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Microscopy imaging plays a vital role in understanding many biological processes in development and disease. The recent advances in automation of microscopes and development of methods and markers for live cell imaging has led to rapid…
Machine learning pipelines for classification tasks often train a universal model to achieve accuracy across a broad range of classes. However, a typical user encounters only a limited selection of classes regularly. This disparity provides…
Histone modifications play a critical role in gene regulation. Consequently, predicting gene expression from histone modification signals is a highly motivated problem in epigenetics. We build upon the work of DeepChrome by Singh et al.…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
Text-guided 3D editing aims to modify existing 3D assets using natural-language instructions. Current methods struggle to jointly understand complex prompts, automatically localize edits in 3D, and preserve unedited content. We introduce…
In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure,…
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
The discovery of CRISPR-mediated gene activation (CRISPRa) has transformed the way in which we perform genetic screening, bioproduction and therapeutics through its ability to scale and multiplex. However, the emergence of loads on the key…
Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation…
Therapeutic antibody candidates often require extensive engineering to improve key functional and developability properties before clinical development. This can be achieved through iterative design, where starting molecules are optimized…
Genomic selection (GS), as a critical crop breeding strategy, plays a key role in enhancing food production and addressing the global hunger crisis. The predominant approaches in GS currently revolve around employing statistical methods for…
Raman spectroscopy (RS) has been widely used for disease diagnosis, e.g., cardiovascular disease (CVD), owing to its efficiency and component-specific testing capabilities. A series of popular deep learning methods have recently been…
Advances in unsupervised learning of object-representations have culminated in the development of a broad range of methods for unsupervised object segmentation and interpretable object-centric scene generation. These methods, however, are…
Protein tertiary structure prediction has improved dramatically in recent years. A considerable fraction of various proteomes can be modelled in the absence of structural templates. We ask whether our DMPfold method can model all the…
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this…
Program synthesis aims to {\it automatically} find programs from an underlying programming language that satisfy a given specification. While this has the potential to revolutionize computing, how to search over the vast space of programs…
The three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput…
CVTree is an alignment-free methodology for inferring species phylogeny and taxonomy. This method allows for the efficient and accurate resolution of evolutionary relationships among large numbers of species based on whole-genome sequence…
DNA and other biopolymers are being investigated as new computing substrates and alternative to silicon-based digital computers. However, the established top-down design of biomolecular interaction networks remains challenging and does not…
Background: Creeping bentgrass (Agrostis soionifera) is a perennial grass of Gramineae, belonging to cold season turfgrass, but has poor disease resistance. Up to now, little is known about the induced systemic resistance (ISR) mechanism,…