Jean-daniel Zucker

Institute of Research for Development | IRD · Mathematical and Computer Modelling of Dynamical Systems (UMMISCO) - UMI 209 SU/IRD

Abstraction is a fundamental mechanism underlying both human and artificial perception, representation of knowledge, reasoning and learning. This mechanism plays a crucial role in many disciplines, notably Computer Programming, Natural and Artificial Vision, Complex Systems, Artificial Intelligence and Machine Learning, Art, and Cognitive Sciences....

Feature selection is an important step when building a classifier on high dimensional data. As the number of observations is small, the feature selection tends to be unstable. It is common that two feature subsets, obtained from different datasets but dealing with the same classification problem, do not overlap significantly. Although it is a cruci...

We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previo...

Background Microbiome biomarker discovery for patient diagnosis, prognosis, and risk evaluation is attracting broad interest. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as bl...

Agent-based modeling is now widely used to investigate complex systems but still lacks integrated and generic tools to support the representation of features usually associated with real complex systems, namely rich, dynamic and realistic environments or multiple levels of agency. The GAMA platform has been developed to address such issues and allo...

The METAPLANTCODE project is dedicated to advancing and optimizing pan-European case studies on metabarcoding. The project's objectives include providing best practice recommendations, optimizing analysis pipelines for species identification, and creating user-friendly reference databases. To accomplish these objectives, METAPLANTCODE will identify...

Global digitization efforts have archived millions of specimen scans worldwide in herbarium collections, which are essential for studying plant evolution and biodiversity. ReColNat hosts, at present, over 10 million images. However, analyzing these datasets poses crucial challenges for botanical research. The application of deep learning in biodive...

Background Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked to sexual preference and others to the HIV infection. The relationship between these lineages and metabolic a...

In this work, we address the challenge of reconstructing the complete 12-lead ECG signal from incomplete parts of it. We focus on two main scenarii: (i) reconstructing missing signal segments within an ECG lead and (ii) recovering missing leads from a single-lead. We propose a model with a U-Net architecture trained on a novel objective function to...

The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital informatio...

Individual lifestyle factors moderately impact the gut microbiome and host biology. This study explores whether their combined influence significantly alters the gut microbiome and determines the mediating role of the gut microbiota in the relationship between lifestyle and phenomes. Analyzing 1,643 individuals from the Metacardis European cross-se...

Background. Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked to sexual preference and others to the HIV infection. The relationship between these lineages and metabolic...

The gut microbiome plays a significant role in the development of Type 2 Diabetes Mellitus (T2DM), but the functional mechanisms behind this association merit deeper investigation. Here, we used the nanopore sequencing technology for metagenomic analyses to compare the gut microbiome of individuals with T2DM from the United Arab Emirates (n = 40) w...

Abstract The host-microbiota co-metabolite trimethylamine N-oxide (TMAO) is linked to increased cardiovascular risk but how its circulating levels are regulated remains unclear. We applied “explainable” machine learning, univariate, multivariate and mediation analyses of fasting plasma TMAO concentration and a multitude of phenotypes in 1,741 adult...

Herbarium specimen scans constitute a valuable source of raw data. Herbarium collections are gaining interest in the scientific community as their exploration can lead to understanding serious threats to biodiversity. Data derived from scanned specimen images can be analyzed to answer important questions such as how plants respond to climate change...

The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital informatio...

The digitization of electrocardiogram paper records is an essential step to preserve and analyze cardiac data. This digitization process is not flawless as it involves several challenges, such as skew correction, binarization, and signal extraction. Various approaches have been proposed to address these challenges and recent studies have introduced...

The exploration of heath data by clustering algorithms allows to better describe the populations of interest by seeking the sub-profiles that compose it. This therefore reinforces medical knowledge, whether it is about a disease or a targeted population in real life. Nevertheless, contrary to the so-called conventional biostatistical methods where...

Nombreuses applications potentielles à venir : compréhension et construction de cartes d'activation en arythmie, identification des sources focales ou des activités réentrantes, analyse de l'ECG, stratification du risque rythmique ou prédiction individualisée du risque d'événements à partir de l'ECG (accident vasculaire cérébral, évolution de la fi...

The exploration of heath data by clustering algorithms allows to better describe the populations of interest by seeking the sub-profiles that compose it. This therefore reinforces medical knowledge, whether it is about a disease or a targeted population in real life. Nevertheless, contrary to the so-called conventional biostatistical methods where...

Introduction Detecting safety signals attributed to a drug in scientific literature is a fundamental issue in pharmacovigilance. The constant increase in the volume of publications requires the automation of this tedious task, in order to find and extract relevant articles from the pack. This task is critical, as serious Adverse Drug Reactions (ADR...

Objectives: The host-microbiota co-metabolite trimethylamine N-oxide (TMAO) is linked to increased thrombotic and cardiovascular risks. Here we, sought to i) characterize which host variables contribute to fasting serum TMAO levels in real-life settings ii) identify potential actionable therapeutic means related to circulating TMAO. Design: We appl...

Artificial Intelligence has opened new doors for customer relationship personalization by capturing life events to tailor front and back-office interactions. Individual bank account data are particularly rich in information on these life events, but few banks have gone beyond its basic use. In this paper, we describe an innovative and original meth...

At a time when the impacts of climate change and increasing urbanization are making risk management more complex, there is an urgent need for tools to better support risk managers. One approach increasingly used in crisis management is preventive mass evacuation. However, to implement and evaluate the effectiveness of such strategy can be complex,...

The exploration of heath data by clustering algorithms allows to better describe the populations of interest by seeking the sub-profiles that compose it. This therefore reinforces medical knowledge, whether it is about a disease or a targeted population in real life. Nevertheless, contrary to the so-called conventional biostatistical methods where...

Roux-en-Y gastric bypass (RYGB) is efficient at inducing drastic albeit variable weight loss and type-2 diabetes (T2D) improvements in patients with severe obesity and T2D. We hypothesized a causal implication of the gut microbiota (GM) in these metabolic benefits, as RYGB is known to deeply impact its composition. In a cohort of 100 patients with...

Previous microbiome and metabolome analyses exploring non-communicable diseases have paid scant attention to major confounders of study outcomes, such as common, pre-morbid and co-morbid conditions, or polypharmacy. Here, in the context of ischemic heart disease (IHD), we used a study design that recapitulates disease initiation, escalation and res...

Objectives Gut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome’s functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the rol...

Background: Dietary intervention is a cornerstone of weight loss therapies. In obesity, a dysbiotic gut microbiota (GM) is characterized by high levels of Bacteroides lineages and low diversity. We examined the GM composition changes, including the Bacteroides 2 enterotype (Bact2), in a real-world weight loss study in subjects following a high-pro...

During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1,2,3,4,5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the ex...

The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed for characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenge. To f...

Aims Congenital long-QT syndromes (cLQTS) or drug-induced long-QT syndromes (diLQTS) can cause torsade de pointes (TdP), a life-threatening ventricular arrhythmia. The current strategy for the identification of drugs at the high risk of TdP relies on measuring the QT interval corrected for heart rate (QTc) on the electrocardiogram (ECG). However, Q...

Background: The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challen...

Interactions between diet and gut microbiota are critical regulators of energy metabolism. The effects of fibre intake have been deeply studied but little is known about the impact of proteins. Here, we investigated the effects of high protein supplementation (Investigational Product, IP) in a double blind, randomised placebo-controled intervention...

Like a hydra, fraudsters adapt and circumvent increasingly sophisticated barriers erected by public or private institutions. Among these institutions, banks must quickly take measures to avoid losses while guaranteeing the satisfaction of law-abiding customers. Facing an expanding flow of operations, effective banking relies on data analytics to su...

According to recent studies, Vietnam is one of the twenty countries most affected by natural disasters in the world, and particularly by floods either on the low elevation coastal zones (risk of submersion) or along the Red River and the Mekong River (risk of flooding). In this context, dams are both means of mitigation but also threats given the p...

The need to adapt human resources to the activity workload is omnipresent in most sectors, especially when the activity variability depends on exogenous factors. Artificial intelligence seems to offer unprecedented opportunities for improving forecasting. However, its application to real-world business contexts still reveals critical breaches. In t...

Congenital or drug-induced long-QT syndromes can cause Torsade-de-Pointes (TdP), a life-threatening ventricular arrhythmia. The current strategy to identify individuals at high risk of TdP consists on measuring the QT duration on the electrocardiogram (ECG), shown to provide limited information. We propose an original method, including training dee...

Over the past decade, technological advances have made high-speed, high-resolution sequencing of genetic material possible at ever lower cost (from millions to one hundred dollars). In this context, the human microbiome has demonstrated its ability to support the stratification and the classification of various human diseases. Thus, the gut microbi...

Background: The gut microbiome plays a major role in chronic diseases, several of which are characterized by an altered diversity and composition of bacterial communities. Large-scale sequencing projects allowed the characterization of these microbial community perturbations. However, a gap remains in how these discoveries can be translated into cl...

Gut microbes are considered as major factors contributing to human health. Nowadays, the vast majority of the data available in the literature are mostly exhibiting negative or positive correlations between specific bacteria and metabolic parameters. From these observations, putative detrimental or beneficial effects are then inferred. Akkermansia...

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20412-9.

Addressing the heterogeneity of both the outcome of a disease and the treatment response to an intervention is a mandatory pathway for regulatory approval of medicines. In randomized clinical trials (RCTs), confirmatory subgroup analyses focus on the assessment of drugs in predefined subgroups, while exploratory ones allow a posteriori the identifi...

Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propio...

A bstract Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DN...