Related papers: MOSGA: Modular Open-Source Genome Annotator
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…
Genomic data has become increasingly accessible to the general public with the advent of companies offering whole genome sequencing at a relatively low cost. However, their reports are not verifiable due to a lack of crucial details and…
Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
Academic research in static analysis produces software implementations. These implementations are time-consuming to develop and some need to be maintained in order to enable building further research upon the implementation. While…
Motivation Modern molecular sequence analysis increasingly relies on automated and robust software tools for interpretation, annotation, and biological insight. The Analysis of Orthologous Collections (AOC) application automates the…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
In cross-modal music processing, translation between visual, auditory, and semantic content opens up new possibilities as well as challenges. The construction of such a transformative scheme depends upon a benchmark corpus with a…
Most existing swarm pattern formation methods depend on a predefined gene regulatory network (GRN) structure that requires designers' priori knowledge, which is difficult to adapt to complex and changeable environments. To dynamically adapt…
Semantic code search, retrieving code that matches a given natural language query, is an important task to improve productivity in software engineering. Existing code search datasets face limitations: they rely on human annotators who…
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
We study sample-efficient molecular optimization under a limited budget of oracle evaluations. We propose MolLIBRA (MultimOdaLity and Language Integrated Bayesian and evolutionaRy optimizAtion), a genetic algorithm based framework that…
Genomics, especially multi-omics, has made precision medicine feasible. The completion and publicly accessible multi-omics resource with clinical outcome, such as The Cancer Genome Atlas (TCGA) is a great test bed for developing…
We developed NameMyGene, a web tool and a stand alone program to easily generate putative family-based names for small RNA sequences so that laboratories can easily organize, analyze, and observe patterns from, the massive amount of data…
Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data…
Ontologies present an attractive technology for describing bio-medicine, because they can be shared, and have rich computational properties. However, they lack the rich expressivity of English and fit poorly with the current scientific…
Selecting the most relevant or informative features is a key issue in actual machine learning problems. Since an exhaustive search is not feasible even for a moderate number of features, an intelligent search strategy must be employed for…