Characterizing Different Modes of Interplay between Rap1 and H3 using Inducible H3-depletion Yeast

Genome-wide gene expression responses to experimental manipulation of Saccharomyces cerevisiae repressor activator protein 1 (Rap1) expression level

(2023) S. Kalra et al.   GENOMICS

Topography of mutational signatures in human cancer

(2023) Burçak Otlu et al.   Cell Reports

YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis

(2022) Miguel Cacho Teixeira et al.   NUCLEIC ACIDS RESEARCH

On the role of transcription in positioning nucleosomes

(2021) Zhongling Jiang et al.   PLoS Computational Biology

Primary Role of the Nucleosome

(2020) Roger D. Kornberg et al.   MOLECULAR CELL

Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

(2019) Benjamin T Donovan et al.   eLife

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Rap1‐mediated nucleosome displacement can regulate gene expression in senescent cells without impacting the pace of senescence

(2019) Shufei Song et al.   AGING CELL

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast

(2019) Wu Wei et al.   GENOME RESEARCH

Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor

(2019) Maxime Mivelaz et al.   MOLECULAR CELL

Systematic Study of Nucleosome-Displacing Factors in Budding Yeast

(2018) Chao Yan et al.   MOLECULAR CELL

Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor

(2018) Andrew C.K. Wu et al.   MOLECULAR CELL

General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation

(2018) Drice Challal et al.   MOLECULAR CELL

Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis

(2017) Sandra Cortijo et al.   Molecular Plant

The coupled effect of nucleosome organization on gene transcription level and transcriptional plasticity

(2017) Jian Chen et al.   Nucleus

The coupled effect of nucleosome organization on gene transcription level and transcriptional plasticity

(2017) Jian Chen et al.   Nucleus

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Promoter architectures and developmental gene regulation

(2016) Vanja Haberle et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The topography of mutational processes in breast cancer genomes

(2016) Sandro Morganella et al.   Nature Communications

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

DiffLogo: a comparative visualization of sequence motifs

(2015) Martin Nettling et al.   BMC BIOINFORMATICS

Molecular mechanisms of ribosomal protein gene coregulation

(2015) Rohit Reja et al.   GENES & DEVELOPMENT

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Nucleosome organization in the vicinity of transcription factor binding sites in the human genome

(2014) Yumin Nie et al.   BMC GENOMICS

Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding

(2013) Ximiao He et al.   BMC GENOMICS

Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence

(2013) J. M. Platt et al.   GENES & DEVELOPMENT

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

(2013) Ronnie Blecher-Gonen et al.   Nature Protocols

DNA Sequence Preferences of Transcriptional Activators Correlate More Strongly than Repressors with Nucleosomes

(2012) Varodom Charoensawan et al.   MOLECULAR CELL

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

In Vivo Effects of Histone H3 Depletion on Nucleosome Occupancy and Position in Saccharomyces cerevisiae

(2012) Andrea J. Gossett et al.   PLoS Genetics

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

(2011) Raluca Gordân et al.   GENOME BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Genomic repertoires of DNA-binding transcription factors across the tree of life

(2010) Varodom Charoensawan et al.   NUCLEIC ACIDS RESEARCH

Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local

(2010) Wee Siong Goh et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence

(2009) Zhiming Dai et al.   BMC GENOMICS

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome

(2009) R. Thomas Koerber et al.   MOLECULAR CELL

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

(2009) Yong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY