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1. DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species

   https://doi.org/10.10106  

   Hu Y, Tattikota SG (January 2021, Computational and Structural Biotechnology Journal)

   null (Ed.)

   With the advent of single-cell RNA sequencing (scRNA-seq) technologies, there has been a spike in stud-ies involving scRNA-seq of several tissues across diverse species includingDrosophila. Although a fewdatabases exist for users to query genes of interest within the scRNA-seq studies, search tools that enableusers to find orthologous genes and their cell type-specific expression patterns across species are limited.Here, we built a new search database, DRscDB (https://www.flyrnai.org/tools/single_cell/web/), toaddress this need. DRscDB serves as a comprehensive repository for published scRNA-seq datasets forDrosophilaand relevant datasets from human and other model organisms. DRscDB is based on manualcuration ofDrosophilascRNA-seq studies of various tissue types and their corresponding analogoustissues in vertebrates including zebrafish, mouse, and human. Of note, our search database provides mostof the literature-derived marker genes, thus preserving the original analysis of the published scRNA-seqdatasets. Finally, DRscDB serves as a web-based user interface that allows users to mine gene expressiondata from scRNA-seq studies and perform cell cluster enrichment analyses pertaining to variousscRNA-seq studies, both within and across species. 

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2. A Web Service for Author Name Disambiguation in Scholarly Databases

   Kunho Kim, Athar Sefid (July 2018, Web/online services)

   Author Name Disambiguation (AND) is the task of clustering unique author names from publication records in scholarly or related databases. Although AND has been extensively studied and has served as an important preprocessing step for several tasks (e.g. calculating bibliometrics and scientometrics for authors), there are few publicly available tools for disambiguation in large-scale scholarly databases. Furthermore, most of the disambiguated data is embedded within the search engines of the scholarly databases, and existing application programming interfaces (APIs) have limited features and are often unavailable for users for various reasons. This makes it difficult for researchers and developers to use the data for various applications (e.g. author search) or research. Here, we design a novel, web-based, RESTful API for searching disambiguated authors, using the PubMed database as a sample application. We offer two type of queries, attribute-based queries and record-based queries which serve different purposes. Attribute-based queries retrieve authors with the attributes available in the database. We study different search engines to find the most appropriate one for processing attribute-based queries. Record-based queries retrieve authors that are most likely to have written a query publication provided by a user. To accelerate record-based queries, we develop a novel algorithm that has a fast record-to-cluster match. We show that our algorithm can accelerate the query by a factor of 4.01 compared to a baseline naive approach. 

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3. Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications

   https://doi.org/10.3390/bioengineering12010056  

   Manzoor, Farhana; Tsurgeon, Cyruss A; Gupta, Vibhuti (January 2025, Bioengineering)

   RNA sequencing (RNA-seq) has emerged as a prominent resource for transcriptomic analysis due to its ability to measure gene expression in a highly sensitive and accurate manner. With the increasing availability of RNA-seq data analysis from clinical studies and patient samples, the development of effective visualization tools for RNA-seq analysis has become increasingly important to help clinicians and biomedical researchers better understand the complex patterns of gene expression associated with health and disease. This review aims to outline the current state-of-the-art data visualization techniques and tools commonly used to frame clinical inferences from RNA-seq data and point out their benefits, applications, and limitations. A systematic review of English articles using PubMed, Scopus, Web of Science, and IEEE Xplore databases was performed. Search terms included “RNA-seq”, “visualization”, “plots”, and “clinical”. Only full-text studies reported between 2017 and 2024 were included for analysis. Following PRISMA guidelines, a total of 126 studies were identified, of which 33 studies met the inclusion criteria. We found that 18% of studies have visualization techniques and tools for circular RNA-seq data, 56% for single-cell RNA-seq data, 23% for bulk RNA-seq data, and 3% for long non-coding RNA-seq data. Overall, this review provides a comprehensive overview of the common visualization tools and their potential applications, which is a useful resource for researchers and clinicians interested in using RNA-seq data for various clinical purposes (e.g., diagnosis or prognosis). 

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4. FlyBase: updates to the Drosophila melanogaster knowledge base

   https://doi.org/10.1093/nar/gkaa1026  

   Larkin, Aoife; Marygold, Steven J; Antonazzo, Giulia; Attrill, Helen; dos Santos, Gilberto; Garapati, Phani V; Goodman, Joshua L; Gramates, L Sian; Millburn, Gillian; Strelets, Victor B; et al (November 2020, Nucleic Acids Research)

   null (Ed.)

   Abstract FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays (‘ribbons’) of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool. 

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5. Database Forensic Analysis with DBCarver

   Wagner, James; Rasin, Alexander; Malik, Tanu; Heart, Karen; Jehle, Hugo; Grier, Jonathan (January 2017, CIDR 2017, 8th Biennial Conference on Innovative Data Systems Research)

   The increasing use of databases in the storage of critical and sensitive information in many organizations has lead to an increase in the rate at which databases are exploited in computer crimes. While there are several techniques and tools available for database forensics, they mostly assume apriori database preparation, such as relying on tamper-detection software to be in place or use of detailed logging. Investigators, alternatively, need forensic tools and techniques that work on poorly-configured databases and make no assumptions about the extent of damage in a database. In this paper, we present DBCarver, a tool for reconstructing database content from a database image without using any log or system metadata. The tool uses page carving to reconstruct both query-able data and non-queryable data (deleted data). We describe how the two kinds of data can be combined to enable a variety of forensic analysis questions hitherto unavailable to forensic investigators. We show the generality and efficiency of our tool across several databases through a set of robust experiments. 

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