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

22. M. Santolini, A. Krishna, L. Blondel, M.J. Palmer, T.E. Landrain, A-L Barabasi, A large scale laboratory notebook analysis predicts team success in a scientific competition (in preparation) [abstract] [best presentation at Complex Networks 2017] [iGEMeta collaboration]

21. A. Dhand, S. Cornelius, M. Santolini, A-L Barabasi, Hospital network centrality predicts mortality (in preparation) [abstract]

20. B. Wang, M. Santolini, K. Glass, DC Chonka, B. Raby, A. Sharma. The peripheral and core properties of a disease module in the interactome (in preparation)

19. M. Santolini*, B. Winborn*, S. Liu, H. Joo Kim, J.P. Taylor, A. Sharma. A disease centrality identifies multi-system proteinopathy disease genes (in preparation) [poster]

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. (in preparation)

17. M. Sumathipala, B. Klein, A. Sharma, M. SantoliniNext Generation Drug Discovery: A Novel In Silico Network Approach to miRNA Drug Target Identification (in preparation)

16. C. Rees, JH Yang, M. Santolini, JN Weiss and A. Karma. Variability and compensation in cardiac electrophysiology at cellular, organ, and population levels. (in revision).

15. A. Sharma, X. Zhou, Z. Jiang, M. Cho, J. Menche, M. Kitsak, M. Santolini, A.-L. Barabási, E. K. Silverman. Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease module (in revision)


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

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] [in the news]


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]


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]

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]

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]


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]

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]

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]


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]

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]

Book chapters

  • Epidemium White Paper: Measuring the program [English] [French]

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.


  • 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.