Database J. Biol. Databases Curation

Keyphrases

Publications

volume 2024, 2024

Bharathram Uppili, Mohammed Faruq
STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome. Database J. Biol. Databases Curation 2024 (2024)
Jiabei Liu, Yiyi Yu, Mingyue Li, Yixuan Wu, Weijun Chen, Guanru Liu, Lingxian Liu, Jiechun Lin, Chujun Peng, Weijun Sun, Xiaoli Wu, Xin Chen
PMBC: a manually curated database for prognostic markers of breast cancer. Database J. Biol. Databases Curation 2024 (2024)
Tao Wu, Yaopan Hou, Guanghao Xin, Jingyan Niu, Shanshan Peng, Fanfan Xu, Ying Li, Yuling Chen, Yifangfei Yu, Huixue Zhang, Xiaotong Kong, Yuze Cao, Shangwei Ning, Lihua Wang, Junwei Hao
MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis. Database J. Biol. Databases Curation 2024 (2024)
Eléonore Bettacchioli, Laurent Chiche, Damien Chaussabel, Divi Cornec, Noémie Jourde-Chiche, Darawan Rinchai
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity. Database J. Biol. Databases Curation 2024 (2024)
Serena Baini, Alessio De Biase
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives. Database J. Biol. Databases Curation 2024 (2024)
Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank. Database J. Biol. Databases Curation 2024 (2024)
Fuyuan Zhang, Hongzhe Cao, Helong Si, Jinping Zang, Jingao Dong, Jihong Xing, Kang Zhang
FGCD: a database of fungal gene clusters related to secondary metabolism. Database J. Biol. Databases Curation 2024 (2024)
Zhiwei Zhou, Jingyi Du, Jianhua Wang, Liangyi Liu, M. Gracie Gordon, Chun Jimmie Ye, Joseph E. Powell, Mulin Jun Li, Shuquan Rao
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues. Database J. Biol. Databases Curation 2024 (2024)
Qingkang Meng, Yiyang Cai, Kun Zhou, Fei Xu, Diwei Huo, Hongbo Xie, Meini Yu, Denan Zhang, Xiujie Chen
DAPredict: a database for drug action phenotype prediction. Database J. Biol. Databases Curation 2024 (2024)
Daniel Walke, Daniel Micheel, Kay Schallert, Thilo Muth, David Broneske, Gunter Saake, Robert Heyer
The importance of graph databases and graph learning for clinical applications. Database J. Biol. Databases Curation 2024 (2024)
Leho Tedersoo, Mahdieh S. Hosseyni Moghaddam, Vladimir Mikryukov, Ali Hakimzadeh, Mohammad Bahram, R. Henrik Nilsson, Iryna Yatsiuk, Stefan Geisen, Arne Schwelm, Kasia Piwosz, Marko Prous, Sirje Sildever, Dominika Chmolowska, Sonja Rueckert, Pavel Skaloud, Peeter Laas, Marco Tines, Jae-Ho Jung, Ji Hye Choi, Saad Alkahtani, Sten Anslan
EUKARYOME: the rRNA gene reference database for identification of all eukaryotes. Database J. Biol. Databases Curation 2024 (2024)
Nie Kai, Cai Qingsong, Ma Kejia, Luo Weiwei, Xing Wu, Chen Xuejie, Cai Lixia, Deng Minzi, Yuan-Yuan Yang, Wang Xiaoyan
An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP). Database J. Biol. Databases Curation 2024 (2024)
Yuanyuan Wang, Yexin Yang, Yi Liu, Chao Liu, Meng Xu, Miao Fang, Xidong Mu
CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish. Database J. Biol. Databases Curation 2024 (2024)
Victor Avram, Shweta Yadav, Pranav Sahasrabudhe, Dan Chang, Jing Wang
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease. Database J. Biol. Databases Curation 2024 (2024)
Carlos Vega, Marek Ostaszewski, Valentin Grouès, Reinhard Schneider, Venkata P. Satagopam
BioKC: a collaborative platform for curation and annotation of molecular interactions. Database J. Biol. Databases Curation 2024 (2024)
Shumin Ren, Lin Yang, Jiale Du, Mengqiao He, Bairong Shen
DRGKB: a knowledgebase of worldwide diagnosis-related groups' practices for comparison, evaluation and knowledge-guided application. Database J. Biol. Databases Curation 2024 (2024)
Ismahene Mesbah, Bianca Habermann, Felix Rico
MechanoProDB: a web-based database for exploring the mechanical properties of proteins. Database J. Biol. Databases Curation 2024 (2024)
Rahel Paloots, Michael Baudis
cancercelllines.org - a novel resource for genomic variants in cancer cell lines. Database J. Biol. Databases Curation 2024 (2024)
Christophe Jenny, Valentin Guignon, Felip Manyer I Ballester, Max Ruas, Mathieu Rouard
spp.) using online resources and citizen science. Database J. Biol. Databases Curation 2024 (2024)
Shahin Ramazi, Seyed Amir Hossein Tabatabaei, Elham Khalili, Amirhossein Golshan Nia, Kiomars Motarjem
Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences. Database J. Biol. Databases Curation 2024 (2024)
Correction to: Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. Database J. Biol. Databases Curation 2024 (2024)
Shuchang Xiong, Zhengwen Liu, Xin Yi, Kai Liu, Bingding Huang, Xin Wang
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application. Database J. Biol. Databases Curation 2024 (2024)
Junkang Wei, Jin Xiao, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles. Database J. Biol. Databases Curation 2024 (2024)
Tae Jin Lee, Arnav Goyal, Garrett Jones, Joshua Glass, Vishal Doshi, Kathryn Bollinger, Lane Ulrich, Saleh Ahmed, Sai Karthik Kodeboyina, Amy Estes, Marc Töteberg-Harms, Wenbo Zhi, Shruti Sharma, Ashok Sharma
AHP DB: a reference database of proteins in the human aqueous humor. Database J. Biol. Databases Curation 2024 (2024)
proteins. Database J. Biol. Databases Curation 2024 (2024)
Darawan Rinchai, Tobias Brummaier, Alexandra A. Marr, Tanwir Habib, Mohammed Toufiq, Tomoshigue Kino, Francois Nosten, Souhaila Al Khodor, Annalisa Terranegra, Rose McGready, Basirudeen Syed Ahamed Kabeer, Damien Chaussabel
A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings. Database J. Biol. Databases Curation 2024 (2024)
Anmol M. Kiran, Mariem Hanachi, Nihad Alsayed, Meriem Fassatoui, Ovokeraye Achinike-Oduaran, Imane Allali, Suresh Maslamoney, Ayton Meintjes, Lyndon Zass, Jorge Da Rocha, Rym Kefi, Alia Benkahla, Kais Ghedira, Sumir Panji, Nicola J. Mulder, Faisal M. Fadlelmola, Oussema Souiai
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata. Database J. Biol. Databases Curation 2024 (2024)
Alexander Kellmann, Max Postema, Joris de Keijser, Pjotr Svetachov, Rebecca C. Wilson, Esther van Enckevort, Morris A. Swertz
Visualization and exploration of linked data using virtual reality. Database J. Biol. Databases Curation 2024 (2024)
Yanhong Xiong, Shiyu Li, Yuxuan Zhang, Qianqian Chen, Mengtan Xing, Yong Zhang, Qi Wang
MechanoBase: a comprehensive database for the mechanics of tissues and cells. Database J. Biol. Databases Curation 2024 (2024)
Tzu-Hsien Yang, Yu-Huai Yu, Sheng-Hang Wu, Fang-Yuan Chang, Hsiu-Chun Tsai, Ya-Chiao Yang
modular transcription regulators and targets from massive literature articles. Database J. Biol. Databases Curation 2024 (2024)
Kunjulakshmi R, Ambuj Kumar, Keerthana Vinod Kumar, Avik Sengupta, Kavita Kundal, Simran Sharma, Ankita Pawar, Pithani Sai Krishna, Mohammad Alfatah, Sandipan Ray, Bhavana Tiwari, Rahul Kumar
AagingBase: a comprehensive database of anti-aging peptides. Database J. Biol. Databases Curation 2024 (2024)
Pengyu Du, Yingli Chen, Qianzhong Li, Zhimin Gai, Hui Bai, Luqiang Zhang, Yuxian Liu, Yanni Cao, Yuanyuan Zhai, Wen Jin
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer. Database J. Biol. Databases Curation 2024 (2024)
Wenhui Zhou, Tao Yang, Liucui Zeng, Jing Chen, Yayu Wang, Xing Guo, Lijin You, Yiqun Liu, Wensi Du, Fan Yang, Cong Hua, Jia Cai, Theo van Hintum, Huan Liu, Ying Gu, Xiaofeng Wei, Tong Wei
LettuceDB: an integrated multi-omics database for cultivated lettuce. Database J. Biol. Databases Curation 2024 (2024)
Correction to: ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides. Database J. Biol. Databases Curation 2024 (2024)
Chong Peng, Xiaofeng Liu, Xiangbo Meng, Congge Chen, Xinming Wu, Lin Bai, Fuping Lu, Fufeng Liu
IPAD-DB: a manually curated database for experimentally verified inhibitors of proteins associated with Alzheimer's disease. Database J. Biol. Databases Curation 2024 (2024)
Feng Shao, Minzhi Zeng, Xiaofei Xu, Huahao Zhang, Zuogang Peng
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research. Database J. Biol. Databases Curation 2024 (2024)
Wenqian Li, Yinliang Chen, Ruofei Yang, Zilong Hu, Shaozhong Wei, Sheng Hu, Xinjun Xiong, Meijuan Wang, Ammar Lubeiny, Xiaohua Li, Minglei Feng, Shuang Dong, Xinlu Xie, Chao Nie, Jingyi Zhang, Yunhao Luo, Yichen Zhou, Ruodi Liu, Jinhai Pan, De-Xin Kong, Xuebo Hu
A terpenoids database with the chemical content as a novel agronomic trait. Database J. Biol. Databases Curation 2024 (2024)
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait. Database J. Biol. Databases Curation 2024 (2024)
Laha Ale, Robert Gentleman, Teresa Filshtein Sonmez, Deepayan Sarkar, Christopher Endres
nhanesA: achieving transparency and reproducibility in NHANES research. Database J. Biol. Databases Curation 2024 (2024)
Jorge Novoa, Javier López-Ibáñez, Monica Chagoyen, Juan Antonio Garcia-Ranea, Florencio Pazos
CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature. Database J. Biol. Databases Curation 2024 (2024)
Daniel Faria, Patrícia Eugénio, Marta Contreiras Silva, Laura Balbi, Georges Bedran, Ashwin Adrian Kallor, Susana Nunes, Aleksander Palkowski, Michal Waleron, Javier Antonio Alfaro, Catia Pesquita
The Immunopeptidomics Ontology (ImPO). Database J. Biol. Databases Curation 2024 (2024)
Charlotte Nachtegael, Jacopo De Stefani, Anthony Cnudde, Tom Lenaerts
DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations. Database J. Biol. Databases Curation 2024 (2024)
Ruiqing Wang, Chao Ren, Tian Gao, Hao Li, Xiaochen Bo, Dahai Zhu, Dan Zhang, Hebing Chen, Yong Zhang
SEPDB: a database of secreted proteins. Database J. Biol. Databases Curation 2024 (2024)
Renzo Angles, Mauricio Arenas-Salinas, Roberto García, Ben Ingram
An optimized relational database for querying structural patterns in proteins. Database J. Biol. Databases Curation 2024 (2024)
Subhashini Sivagnanam, Steven Yeu, Kai Lin, S. Sakai, F. Garzon, Kenneth Yoshimoto, Katrina Prantzalos, D. P. Upadhyaya, Amitava Majumdar, Satya S. Sahoo, William W. Lytton
Towards building a trustworthy pipeline integrating Neuroscience Gateway and Open Science Chain. Database J. Biol. Databases Curation 2024 (2024)
Yue Liu, Yuhuan Zhou, Xiumei Hu, Wuri Le-Ge, Haoyan Wang, Tao Jiang, Junyi Li, Yang Hu, Yadong Wang
DIRMC: a database of immunotherapy-related molecular characteristics. Database J. Biol. Databases Curation 2024 (2024)
Puneet K. Singh, Razvan C. Stan
ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures. Database J. Biol. Databases Curation 2024 (2024)
Correction to: The importance of graph databases and graph learning for clinical applications. Database J. Biol. Databases Curation 2024 (2024)
Alexander Bach, Florian Raub, Hubert Höfer, Richard Ottermanns, Martina Roß-Nickoll
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data. Database J. Biol. Databases Curation 2024 (2024)
Kai Wang, Bambarendage P. U. Perera, Rachel K. Morgan, Kimberley Sala-Hamrick, Viviana Geron, Laurie K. Svoboda, Christopher Faulk, Dana C. Dolinoy, Maureen A. Sartor
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation. Database J. Biol. Databases Curation 2024 (2024)