Related papers: Methylator: A Modular Framework for DNA Methylatio…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
Mitosis detection is one of the fundamental tasks in computational pathology, which is extremely challenging due to the heterogeneity of mitotic cell. Most of the current studies solve the heterogeneity in the technical aspect by increasing…
Large Genomic Foundation Models have recently achieved remarkable results and in-vivo translation capabilities. However these models quickly grow to over a few Billion of parameters and are expensive to run when compute is limited. To…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
Detecting microbial biomarkers used to predict disease phenotypes and clinical outcomes is crucial for disease early-stage screening and diagnosis. Most methods for biomarker identification are linear-based, which is very limited as…
Deep learning segmentation and fluorescence imaging techniques allow the cellular morphology of living embryos to be constructed spatiotemporally. These development processes involve numerous molecules distributed at the subcellular scale,…
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…
Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
GELATIO is a new software framework for advanced data analysis and digital signal processing developed for the GERDA neutrinoless double beta decay experiment. The framework is tailored to handle the full analysis flow of signals recorded…
We present a software framework for statistical data analysis, called HistFitter, that has been used extensively by the ATLAS Collaboration to analyze big datasets originating from proton-proton collisions at the Large Hadron Collider at…
In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling…
Methane ($CH_4$) is a potent anthropogenic greenhouse gas, contributing 86 times more to global warming than Carbon Dioxide ($CO_2$) over 20 years, and it also acts as an air pollutant. Given its high radiative forcing potential and…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Flow cytometry mainly used for detecting the characteristics of a number of biochemical substances based on the expression of specific markers in cells. It is particularly useful for detecting membrane surface receptors, antigens, ions, or…
Reducing methane emissions is essential for mitigating global warming. To attribute methane emissions to their sources, a comprehensive dataset of methane source infrastructure is necessary. Recent advancements with deep learning on…
Digitization of histopathology slides has led to several advances, from easy data sharing and collaborations to the development of digital diagnostic tools. Deep learning (DL) methods for classification and detection have shown great…
DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits different behavior from that in free solutions. The system of…