相关论文: DNA hybridization to mismatched templates: a chip …
Defect-free single atom array in optical tweezers is a promising platform for scalable quantum computing, quantum simulation, and quantum metrology. Extending single-species array to mixed-species one promise to offer new possibilities. In…
A novel combination of established data analysis techniques for reconstructing all charged-particle tracks in high energy collisions is proposed. It uses all information available in a collision event while keeping competing choices open as…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Deep predictive models of neuronal activity have recently enabled several new discoveries about the selectivity and invariance of neurons in the visual cortex. These models learn a shared set of nonlinear basis functions, which are linearly…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…
Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic…
The large beamforming gain used to operate at millimeter wave (mmWave) frequencies requires obtaining channel information to configure hybrid antenna arrays. Previously proposed wideband channel estimation strategies, however, assume…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
Small target detection is inherently challenging due to the minimal size, lack of distinctive features, and the presence of complex backgrounds. Heavy noise further complicates the task by both obscuring and imitating the target appearance.…
Due to the redundant nature of DNA synthesis and sequencing technologies, a basic model for a DNA storage system is a multi-draw "shuffling-sampling" channel. In this model, a random number of noisy copies of each sequence is observed at…
Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence…
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is…
Background: The evolution of microRNA regulation in metazoans is a mysterious process: MicroRNA sequences are highly conserved among distal organisms, but on the other hand, there is no evident conservation of their targets. Results: We…
For large libraries of small molecules, exhaustive combinatorial chemical screens become infeasible to perform when considering a range of disease models, assay conditions, and dose ranges. Deep learning models have achieved state of the…
Hybrid neural ordinary differential equations (neural ODEs) integrate mechanistic models with neural ODEs, offering strong inductive bias and flexibility, and are particularly advantageous in data-scarce healthcare settings. However,…
Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…
Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…
Reconstructing charged particle tracks is a fundamental task in modern collider experiments. The unprecedented particle multiplicities expected at the High-Luminosity Large Hadron Collider (HL-LHC) pose significant challenges for track…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…