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Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
evortran is a modern Fortran library designed for high-performance genetic algorithms and evolutionary optimization. evortran can be used to tackle a wide range of problems in high-energy physics and beyond, such as derivative-free…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
Deep generative modeling for biological sequences presents a unique challenge in reconciling the bias-variance trade-off between explicit biological insight and model flexibility. The deep manifold sampler was recently proposed as a means…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Protein variant libraries produced by site-directed mutagenesis are a useful tool utilized by protein engineers to explore variants with potentially improved properties, such as activity and stability. These libraries are commonly built by…
Recent advancements in deep learning for automated image processing and classification have accelerated many new applications for medical image analysis. However, most deep learning applications have been developed using reconstructed,…
The increased availability and usage of modern medical imaging induced a strong need for automatic medical image segmentation. Still, current image segmentation platforms do not provide the required functionalities for plain setup of…
Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproducing published results, either experimental data or…
Ptychography has rapidly grown in the fields of X-ray and electron imaging for its unprecedented ability to achieve nano or atomic scale resolution while simultaneously retrieving chemical or magnetic information from a sample. A…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
The advent of large scale, high-throughput genomic screening has introduced a wide range of tests for diagnostic purposes. Prominent among them are tests using miRNA expression levels. Genomics and proteomics now provide expression levels…
Epitopes are short antigenic peptide sequences which are recognized by antibodies or immune cell receptors. These are central to the development of immunotherapies, vaccines, and diagnostics. However, the rational design of synthetic…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…