Quantitative Biology
ESCI-ISI SCOPUS (2013-2025)
2095-4697
2095-4689
Cơ quản chủ quản: Higher Education Press
Lĩnh vực:
Modeling and SimulationComputer Science ApplicationsBiochemistry, Genetics and Molecular Biology (miscellaneous)Applied Mathematics
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Các bài báo tiêu biểu
Variable importance-weighted random forests
Tập 5 - Trang 338-351 - 2017
Random Forests is a popular classification and regression method that has proven
powerful for various prediction problems in biological studies. However, its
performance often deteriorates when the number of features increases. To address
this limitation, feature elimination Random Forests was proposed that only uses
features with the largest variable importance scores. Yet the performance of
this...
Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA‐seq data
- 2018
BackgroundMost eukaryotic protein‐coding genes exhibit alternative cleavage and
polyadenylation (APA), resulting in mRNA isoforms with different 3′ untranslated
regions (3′ UTRs). Studies have shown that brain cells tend to express long 3′
UTR isoforms using distal cleavage and polyadenylation sites (PASs).MethodsUsing
our recently developed, comprehensive PAS database PolyA_DB, we developed an
ef...
Computational methodology for ChIP‐seq analysis
Tập 1 Số 1 - Trang 54-70 - 2013
Chromatin immunoprecipitation coupled with massive parallel sequencing
(ChIP‐seq) is a powerful technology to identify the genome‐wide locations of DNA
binding proteins such as transcription factors or modified histones. As more and
more experimental laboratories are adopting ChIP‐seq to unravel the
transcriptional and epigenetic regulatory mechanisms, computational analyses of
ChIP‐seq also becom...
Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP‐seq and chromatin accessibility data
Tập 8 Số 3 - Trang 267-276 - 2020
The Cistrome Data Browser (DB) at the website (cistrome.org/db) provides about
56,000 published human and mouse ChIP‐seq, DNase‐seq, and ATAC‐seq chromatin
profiles, which we have processed using uniform analysis and quality control
pipelines. The Cistrome DB Toolkit at the website (dbtoolkit.cistrome.org) was
developed to allow users to investigate fundamental questions using this data
collection...
Identifying miRNA‐disease association based on integrating miRNA topological similarity and functional similarity
Tập 7 Số 3 - Trang 202-209 - 2019
BackgroundMicroRNAs (miRNAs) are a significant type of non‐coding RNAs, which
usually were encoded by endogenous genes with about ~22 nt nucleotides.
Accumulating biological experiments have shown that miRNAs have close
associations with various human diseases. Although traditional experimental
methods achieve great successes in miRNA‐disease interaction identification,
these methods also have som...
Perspective on the q‐bio Summer School and Conference: 2007 – 2014 and beyond
Tập 2 Số 1 - Trang 54-58 - 2014
A resistant method for landmark‐based analysis of individual asymmetry in two dimensions
- 2016
BackgroundSymmetry of biological structures can be thought as the repetition of
their parts in different positions and orientations. Asymmetry analyses,
therefore, focuses on identifying and measuring the location and extent of
symmetry departures in such structures. In the context of geometric
morphometrics, a key step when studying morphological variation is the
estimation of the symmetric shape...
Transcriptome assembly strategies for precision medicine
- 2017
BackgroundPrecision medicine approach holds great promise to tailored diagnosis,
treatment and prevention. Individuals can be vastly different in their genomic
information and genetic mechanisms hence having unique transcriptomic
signatures. The development of precision medicine has demanded moving beyond DNA
sequencing (DNA‐Seq) to much more pointed RNA‐sequencing (RNA‐Seq) [ Cell, 2017,
168: 584...
TACO: Taxonomic prediction of unknown OTUs through OTU co‐abundance networks
- 2016
BackgroundA main goal of metagenomics is taxonomic characterization of microbial
communities. Although sequence comparison has been the main method for the
taxonomic classification, there is not a clear agreement on similarity
calculation and similarity thresholds, especially at higher taxonomic levels
such as phylum and class. Thus taxonomic classification of novel metagenomic
sequences without c...