Decoding enhancer complexity with machine learning and high-throughput discovery
GD Smith, WH Ching, P Cornejo-Páramo, ES Wong - Genome biology, 2023 - Springer
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their
flexible organization and functional redundancies make deciphering their sequence-function …
flexible organization and functional redundancies make deciphering their sequence-function …
Mechanisms of binding specificity among bHLH transcription factors
The transcriptome of every cell is orchestrated by the complex network of interaction
between transcription factors (TFs) and their binding sites on DNA. Disruption of this network …
between transcription factors (TFs) and their binding sites on DNA. Disruption of this network …
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression
The proximal tubule is a key regulator of kidney function and glucose metabolism. Diabetic
kidney disease leads to proximal tubule injury and changes in chromatin accessibility that …
kidney disease leads to proximal tubule injury and changes in chromatin accessibility that …
Cell-type-directed design of synthetic enhancers
II Taskiran, KI Spanier, H Dickmänken, N Kempynck… - Nature, 2024 - nature.com
Transcriptional enhancers act as docking stations for combinations of transcription factors
and thereby regulate spatiotemporal activation of their target genes. It has been a long …
and thereby regulate spatiotemporal activation of their target genes. It has been a long …
[HTML][HTML] Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation
C Bravo Gonzalez-Blas, I Matetovici, H Hillen… - Nature Cell …, 2024 - nature.com
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based
on their location within the liver lobule. However, it is unclear whether this spatial variation …
on their location within the liver lobule. However, it is unclear whether this spatial variation …
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation
KJ Brennan, M Weilert, S Krueger, A Pampari, H Liu… - Developmental cell, 2023 - cell.com
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out
cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive …
cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive …
Decoding gene regulation in the fly brain
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome
analysis,,,,–, three-dimensional morphological classification and electron microscopy …
analysis,,,,–, three-dimensional morphological classification and electron microscopy …
Evaluating deep learning for predicting epigenomic profiles
Deep learning has been successful at predicting epigenomic profiles from DNA sequences.
Most approaches frame this task as a binary classification relying on peak callers to define …
Most approaches frame this task as a binary classification relying on peak callers to define …
Dirichlet flow matching with applications to dna sequence design
Discrete diffusion or flow models could enable faster and more controllable sequence
generation than autoregressive models. We show that na\" ive linear flow matching on the …
generation than autoregressive models. We show that na\" ive linear flow matching on the …
Predictive analyses of regulatory sequences with EUGENe
Deep learning has become a popular tool to study cis-regulatory function. Yet efforts to
design software for deep-learning analyses in regulatory genomics that are findable …
design software for deep-learning analyses in regulatory genomics that are findable …