A. Taylor-Weiner*, F. Aguet*, N. Haradhvala, S. Gosai, J. Kim, K. Ardlie, E. Van Allen, G. Getz, "Scaling computational genomics to millions of individuals with GPUs," bioRxiv, 2018.
K. Yizhak, F. Aguet, J. Kim, J. Hess, K. Kubler, J. Grimsby, R. Frazer, H. Zhang, N. Haradhvala, D. Rosebrock, D. Livitz, X. Li, E. Arich-Landkof, N. Shoresh, C. Stewart, A. Segrè, P. Branton, P. Polak, K. Ardlie, G. Getz, "A comprehensive analysis of RNA sequences reveals macroscopic somatic clonal expansion across normal tissues," bioRxiv, 2018.
S. Castel, A. Cervera, P. Mohammadi, F. Aguet, F. Reverter, A. Wolman, R. Guigó, I. Iossifov, A. Vasileva, T. Lappalainen, "Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk," Nat. Genet. 50, 1327-1334, 2018.
E.R. Gamazon, A.V. Segrè, M. van de Bunt, X. Wen, H.S. Xi, F. Hormozdiari, H. Ongen, A. Konkashbaev, E.M. Derks, F. Aguet, J. Quan, GTEx Consortium, D.L. Nicolae, E. Eskin, M. Kellis, G. Getz, M.I. McCarthy, E.T. Dermitzakis, N.J. Cox, K.G. Ardlie, "Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation," Nat. Genet. 50, 956-967, 2018.
P.G. Ferreira, M. Muñoz-Aguirre, F. Reverter, C.P. Sá Godinho, A. Sousa, A. Amadoz, R. Sodaei, M.R. Hidalgo, D. Pervouchine, J. Carbonell-Caballero, R. Nurtdinov, A. Breschi, R. Amador, P. Oliveira, C. Çubuk, J. Curado, F. Aguet, C. Oliveira, J. Dopazo, M. Sammeth, K.G. Ardlie, R. Guigó, "The effects of death and post-mortem cold ischemia on human tissue transcriptomes," Nat. Comm. 9, 490, 2018.
GTEx Consortium*, "Genetic effects on gene expression across human tissues," Nature 550, 204-213, 2017.*co-first author[Nature News & Views][Coverage in The Scientist]
T. Tukiainen, A.-C. Villani, A. Yen, M. Rivas, J.L. Marshall, R. Satija, M. Aguirre, L. Gauthier, M. Fleharty, A. Kirby, B. Cummings, S.E. Castel, K. Karczewski, F. Aguet, A. Byrnes, GTEx Consortium, T. Lappalainen, A. Regev, K. Ardlie, N. Hacohen, D. MacArthur, "Landscape of X chromosome inactivation across human tissues," Nature 550, 244-248, 2017.
N. Habib, I. Avraham-Davidi, A. Basu, T. Burks, K. Shekhar, M. Hofree, S. Choudhury, F. Aguet, E. Gelfand, K. Ardlie, D. Weitz, O. Rozenblatt-Rosen, F. Zhang, A. Regev, "Massively-parallel single nucleus RNA-seq with DroNc-seq," Nat. Methods 14, 955-958, 2017.
J. Joung, J.M. Engreitz, S. Konermann, O.O. Abudayyeh, V.K. Verdine, F. Aguet, J.S. Gootenberg, N.E. Sanjana, J.B. Wright, C.P. Fulco, Y.-Y. Tseng, C.H. Yoon, J.S. Boehm, E.S. Lander, F. Zhang, "Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood," Nature 548, 343-346, 2017.
D. Klarin, Q.M. Zhu, C.A. Emdin, M. Chaffin, S. Horner, B.J. McMillan, A. Leed, M.E. Weale, C.C.A Spencer, F. Aguet, A.V. Segrè, K.G. Ardlie, A.V. Khera, V.K. Kaushik, P. Natarajan, CARDIoGRAMplusC4D Consortium, S. Kathiresan, "Genetic analysis in UK Biobank links insulin resistance and transendothelial migration pathways to coronary artery disease," Nat. Genet. 49, 1392-1397, 2017.
F. Aguet*, S. Upadhyayula*, R. Gaudin*, Y.-y. Chou, E. Cocucci, K. He, B.-C. Chen, K. Mosaliganti, M. Pasham, W. Skillern, W.R. Legant, T.-L. Liu, G. Findlay, E. Marino, G. Danuser, S. Megason, E. Betzig, T. Kirchhausen, "Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy," Mol. Biol. Cell 27(22), 3418-3435, 2016. [pdf]* equal contribution
C.R. Reis, P.-H. Chen, S. Srinivasan, F. Aguet, M. Mettlen, S.L. Schmid, "Crosstalk between Akt/GSK3β signaling and dynamin‐1 regulates clathrin‐mediated endocytosis," EMBO J 34(16), 2132-2146, 2015. [pdf]
F. Aguet, C.N. Antonescu, M. Mettlen, S.L. Schmid, and G. Danuser, "Advances in Analysis of Low Signal-to-Noise Images Link Dynamin and AP2 to the Functions of an Endocytic Checkpoint," Dev. Cell 26(3), 279-291, 2013. [pdf]
H. Kirshner, F. Aguet, D. Sage, and M. Unser, "3-D PSF fitting for fluorescence microscopy: implementation and localization application," J. Microsc. 249(1), 13-25, 2013. [ ➡ Cover article] [pdf]
E. Cocucci, F. Aguet, S. Boulant, and T. Kirchhausen, "The first five seconds in the life of a clathrin-coated pit," Cell 150(3), 495-507, 2012. [ ➡ Coverage in Science (pdf), Nat. Methods (pdf), Nat. Rev. Mol. Cell Biol. (pdf)] [pdf]
C.N. Antonescu, F. Aguet, G. Danuser, and S.L. Schmid, "Phosphatidylinositol-(4,5)-bisphosphate regulates clathrin-coated pit initiation, stabilization and size," Mol. Biol. Cell 22(14), 2588-2600, 2011. [pdf]
T. Böcking, F. Aguet, S.C. Harrison, and T. Kirchhausen, "Single-molecule analysis of a molecular disassemblase reveals the mechanism of Hsc70-driven clathrin uncoating," Nat. Struct. Mol. Biol. 18(3), 295-301, 2011. [ ➡ Coverage in Nat. Rev. Mol. Cell Biol. (pdf)] [ ➡ Cover article] [pdf]
A.P. Liu, F. Aguet, G. Danuser, and S.L. Schmid, "Local clustering of transferrin receptors promotes clathrin-coated pit initiation," J. Cell Biol. 191(7), 1381-1393, 2010. [pdf]
I. Märki, N.L. Bocchio, S. Geissbühler, F. Aguet, A. Bilenca, and T. Lasser, "Three-dimensional nano-localization of single fluorescent emitters," Opt. Express 18(19), 20263-20272, 2010. [ ➡ Selected for Virtual J. Biomed. Opt. 5(13), 2010] [pdf]
F. Aguet, S. Geissbühler, I. Märki, T. Lasser, and M. Unser, "Super-resolution orientation estimation and localization of fluorescent dipoles using 3-D steerable filters," Opt. Express 17(8), 6829-6848, 2009. [ ➡ Selected for Virtual J. Biomed. Opt. 4(6), 2009] [pdf]
F. Aguet, D. Van De Ville, and M. Unser "Model-based 2.5-D deconvolution for extended depth of field in brightfield microscopy," IEEE Trans. Image Process. 17(7), 1144-1153, 2008. [pdf]
F. Aguet, D. Van De Ville, and M. Unser, "A maximum-likelihood formalism for sub-resolution axial localization of fluorescent nanoparticles," Opt. Express 13(26), 10503-10522, 2005. [ ➡ Coverage in Photonics Showcase and EuroPhotonics] [ ➡ Selected for Virtual J. Biomed. Opt. 1(1), 2006] [pdf]
F. Aguet, K.G. Ardlie, "Tissue Specificity of Gene Expression," Curr. Genet. Med. Rep. 4, 163-169, 2016.
F. Aguet, C. Vonesch, J.-L. Vonesch, and M. Unser, "An introduction to fluorescence microscopy: basic principles, challenges, and opportunities," Microscopic Image Analysis for Life Science Applications, Artech House (Eds. J. Rittscher, R. Machiraju, S. T. C. Wong), 85-114, 2008.
F. Aguet, "Super-resolution fluorescence microscopy based on physical models," Swiss Federal Institute of Technology, Lausanne, EPFL Thesis no. 4418, 209 p., May 28, 2009. [ ➡ 2010 Research Award of the Swiss Society for Biomedical Engineering]
S. Geissbühler, F. Aguet, I. Märki, and T. Lasser, "Super-resolved position and orientation estimation of fluorescent dipoles using 3D steerable filters," Proc. SPIE, vol. 7571(75710P), 2010.
G. González, F. Aguet, F. Fleuret, M. Unser, and P. Fua, "Steerable features for statistical 3D dendrite detection," Medical Image Computing and Computer-Assisted Intervention (MICCAI 2009) - Lecture Notes in Computer Science 5762, 625-632, 2009.
F. Aguet, S. Geissbühler, I. Märki, T. Lasser, and M. Unser, "Steerable filters for orientation estimation and localization of fluorescent dipoles," Proc. 6th IEEE International Symposium on Biomedical Imaging, ISBI 2009 (June 28-July 1), 1166-1169, 2009.
F. Aguet, S. Geissbühler, I. Märki, T. Lasser, and M. Unser, "Super-resolved position and orientation of fluorescent dipoles," Proc. OSA/SPIE European Conference on Biomedical Optics (ECBO'09), vol. 7367(73670Y), 2009.
S. C. Sekhar, F. Aguet, S. Romain, P. Thévenaz, and M. Unser, "Parametric B-spline snakes on distance maps—application to segmentation of histology images," Proc. 16th European Signal Processing Conference, EUSIPCO 2008 (August 25-29), 2008.
F. Aguet, D. Van De Ville, and M. Unser, "An accurate PSF model with few parameters for axially shift-variant deconvolution," Proc. 5th IEEE International Symposium on Biomedical Imaging, ISBI 2008 (May 14-17), 157-160, 2008. [pdf].
F. Aguet, D. Van De Ville, M. Unser, "Sub-resolution maximum-likelihood based localization of fluorescent nanoparticles in three dimensions," Proc. 4th IEEE International Symposium on Biomedical Imaging, ISBI 2007 (April 12-15), 932-935, 2007. [ ➡ Invited paper]
F. Aguet, D. Van De Ville, M. Unser, "Joint Texture and Topography Estimation for Extended Depth of Field in Brightfield Microscopy Proc. 3rd IEEE International Symposium on Biomedical Imaging, ISBI 2006 (April 6-9), 778-781, 2006.
F. Aguet, M. Jacob, M. Unser, "Three-Dimensional Feature Detection Using Optimal Steerable Filters," Proc. 2005 IEEE International Conference on Image Processing (ICIP'05), Genova, Italy, September 11-14, 2005, II 1158-1161. [pdf].
F. Aguet, D. Van De Ville, M. Unser, "Sub-Resolution Axial Localization of Nanoparticles in Fluorescence Microscopy," Proc. OSA/SPIE European Conference on Biomedical Optics (ECBO'05), vol. 5860(58600P), 2005.