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Chi Hoang

dblp:01/1812 · DBLP profile ↗
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2ranked-venue papers
0as first author
1since 2021 · last 2024
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Databases, data management, data science and information retrieval · 1Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Databases, data mining, and information retrieval
1 paper
Query processing and optimization · 77% Database system architecture and tuning · 23%

Topics — the 2 heaviest of 5, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
protein sequence analysis
0.812024
Fast and scalable querying of eukaryotic linear motifs with gget elm · Bioinform. 2024
Bioinformatics and computational biology › sequence analysis › motif discovery
short linear motif discovery
0.812024
Fast and scalable querying of eukaryotic linear motifs with gget elm · Bioinform. 2024
YearPublicationVenuePosition
2024 Fast and scalable querying of eukaryotic linear motifs with gget elm
abstract
MOTIVATION: Eukaryotic linear motifs (ELMs), or Short Linear Motifs, are protein interaction modules that play an essential role in cellular processes and signaling networks and are often involved in diseases like cancer. The ELM database is a collection of manually curated motif knowledge from scientific papers. It has become a crucial resource for investigating motif biology and recognizing candidate ELMs in novel amino acid sequences. Users can search amino acid sequences or UniProt Accessions on the ELM resource web interface. However, as with many web services, there are limitations in the swift processing of large-scale queries through the ELM web interface or API calls, and, therefore, integration into protein function analysis pipelines is limited. RESULTS: To allow swift, large-scale motif analyses on protein sequences using ELMs curated in the ELM database, we have extended the gget suite of Python and command line tools with a new module, gget elm, which does not rely on the ELM server for efficiently finding candidate ELMs in user-submitted amino acid sequences and UniProt Accessions. gget elm increases accessibility to the information stored in the ELM database and allows scalable searches for motif-mediated interaction sites in the amino acid sequences. AVAILABILITY AND IMPLEMENTATION: The manual and source code are available at https://github.com/pachterlab/gget.
Laura Luebbert, Chi Hoang, Manjeet Kumar, Lior Pachter
Bioinform.2
1996 EROC: A Toolkit for Building NEATO Query Optimizers
William J. McKenna, Louis Burger, Chi Hoang, Melissa Truong
VLDB3