Microfluidics: reframing biological enquiry

TA Duncombe, AM Tentori, AE Herr - Nature Reviews Molecular Cell …, 2015 - nature.com
The underlying physical properties of microfluidic tools have led to new biological insights
through the development of microsystems that can manipulate, mimic and measure biology …

Deciphering the transcriptional cis-regulatory code

JO Yáñez-Cuna, EZ Kvon, A Stark - Trends in Genetics, 2013 - cell.com
Information about developmental gene expression resides in defined regulatory elements,
called enhancers, in the non-coding part of the genome. Although cells reliably utilize …

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

KR Nitta, A Jolma, Y Yin, E Morgunova, T Kivioja… - elife, 2015 - elifesciences.org
Divergent morphology of species has largely been ascribed to genetic differences in the
tissue-specific expression of proteins, which could be achieved by divergence in cis …

Transcriptional regulators form diverse groups with context-dependent regulatory functions

G Stampfel, T Kazmar, O Frank, S Wienerroither… - Nature, 2015 - nature.com
One of the most important questions in biology is how transcription factors (TFs) and
cofactors control enhancer function and thus gene expression. Enhancer activation usually …

[HTML][HTML] A genome-scale resource for the functional characterization of Arabidopsis transcription factors

JL Pruneda-Paz, G Breton, DH Nagel, SE Kang… - Cell reports, 2014 - cell.com
Extensive transcriptional networks play major roles in cellular and organismal functions.
Transcript levels are in part determined by the combinatorial and overlapping functions of …

Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Populus trichocarpa

H Chen, JP Wang, H Liu, H Li, YCJ Lin, R Shi… - The Plant …, 2019 - academic.oup.com
Wood remains the world's most abundant and renewable resource for timber and pulp and
is an alternative to fossil fuels. Understanding the molecular regulation of wood formation …

Spatial expression of transcription factors in Drosophilaembryonic organ development

AS Hammonds, CA Bristow, WW Fisher, R Weiszmann… - Genome biology, 2013 - Springer
Background Site-specific transcription factors (TFs) bind DNA regulatory elements to control
expression of target genes, forming the core of gene regulatory networks. Despite decades …

A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing

H Zhu, SD Zhao, A Ray, Y Zhang, X Li - Nature communications, 2022 - nature.com
During development, neural progenitors are temporally patterned to sequentially generate a
variety of neural types. In Drosophila neural progenitors called neuroblasts, temporal …

A comprehensive Drosophila melanogaster transcription factor interactome

L Shokri, S Inukai, A Hafner, K Weinand, K Hens… - Cell reports, 2019 - cell.com
Combinatorial interactions among transcription factors (TFs) play essential roles in
generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid …

Cell type–specific genomics of Drosophila neurons

GL Henry, FP Davis, S Picard, SR Eddy - Nucleic acids research, 2012 - academic.oup.com
Many tools are available to analyse genomes but are often challenging to use in a cell type–
specific context. We have developed a method similar to the isolation of nuclei tagged in a …