Publications

A complete list of my publications can be found on my Google Scholar profile. Red color indicates key publications. My complete CV can be found here.

In preparation

M. Santolini, A. Krishna, L. Blondel, M.J. Palmer, T.E. Landrain, A-L Barabasi, Collaboration and Innovation in an International Science and Engineering Competition (in preparation) [abstract] [best presentation at Complex Networks 2017] [iGEM Insights collaboration]


2020

23. Santolini,M., Ellinas,C. and Nicolaides,C. (2020) Uncovering the fragility of large-scale engineering project networks. arXiv:2009.11752 [pdf]

22. Mellors,T., Withers,J.B., Ameli,A., Jones,A., Wang,M., Zhang,L., Sanchez,H.N., Santolini,M., Do Valle,I., Sebek,M., et al. (2020) Clinical Validation of a Blood-Based Predictive Test for Stratification of Response to Tumor Necrosis Factor Inhibitor Therapies in Rheumatoid Arthritis Patients. Network and Systems Medicine, 3, 91–104. [pdf]

21. Charles Auffray, Rudi Balling, Niklas Blomberg, MYRNA BONALDO, Bertrand Boutron, Samir Brahmachari, Christian Bréchot, Alfredo Cesario, Sai-Juan Chen, Karine Clément, Daria Danilenko, Alberto Di Meglio, Andrea Gelemanovic, Carole Goble, Takashi Gojobori, Jason D Goldman, Michel Goldman, Yi-Ke Guo, James Heath, Leroy Hood, Peter Hunter, Li Jin, Hiroaki Kitano, Bartha Maria Knoppers, Doron Lancet, Catherine Larue, Mark Lathrop, Martine Laville, Ariel B Lindner, Antoine Magnan, Andres Metspalu, Edgar Morin, Lisa FP Ng, Laurent Nicod, Denis Noble, Laurent Nottale, Helga Nowotny, Iruna Okeke, Tolu Oni, Peter Openshaw, Mehmet Oztürk, Susanna Palkonen, Janusz Paweska, Christophe Pison, Mihael Polymeropoulos, Christian Pristipino, Ulrike Protzer, Josep Roca, Damjana Rozman, Marc Santolini, Ferran Sanz, Giovanni Scambia, Eran Segal, Ismail Serageldin, Marcelo Bento Soares, Peter Sterk, Sumio Sugano, Julio Superti-Furga, David Supple, Jesper Tegnér, Mathias Uhlen, Andrea Urbani, Alfonso Valencia, Vincenzo Valentini, Sylvie van der Werf, Manlio Vinciguerra, Olaf Wolkenhauer, Emiel Wouters. COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight F1000Research 2020, 9:1130 [pdf]

20. A Meignié, C Combredet, M Santolini, I Kovacs, T Douche, Q Giai, H Eun, M Matondo, Y Jacob, R Grailhe, F Tangy, and A. V. Komarova. Proteomic Analysis Uncovers Measles Virus Protein C Interaction with p65/iASPP/p53 Protein Complex, bioRxiv [pdf]

19. O. Poquet, L. Tupikina, and M. Santolini. Are Forum Networks Social Networks? A Methodological Perspective. In Proceedings of the 10th International Conference on Learning Analytics and Knowledge (LAK ’20), March 23–27, 2020, Frankfurt, Germany. [pdf]

2019

18. A. Kılıç, A. Ameli, J-A Park, A Koh, K Tantisira, M. Santolini, F. Cheng, J. Mitchel, M. McGill, A. Sharma, S. H Randell, J. M Drazen, J. Fredberg, and S. T. Weiss.  Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. Scientific Reports (in press)

17. B Wang, K Glass, A Röhl, M Santolini, D.C. Croteau-Chonka, S. T. Weiss, B. A. Raby, A. Sharma. The periphery and the core properties explain the omnigenic model in the human interactome. bioRxiv [web] [pdf]

2018

16. C. Rees, JH Yang, M. Santolini, JN Weiss and A. Karma. The Ca2+ transient as a feedback sensor controlling cardiomyocyte ionic conductances in mouse populations. eLife [web] [pdf]

15. A. Sharma, M. Kitsak, M. Cho, A. Ameli, X. Zhou, Z. Jiang, J D Crapo, T beaty, J. Menche, P S Bakke, M. Santolini, E. K. Silverman. Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease module. Scientific Reports  [web] [pdf]

14. M. Santolini, A-L Barabasi, Predicting perturbation patterns from the topology of biological networks. PNAS [web][pdf]

13. A. Kilic, M. Santolini, A. Al Garawi, S. Uchida, H. Renz, S. T. Weiss, A. Sharma, A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. JCI Insight [web] [pdf]

12. M Benchoufi, M Fournier, D Magrez, G Macaux, V Barué, A Mansilla Sanchez, O de Fresnoye, R Fillaudeau, O Tauvel-Mocquet, N Chalabi, J-F Petit-Nivard, L Blondel, M Santolini, and B Ben Hadj Yahia. Epidemium: A multidisciplinary community to tackle cancer using big and open data. Journal of Clinical Oncology [web] [pdf]

11. A Sharma, A Halu, J.L. Decano, M Padi, Y-Y Liu, RB Prasad, J Fadista,
M Santolini, J Menche, ST. Weiss, M. Vidal, EK. Silverman, M Aikawa, A-L Barabási, L Groop and J Loscalzo Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. npj Systems Biology and Applications [web] [pdf]

10. M. Santolini, MC. Romay, C. Rau, S. Ren, J. Saucerman, J. Wang, J. Weiss, Y. Wang, A. Lusis, A. Karma. A personalized, multi-omics approach identifies genes involved in cardiac hypertrophy and heart failure. npj Systems Biology and Applications  [web] [pdf] [in the news


2017

9. CD Rau, MC Romay, M Tuteryan, JC Wang, M. Santolini, S Ren, A Karma, JN Weiss, Y Wang, AJ Lusis. Systems Genetics Approach Identifies Gene Pathways and Adamts2 as Drivers of Isoproterenol-Induced Cardiac Hypertrophy and Cardiomyopathy in Mice. Cell Systems [web] [pdf]


2016

8. H Mirzakhani, AA Litonjua, T McElrath, G O’Connor, A Lee-Parritz, R Iverson, G Ma- cones, R Strunk, LB Bacharier, R Zeiger, BW Hollis, DE Handy, A Sharma, N Laranjo, V Carey, W Qiu, M. Santolini, S Liu, D Chhabra, DA Enquobahrie, MA Williams, J Localzo, ST Weiss. Early pregnancy vitamin D status and risk of preeclampsia. J Clin Invest.  [web] [pdf]

7. I. Sakakibara, M. Wurmser, M. Santolini, R. Davaze, S. Ducommun, K. Sakamoto, P. Maire. Six1 homeoprotein drives myofiber type IIA specialization in soleus muscle. Skeletal Muscle [web] [pdf]

6. M. Santolini*, I. Sakakibara*, M. Gauthier, V. Mouly, JP. Concordet, PA. Defossez, V. Hakim, P. Maire. MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis. Nucleic Acids Research [web] [pdf]


2014

5. M. Santolini, T. Mora, and V. Hakim. A general pairwise interaction model provides an accurate description of in vivo transcription factor binding sites. PLoS One  [web] [pdf]

4. I. Sakakibara, M. Santolini, A. Ferry, V. Hakim, and P. Maire. Six homeoproteins and a linc-RNA at the fast MYH locus lock fast myofiber terminal phenotype. PLoS Genetics [web] [pdf]

3. M. Santolini*, H. Rouault*, F. Schweisguth, and V. Hakim. Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. Nucleic Acids Research [web] [pdf]


2013

2. M. Santolini*, D. Menoret*, I. Fernandes, R. Spokony, J. Zanet, I. Gonzalez, Y. Latapie, P. Ferrer, H. Rouault, K. P. White, P. Besse, V. Hakim, S. Aerts, F. Payre, and S. Plaza. Genome-wide analyses of shavenbaby target genes reveals distinct features of enhancer organization. Genome Biology [web] [pdf]

1. F. Relaix, J. Demignon, C. Laclef, J. Pujol, M. Santolini, C. Niro, M. Lagha, D. Ro- cancourt, M. Bucking- ham, and P. Maire. Six homeoproteins directly activate Myod expression in the gene regulatory networks that control early myogenesis. PLoS Genetics [web] [pdf]


Book chapters

The Epidemium challenge is a community-based open science program exploring new paths to cancer research. In this chapter we reflect on the program by analyzing the digital traces of teams from the various collaborative tools used during the challenge.


News

Comment naissent les idées lumineuses ? Le grand mystère de la créativité, in Le Monde (23 Dec 2019) [pdf]

Theses

  • Computational analysis of cis-regulatory elements in drosophila and mammalian genomes. (French) [pdf]

My PhD thesis of physics done at the Laboratoire de Physique Statistique (LPS) of ENS under the supervision of Vincent Hakim.

  • Le Principe Anthropique – La place de l’Homme dans l’Univers.  (French) [pdf]

My Master’s thesis of History and Philosophy of Science done at ENS under the supervision of Marc Lachièze-Rey during 2008.

  • Estimating cosmological parameters through cross-correlation of galaxy surveys and Cosmic Microwave Background fluctuations. [pdf]

Thesis from my internship done at the Departement of Astrophysical Sciences at Princeton University under the supervision of David Spergel during spring 2007.