A tissue dissociation method for ATAC-seq and CUT&RUN in Drosophila pupal tissues

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Damage-responsive, maturity-silenced enhancers regulate multiple genes that direct regeneration in Drosophila

(2020) Robin E Harris et al.   eLife

Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis

(2020) Matthew J Niederhuber et al.   Current Opinion in Insect Science

Direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone in Drosophila

(2019) Christopher M. Uyehara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Improved CUT&RUN chromatin profiling tools

(2019) Michael P Meers et al.   eLife

Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells

(2019) Yiqin Ma et al.   PLOS BIOLOGY

Separate Polycomb Response Elements control chromatin state and activation of the vestigial gene

(2019) Kami Ahmad et al.   PLoS Genetics

Damage-responsive elements in Drosophila regeneration

(2018) Elena Vizcaya-Molina et al.   GENOME RESEARCH

Hormone-dependent control of developmental timing through regulation of chromatin accessibility

(2017) Christopher M. Uyehara et al.   GENES & DEVELOPMENT

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development

(2016) Vincent Loubiere et al.   NATURE GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Dynamic CRM occupancy reflects a temporal map of developmental progression

(2010) Bartek Wilczyński et al.   Molecular Systems Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY