Related papers: RNASeqR: an R package for automated two-group RNA-…
A key challenge in enzyme annotation is identifying the biochemical reactions catalyzed by proteins. Most existing methods rely on Enzyme Commission (EC) numbers as intermediaries: they first predict an EC number and then retrieve the…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…
Major advancements in fields as diverse as biology and quantum computing have relied on a multitude of microscopic techniques. All optical, electron and scanning probe microscopy advanced with new detector technologies and integration of…
Deep learning methods are widely applied in digital pathology to address clinical challenges such as prognosis and diagnosis. As one of the most recent applications, deep models have also been used to extract molecular features from whole…
The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information…
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various…
The advent of powerful neural classifiers has increased interest in problems that require both learning and reasoning. These problems are critical for understanding important properties of models, such as trustworthiness, generalization,…
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.…
Microbiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences of changes in the intestinal microbiome may…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
Single-cell RNA sequencing (scRNA-seq) has made significant strides in unraveling the intricate cellular diversity within complex tissues. This is particularly critical in the brain, presenting a greater diversity of cell types than other…
Mean residual lifetime is an important measure utilized in various fields, including pharmaceutical companies, manufacturing companies, and insurance companies for survival analysis. However, the computation of mean residual lifetime can be…
Motivation: Single cell RNA sequencing (scRNA-seq) data makes studying the development of cells possible at unparalleled resolution. Given that many cellular differentiation processes are hierarchical, their scRNA-seq data is expected to be…
BioStatFlow is a free web application, useful to facilitate the performance of statistical analyses of "omics", including metabolomics, data using R packages. It is a fast and easy on-line tool for biologists who are not experts in…
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…
Most human protein-coding genes can be transcribed into multiple possible distinct mRNA isoforms. These alternative splicing patterns encourage molecular diversity and dysregulation of isoform expression plays an important role in disease…
Graphical models provide powerful tools to uncover complicated patterns in multivariate data and are commonly used in Bayesian statistics and machine learning. In this paper, we introduce the R package BDgraph which performs Bayesian…
Database research and development rely heavily on realistic user workloads for benchmarking, instance optimization, migration testing, and database tuning. However, acquiring real-world SQL queries is notoriously challenging due to strict…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
Identifying phenotype-associated genes is a common first step in polygenic risk score construction, enrichment testing, target prioritisation and variant interpretation, but relevant evidence is distributed across heterogeneous databases…