Marc Santolini

Inserm, CRI Paris, Faculty Member

Harvard Medical School, Channing Division of Network Medicine, Research collaborator

Northeastern University, Network Science Institute, Visiting researcher

Followers

171

Following

Co-author

Public Views

Network science for medicine and collaborative projects

less

InterestsView All (28)

Uploads

Papers by Marc Santolini

Uncovering the fragility of large-scale engineering project networks

Engineering projects are notoriously hard to complete on-time, with project delays often theorise... more Engineering projects are notoriously hard to complete on-time, with project delays often theorised to propagate across interdependent activities. Here, we use a novel dataset consisting of activity networks from 14 diverse, large-scale engineering projects to uncover network properties that impact timely project completion. We provide the first empirical evidence of the infectious nature of activity deviations, where perturbations in the delivery of a single activity can impact up to 4 activities downstream, leading to large perturbation cascades. We further show that perturbation clustering significantly affects project overall delays. Finally, we find that poorly performing projects have their highest perturbations in high reach nodes, which can lead to largest cascades, while well performing projects have perturbations in low reach nodes, resulting in localised cascades. Altogether, these findings pave the way for a network-science framework that can materially enhance the delive...

format_quoteExtensive cascades occur from major perturbations affecting 'fragile' nodes with significant reach, emphasizing vulnerability points in networks.format_quote

Download

Network-based response module comprised of gene expression biomarkers predicts response to infliximab at treatment initiation in ulcerative colitis

Translational Research, 2022

Impasse in Doha Development Agenda has been generating new alternatives which can drive a wedge b... more Impasse in Doha Development Agenda has been generating new alternatives which can drive a wedge between export and import prices and the role of trade facilitation policies in bridging that wedge has been recognized among economic and trade pundits. Trade facilitation is multi-faceted area which can shape the competitiveness of trade by interacting with multidimensional spheres of increasing complexity of trade by reducing trade transaction cost.In the case of Pakistan, its global share of export is decreasing since 1999 and export growth is stagnant. Many factors and policies are stayed responsible owing to external and internal environment, political and economic reasons and regional and national policies. Since 1970s, she has not prioritized trade development agenda especially trade facilitation measures aggressively. Many regional as well as East-Asian countries adopted trade facilitation measures vigorously besides trade policies and results have been yielded in the form of elevated share of their products in world markets. Trade facilitation measures particularly custom efficiency, port and logistic efficiency, regulatory environment and e-business usages apart from other traditional trade policies needs to be improved to enhance trade competitiveness in Pakistan.

Download

Estimation de paramètres cosmologiques par corrélation croisée d'observations de galaxies et du fond de rayonnement cosmologique-Estimating cosmological parameters through cross-correlation of galaxy surveys and Cosmic Microwave Background fluctuations

Au cours de la dernière décennie, l'étude de plus en plus précise du fond de rayonnement cosmolog... more Au cours de la dernière décennie, l'étude de plus en plus précise du fond de rayonnement cosmologique (CMB), relique des âges obscurs qui ont suivi le Big-Bang, a permis une profonde amélioration de la connaissance de l'univers dans lequel nous vivons, de sa composition et de son histoire. Tous ces éléments sont résumés en quelques simples paramètres, les paramètres cosmologiques. En comparant les observations I would like to genuinely thank Prof. David Spergel for welcoming me in his group and for the very interesting work he suggested to me; Aurélien Fraisse, former ENS student and now second year graduate student in the group, for his help to prepare my arrival in Princeton, his availability to recommend introductory readings about cosmology and to answer my questions about programming; Sudeep Das, third year graduate student in the group, for answering the numerous questions I had about weak lensing, parameters constraints, and Fortran 90 computation; Charlotte Zanidakis, Academic Programs Administrator, for her kindness and her help when I arrived; Pr. Steven Balbus (ENS, Paris) for advising me when I was looking for this internship; and nally all the people I met here who made this internship a very pleasant experience.

Download

COVID-19 and Beyond: A Call for Action and Audacious Solidarity to All the Citizens and Nations, It Is Humanity’s Fight

Background: SARS-CoV-2 belongs to a subgroup of coronaviruses rampant in bats for centuries. It h... more Background: SARS-CoV-2 belongs to a subgroup of coronaviruses rampant in bats for centuries. It has caused the COVID-19 pandemic. Most patients recover, but a minority of severe cases experience acute respiratory distress or an inflammatory storm devastating many organs that can lead to patient death. The spread of SARS-CoV-2 has been facilitated by the increasing intensity of air travel, urban congestion and human contact during the last half century. Until therapies and vaccines are available, tests for virus and exposure, confinement measures and physical distancing have helped curb the pandemic. Vision: The COVID-19 pandemic calls for safeguards and remediation measures through a systemic response. A myriad of self-organizing initiatives by scientists and citizens is developing an advanced collective intelligence response to the coronavirus crisis. Their integration forms Olympiads of Solidarity and Health. Their ability to optimize our response to COVID-19 could serve as a mode...

Download

Quantifying the rise and fall of scientific fields

Science advances by pushing the boundaries of the adjacent possible. While the global scientific ... more Science advances by pushing the boundaries of the adjacent possible. While the global scientific enterprise grows at an exponential pace, at the mesoscopic level the exploration and exploitation of research ideas is reflected through the rise and fall of research fields. The empirical literature has largely studied such dynamics on a case-by-case basis, with a focus on explaining how and why communities of knowledge production evolve. Although fields rise and fall on different temporal and population scales, they are generally argued to pass through a common set of evolutionary stages.To understand the social processes that drive these stages beyond case studies, we need a way to quantify and compare different fields on the same terms. In this paper we develop techniques for identifying scale-invariant patterns in the evolution of scientific fields, and demonstrate their usefulness using 1.5 million preprints from the arXiv repository covering 175 research fields spanning Physics, M...

format_quoteThe evolution of research fields follows a right-tailed Gumbel distribution, with significant parameters for peak location and distribution width identified across 1.45 million articles.format_quote

Download

Uncovering the fragility of large-scale engineering projects

EPJ Data Science, 2021

Engineering projects are notoriously hard to complete on-time, with project delays often theorise... more Engineering projects are notoriously hard to complete on-time, with project delays often theorised to propagate across interdependent activities. Here, we use a novel dataset consisting of activity networks from 14 diverse, large-scale engineering projects to uncover network properties that impact timely project completion. We provide empirical evidence of perturbation cascades, where perturbations in the delivery of a single activity can impact the delivery of up to 4 activities downstream, leading to large perturbation cascades. We further show that perturbation clustering significantly affects project overall delays. Finally, we find that poorly performing projects have their highest perturbations in high reach nodes, which can lead to largest cascades, while well performing projects have perturbations in low reach nodes, resulting in localised cascades. Altogether, these findings pave the way for a network-science framework that can materially enhance the delivery of large-scale...

Download

Co-Immune: a case study on open innovation for vaccination hesitancy and access (Preprint)

Journal of Participatory Medicine, 2021

Background: The rise of major complex public health problems, such as vaccination hesitancy and a... more Background: The rise of major complex public health problems, such as vaccination hesitancy and access to vaccination, requires innovative, open and transdisciplinary approaches. In spite of this, institutional silos, paywalls and lack of participation of non-academic citizens in the design of solutions hamper efforts to meet these challenges. Against this background, new solutions have been explored, with participatory research, citizen science, hackathon and challenge-based approaches being applied in the context of public health. Objectives: Our ambition was to develop a framework for creating citizen science and open innovation projects that address the contemporary challenges of vaccination in France and around the globe. Methods: We designed and implemented Co-Immune, a programme created to tackle the question of vaccination hesitancy and access to vaccination through an online and offline challenge-based open innovation approach. The programme was run on the open science platform Just One Giant Lab. Results: Over a 6-month period, the Co-Immune programme gathered 234 participants of diverse backgrounds and 13 partners from the public and private sectors and organized 8 events to facilitate the creation of 20 new projects as well as the continuation of 2 existing projects to address the issues of vaccination hesitancy and access, ranging from app development and data mining to analysis and game design. In an open framework, the projects made their data, code, and solutions publicly available. Conclusion: Co-Immune highlights how open innovation approaches and online platforms can help to gather and coordinate non-institutional communities in a rapid, distributed and global way towards solving public health issues. Through the ideas of hackathons and other contest approaches, such initiatives can lead to the production and transfer of knowledge, creating novel solutions in the public health sector. The example of Co-Immune contributes to paving the way for organisations and individuals to collaboratively tackle future global challenges. .

format_quoteThe Co-Immune programme launched 20 projects addressing vaccination hesitancy, engaging 234 diverse participants over six months through eight events.format_quote

Download

Quantified Us: A group-in-the-loop approach to team network reconstruction

Adjunct Proceedings of the 2021 ACM International Joint Conference on Pervasive and Ubiquitous Computing and Proceedings of the 2021 ACM International Symposium on Wearable Computers, 2021

Understanding team collaboration processes is key for the development of new technologies towards... more Understanding team collaboration processes is key for the development of new technologies towards increasing groups effectiveness. In particular, the need and challenges of coordinating potentially large-scale, self-organized, collaborative initiatives have been made even more salient by the COVID-19 pandemic. Key to this challenge is the difficulty for participants to situate themselves within the larger social context. At the individual level, the Quantified-Self movement has showcased how insights from one's own data can trigger changes in behavior, sometimes leading to fundamental insights through self-research. Building on these premises, here we present CoSo (Collaborative Sonar), a digital platform for participatory collective sensing and social research. CoSo is a web and mobile data collection platform for team network reconstruction and visualization. It leverages a "group-in-the-loop" intrinsic motivator to collect data on collaborative activities performed by a team through a mobile app, with summary statistics and visualizations of the collected data made available on a web dashboard. We showcase its use and discuss the perspectives offered by promoting grouplevel metacognition and collective introspection. By highlighting the invisible relationships in a group, CoSo facilitates in-the-wild studies, remote/hybrid data collection, and multi-modal sensing approaches of group interactions within professional and other social contexts. CCS CONCEPTS • Software and its engineering → Software libraries and repositories; • Information systems → Information systems applications; Open source software; Retrieval on mobile devices; • Human-centered computing → Scientific visualization.

format_quoteEcological momentary assessment (EMA) significantly reduces retrospective bias, gathering real-time data about user experiences and interactions.format_quote

Download

Detection of Spatiotemporal Clusters of COVID-19–Associated Symptoms and Prevention Using a Participatory Surveillance App: Protocol for the @choum Study

JMIR Research Protocols, 2021

Background The early detection of clusters of infectious diseases such as the SARS-CoV-2–related ... more Background The early detection of clusters of infectious diseases such as the SARS-CoV-2–related COVID-19 disease can promote timely testing recommendation compliance and help to prevent disease outbreaks. Prior research revealed the potential of COVID-19 participatory syndromic surveillance systems to complement traditional surveillance systems. However, most existing systems did not integrate geographic information at a local scale, which could improve the management of the SARS-CoV-2 pandemic. Objective The aim of this study is to detect active and emerging spatiotemporal clusters of COVID-19–associated symptoms, and to examine (a posteriori) the association between the clusters’ characteristics and sociodemographic and environmental determinants. Methods This report presents the methodology and development of the @choum (English: “achoo”) study, evaluating an epidemiological digital surveillance tool to detect and prevent clusters of individuals (target sample size, N=5000), age...

Download

A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation

JCI insight, Jan 7, 2018

Allergic asthma is a chronic inflammatory disease dominated by a CD4+ T helper 2 (Th2) cell signa... more Allergic asthma is a chronic inflammatory disease dominated by a CD4+ T helper 2 (Th2) cell signature. The immune response amplifies in self-enforcing loops, promoting Th2-driven cellular immunity and leaving the host unable to terminate inflammation. Posttranscriptional mechanisms, including microRNAs (miRs), are pivotal in maintaining immune homeostasis. Since an altered expression of various miRs has been associated with T cell-driven diseases, including asthma, we hypothesized that miRs control mechanisms ensuring Th2 stability and maintenance in the lung. We isolated murine CD4+ Th2 cells from allergic inflamed lungs and profiled gene and miR expression. Instead of focusing on the magnitude of miR differential expression, here we addressed the secondary consequences for the set of molecular interactions in the cell, the interactome. We developed the Impact of Differential Expression Across Layers, a network-based algorithm to prioritize disease-relevant miRs based on the centra...

Download

Predicting perturbation patterns from the topology of biological networks

Proceedings of the National Academy of Sciences of the United States of America, Jul 20, 2018

High-throughput technologies, offering an unprecedented wealth of quantitative data underlying th... more High-throughput technologies, offering an unprecedented wealth of quantitative data underlying the makeup of living systems, are changing biology. Notably, the systematic mapping of the relationships between biochemical entities has fueled the rapid development of network biology, offering a suitable framework to describe disease phenotypes and predict potential drug targets. However, our ability to develop accurate dynamical models remains limited, due in part to the limited knowledge of the kinetic parameters underlying these interactions. Here, we explore the degree to which we can make reasonably accurate predictions in the absence of the kinetic parameters. We find that simple dynamically agnostic models are sufficient to recover the strength and sign of the biochemical perturbation patterns observed in 87 biological models for which the underlying kinetics are known. Surprisingly, a simple distance-based model achieves 65% accuracy. We show that this predictive power is robust...

format_quoteNetwork model predicts perturbation spreading with ∼80% accuracy, revealing its potential for understanding gene expression and drug development.format_quote

Download

Six1 homeoprotein drives myofiber type IIA specialization in soleus muscle

Skeletal muscle, 2016

Adult skeletal muscles are composed of slow and fast myofiber subtypes which each express selecti... more Adult skeletal muscles are composed of slow and fast myofiber subtypes which each express selective genes required for their specific contractile and metabolic activity. Six homeoproteins are transcription factors regulating muscle cell fate through activation of myogenic regulatory factors and driving fast-type gene expression during embryogenesis. We show here that Six1 protein accumulates more robustly in the nuclei of adult fast-type muscles than in adult slow-type muscles, this specific enrichment takes place during perinatal growth. Deletion of Six1 in soleus impaired fast-type myofiber specialization during perinatal development, resulting in a slow phenotype and a complete lack of Myosin heavy chain 2A (MyHCIIA) expression. Global transcriptomic analysis of wild-type and Six1 mutant myofibers identified the gene networks controlled by Six1 in adult soleus muscle. This analysis showed that Six1 is required for the expression of numerous genes encoding fast-type sarcomeric pro...

Download

MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis

Nucleic acids research, Jan 14, 2016

Myogenic regulatory factors of the MyoD family have the ability to reprogram differentiated cells... more Myogenic regulatory factors of the MyoD family have the ability to reprogram differentiated cells toward a myogenic fate. In this study, we demonstrate that Six1 or Six4 are required for the reprogramming by MyoD of mouse embryonic fibroblasts (MEFs). Using microarray experiments, we found 761 genes under the control of both Six and MyoD. Using MyoD ChIPseq data and a genome-wide search for Six1/4 MEF3 binding sites, we found significant co-localization of binding sites for MyoD and Six proteins on over a thousand mouse genomic DNA regions. The combination of both datasets yielded 82 genes which are synergistically activated by Six and MyoD, with 96 associated MyoD+MEF3 putative cis-regulatory modules (CRMs). Fourteen out of 19 of the CRMs that we tested demonstrated in Luciferase assays a synergistic action also observed for their cognate gene. We searched putative binding sites on these CRMs using available databases and de novo search of conserved motifs and demonstrated that the...

Download

COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight

F1000Research

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to a subgroup of... more Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to a subgroup of coronaviruses rampant in bats for centuries. It caused the coronavirus disease 2019 (COVID-19) pandemic. Most patients recover, but a minority of severe cases experience acute respiratory distress or an inflammatory storm devastating many organs that can lead to patient death. The spread of SARS-CoV-2 was facilitated by the increasing intensity of air travel, urban congestion and human contact during the past decades. Until therapies and vaccines are available, tests for virus exposure, confinement and distancing measures have helped curb the pandemic. Vision: The COVID-19 pandemic calls for safeguards and remediation measures through a systemic response. Self-organizing initiatives by scientists and citizens are developing an advanced collective intelligence response to the coronavirus crisis. Their integration forms Olympiads of Solidarity and Health. Their ability to optimize our res...

Proteomic Analysis Uncovers Measles Virus Protein C Interaction with p65/iASPP/p53 Protein Complex

Viruses manipulate central machineries of host cells to their advantage. They prevent host cell a... more Viruses manipulate central machineries of host cells to their advantage. They prevent host cell antiviral responses to create a favorable environment for their survival and propagation. Measles virus (MV) encodes two non-structural proteins MV-V and MV-C known to counteract the host interferon response and to regulate cell death pathways. Several molecular mechanisms underlining MV-V regulation of innate immunity and cell death pathways have been proposed, whereas MV-C host protein partners are less studied. We suggest that some cellular factors that are controlled by MV-C protein during viral replication could be components of innate immunity and the cell death pathways. To determine which host factors are targeted by MV-C, we captured both direct and indirect host protein partners of MV-C protein. For this, we used a strategy based on recombinant viruses expressing tagged viral proteins followed by affinity purification and a bottom-up mass spectrometry analysis. From the list of ...