Submitted papers

• Bleakley, K., Fortas, C., Duong, V., Ly, S., Cantaert, T., Sothy, H., Laurent, D., Buchy, P., Dussart, P., and Sakuntabhai, A. (2019). Multivariate evidence-based pediatric dengue severity prediction at hospital arrival.

• Bleakley, K. and Vert, J.-P. (2011). The group fused Lasso for multiple change-point detection.    Software.   (163 citations as of 3/05/2021, not bad for a preprint!)

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Publications

• Pommier, J.-D., Martino, F., Bleakley, K., Flurin, L., Van Roy, F., Carles, M., Valette, M., and Camous, L. (2021). A tale of a two-wave epidemic: Characteristics and mortality risk factors for Covid-19 ICU patients in the French West Indies. Journal of Biology and Today's World.

• Dussart, P., Duong, V., Bleakley, K., Fortas, C., Lorn Try, P., Kim, K. S., Choeung, R., In, S., Andries, A.-C., Cantaert, T., Flamand, M., Buchy, P., and Sakuntabhai, A. (2020). Comparison of dengue case classification schemes and evaluation of biological changes in different dengue clinical patterns in a longitudinal follow-up of hospitalized children in Cambodia. PLOS Neglected Tropical Diseases.

• Lachuer, H., Mathur, P., Bleakley, K., and Schauer, K. (2020). Quantifying spatiotemporal parameters of cellular exocytosis in micropattered cells. JoVE Journal.

• Fourati, S, ... , Bleakley, K, ... , et al. (2018). A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Nature Communications.

• Le Billan, F, ... , Bleakley, K, ... , et al. (2018). A specific signature of cyclical transcriptional clocks dictates renal corticosteroid signaling. The FASEB journal.

• Nikolayeva, I, ... , Bleakley, K, ... , et al. (2018). A blood RNA signature detecting severe disease in young dengue patients at hospital arrival. Journal of Infectious Diseases.

• Simon-Lorière, E, ... , Bleakley, K, ... , et al. (2017). Increased and controlled adaptive immune responses protect against clinical dengue. Science Translational Medicine.

• Biau, G., Bleakley, K and Cadre, B. (2016). The statistical performance of collaborative inference. . Journal of Machine Learning Research.

• Biau, G., Bleakley, K and Mason, D. (2016). Long signal change-point detection. Electronic Journal of Statistics.

• Mbogning, C., Bleakley, K. and Lavielle, M. (2014). Joint modeling of longitudinal and repeated time-to-event data with maximum likelihood estimation via the SAEM algorithm. Journal of Statistical Computation and Simulation.

• Mbogning, C., Bleakley, K. and Lavielle, M. (2012). Between-subject and within-subject model mixtures for classifying HIV treatment response. Progress in Applied Mathematics.

• Servant, N., Bollet, M. A., Halfwerk, H., Bleakley, K., Kreike, B., Jacob, L., Sie, D., Kerkhoven, R., Hupé, P., Hadhri, R., Fourquet, A., Bartelink, H., Barillot, E., Sigal-Zafrani, B. and van de Vijver, M. J. (2012). Search for a gene-expression signature of breast cancer local recurrence in young women. Clinical Cancer Research.

• Boeva, V., Popova, T., Bleakley, K., Chiche, P., Janoueix-Lerosey, I., Cappo, J., Schleiermacher, G., Delattre, O. and Barillot, E. (2011). Control-FREEC: a tool for assessing copy number and genotype using next generation sequencing data. Bioinformatics.

• Lavielle, M. and Bleakley, K. (2011). Automatic data binning for improved visual diagnosis of pharmacometric models. Journal of Pharmacokinetics and Pharmacodynamics.

• Boeva, V., Zinovyev, A., Bleakley, K., Vert, J.-P., Janoueix-Lerosey, I., Delattre, O. and Barillot, E. (2010). Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics.

• Vert, J.-P. and Bleakley, K. (2010). Fast detection of multiple change-points shared by many signals using group LARS. Advances in Neural Information Processing Systems 2010.

• Schauer, K., Duong, T., Bleakley, K., Bardin, S., Bornens, M. and Goud, B. (2010). Probabilistic density maps to study global endomembrane organization, Nature Methods, (doi:10.1038/nmeth.1462).

• Biau, G., Bleakley, K., Györfi, L. and 0ttucsák, G. (2010). Nonparametric sequential prediction of time series, Journal of Nonparametric Statistics, Vol. 22, pp. 297-317.

• Austerlitz, F., David, O., Schaeffer, B., Bleakley, K., Olteanu, M., Leblois, R., Veuille, M. and Laredo, C. (2009). DNA barcode analysis: a comparison of phylogenetic and statistical classification methods, BMC Bioinformatics, Vol. 10(Suppl 14):S10.

• Bleakley, K. and Yamanishi, Y. (2009). Supervised prediction of drug-target interactions using bipartite local models, Bioinformatics, Vol. 25(18), pp. 2397-2403. Software

• Bleakley, K., Lefranc, M.-P. and Biau, G. (2008). Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools, BMC Bioinformatics, 9:408.

• Bleakley, K., Biau, G. and Vert, J.-P. (2007). Supervised reconstruction of biological networks with local models, Bioinformatics, Vol. 23, pp. i57-i65. Software

• Bleakley, K., Giudicelli, V., Wu, Y., Lefranc, M.-P. and Biau, G. (2006). IMGT standardization for statistical analyses of T cell receptor junctions: The TRAV-TRAJ example, In Silico Biology, Vol. 6, 0051.

• Biau, G. and Bleakley, K. (2006). Statistical inference on graphs, Statistics & Decisions, Vol. 24(2), pp. 209-232. (S&D website)

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Books and translations

• Bécue-Bertaut, M. (2019). Textual Data Science with R, CRC Press, Abingdon (194 pages).

• Simultaneous translation (French to English) of the "Horizons of Statistics" day at the Institut Henri Poincaré, Paris. (2014).

• Lavielle, M. with contributions by Bleakley, K. (2014). Mixed Effects Models for the Population Approach, Taylor & Francis, New York (383 pages).

• Lavielle, M. (2012). Statistical analysis of the paper of G.E. Séralini et al. The paper, "Long term toxicity of a Roundup herbicide and a Roundup-tolerant genetically modified maize", purported to show the toxicity of a GMO. The scandal, followed by refutation of the study's conclusions, even reached the New York Times.

• Gaetan, C. and Guyon, X. (2010). Spatial Statistics and Modeling, Springer, New York (302 pages).