Protocols and Manuscripts

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2025

Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model

[preprint] PISA: a versatile interpretation tool for visualizing cis-regulatory rules in genomic data

2024

Co-option of the trichome-forming network initiated the evolution of a morphological novelty in Drosophila eugracilis

2023

***Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development

Off the deep end: What can deep learning do for the gene expression field?

Emerging questions in transcriptional regulation

The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

[preprint] De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding

2021

The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters

TATA and paused promoters active in differentiated tissues have distinct expression characteristics

Evaluation of facial aesthetics by laypersons in patients undergoing intraoral quadrangular Le Fort II osteotomy compared with conventional Le Fort I osteotomy

***Base-resolution models of transcription-factor binding reveal soft motif syntax

2020

Seven myths of how transcription factors read the cisregulatory code

b-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells

2019

An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster

A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing

2018

Capicua controls Toll/IL-1 signaling targets independently of RTK regulation

Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing

Author Correction: Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion

2017

Paused RNA polymerase II inhibits new transcriptional initiation

Hippo Reprograms the Transcriptional Response to Ras Signaling

Drosophila poised enhancers are generated during tissue patterning with the help of repression

Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis

***HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets

2016

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

2015

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

2014

TRF2, but not TBP, mediates the transcription of ribosomal protein genes

Molecular Evolution of the Yap/Yorkie Proto-Oncogene and Elucidation of Its Core Transcriptional Program

RNA polymerase II pausing during development

2013

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

Identification of transcription factor binding sites from ChIP-seq data at high resolution

2012

Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression

2011

Developmental gene regulation in the era of genomics

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

A computational pipeline for comparative ChIP-seq analyses

2008

Promoter elements associated with RNA Pol II stalling in the Drosophila

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