scholarly journals GIGGLE: a search engine for large-scale integrated genome analysis

2017 ◽  
Author(s):  
Ryan M. Layer ◽  
Brent S. Pedersen ◽  
Tonya DiSera ◽  
Gabor T. Marth ◽  
Jason Gertz ◽  
...  
Keyword(s):  
Data Integration ◽  
Search Engine ◽  
Genome Analysis ◽  
Large Scale ◽  
Hypothesis Generation ◽  
Link Type

AbstractGIGGLE is a genomics search engine that identifies and ranks the significance of shared genomic loci between query features and thousands of genome interval files. GIGGLE scales to billions of intervals, is faster (+1,000X) than existing methods, and its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEX by facilitating data integration and hypothesis generation. GIGGLE is available at https://github.com/ryanlayer/giggle.

scholarly journals GIGGLE: a search engine for large-scale integrated genome analysis

2018 ◽  
Vol 15 (2) ◽  
pp. 123-126 ◽  
Author(s):  
Ryan M Layer ◽  
Brent S Pedersen ◽  
Tonya DiSera ◽  
Gabor T Marth ◽  
Jason Gertz ◽  
...  
Keyword(s):  
Search Engine ◽  
Genome Analysis ◽  
Large Scale

scholarly journals Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Deborah O. Dele-Oni ◽  
Karen E. Christianson ◽  
Shawn B. Egri ◽  
Alvaro Sebastian Vaca Jacome ◽  
Katherine C. DeRuff ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Model ◽  
Cellular Responses ◽  
Proteomic Profiling ◽  
Reduced Representation ◽  
Link Type ◽  
Original Dataset ◽  
Quality Control Metrics ◽  
Biological Insight ◽  
Chromatin Profiling

AbstractWhile gene expression profiling has traditionally been the method of choice for large-scale perturbational profiling studies, proteomics has emerged as an effective tool in this context for directly monitoring cellular responses to perturbations. We previously reported a pilot library containing 3400 profiles of multiple perturbations across diverse cellular backgrounds in the reduced-representation phosphoproteome (P100) and chromatin space (Global Chromatin Profiling, GCP). Here, we expand our original dataset to include profiles from a new set of cardiotoxic compounds and from astrocytes, an additional neural cell model, totaling 5300 proteomic signatures. We describe filtering criteria and quality control metrics used to assess and validate the technical quality and reproducibility of our data. To demonstrate the power of the library, we present two case studies where data is queried using the concept of “connectivity” to obtain biological insight. All data presented in this study have been deposited to the ProteomeXchange Consortium with identifiers PXD017458 (P100) and PXD017459 (GCP) and can be queried at https://clue.io/proteomics.

scholarly journals The Matter of Chance: Auditing Web Search Results Related to the 2020 U.S. Presidential Primary Elections Across Six Search Engines

2021 ◽  
pp. 089443932110068
Author(s):  
Aleksandra Urman ◽  
Mykola Makhortykh ◽  
Roberto Ulloa
Keyword(s):  
Search Engine ◽  
Search Engines ◽  
Large Scale ◽  
Web Search ◽  
Primary Elections ◽  
Virtual Agents ◽  
Search Results ◽  
Presidential Primary ◽  
Large Scale Analysis ◽  
Algorithmic Information

We examine how six search engines filter and rank information in relation to the queries on the U.S. 2020 presidential primary elections under the default—that is nonpersonalized—conditions. For that, we utilize an algorithmic auditing methodology that uses virtual agents to conduct large-scale analysis of algorithmic information curation in a controlled environment. Specifically, we look at the text search results for “us elections,” “donald trump,” “joe biden,” “bernie sanders” queries on Google, Baidu, Bing, DuckDuckGo, Yahoo, and Yandex, during the 2020 primaries. Our findings indicate substantial differences in the search results between search engines and multiple discrepancies within the results generated for different agents using the same search engine. It highlights that whether users see certain information is decided by chance due to the inherent randomization of search results. We also find that some search engines prioritize different categories of information sources with respect to specific candidates. These observations demonstrate that algorithmic curation of political information can create information inequalities between the search engine users even under nonpersonalized conditions. Such inequalities are particularly troubling considering that search results are highly trusted by the public and can shift the opinions of undecided voters as demonstrated by previous research.

Large-scale Data Integration for Facilities Analytics: Challenges and Opportunities

2020 ◽  
Author(s):  
Balaje T. Thumati ◽  
Halasya Siva Subramania ◽  
Rajeev Shastri ◽  
Karthik Kalyana Kumar ◽  
Nicole Hessner ◽  
...  
Keyword(s):  
Data Integration ◽  
Large Scale ◽  
Large Scale Data ◽  
Challenges And Opportunities ◽  
Scale Data

scholarly journals Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration

2011 ◽  
Vol 5 ◽  
Author(s):  
Leon French ◽  
Powell Patrick Cheng Tan ◽  
Paul Pavlidis
Keyword(s):  
Gene Expression ◽  
Data Integration ◽  
Large Scale ◽  
Scale Analysis ◽  
Rodent Brain ◽  
Large Scale Analysis

Reliability of a Distributed Search Engine for Fresh Information Retrieval in Large-Scale Intranet

2006 ◽  
pp. 203-216
Author(s):  
Nobuyoshi Sato ◽  
Minoru Udagawa ◽  
Minoru Uehara ◽  
Yoshifumi Sakai ◽  
Hideki Mori
Keyword(s):  
Information Retrieval ◽  
Search Engine ◽  
Large Scale ◽  
Distributed Search

scholarly journals SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

2020 ◽  
Vol 16 (12) ◽  
pp. e1008439
Author(s):  
Jennifer Lu ◽  
Steven L. Salzberg
Keyword(s):  
Large Scale ◽  
Analysis Tool ◽  
Index Test ◽  
Bacterial Genomes ◽  
Phylogenetic Groups ◽  
Bacterial Phyla ◽  
Link Type ◽  
Gc Skew ◽  
A Genome ◽  
Web App

GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands of the same chromosome contain different proportions of guanine and cytosine nucleotides. Here we demonstrate that this phenomenon, which was first discovered in the mid-1990s, can be used today as an analysis tool for the 15,000+ complete bacterial genomes in NCBI’s Refseq library. In order to analyze all 15,000+ genomes, we introduce a new method, SkewIT (Skew Index Test), that calculates a single metric representing the degree of GC skew for a genome. Using this metric, we demonstrate how GC skew patterns are conserved within certain bacterial phyla, e.g. Firmicutes, but show different patterns in other phylogenetic groups such as Actinobacteria. We also discovered that outlier values of SkewIT highlight potential bacterial mis-assemblies. Using our newly defined metric, we identify multiple mis-assembled chromosomal sequences in previously published complete bacterial genomes. We provide a SkewIT web app https://jenniferlu717.shinyapps.io/SkewIT/ that calculates SkewI for any user-provided bacterial sequence. The web app also provides an interactive interface for the data generated in this paper, allowing users to further investigate the SkewI values and thresholds of the Refseq-97 complete bacterial genomes. Individual scripts for analysis of bacterial genomes are provided in the following repository: https://github.com/jenniferlu717/SkewIT.

scholarly journals PaperBLAST: Text-mining papers for information about homologs

2017 ◽  
Author(s):  
Morgan N. Price ◽  
Adam P. Arkin
Keyword(s):  
Text Mining ◽  
Genome Sequencing ◽  
Full Text ◽  
Large Scale ◽  
Scientific Literature ◽  
Protein Sequences ◽  
Protein Coding ◽  
Link Protein ◽  
Protein Coding Genes ◽  
Link Type

AbstractLarge-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources that link protein sequences to scientific articles (Swiss-Prot, GeneRIF, and EcoCyc). PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/.

scholarly journals Identity and compatibility of reference genome resources

2021 ◽  
Author(s):  
Michał Stolarczyk ◽  
Bingjie Xue ◽  
Nathan C. Sheffield
Keyword(s):  
Coordinate System ◽  
Genome Analysis ◽  
Reference Genome ◽  
Reference Data ◽  
Coordinate Systems ◽  
Link Type ◽  
Novel Approach ◽  
Many Sources ◽  
Parent Child Relationships ◽  
Parent Child

Genome analysis relies on reference data like sequences, feature annotations, and aligner indexes. These data can be found in many versions from many sources, making it challenging to identify and assess compatibility among them. For example, how can you determine which indexes are derived from identical raw sequence files, or which annotations share a compatible coordinate system? Here, we describe a novel approach to establish identity and compatibility of reference genome resources. We approach this with three advances: First, we derive unique identifiers for each resource; second, we record parent-child relationships among resources; and third, we describe recursive identifiers that determine identity as well as compatibility of coordinate systems and sequence names. These advances facilitate portability, reproducibility, and re-use of genome reference data.Availabilityhttps://refgenie.databio.org

scholarly journals Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Gongchao Jing ◽  
Lu Liu ◽  
Zengbin Wang ◽  
Yufeng Zhang ◽  
Li Qian ◽  
...  
Keyword(s):  
Big Data ◽  
User Interface ◽  
Search Engine ◽  
Functional Similarity ◽  
Metagenomic Data ◽  
Data Sets ◽  
Data Space ◽  
Link Type ◽  
Database Platform ◽  
Microbiome Data

ABSTRACT Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes in the global metagenome data space based on the taxonomic or functional similarity of a whole microbiome to those in the database. MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a Web-based graphical user interface for user-friendly searching, data browsing, and tutoring. MSE 2 is freely accessible via http://mse.ac.cn. For standalone searches of customized microbiome databases, the kernel of the MSE 2 search engine is provided at GitHub (https://github.com/qibebt-bioinfo/meta-storms). IMPORTANCE A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird’s-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile. Key improvements include database extension, data compatibility, a search engine kernel, and a user interface. The new ability to search the microbiome space via functional similarity greatly expands the scope of search-based mining of the microbiome big data.

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