Related papers: Agptools: a utility suite for editing genome assem…
Gene assembly is an important step in functional analysis of shotgun metagenomic data. Nonetheless, strain aware assembly remains a challenging task, as current assembly tools often fail to distinguish among strain variants or require…
Scatterplots are a common tool for exploring multidimensional datasets, especially in the form of scatterplot matrices (SPLOMs). However, scatterplots suffer from overplotting when categorical variables are mapped to one or two axes, or the…
Large language models have demonstrated promising performance across various software engineering tasks. While fine-tuning is a common practice to adapt these models for downstream tasks, it becomes challenging in resource-constrained…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies - a crucial step…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…
This Chapter, "A Guide to General-Purpose ABC Software", is to appear in the forthcoming Handbook of Approximate Bayesian Computation (2018). We present general-purpose software to perform Approximate Bayesian Computation (ABC) as…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
Evolution can be broadly described in terms of mutations of the genotype and the subsequent selection of the phenotype. The full enumeration of a given genotype-phenotype (GP) map is therefore a powerful technique in examining evolutionary…
Program synthesis with Genetic Programming searches for a correct program that satisfies the input specification, which is usually provided as input-output examples. One particular challenge is how to effectively handle loops and recursion…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…
We study a generic program to investigate the scope for automatically customising it for a vital current task, which was not considered when it was first written. In detail, we show genetic programming (GP) can evolve models of aspects of…
Cartesian Genetic Programming (CGP) has previously shown capabilities in image processing tasks by evolving programs with a function set specialized for computer vision. A similar approach can be applied to Atari playing. Programs are…
In this paper we will present a general agglomeration law for sorting networks. Agglomeration is a common technique when designing parallel programmes to control the granularity of the computation thereby finding a better fit between the…
This paper proposes the use of notebooks for the design documentation and tool interaction in the rigorous design of embedded systems. Conventionally, a notebook is a sequence of cells alternating between (textual) code and prose to form a…
There is an abundance of prior research on the optimization of production systems, but there is a research gap when it comes to optimizing which components should be included in a design, and how they should be connected. To overcome this…