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2024
Gene regulatory network co-option is sufficient to induce a morphological novelty in Drosophila
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
***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
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
2015
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints
2014
TRF2, but not TBP, mediates the transcription of ribosomal protein genes
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
A computational pipeline for comparative ChIP-seq analyses
2008
Promoter elements associated with RNA Pol II stalling in the Drosophila