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Luca Albergante

Luca Albergante
Institut Curie · Département de Bioinformatique et Biologie des systèmes

PhD

About

38
Publications
3,657
Reads
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811
Citations
Introduction
I use a combination of mathematical modelling and computational data analysis to study complex biological processes. My primary interests include cancer, immunology, genetic networks and DNA replication.
Additional affiliations
September 2016 - present
Institut Curie
Position
  • PostDoc Position
September 2015 - February 2016
University of Dundee
Position
  • Lecturer in Research Methods
March 2014 - June 2015
University of Dundee
Position
  • Lecturer in Statistics and Data Analysis
Description
  • I taught undergraduate and graduate courses on statistics and data analysis using R
Education
November 2006 - December 2010
University of Milan
Field of study
  • Applied Mathematics and Statistics

Publications

Publications (38)
Article
Full-text available
The gene regulatory network (GRN) is the central decision‐making module of the cell. We have developed a theory called Buffered Qualitative Stability (BQS) based on the hypothesis that GRNs are organised so that they remain robust in the face of unpredictable environmental and evolutionary changes. BQS makes strong and diverse predictions about the...
Article
Full-text available
The replication of DNA is initiated at particular sites on the genome called replication origins (ROs). Understanding the constraints that regulate the distribution of ROs across different organisms is fundamental for quantifying the degree of replication errors and their downstream consequences. Using a simple probabilistic model, we generate a se...
Article
Full-text available
To prevent rereplication of genomic segments, the eukaryotic cell cycle is divided into two nonoverlapping phases. During late mitosis and G1 replication origins are "licensed" by loading MCM2-7 double hexamers and during S phase licensed replication origins activate to initiate bidirectional replication forks. Replication forks can stall irreversi...
Article
Full-text available
Author Summary Granulomatous inflammation is a common feature of chronic infectious and non-infectious disease. In the parasitic disease visceral leishmaniasis, the formation of granulomas in the liver is a hallmark of effective cellular immunity and host resistance to infection. Conventional experimental models, however, have inherent limitations...
Article
Full-text available
The complexity of signalling pathways was boosted at the origin of the vertebrates, when two rounds of whole genome duplication (2R-WGD) occurred. Those genes and proteins that have survived from the 2R-WGD-termed 2R-ohnologues-belong to families of two to four members, and are enriched in signalling components relevant to cancer. Here, we find tha...
Article
Full-text available
A subset of cancer-associated fibroblasts (FAP+/CAF-S1) mediates immunosuppression in breast cancers, but its heterogeneity and its impact on immunotherapy response remain unknown. Here, we identify 8 CAF-S1 clusters by analyzing more than 19,000 single CAF-S1 fibroblasts from breast cancer. We validate the five most abundant clusters by flow cytom...
Article
Full-text available
In order to maintain functional robustness and species integrity, organisms must ensure high fidelity of the genome duplication process. This is particularly true during early development, where cell division is often occurring both rapidly and coherently. By studying the extreme limits of suppressing DNA replication failure due to double fork stal...
Article
Full-text available
Multidimensional datapoint clouds representing large datasets are frequently characterized by non-trivial low-dimensional geometry and topology which can be recovered by unsupervised machine learning approaches, in particular, by principal graphs. Principal graphs approximate the multivariate data by a graph injected into the data space with some c...
Article
Full-text available
Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-ce...
Preprint
Full-text available
Modern large-scale datasets are frequently said to be high-dimensional. However, their data point clouds frequently possess structures, significantly decreasing their intrinsic dimen-sionality (ID) due to the presence of clusters, points being located close to low-dimensional varieties or fine-grained lumping. We test a recently introduced dimensio...
Preprint
Full-text available
Modern large-scale datasets are frequently said to be high-dimensional. However, their data point clouds frequently possess structures, significantly decreasing their intrinsic dimensionality (ID) due to the presence of clusters, points being located close to low-dimensional varieties or fine-grained lumping. We test a recently introduced dimension...
Preprint
Differences in gene dosages between and within species are widely observed. Nevertheless, our understanding of the impacts of gene dosages on transcriptional regulation is far from complete and it is largely ignored in many genetic studies. In this article, we showed that dynamic properties of three genetic structures became significantly different...
Article
Full-text available
The parasitic African trypanosome, Trypanosoma brucei, evades the adaptive host immune response by a process of antigenic variation that involves the clonal switching of variant surface glycoproteins (VSGs). The VSGs that come to dominate in vivo during an infection are not entirely random, but display a hierarchical order. How this arises is not f...
Preprint
Full-text available
We present ElPiGraph, a method for approximating data distributions having non-trivial topological features such as the existence of excluded regions or branching structures. Unlike many existing methods, ElPiGraph is not based on the construction of a k-nearest neighbour graph, a procedure that can perform poorly in the case of multidimensional an...
Preprint
Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-ce...
Article
Full-text available
For many cancer types, incidence rises rapidly with age as an apparent power law, supporting the idea that cancer is caused by a gradual accumulation of genetic mutations. Similarly, the incidence of many infectious diseases strongly increases with age. Here, combining data from immunology and epidemiology, we show that many of these dramatic age-r...
Article
How do social interactions in fictional words? Here we show that network theory can be used to systematically and quantitatively analyse relationships among noble houses and how the web of alliances and conflicts changes over time in the fantasy drama TV series \textit{Game of Thrones}. Network analysis proved to be a powerful tool in capturing str...
Article
Full-text available
Using a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression of upstream genes, and thus LR...
Preprint
Full-text available
The parasitic African trypanosome, Trypanosoma brucei , evades the adaptive host immune response by a process of antigenic variation that involves the clonal switching of variant surface glycoproteins (VSGs). The VSGs that periodically come to dominate in vivo display a hierarchy, but how this hierarchy arises is not well-understood. Combining publ...
Preprint
Full-text available
Using a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression of upstream genes, and thus LR...
Chapter
We discuss an overtly “simple approach” to complex biological systems borrowing selectively from theoretical physics. The approach is framed by three maxims, and we show examples of its success in two different applications: investigating cellular robustness at the level of gene regulatory networks and quantifying rare events of DNA replication err...
Article
Full-text available
Tumour heterogeneity presents a significant obstacle for cancer therapeutics. Tumour cell karyotyping has the potential to uncover chromosomal heterogeneity at a single cell resolution, but it relies on a slow and laborious method that restricts its utility for solid tumours in a clinical setting. Here, we report a reproducible high throughput comp...
Data
Edges that result in the formation of at least one long feedback loop when inserted in the GM12878 GRN. The number of long feedback loops created and the length of the longest feedback loops are also indicated. Supplementary file 1 lists all the 48 edge insertions that result in the creation of long feedback loops when inserted in the GM12878 GRN....
Article
This paper presents a protocol to eliminate the necessity for human moderators in forums, thus automatising the moderation process. The protocol uses a bio-inspired approach: well- and ill-behaving posters are modelled as healthy and infected cells of a living organism. Moderators are modelled as leukocytes that remove infected cells. The identific...
Conference Paper
Leishmania donovani is an obligate intracellular parasite responsible for the systemic disease visceral leishmaniasis. During the course of the disease, the parasite is found in the spleen, liver and bone marrow. Characteristic of the liver immune response to leishmaniasis is a type of inflammation (“ggranulomatous inflammation”) that results in th...
Chapter
The notion of identity has been discussed extensively in the past. Leibniz was the first to present this notion in a logically coherent way, using a formulation generally recognized as "Leibniz's Law". Although some authors criticized this formulation, Leibniz's Law is generally accepted as the definition of identity. This chapter interprets Leibni...
Chapter
The notion of identity has been discussed extensively in the past. Leibniz was the first to present this notion in a logically coherent way, using a formulation generally recognized as “Leibniz's Law”. Although some authors criticized this formulation, Leibniz's Law is generally accepted as the definition of identity. This work interprets Leibniz's...
Conference Paper
This paper describes a distributed moderation protocol for wireless discussion forums. Moderating a large discussion forum is a complex task that requires knowledgeable human moderators to check newly posted messages, and ban users that break the rules. The presented protocol uses a bio-inspired approach: well-behaving posters are modelled as healt...

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Projects

Projects (2)
Archived project
This project aim at exploring the potentialities of principal graph as a methodology to explore the dynamics and heterogeneity of single cell data. Intermediate goals include the exploration of cell cycle structure, heterogeneity, and DNA repair