Deep cis-regulatory homology of the butterfly wing pattern ground plan

Enhancer redundancy in development and disease

(2021) Evgeny Z. Kvon et al.   NATURE REVIEWS GENETICS

Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms

(2021) Frank Grosveld et al.   Annual Review of Genomics and Human Genetics

HALPER facilitates the identification of regulatory element orthologs across species

(2020) Xiaoyu Zhang et al.   BIOINFORMATICS

Cross-species analysis of enhancer logic using deep learning

(2020) Liesbeth Minnoye et al.   GENOME RESEARCH

Contrasting Roles of Transcription Factors Spineless and EcR in the Highly Dynamic Chromatin Landscape of Butterfly Wing Metamorphosis

(2019) Karin R.L. van der Burg et al.   Cell Reports

Multi-enhancer transcriptional hubs confer phenotypic robustness

(2019) Albert Tsai et al.   eLife

Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry

(2019) James J. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interplay between Developmental Flexibility and Determinism in the Evolution of Mimetic Heliconius Wing Patterns

(2019) Carolina Concha et al.   CURRENT BIOLOGY

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

(2018) Jianhong Ou et al.   BMC GENOMICS

A Comprehensive and Dated Phylogenomic Analysis of Butterflies

(2018) Marianne Espeland et al.   CURRENT BIOLOGY

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

(2018) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Macroevolutionary shifts ofWntAfunction potentiate butterfly wing-pattern diversity

(2017) Anyi Mazo-Vargas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome

(2017) Ha Youn Shin et al.   Nature Communications

Complex modular architecture around a simple toolkit of wing pattern genes

(2017) Steven M. Van Belleghem et al.   Nature Ecology & Evolution

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems

(2014) Arnaud Martin et al.   DEVELOPMENTAL BIOLOGY

Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects

(2014) Majid Kazemian et al.   Genome Biology and Evolution

Ancient homology underlies adaptive mimetic diversity across butterflies

(2014) Jason R. Gallant et al.   Nature Communications

HAL: a hierarchical format for storing and analyzing multiple genome alignments

(2013) Glenn Hickey et al.   BIOINFORMATICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand

(2012) A. Martin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS