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@article{omodei2014modelisation,

title = {Modélisation multiniveau de la morphogenèse de familles de citations},

author = {Elisa Omodei and Jean-Philippe Cointet},

url = {https://journals.openedition.org/rsl/510},

doi = {10.4000/rsl.510},

year  = {2014},

date = {2014-01-01},

urldate = {2014-01-01},

journal = {Revue Sciences/Lettres},

number = {2},

publisher = {École normale supérieure},

abstract = {Dans cet article, nous étudions les dynamiques de prolifération et de diversification des « citations » dans la blogosphère. Dans la continuité des travaux séminaux de Leskovec et Simmons sur les dynamiques « culturelles » dans les médias sociaux, nous analysons en profondeur les transformations que les citations subissent au cours de leur diffusion en ligne. Nous ne visons pas dans notre approche à modéliser la dynamique temporelle du processus de diffusion mais plutôt de décrire finement la nature des changements qui affectent les expressions placées entre guillemets. Quelles sont les grands types de transformations observées et quelles propriétés des citations les rendent plus ou moins sensibles à ces mutations ? En poursuivant la métaphore biologique, nous essayons de comprendre comment des mutations à différentes échelles génèrent des « espèces » de citations (familles).},

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}

@article{tancoigne2014place,

title = {The place of agricultural sciences in the literature on ecosystem services},

author = {Elise Tancoigne and Marc Barbier and Jean-Philippe Cointet and Guy Richard},

doi = {10.1016/j.ecoser.2014.07.004},

year  = {2014},

date = {2014-01-01},

urldate = {2014-01-01},

journal = {Ecosystem Services},

volume = {10},

pages = {35-48},

publisher = {Elsevier},

abstract = {We performed a quantitative and qualitative analysis of the scientific literature on ecosystem services in order to help tracing a research agenda for agricultural sciences. The ecosystem services concept now lies at the heart of current developments to address global environmental change. Do agricultural sciences generate knowledge that covers this emerging theme? An analysis of scientific production allowed us to return to the ecological origins of this concept and see how little it has been appropriated by agricultural sciences until now, despite major focus on the issue of agro-ecosystems in the literature. Agricultural sciences tend to be more active in the field of environmental services, defined as services rendered by humans to ecosystems. The main studied services are those which have already been clearly identified and which act in synergy. Less attention is paid to the antagonisms between different services. These findings call for the implementation of agricultural research programmes that will consider the socio-agro-ecosystem as a whole and broaden the traditional issues addressed by agricultural sciences. We insist on three main management and operational issues that needs to be overcome if this is to be done: working at the landscape scale, increasing inter-disciplinary collaborations and take uncertainties into account.},

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@article{venturini2014three,

title = {Three maps and three misunderstandings: A digital mapping of climate diplomacy},

author = {Tommaso Venturini and Nicolas Baya-Laffite and Jean-Philippe Cointet and Ian Gray and Vinciane Zabban and Kari De Pryck},

url = {https://doi.org/10.1177/2053951714543804},

doi = {10.1177/2053951714543804},

year  = {2014},

date = {2014-01-01},

urldate = {2014-01-01},

journal = {Big Data & Society},

volume = {1},

number = {2},

pages = {1-19},

publisher = {SAGE Publications Sage UK: London, England},

abstract = {This article proposes an original analysis of the international debate on climate change through the use of digital methods. Its originality is twofold. First, it examines a corpus of reports covering 18 years of international climate negotiations, a dataset never explored before through digital techniques. This corpus is particularly interesting because it provides the most consistent and detailed reporting of the negotiations of the United Nations Framework Convention on Climate Change. Second, in this paper we test an original approach to text analysis that combines automatic extractions and manual selection of the key issue-terms. Through this mixed approach, we tried to obtain relevant findings without imposing them on our corpus. The originality of our corpus and of our approach encouraged us to question some of the habits of digital research and confront three common misunderstandings about digital methods that we discuss in the first part of the article (section ‘Three misunderstandings on digital methods in social sciences’). In addition to reflecting on methodology, however, we also wanted to offer some substantial contribution to the understanding of UN-framed climate diplomacy. In the second part of the article (section ‘Three maps on climate negotiations’) we will therefore introduce some of the preliminary results of our analysis. By discussing three visualizations, we will analyze the thematic articulation of the climatic negotiations, the rise and fall of these themes over time and the visibility of different countries in the debate. },

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@article{Baya-Laffite2014,

title = {Cartographier la trajectoire de l'adaptation dans l'espace des négociations sur le climat. Changer d'échelle, red(u)ire la complexité},

author = {Nicolas Baya-Laffite and Jean-Philippe Cointet},

url = {https://doi.org/10.3917/res.188.0159},

doi = {10.3917/res.188.0159},

year  = {2014},

date = {2014-01-01},

urldate = {2014-01-01},

journal = {Réseaux},

volume = {188},

number = {6},

pages = {159-198},

abstract = {Les négociations au sein de Convention cadre des Nations Unies sur les changements climatiques (CCNUCC) connaissaient une inflation thématique incessante à l’aune des intérêts et cadrages souvent concurrents des Parties. En témoigne la place acquise par le thème controversé de l’adaptation aux impacts du changement climatique. Cartographier ce phénomène complexe constitue un défi pour l’analyse quali-quantitative des problèmes publics que cet article adresse en présentant et en discutant une expérience de production et visualisation de données sur configuration de l’espace thématique des négociations et son déploiement dans le temps. Par un changement d’échelle et des allers-retours entre visualisation et narration, il est dès lors possible de réduire et redire la complexité pour rendre compte de la trajectoire de l’adaptation. Celui-ci n’est, cependant, qu’un exemple parmi les multiples histoires, fondées sur la modélisation des données, qui peuvent être produites. Ainsi, ce type de visualisations porte un potentiel en tant qu’objet frontière pour discuter les enjeux passés, présents et futurs à l’aune d’une vue synoptique du processus.},

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@article{chavalarias2013phylomemetic,

title = {Phylomemetic patterns in science evolution - the rise and fall of scientific fields},

author = {David Chavalarias and Jean-Philippe Cointet},

url = {https://doi.org/10.1371/journal.pone.0054847},

doi = {10.1371/journal.pone.0054847},

year  = {2013},

date = {2013-01-01},

urldate = {2013-01-01},

journal = {PloS one},

volume = {8},

number = {2},

pages = {e54847},

publisher = {Public Library of Science},

abstract = {We introduce an automated method for the bottom-up reconstruction of the cognitive evolution of science, based on big-data issued from digital libraries, and modeled as lineage relationships between scientific fields. We refer to these dynamic structures as phylomemetic networks or phylomemies, by analogy with biological evolution; and we show that they exhibit strong regularities, with clearly identifiable phylomemetic patterns. Some structural properties of the scientific fields - in particular their density -, which are defined independently of the phylomemy reconstruction, are clearly correlated with their status and their fate in the phylomemy (like their age or their short term survival). Within the framework of a quantitative epistemology, this approach raises the question of predictibility for science evolution, and sketches a prototypical life cycle of the scientific fields: an increase of their cohesion after their emergence, the renewal of their conceptual background through branching or merging events, before decaying when their density is getting too low.},

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@article{keating2013therapy,

title = {Therapy’s shadow: a short history of the study of resistance to cancer chemotherapy},

author = {Peter Keating and Alberto Cambrosio and Nicole Nelson and Andrei Mogoutov and Jean-Philippe Cointet},

url = {https://doi.org/10.3389/fphar.2013.00058},

doi = {10.3389/fphar.2013.00058},

year  = {2013},

date = {2013-01-01},

urldate = {2013-01-01},

journal = {Frontiers in pharmacology},

volume = {4},

pages = {58},

publisher = {Frontiers},

abstract = {This article traces the history of research on resistance to drug therapy in oncology using scientometric techniques and qualitative analysis. Using co-citation analysis, we generate maps to visualize subdomains in resistance research in two time periods, 1975–1990 and 1995–2010. These maps reveal two historical trends in resistance research: first, a shift in focus from generic mechanisms of resistance to chemotherapy to a focus on resistance to targeted therapies and molecular mechanisms of oncogenesis; and second, a movement away from an almost exclusive reliance on animal and cell models and toward the generation of knowledge about resistance through clinical trial work. A close reading of highly cited articles within each subdomain cluster reveals specific points of transition from one regime to the other, in particular the failure of several promising theories of resistance to be translated into clinical insights and the emergence of interest in resistance to a new generation of targeted agents such as imatinib and trastuzumab. We argue that the study of resistance in the oncology field has thus become more integrated with research into cancer therapy – rather than constituting it as a separate domain of study, as it has done in the past, contemporary research treats resistance as the flip side to treatment, as therapy’s shadow.},

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@article{raimbault2013caracterisation,

title = {Caractérisation du processus d’émergence de la biologie synthétique à partir d’une approche scientomiétrique},

author = {Benjamin Raimbault and Jean-Philippe Cointet and Pierre-Benoît Joly},

url = {https://doi.org/10.1051/medsci/201329s213},

doi = {10.1051/medsci/201329s213},

year  = {2013},

date = {2013-01-01},

urldate = {2013-01-01},

journal = {médecine/sciences},

volume = {29},

pages = {47-55},

publisher = {Éditions EDK, Groupe EDP Sciences},

abstract = {La biologie de synthèse est un espace hétérogène dont la définition n’est pas stabilisée. Elle se situe à l’intersection de différents champs disciplinaires : chimie, biologie moléculaire, bio-informatique, et est classiquement abordée par la littérature selon trois angles [1–3] : 1 une approche « DNA based device construction » (biobrick), ou approche bottom-up, focalisée sur l’ingénierie de circuits de gènes synthétiques ; 2 une approche « genome-driven cell engineering », ou approche top-down, focalisée sur la synthèse d’un génome dans son intégralité ; 3 une approche « proto-cell creation » qui vise à recréer des systèmes cellulaires minimaux, et en vertu de laquelle les recherches sont focalisées sur le principe de l’émergence, ouvertement présenté comme un obstacle par les tenants de la première approche.

},

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@article{Parasie2012b,

title = {La presse en ligne au service de la démocratie locale, une analyse morphologique de forums politiques},

author = {Sylvain Parasie and Jean-Philippe Cointet},

url = {https://doi.org/10.3917/rfsp.621.0045},

doi = {10.3917/rfsp.621.0045},

year  = {2012},

date = {2012-02-01},

urldate = {2012-02-01},

journal = {Revue Française de Science Politique},

volume = {62},

number = {1},

pages = {45-70},

abstract = {Les sciences sociales dressent souvent un constat critique du rôle que joue la presse dans la vie politique locale. À travers une analyse statistique et lexicométrique de forums web mis en place par La Voix du Nord à l’occasion des élections municipales de 2008, cet article montre qu’une organisation de presse peut tirer parti du web pour modifier le rôle qu’elle joue dans les espaces démocratiques locaux. Pour ce faire, il montre que la prise de parole se déploie en ligne d’une façon spécifique selon la morphologie des communes. En proposant des espaces de discussion en ligne, le journal joue le rôle d’un « voile » dans les petites communes ­ mettant en suspens les identités dans un contexte d’interconnaissance ­ et d’un « catalyseur » dans les communes moyennes ­ favorisant l’émergence d’une opinion locale.},

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}

@article{cointet2012reseaux,

title = {Les réseaux de l’expression génique - Émergence et développement d’un domaine clé de la génomique},

author = {Jean-Philippe Cointet and Andrei Mogoutov and Pascale Bourret and Rim El Abed and Alberto Cambrosio},

url = {https://doi.org/10.1051/medsci/2012281s104},

doi = {10.1051/medsci/2012281s104},

year  = {2012},

date = {2012-01-01},

urldate = {2012-01-01},

journal = {médecine/sciences},

volume = {28},

pages = {7--13},

publisher = {Éditions EDK, Groupe EDP Sciences},

abstract = {Cet article analyse l’émergence et le développement d’un des domaines clés de la génomique, celui de l’expression génique (gene expression profiling), en utilisant des méthodes d’analyse informatisée et de cartographie du contenu des publications scientifiques. Les résultats de cette analyse détaillent le rôle central joué par l’oncologie dans le développement de ce domaine de recherche. Des démonstrations de principe utilisant un organisme modèle végétal ont rapidement débouché sur des preuves de l’utilité de cette approche dans le cas des hémopathies malignes et des applications dans le domaine des tumeurs solides, notamment les cancers du sein. L’étude met également en relief l’importance de la bioinformatique et des biostatistiques comme conditions de possibilité de ce type de recherches, qui s’imposent dès lors comme le troisième pôle, en plus du laboratoire et de la clinique, du triangle de la recherche translationnelle.},

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@article{parasie2012online,

title = {Online press serving local democracy},

author = {Sylvain Parasie and Jean-Philippe Cointet and Michael O’Mahony},

url = {http://dx.doi.org/10.3917/rfsp.621.0045},

doi = {10.3917/rfsp.621.0045},

year  = {2012},

date = {2012-01-01},

urldate = {2012-01-01},

journal = {Revue française de science politique},

volume = {62},

number = {1},

pages = {45--70},

publisher = {Presses de Sciences Po},

abstract = {For decades, research has been quite sceptical towards the role journalism plays in local political life. This article shows that news organizations can take advantage of the web to play a new role in local democratic arenas. Based on a statistical and lexicometric analysis of online forums set up by a French regional newspaper (La Voix du Nord), this study shows how the morphology of municipalities impacts the way online discussion unfolds. In providing such online discussion arenas to citizens, the news organization plays the part of a “veil” in small cities – playing down the effects of strong acquaintanceship among individuals – and the part of a “catalyst” in medium-sized cities – promoting the rise of local opinion.},

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