Related papers: Introgression Browser: High throughput whole-genom…
Quality traits are some of the most important and time-consuming phenotypes to evaluate in plant breeding programs. These traits are often evaluated late in the breeding pipeline due to their cost, resulting in the potential advancement of…
Complete genome sequences contain valuable information about natural selection, but extracting this information for short, widely scattered noncoding elements remains a challenging problem. Here we introduce a new computational method for…
Background: Cancers are highly heterogeneous with different subtypes. These subtypes often possess different genetic variants, present different pathological phenotypes, and most importantly, show various clinical outcomes such as varied…
Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…
Recently, the EAGL-I system was developed to rapidly create massive labeled datasets of plants intended to be commonly used by farmers and researchers to create AI-driven solutions in agriculture. As a result, a publicly available plant…
Background: To understand individual genomes it is necessary to look at the variations that lead to changes in phenotype and possibly to disease. However, genotype information alone is often not sufficient and additional knowledge regarding…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of…
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor…
Machine Learning (ML) has achieved unprecedented performance in several applications including image, speech, text, and data analysis. Use of ML to understand underlying patterns in gene mutations (genomics) has far-reaching results, not…
Genomic Selection (GS) uses whole-genome information to predict crop phenotypes and accelerate breeding. Traditional GS methods, however, struggle with prediction accuracy for complex traits and large datasets. We propose DPCformer, a deep…
This paper presents SWNet, a bimodal end-to-end cross-spectral network specifically engineered for the detection of camouflaged weeds in dense agricultural environments. Plant camouflage, characterized by homochromatic blending where…
We present LINSPECTOR WEB, an open source multilingual inspector to analyze word representations. Our system provides researchers working in low-resource settings with an easily accessible web based probing tool to gain quick insights into…
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
Recent studies show that Transformer has strong capability of building long-range dependencies, yet is incompetent in capturing high frequencies that predominantly convey local information. To tackle this issue, we present a novel and…
Bacterial phase variation enables reversible, locus-specific phenotypic switching, often driven by DNA inversion (invertons). To identify these events, researchers commonly rely on sequencing reads that provide orientation-specific support.…
Single-strand breaks (SSBs) are the major DNA damage in the genome arising spontaneously as the outcome of genotoxins and intermediates of DNA transactions. SSBs play a crucial role in various biological processes and show a non-random…
Pathological images play an essential role in cancer prognosis, while survival analysis, which integrates computational techniques, can predict critical clinical events such as patient mortality or disease recurrence from whole-slide images…
A panel of large number of common Single Nucleotide Polymorphisms (SNPs) distributed across an entire porcine genome has been widely used to represent genetic variability of pig. With the advent of SNP-array technology, a genome-wide…