Methods in molecular biology (Clifton, N.J.)
34590279
Advances in molecular genetics through high-throughput gene mutagenesis and genetic crossing have enabled gene interaction mapping across whole genomes. Detecting gene interactions in even small microbial genomes relies on measuring growth phenotypes...
Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical bio...
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs usin...
Stomata are adjustable pores on leaf surfaces that regulate the tradeoff of CO2 uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping ep...
In higher eukaryotic cells, chromosomes are folded inside the nucleus. Recent advances in whole-genome mapping technologies have revealed the multiscale features of 3D genome organization that are intertwined with fundamental genome functions. Howeve...
Bulked segregant analysis (BSA) is a rapid, cost-effective method for mapping mutations and quantitative trait loci (QTLs) in animals and plants based on high-throughput sequencing. However, the algorithms currently used for BSA have not been systema...
The ubiquitous availability of genome sequencing data explains the popularity of machine learning-based methods for the prediction of protein properties from their amino acid sequences. Over the years, while revising our own work, reading submitted m...
Globally, millions of lives are impacted every year by infectious diseases outbreaks. Comprehensive and innovative surveillance strategies aiming at early alert and timely containment of emerging and reemerging pathogens are a pressing priority. Shor...
IEEE transactions on biomedical circuits and systems
38157470
In this article, we introduce GEMA, a genome exact mapping accelerator based on learned indexes, specifically designed for FPGA implementation. GEMA utilizes a machine learning (ML) algorithm to precisely locate the exact position of read sequences w...
Chemical mutagenesis-driven forward genetic screens are pivotal in unveiling gene functions, yet identifying causal mutations behind phenotypes remains laborious, hindering their high-throughput application. Here, we reveal a non-uniform mutation rat...