Hold out the genome: a roadmap to solving the cis-regulatory code
CG de Boer, J Taipale - Nature, 2024 - nature.com
Gene expression is regulated by transcription factors that work together to read cis-
regulatory DNA sequences. The 'cis-regulatory code'—how cells interpret DNA sequences …
regulatory DNA sequences. The 'cis-regulatory code'—how cells interpret DNA sequences …
Machine-guided design of cell-type-targeting cis-regulatory elements
Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity,
developmental timing and stimulus responses, which collectively define the thousands of …
developmental timing and stimulus responses, which collectively define the thousands of …
LegNet: a best-in-class deep learning model for short DNA regulatory regions
Motivation The increasing volume of data from high-throughput experiments including
parallel reporter assays facilitates the development of complex deep-learning approaches …
parallel reporter assays facilitates the development of complex deep-learning approaches …
Improving the generalization of protein expression models with mechanistic sequence information
Y Shen, G Kudla, DA Oyarzún - Nucleic Acids Research, 2025 - academic.oup.com
The growing demand for biological products drives many efforts to maximize expression of
heterologous proteins. Advances in high-throughput sequencing can produce data suitable …
heterologous proteins. Advances in high-throughput sequencing can produce data suitable …
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints …
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with
chromatin accessibility assays, the sequence syntax and genetic variants that regulate …
chromatin accessibility assays, the sequence syntax and genetic variants that regulate …
A generative framework for enhanced cell-type specificity in rationally designed mRNAs
mRNA delivery offers new opportunities for disease treatment by directing cells to produce
therapeutic proteins. However, designing highly stable mRNAs with programmable cell type …
therapeutic proteins. However, designing highly stable mRNAs with programmable cell type …
Predicting gene expression using millions of yeast promoters reveals cis-regulatory logic
T Dash, S Bornelöv - bioRxiv, 2025 - biorxiv.org
Motivation: Gene regulation involves complex interactions between multiple transcription
factors. While early attempts to train deep neural networks to predict gene expression were …
factors. While early attempts to train deep neural networks to predict gene expression were …
Functional yeast promoter sequence design using temporal convolutional generative language models
I Alsaggaf, C Wan - bioRxiv, 2024 - biorxiv.org
Promoter sequence design is the key to accurately control gene expression processes that
play a crucial role in biological systems. Thanks to the recent community effort, we are now …
play a crucial role in biological systems. Thanks to the recent community effort, we are now …
Guiding future genomics research through machine learning: functional DNA analysis and benchmarking
I Luthra - 2024 - open.library.ubc.ca
Differences in gene expression can drive variation in phenotypes and disease. Gene
expression is modulated, in part, by proteins called transcription factors that bind specific …
expression is modulated, in part, by proteins called transcription factors that bind specific …