CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data-Reference-Cited by-同舟云学术

CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data

Published:2017-12-21 Issue:10 Volume:34 Page:1733-1740
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Chen Xi¹,Gu Jinghua¹,Wang Xiao¹,Jung Jin-Gyoung²,Wang Tian-Li²,Hilakivi-Clarke Leena³,Clarke Robert³,Xuan Jianhua¹^ORCID

Affiliation:

1. Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA

2. Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA

3. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA

Funder

National Institutes of Health

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/article-pdf/34/10/1733/25118178/btx827.pdf

Reference31 articles.

1. Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems;Angelini;Front. Cell. Dev. Biol,2014

2. Clustering of genes into regulons using integrated modeling-COGRIM;Chen;Genome Biol,2007

3. ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles;Chen;Nucleic Acids Res,2016

4. Reconstruction of transcriptional regulatory networks by stability-based network component analysis;Chen;IEEE/ACM Trans. Comput. Biol. Bioinform,2013

5. The functional consequences of variation in transcription factor binding;Cusanovich;PLoS Genet,2014

Cited by 17 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Using single cell atlas data to reconstruct regulatory networks;Nucleic Acids Research;2023-02-10

2. Novel estrogen-responsive genes (ERGs) for the evaluation of estrogenic activity;PLOS ONE;2022-08-17

3. APT: An Automated Probe Tracker From Gene Expression Data;IEEE/ACM Transactions on Computational Biology and Bioinformatics;2021-09-01

4. ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements;PLOS Computational Biology;2021-07-22

5. ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach;BMC Bioinformatics;2021-04-15