26 papers · ranked by Valyu relevance
Mikołaj Danielewski, Marlena Szalata, Jan Krzysztof Nowak, Jarosław Walkowiak + 3 more
With the development of genome sequencing technologies, the amount of data produced has greatly increased in the last two decades. The abundance of digital sequence information (DSI) has provided research opportunities, improved our understanding of the genome, and led to the discovery of new solutions in industry and…
Bohdan B. Khomtchouk, Kasra A. Vand, Thor Wahlestedt, Kelly Khomtchouk + 2 more
We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence…
Daniel J Rigden, Xosé M Fernández
The 2026 Nucleic Acids Research database issue has 182 papers from across biology and neighbouring fields. Eighty-four of these papers describe new databases, while 86 are updates on databases that have previously appeared here. Twelve more papers cover databases most recently published elsewhere. New nucleic acid…
Sohrab P Shah, Yong Huang, Tao Xu, Macaire MS Yuen + 2 more
Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for…
Gerda Cristal Villalba, Ursula Matte
Public databases are essential to the development of multi-omics resources. The amount of data created by biological technologies needs a systematic and organized form of storage, that can quickly be accessed, and managed. This is the objective of a biological database. Here, we present an overview of human databases…
Shahid Ullah, Wajeeha Rahman, Farhan Ullah, Gulzar Ahmad + 2 more
'Muhmmad Ijaz' 'Tianshun Gao'] Background: The achievement of the human genome project provides a basis for the systematic study of the human genome from evolutionary history to disease-specific medicine. With the explosive growth of biological data, a growing number of biological databases are being established to…
Raja A. Moftah, Abdelsalam M. Maatuk, Richard White
There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in terms of their ability to efficiently access bioinformatics databases using webbased…
Michael J. Bell, Phillip Lord
As the quantity of data being depositing into biological databases continues to increase, it becomes ever more vital to develop methods that enable us to understand this data and ensure that the knowledge is correct. It is widely-held that data percolates between different databases, which causes particular concerns…
Saeid Kadkhodaei, Fatemeh Barantalab, Sima Taheri, Majid Foroughi + 19 more
'Farahnaz Golestan Hashemi' 'Mahmood Reza Shabanimofrad' 'Hossein Hosseinimonfared' 'Morvarid Akhavan Rezaei' 'Ali Ranjbarfard' 'Mahbod Sahebi' 'Parisa Azizi' 'Maryam Dadar' 'Rambod Abiri' 'Mohammad Fazel Harighi' 'Nahid Kalhori' 'Mohammad Etemadi' 'Ali Baradaran' 'Mahmoud Danaee' 'Zahra Azhdari' 'Hamid Rajabi Memari'…
Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney + 1 more
'Janet Thornton'] Molecular Biology has been at the heart of the ‘big data’ revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of Dayhoff’s ‘Atlas of Protein Sequence and Structure’ through the Human Genome Project in the late 1990s and…
A. C. Gorakshakar, K. Ghosh
Bioinformatics is a relatively new discipline. It is a field of science in which Computer science, Mathematics, Molecular biology and Information technology merges to form a single discipline. Database development, sequence alignment, protein structure prediction, RNA folding, evolutionary tree construction are some of…
Abhishek Agarwal, Piyush Agrawal, Aditi Sharma, Vinod Kumar + 2 more
IndiaBioDb (https://webs.iiitd.edu.in/raghava/indiabiodb/) is a manually curated comprehensive repository of bioinformatics resources developed and maintained by Indian researchers. This repository maintains information about more than 550 freely accessible functional resources that include around 263 biological…
H Lawrence Perrin, Marion Denorme, Julien Grosjean, Omictools Community + 6 more
'Omictools Community' 'Emeric Dynomant' 'Vincent Henry' 'Fabien Pichon' 'Stéfan Darmoni' 'Arnaud Desfeux' 'Bruno J. Gonzalez'] 1omicX, Seine Innopolis, 72 rue de la republique, 76140 Le-Petit-Quevilly, France, 2Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Normandy Center for Genomic and…
Anurag Priyam, Ben J. Woodcroft, Vivek Rai, Alekhya Munagala + 7 more
The dramatic drop in DNA sequencing costs has created many opportunities for novel biological research. These opportunities largely rest upon the ability to effectively compare newly obtained and previously known sequences. This is commonly done with BLAST, yet using BLAST directly on new datasets requires substantial…
Tetsu Sakamoto, J. Miguel Ortega
NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, taking advantage of its taxonomic tree could be…
Colbie Reed, Rémi Denise, Jacob Hourihan, Jill Babor + 4 more
Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on any specific member of that said family. This step is often performed only superficially or partially by experimentalists as the most common approaches and tools to pursue this…
Clément Levin, Emeric Dynomant, Bruno J. Gonzalez, Laurent Mouchard + 3 more
'David Landsman' 'Eivind Hovig' 'Kristian Vlahoviček'] omicX, Seine Innopolis, 72 rue de la Republique, 76140 Le-Petit-Quevilly, France. Normandie Univ, INSA Rouen, LITIS, 76000 Rouen, France. Département d'Informatique et d'Information Médicales, D2IM, CHU de Rouen, France. Normandie Univ, UNIROUEN, Inserm U1245 and…
Christopher Southan
This article assesses a key aspect of data sharing that has the potential to accelerate the progress and impact of medicinal chemistry. To achieve this the community needs to increase the outward flow of experimental results locked-up in millions of published PDFs into structured open databases that explicitly capture…
Mélanie Dulong de Rosnay
Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds upon research led by Science Commons demonstrating why open data and the freedom…
Ansuman Chattopadhyay, Carrie L. Iwema, Barbara A. Epstein, Adrian V. Lee + 1 more
Biomedical researchers are increasingly reliant on obtaining bioinformatics training in order to conduct their research. Here we present a model that academic institutions may follow to provide such training for their researchers, based on the Molecular Biology Information Service (MBIS) of the Health Sciences Library…
José J. Naveja-Romero, Fernanda I. Saldívar-González, Diana L. Prado-Romero, Angel J. Ruiz-Moreno + 3 more
The manuscript discusses recent advances on computer-aided drug discovery (CADD) with focus on data-dependent drug discovery. Herein, we do not intend to review the many CADD methodologies comprehensively. Instead, the review discusses progress on selected concepts, methodologies, resources, and applications that are…
Alejandro Gómez-García, Daniel A. Acuña Jiménez, William J. Zamora, Haruna L. Barazorda-Ccahuana + 12 more
Natural product (NP) databases are crucial tools in computer-aided drug design (CADD). Over the last decade, there has been a worldwide effort to assemble information regarding natural products (NPs) isolated and characterized in certain geographical regions. In 2023, it was published LANaPDB, to our knowledge, it is…
Authors not listed
Natural products databases are well-structured data sources that offer new molecular development opportunities in drug discovery, agrochemistry, food, cosmetics, and several other research disciplines or chemical industries. The crescent world's interest in the development of these databases is related to the…
Authors not listed
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins these models. By systematically collecting, validating, and indexing these models, the PDB has accelerated structural…
Alejandro Gómez-García, Ann-Kathrin Prinz, Daniel A. Acuña Jiménez, William J. Zamora + 14 more
Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective…
Eric W Deutsch, Juan Antonio Vizcaíno, Andrew R Jones, Pierre-Alain Binz + 25 more
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception twenty years ago. Here we describe the general…