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Biochemistry & Molecular Biology
Bailing Zhou, Baohua Ji, Congcong Shen, Xia Zhang, Xue Yu, Pingping Huang, Ru Yu, Hongmei Zhang, Xianghua Dou, Qingshuai Chen, Qiangcheng Zeng, Xiaoxin Wang, Zanxia Cao, Guodong Hu, Shicai Xu, Huiying Zhao, Yuedong Yang, Yaoqi Zhou, Jihua Wang
Summary: Long noncoding RNAs (lncRNAs) play crucial roles in various biological processes and diseases. The EVLncRNAs database, with its latest update, has expanded significantly by incorporating a wide range of information and functional classifications, as well as improving the web interface.
NUCLEIC ACIDS RESEARCH
(2023)
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Mathematical & Computational Biology
Dorotea Dudas, Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Mueller
Summary: SABIO-RK is a database for biochemical reactions and their kinetics, which involves complex and multidimensional data. Standard tabular views are not effective in representing the relationships between the data. Visualization methods such as heat maps, parallel coordinates, and scatter plots are implemented in SABIO-RK to facilitate interactive exploration of the data.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Biochemistry & Molecular Biology
Bailing Zhou, Baohua Ji, Kui Liu, Guodong Hu, Fei Wang, Qingshuai Chen, Ru Yu, Pingping Huang, Jing Ren, Chengang Guo, Huiying Zhao, Hongmei Zhang, Dongbo Zhao, Zhiwei Li, Qiangcheng Zeng, Jiafeng Yu, Yunqiang Bian, Zanxia Cao, Shicai Xu, Yuedong Yang, Yaoqi Zhou, Jihua Wang
Summary: The EVLncRNAs database is a comprehensive collection of experimentally validated functional lncRNAs, with information on diseases, interactions, and structures, all checked against known retractions and fake articles for reliability.
NUCLEIC ACIDS RESEARCH
(2021)
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Microbiology
Tanyaradzwa R. Ngara, Peiji Zeng, Houjin Zhang
Summary: Biological nitrogen removal (BNR) technologies are effective for treating nitrogen pollutants in wastewater. This study presents BNRdb, a database that integrates various curated BNR-related data. BNRdb contains microbial strains, gene families, enzymes, reactions, treatment datasets, sequencing datasets, and bioreactor systems. It is the first resource to systematically integrate BNR data from archaea, bacteria, and fungi.
Article
Cell Biology
Agathangelos Chatzichristofi, Vasileios Sagris, Aristos Pallaris, Marios Eftychiou, Ioanna Kalvari, Nicholas Price, Theodosios Theodosiou, Ioannis Iliopoulos, Ioannis P. Nezis, Vasilis J. Promponas
Summary: LIRcentral is an online repository that provides comprehensive and high-quality information on LIR motifs for research purposes. It facilitates the characterization of LIR motifs, the development of prediction methods, and the analysis of their biological importance.
Article
Biochemical Research Methods
Dikscha Sapra, Harpreet Kaur, Anjali Dhall, Gajendra P. S. Raghava
Summary: This study created a manually curated database called ProCanBio, which contains detailed information on 2053 potential PCa biomarkers obtained from 412 publications. The database includes protein-based, RNA-based, genomic mutations, miRNA-based, and metabolites-based biomarkers, and provides a user-friendly tabular format for easy access. A web-based interactive platform was also developed to explore the information in the resource, making it a valuable tool for research community in the field of prostate malignancy.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
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Biochemistry & Molecular Biology
Congxue Hu, Tengyue Li, Yingqi Xu, Xinxin Zhang, Feng Li, Jing Bai, Jing Chen, Wenqi Jiang, Kaiyue Yang, Qi Ou, Xia Li, Peng Wang, Yunpeng Zhang
Summary: CellMarker 2.0 is an updated database that provides experimentally supported markers of various cell types in different tissues of human and mouse. It also offers web tools for analyzing single cell sequencing data.
NUCLEIC ACIDS RESEARCH
(2023)
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Biology
Liping Ren, Lin Ning, Yu Yang, Ting Yang, Xinyu Li, Shanshan Tan, Peixin Ge, Shun Li, Nanchao Luo, Pei Tao, Yang Zhang
Summary: Researchers have developed a manually curated database of metabolite markers related to COVID-19, which includes significantly altered metabolites associated with early diagnosis, disease severity, prognosis, and drug response. This database facilitates both basic and clinical research on COVID-19.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
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
Yibo Wang, Yihao Lin, Sicheng Wu, Jiani Sun, Yuyan Meng, Enhui Jin, Demian Kong, Guangya Duan, Shaoqi Bei, Zhuojing Fan, Gangao Wu, Lili Hao, Shuhui Song, Bixia Tang, Wenming Zhao
Summary: BioKA is a curated and integrated knowledgebase that encompasses multiple animal species, diseases/traits, and annotated resources. It provides comprehensive information on biomarkers and an interactive knowledge network, which contributes to a deeper understanding of animal diseases and supports livestock breeding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xiaonan Liu, Dongmei Tian, Cuiping Li, Bixia Tang, Zhonghuang Wang, Rongqin Zhang, Yitong Pan, Yi Wang, Dong Zou, Zhang Zhang, Shuhui Song
Summary: GWAS Atlas is a curated resource of genotype-to-phenotype associations, which incorporates a large amount of association data for various species and provides online analysis tools and a submission platform. As a core resource in the National Genomics Data Center, GWAS Atlas plays an important role in agronomic trait study and molecular breeding.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Food Science & Technology
Xing-Xing Shi, Fan Wang, Zhi-Zheng Wang, Guang-Yi Huang, Min Li, Jesus Simal-Gandara, Ge-Fei Hao, Guang-Fu Yang
Summary: Rigorous risk assessment of chemicals in food and feed is crucial for food safety. However, obtaining fragmented toxicological data remains challenging, hence the need for related resources. This study collected a large amount of experimental toxicity records and established a freely available online database to reveal the toxicological profiles of food-related chemicals, aiding toxicological studies and risk assessments.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Engineering, Biomedical
Abdul Rafay, Waqar Hussain
Summary: Skin diseases are common and often underestimated health issues that affect nearly one-third of the global population. Deep learning algorithms have shown great potential in accurately diagnosing these diseases. This research presents a novel dataset of 31 skin diseases and uses three different CNN types for transfer learning, with EfficientNet achieving the highest testing accuracy and further fine-tuning.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2023)
Article
Biochemistry & Molecular Biology
Aurelien F. A. Moumbock, Mingjie Gao, Ammar Qaseem, Jianyu Li, Pascal A. Kirchner, Bakoh Ndingkokhar, Boris D. Bekono, Conrad Simoben, Smith B. Babiaka, Yvette Malange, Florian Sauter, Paul Zierep, Fidele Ntie-Kang, Stefan Guenther
Summary: Antimicrobial resistance poses a global health threat, necessitating the development of new antimicrobials; most current antibiotics are natural products from streptomycetes NPs, but there is still a large untapped reservoir; StreptomeDB is the only online database allowing exploration of streptomycetes NPs, providing rich data content and real-world use cases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yangjun Zhang, Xiangyang Yao, Hui Zhou, Xiaoliang Wu, Jianbo Tian, Jin Zeng, Libin Yan, Chen Duan, Haoran Liu, Heng Li, Ke Chen, Zhiquan Hu, Zhangqun Ye, Hua Xu
Summary: This study presents an updated version of the OncoSplicing database, which integrates a large number of alternative splicing events across various cancers to provide clinically relevant information on alternative splicing.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Mueller
JOURNAL OF BIOTECHNOLOGY
(2017)
Editorial Material
Biochemistry & Molecular Biology
Neil Swainston, Antonio Baici, Barbara M. Bakker, Athel Cornish-Bowden, Paul F. Fitzpatrick, Peter Halling, Thomas S. Leyh, Claire O'Donovan, Frank M. Raushel, Udo Reschel, Johann M. Rohwer, Santiago Schnell, Dietmar Schomburg, Keith F. Tipton, Ming-Daw Tsai, Hans V. Westerhoff, Ulrike Wittig, Roland Wohlgemuth, Carsten Kettner
Article
Biochemistry & Molecular Biology
Peter Hailing, Paul F. Fitzpatrick, Frank M. Raushel, Johann Rohwer, Santiago Schnell, Ulrike Wittig, Roland Wohlgemuth, Carsten Kettner
BIOPHYSICAL CHEMISTRY
(2018)
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Biochemistry & Molecular Biology
Neil Swainston, Martin Golebiewski, Hanan L. Messiha, Naglis Malys, Renate Kania, Sylvestre Kengne, Olga Krebs, Saqib Mir, Heidrun Sauer-Danzwith, Kieran Smallbone, Andreas Weidemann, Ulrike Wittig, Douglas B. Kell, Pedro Mendes, Wolfgang Mueller, Norman W. Paton, Isabel Rojas
Review
Biochemistry & Molecular Biology
Ulrike Wittig, Maja Rey, Renate Kania, Meik Bittkowski, Lei Shi, Martin Golebiewski, Andreas Weidemann, Wolfgang Mueller, Isabel Rojas
Article
Biochemistry & Molecular Biology
Ulrike Wittig, Renate Kania, Martin Golebiewski, Maja Rey, Lei Shi, Lenneke Jong, Enkhjargal Algaa, Andreas Weidemann, Heidrun Sauer-Danzwith, Saqib Mir, Olga Krebs, Meik Bittkowski, Elina Wetsch, Isabel Rojas, Wolfgang Mueller
NUCLEIC ACIDS RESEARCH
(2012)
Review
Biochemistry & Molecular Biology
Jan Range, Colin Halupczok, Jens Lohmann, Neil Swainston, Carsten Kettner, Frank T. Bergmann, Andreas Weidemann, Ulrike Wittig, Santiago Schnell, Jurgen Pleiss
Summary: EnzymeML is an XML-based data exchange format that supports comprehensive documentation of enzymatic data, extended by implementing the STRENDA Guidelines. It supports the scientific community with a standardized data exchange format and integrates software tools through a Python API.
Article
Biochemical Research Methods
Simone Lauterbach, Hannah Dienhart, Jan Range, Stephan Malzacher, Jan-Dirk Spoering, Doerte Rother, Maria Filipa Pinto, Pedro Martins, Colton E. Lagerman, Andreas S. Bommarius, Amalie Vang Host, John M. Woodley, Sandile Ngubane, Tukayi Kudanga, Frank T. Bergmann, Johann M. Rohwer, Dorothea Iglezakis, Andreas Weidemann, Ulrike Wittig, Carsten Kettner, Neil Swainston, Santiago Schnell, Juergen Pleiss
Summary: The design of biocatalytic reaction systems is complex due to the dependency of kinetic parameters on the enzyme, reaction conditions, and modeling method. Enzymatic experiments and data reusability are challenging, leading to the development of EnzymeML, an XML-based markup language for storing and exchanging enzymatic data. EnzymeML facilitates the communication between experimental platforms, lab notebooks, modeling tools, publication platforms, and enzymatic reaction databases.
Article
Mathematical & Computational Biology
Dorotea Dudas, Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Mueller
Summary: SABIO-RK is a database for biochemical reactions and their kinetics, which involves complex and multidimensional data. Standard tabular views are not effective in representing the relationships between the data. Visualization methods such as heat maps, parallel coordinates, and scatter plots are implemented in SABIO-RK to facilitate interactive exploration of the data.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Biology
Ulrike Wittig, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Stefanie Anstein, Jasmin Saric, Isabel Rojas
DATA INTEGRATION IN THE LIFE SCIENCES, PROCEEDINGS
(2006)