wei-Cheng Huang, Chun-Wei Tung, Ping-Jyun Sung, Lun Kelvin Tsou, Mingzi M. Zhang
Summary: In this study, two covalent probes were developed to identify STING as a direct target of excB in living mammalian cells. The study reveals a possible mechanism-of-action of excB and expands the repertoire of covalent STING inhibitors.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Veterinary Sciences
Chia-Chi Wang, Yu-Ting Hung, Che-Yu Chou, Shih-Ling Hsuan, Zeng-Weng Chen, Pei-Yu Chang, Tong-Rong Jan, Chun-Wei Tung
Summary: Antimicrobial resistance is a global health issue and surveillance of AMR can provide valuable insights. Salmonella, widely found in food-producing animals, is prioritized in the AMR surveillance program by WHO. The study aims to develop WGS-based random forest models for predicting MIC values of 24 drugs using data from labs in Taiwan.
VETERINARY RESEARCH
(2023)