Using graph modularity analysis to identify transcription factor binding sites

Factor Binding ◽

Identify Transcription Factor ◽

Modularity Analysis

A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines

STAR Protocols ◽

10.1016/j.xpro.2021.100750 ◽

2021 ◽

Vol 2 (3) ◽

pp. 100750

Author(s):

Nikki Ruoxi Kong ◽

Li Chai ◽

Daniel Geoffrey Tenen ◽

Mahmoud Adel Bassal

Keyword(s):

Transcription Factor ◽

Cell Lines ◽

Human Cell ◽

Binding Sites ◽

Human Cell Lines ◽

Analysis Pipeline ◽

Factor Binding ◽

Computational Methods to Identify Transcription Factor Binding Sites Using CAGE Information

Cap-Analysis Gene Expression (CAGE) ◽

10.1201/b11146-12 ◽

2009 ◽

pp. 137-151

Author(s):

Vladimir Bajic ◽

Sebastian Schmeier ◽

Cameron MacPherson

Keyword(s):

Transcription Factor ◽

Computational Methods ◽

Binding Sites ◽

Factor Binding ◽

Combining Greedy Method and Genetic Algorithm to Identify Transcription Factor Binding Sites

2006 Sixth International Conference on Hybrid Intelligent Systems (HIS'06) ◽

10.1109/his.2006.264898 ◽

2006 ◽

Cited By ~ 1

Author(s):

Wanyu Wang ◽

Xiaoyu Chang ◽

Chunguang Zhou

Keyword(s):

Genetic Algorithm ◽

Transcription Factor ◽

Binding Sites ◽

Greedy Method ◽

Factor Binding ◽

ConTra v3: a tool to identify transcription factor binding sites across species, update 2017

Nucleic Acids Research ◽

10.1093/nar/gkx376 ◽

2017 ◽

Vol 45 (W1) ◽

pp. W490-W494 ◽

Cited By ~ 33

Author(s):

Łukasz Kreft ◽

Arne Soete ◽

Paco Hulpiau ◽

Alexander Botzki ◽

Yvan Saeys ◽

...

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Factor Binding ◽

Tracing the Evolutionary History of Drosophila Regulatory Regions with Models that Identify Transcription Factor Binding Sites

Molecular Biology and Evolution ◽

10.1093/molbev/msg077 ◽

2003 ◽

Vol 20 (5) ◽

pp. 703-714 ◽

Cited By ~ 48

Author(s):

E. T. Dermitzakis

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Evolutionary History ◽

Regulatory Regions ◽

Factor Binding ◽

Identify Transcription Factor ◽

History Of

ConTra v2: a tool to identify transcription factor binding sites across species, update 2011

Nucleic Acids Research ◽

10.1093/nar/gkr355 ◽

2011 ◽

Vol 39 (suppl_2) ◽

pp. W74-W78 ◽

Cited By ~ 44

Author(s):

Stefan Broos ◽

Paco Hulpiau ◽

Jeroen Galle ◽

Bart Hooghe ◽

Frans Van Roy ◽

...

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Factor Binding ◽

Computational Methods to Identify Transcription Factor Binding Sites Using CAGE Information

Cap-Analysis Gene Expression (Cage) ◽

10.1201/9780429065750-11 ◽

2019 ◽

pp. 137-152

Author(s):

Vladimir B. Bajic ◽

Sebastian Schmeier ◽

Cameron Ross MacPherson

Keyword(s):

Transcription Factor ◽

Computational Methods ◽

Binding Sites ◽

Factor Binding ◽

Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-occurrence Graph

Bioinformatics Research and Applications - Lecture Notes in Computer Science ◽

10.1007/978-3-540-79450-9_21 ◽

2008 ◽

pp. 220-231

Author(s):

Alexandre P. Francisco ◽

Arlindo L. Oliveira ◽

Ana T. Freitas

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Promoter Regions ◽

Factor Binding ◽

Modularity Analysis

USING DNASE DIGESTION DATA TO ACCURATELY IDENTIFY TRANSCRIPTION FACTOR BINDING SITES

Biocomputing 2013 ◽

10.1142/9789814447973_0009 ◽

2012 ◽

Cited By ~ 4

Author(s):

KAIXUAN LUO ◽

ALEXANDER J. HARTEMINK

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Factor Binding ◽

Dnase Digestion ◽

A Bayesian Scoring Scheme based Particle Swarm Optimization algorithm to identify transcription factor binding sites

Applied Soft Computing ◽

10.1016/j.asoc.2012.04.006 ◽

2012 ◽

Vol 12 (9) ◽

pp. 2846-2855 ◽

Cited By ~ 5

Author(s):

Mustafa Karabulut ◽

Turgay Ibrikci

Keyword(s):

Transcription Factor ◽

Particle Swarm Optimization ◽

Optimization Algorithm ◽

Binding Sites ◽

Particle Swarm Optimization Algorithm ◽

Swarm Optimization ◽

Factor Binding ◽