Related papers: TROM: A Testing-based Method for Finding Transcrip…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Research increasingly relies on computational methods to analyze experimental data and predict molecular properties. Current approaches often require researchers to use a variety of tools for statistical analysis and machine learning,…
Spatial transcriptomics data analysis integrates cellular transcriptional activity with spatial coordinates to identify spatial domains, infer cell-type dynamics, and characterize gene expression patterns within tissues. Despite recent…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…
Sample overlap is a common issue in evidence synthesis in the field of medical research, particularly when integrating findings from observational studies utilizing existing databases such as registries. Due to the general inaccessibility…
Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
Assessing whether two patient populations exhibit comparable event dynamics is essential for evaluating treatment equivalence, pooling data across cohorts, or comparing clinical pathways across hospitals or strategies. We introduce a…
Transcriptomic analysis are characterized by being not directly quantitative and only providing relative measurements of expression levels up to an unknown individual scaling factor. This difficulty is enhanced for differential expression…
Optical Music Recognition (OMR) is an important technology in music and has been researched for a long time. Previous approaches for OMR are usually based on CNN for image understanding and RNN for music symbol classification. In this…
In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…
Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…
High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
We present Transfer Orthology Networks (TRON), a novel neural network architecture designed for cross-species transfer learning. TRON leverages orthologous relationships, represented as a bipartite graph between species, to guide knowledge…