Related papers: Agptools: a utility suite for editing genome assem…
Learning ensembles by bagging can substantially improve the generalization performance of low-bias, high-variance estimators, including those evolved by Genetic Programming (GP). To be efficient, modern GP algorithms for evolving (bagging)…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
This article introduces MCNP-GO (https://github.com/afriou/mcnpgo), a Python package designed to manipulate and assemble MCNP input files, allowing users to assemble a set of independent objects, each described by a valid MCNP file, into a…
The authors' "metatools" are a collection of tools for generic programming. This includes generating Java sources from mathematically well-founded specifications, as well as the creation of strictly typed document object models for XML…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
Genetic programming (GP) is an evolutionary computation technique to solve problems in an automated, domain-independent way. Rather than identifying the optimum of a function as in more traditional evolutionary optimization, the aim of GP…
Vectorial Genetic Programming (Vec-GP) extends GP by allowing vectors as input features along regular, scalar features, using them by applying arithmetic operations component-wise or aggregating vectors into scalars by some aggregation…
This paper introduces new tools for genomic signal processing, which can assist for genomic attribute extracting or describing biologically meaningful features embedded in a DNA. The codongrams and a2grams are offered as an alternative to…
In recent years the field of genetic programming has made significant advances towards automatic programming. Research and development of contemporary program synthesis methods, such as PushGP and Grammar Guided Genetic Programming, can…
The Genomic Data Commons (GDC) provides access to high quality, harmonized cancer genomics data through a unified curation and analysis platform centered around patient cohorts. While GDC users can interactively create complex cohorts…
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…
Contemporary genetic programming (GP) systems for general program synthesis have been primarily concerned with evolving programs that can manipulate values from a standard set of primitive data types and simple indexed data structures. In…
To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
The Phylogenetic Genome Annotator (PGA) is a computer program that enables real-time comparison of 'gene trees' versus 'species trees' obtained from predicted open reading frames of whole genome data. The gene phylogenies are inferred for…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
Non-sharable sensitive data collection and analysis in large-scale consortia for genomic research is complicated. Time consuming issues in installing software arise due to different operating systems, software dependencies and running the…
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…