Genomics
In recent studies, non-coding protein RNAs have been identified as microRNA that can be used as biomarkers for early diagnosis and treatment of cancer, that decrease mortality in cancer. A microRNA may target hundreds or thousands of genes…
The ever-increasing number of genome sequencing and resequencing projects is a central source of insights into the ecology and evolution of non-model organisms. An important aspect of genomics is the elucidation of sex determination systems…
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate…
Whole genome amplification (WGA) plays an important role in sample preparation of low-input templates for high-throughput sequencing. Multiple displacement amplification (MDA), a popular isothermal WGA method, suffers a major hurdle of…
Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model…
We train a neural network to predict chemical toxicity based on gene expression data. The input to the network is a full expression profile collected either in vitro from cultured cells or in vivo from live animals. The output is a set of…
The Iberian Mediterranean Basin is home to one of the largest groups of prehistoric rock art sites in Europe. Despite the cultural relevance of prehistoric Spanish Levantine rock art, pigment composition remains partially unknown, and the…
We introduce GeNet, a method for shotgun metagenomic classification from raw DNA sequences that exploits the known hierarchical structure between labels for training. We provide a comparison with state-of-the-art methods Kraken and…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…
Despite the extreme diversity of T cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely-shared sequences, often referred to as `public', have been suggested…
In the context of cancer, internal "checkerboard" structures are normally found in the matrices of gene expression data, which correspond to genes that are significantly up- or down-regulated in patients with specific types of tumors. In…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
The study of human genes and diseases is very rewarding and can lead to improvements in healthcare, disease diagnostics and drug discovery. In this paper, we further our previous study on gene disease relationship specifically with the…
The V(D)J recombination forms the immunoglobulin genes by joining the variable (V), diversity (D), and joining (J) germline genes. Since variations in germline genes have been linked to various diseases, personalized immunogenomics aims at…
It is tempting to believe that we now own the genome. The ability to read and re-write it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has…
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical…
A key focus in current cancer research is the discovery of cancer biomarkers that allow earlier detection with high accuracy and lower costs for both patients and hospitals. Blood samples have long been used as a health status indicator,…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional…