Author details

Full Name

Tao Liu

Affiliation

ORCID

Career Start Year

2006

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37351601	Senescence-related receptor kinase 1 functions downstream of WRKY53 in regulating leaf senescence in Arabidopsis.		2023
34772935	Fast alignment and preprocessing of chromatin profiles with Chromap.	Nature Communications	2021
33258917	movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples.	Bioinformatics	2021
33142319	scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data.	Brief Bioinform	2021
32698196	Benchmarking variant callers in next-generation and third-generation sequencing analysis.	Briefings in Bioinformatics	2021
32767996	Integrative analyses of single-cell transcriptome and regulome using MAESTRO.		2020
31199868	HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.	Nucleic Acids Research	2019
31159718	Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA.	BMC Genomics	2019
27789702	Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.	Nucleic Acids Res	2017
29170441	Genome-wide identification and differential analysis of translational initiation.	Nat Commun	2017
27716038	ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.	BMC Bioinformatics	2016
26371315	Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin.	Proceedings of the National Academy of Sciences of the United States of America	2015
25833190	Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells.	Arthritis Rheumatol	2015
25164756	Comparative analysis of metazoan chromatin organization.	Nature	2014
24948806	An amino terminal phosphorylation motif regulates intranuclear compartmentalization of Olig2 in neural progenitor cells.	J Neurosci	2014
24743991	Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells.	Methods in Molecular Biology	2014
23508969	CistromeFinder for ChIP-seq and DNase-seq data reuse.		2013
25741452	Computational methodology for ChIP-seq analysis.	Quantitative Biology	2013
24315104	Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation.	Cell	2013
24244136	Practical guidelines for the comprehensive analysis of ChIP-seq data.	PLoS Comput Biol	2013
23239736	EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.	Science	2012
22936215	Identifying ChIP-seq enrichment using MACS.		2012
22495751	CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.		2012
22955991	ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.	Genome Res	2012
22522655	Systematic evaluation of factors influencing ChIP-seq fidelity.	Nat Methods	2012
21859476	Cistrome: an integrative platform for transcriptional regulation studies.	Genome Biol	2011
21393543	A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism.	Science	2011
21295131	Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites.	Genomics	2011
21284836	MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.		2011
21177964	Broad chromosomal domains of histone modification patterns in C. elegans.	Genome Res	2011
21633945	Using MACS to identify peaks from ChIP-Seq data.	Current Protocols in Bioinformatics	2011
21940749	A comprehensive view of nuclear receptor cancer cistromes.	Cancer Res	2011
21177976	Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.	Science	2010
19689956	CEAS: cis-regulatory element annotation system.		2009
19182803	Differential chromatin marking of introns and expressed exons by H3K36me3.	Nature Genetics	2009
18492288	MicroRNA-encoding long non-coding RNAs.	BMC Genomics	2008
18000000	NONCODE v2.0: decoding the non-coding.	Nucleic Acids Research	2008
18798982	Model-based analysis of ChIP-Seq (MACS).	Genome Biol	2008
18473345	An unusual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism.	Hum Mutat	2008
17785534	Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.	Genome Research	2007
16738136	Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.	Nucleic Acids Res	2006