[HTML][HTML] Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants

E Yasmeen, J Wang, M Riaz, L Zhang, K Zuo - Plant Communications, 2023 - cell.com
With the development of high-throughput biology techniques and artificial intelligence, it has
become increasingly feasible to design and construct artificial biological parts, modules …

[HTML][HTML] Recent advances in generative adversarial networks for gene expression data: a comprehensive review

M Lee - Mathematics, 2023 - mdpi.com
The evolving field of generative artificial intelligence (GenAI), particularly generative deep
learning, is revolutionizing a host of scientific and technological sectors. One of the pivotal …

How will generative AI disrupt data science in drug discovery?

JP Vert - Nature Biotechnology, 2023 - nature.com
In the short few months since the release of ChatGPT 1, 2, the potential for large language
models (LLMs) and generative artificial intelligence (AI) to disrupt fields as diverse as art …

Dirichlet diffusion score model for biological sequence generation

P Avdeyev, C Shi, Y Tan, K Dudnyk… - … on Machine Learning, 2023 - proceedings.mlr.press
Designing biological sequences is an important challenge that requires satisfying complex
constraints and thus is a natural problem to address with deep generative modeling …

[HTML][HTML] 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 …

[HTML][HTML] Deep flanking sequence engineering for efficient promoter design using DeepSEED

P Zhang, H Wang, H Xu, L Wei, L Liu, Z Hu… - Nature …, 2023 - nature.com
Designing promoters with desirable properties is essential in synthetic biology. Human
experts are skilled at identifying strong explicit patterns in small samples, while deep …

Computational design of mRNA vaccines

YA Kim, K Mousavi, A Yazdi, M Zwierzyna, M Cardinali… - Vaccine, 2024 - Elsevier
Abstract mRNA technology has emerged as a successful vaccine platform that offered a swift
response to the COVID-19 pandemic. Accumulating evidence shows that vaccine efficacy …

Machine learning for heavy metal removal from water: recent advances and challenges

X Yuan, J Li, JY Lim, A Zolfaghari, DS Alessi… - ACS ES&T …, 2023 - ACS Publications
Research on the removal of heavy metals (HMs) from contaminated waters, aiming at
ensuring the safety of water bodies, has shifted from direct experimental tests to machine …

[HTML][HTML] An overview of deep generative models in functional and evolutionary genomics

B Yelmen, F Jay - Annual Review of Biomedical Data Science, 2023 - annualreviews.org
Following the widespread use of deep learning for genomics, deep generative modeling is
also becoming a viable methodology for the broad field. Deep generative models (DGMs) …

[HTML][HTML] Machine-guided design of synthetic cell type-specific cis-regulatory elements

SJ Gosai, RI Castro, N Fuentes, JC Butts, S Kales… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity,
developmental timing, and stimulus responses, which collectively define the thousands of …