françois aguet

Preprints

* denotes equal contribution

Y. Liang, F. Aguet, A. Barbeira, K. Ardlie, H.K. Im, "Scalable unified framework of total and allele-specific counts for cis-QTL, fine-mapping, and prediction," bioRxiv, 2020.

O.M. de Goede, N.M. Ferraro, D.C. Nachun, A.S. Rao, F. Aguet, A.N. Barbeira, S.E. Castel, S. Kim-Hellmuth, Y. Park, A.J. Scott, B.J. Strober, GTEx Consortium, C.D. Brown, X. Wen, I. M. Hall, A. Battle, T. Lappalainen, H.K. Im, K.G. Ardlie, T. Quertermous, K. Kirkegaard, S.B. Montgomery, "Long non-coding RNA gene regulation and trait associations across human tissues," bioRxiv, 2019.

A.N. Barbeira, R. Bonazzola, E.R. Gamazon, Y. Liang, Y. Park, S. Kim-Hellmuth, G. Wang, Z. Jiang, D. Zhou, F. Hormozdiari, B. Liu, A. Rao, A.R. Hamel, M.D. Pividori, F. Aguet, GTEx GWAS Working Group, L. Bastarache, D.M. Jordan, M. Verbanck, R. Do, GTEx Consortium, M. Stephens, K.G. Ardlie, M. McCarthy, S.B. Montgomery, A.V. Segrè, C.D. Brown, T. Lappalainen, X. Wen, H.K. Im, "Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits," bioRxiv, 2019.

Journal papers

* denotes equal contribution

GTEx Consortium (first & co-corresponding author), "The GTEx Consortium atlas of genetic regulatory effects across human tissues," Science 369, 1318-1330, 2020. Coverage: [Science News] [Broad Institute] [NYGC]

S. Kim-Hellmuth*, F. Aguet*, M. Oliva, M. Muñoz-Aguirre, S. Kasela, V. Wucher, S.E. Castel, A.R. Hamel, A. Viñuela, A.L. Roberts, S. Mangul, X. Wen, G. Wang, A.N. Barbeira, D. Garrido-Martín, B. Nadel, Y. Zou, R. Bonazzola, J. Quan, A. Brown, A. Martinez-Perez, J.M. Soria, GTEx Consortium, G. Getz, E.T. Dermitzakis, K.S. Small, M. Stephens, H.S. Xi, H.K. Im, R. Guigó, A.V. Segrè, B.E. Stranger, K.G. Ardlie, T. Lappalainen "Cell type specific genetic regulation of gene expression across human tissues," Science 369, eaaz8528, 2020.

N.M. Ferraro, B.J. Strober, J. Einson, N.S. Abell, F. Aguet, A.N. Barbeira, M. Brandt, M. Bucan, S.E. Castel, J.R. Davis, E. Greenwald, G.T. Hess, A.T. Hilliard, R.L. Kember, B. Kotis, Y. Park, G. Peloso, S. Ramdas, A.J. Scott, C. Smail, E.K. Tsang, S.M. Zekavat, M. Ziosi, Aradhana, TOPMed Lipids Working Group, K.G. Ardlie, T.L. Assimes, M.C. Bassik, C.D. Brown, A. Correa, I. Hall, H.K. Im, X. Li, P. Natarajan, GTEx Consortium, T. Lappalainen, P. Mohammadi, S.B. Montgomery, A. Battle, "Transcriptomic signatures across human tissues identify functional rare genetic variation," Science 369, eaaz5900, 2020.

K. Demanelis, F. Jasmine, L.S. Chen, M. Chernoff, L. Tong, D. Delgado, C. Zhang, J. Shinkle, M. Sabarinathan, H. Lin, E. Ramirez, M. Oliva, S. Kim-Hellmuth, B.E. Stranger, T.-P. Lai, A. Aviv, K.G. Ardlie, F. Aguet, H. Ahsan, GTEx Consortium, J. Doherty, M.G. Kibriya, B.L. Pierce, "Determinants of telomere length across human tissues," Science 369, eaaz6876, 2020.

M. Oliva, M. Muñoz-Aguirre, S. Kim-Hellmuth, V. Wucher, A.D.H. Gewirtz, D.J. Cotter, P. Parsana, S. Kasela, B. Balliu, A. Viñuela, S.E. Castel, P. Mohammadi, F. Aguet, Y. Zou, E.A. Khramtsova, A.D. Skol, D. Garrido-Martín, F. Reverter, A. Brown, P. Evans, E.R. Gamazon, A. Payne, R. Bonazzola, A.N. Barbeira, A.R. Hamel, A. Martinez-Perez, J.M. Soria, G. Consortium, B.L. Pierce, M. Stephens, E. Eskin, E.T. Dermitzakis, A.V. Segrè, H.K. Im, B.E. Engelhardt, K.G. Ardlie, S.B. Montgomery, A.J. Battle, T. Lappalainen, R. Guigó, B.E. Stranger "The impact of sex on gene expression across human tissues, Science 369, eaba3066, 2020.

S.E. Castel, F. Aguet, P. Mohammadi, GTEx Consortium, K.G. Ardlie, T. Lappalainen, "A vast resource of allelic expression data spanning human tissues," Genome Biol 21, 234, 2020.

N.R. Gay, M. Gloudemans, M.L. Antonio, N.S. Abell, B. Balliu, Y. Park, A.R. Martin, S. Musharoff, A. Rao, F. Aguet, A. Barbeira, R. Bonazzola, F. Hormozdiari, GTEx Consortium, K.G. Ardlie, C.D. Brown, H.K. Im, T. Lappalainen, X. Wen, S.B. Montgomery, "Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx," Genome Biol 21, 233, 2020.

N.R. Tucker, M. Chaffin, S.J. Fleming, A.W. Hall, V.A. Parsons, K.C. Bedi Jr, A.-D. Akkad, C.N. Herndon, A. Arduini, I. Papangeli , C. Roselli, F. Aguet, S.H. Choi, K.G. Ardlie, M. Babadi, K.B. Margulies, C.M. Stegmann, P.T. Ellinor, "Transcriptional and Cellular Diversity of the Human Heart," Circulation 142, 466-482, 2020.

M. Bustoros, R. Sklavenitis-Pistofidis, J. Park, R. Redd, B. Zhitomirsky, A.J. Dunford, K. Salem, Y.-T. Tai, S. Anand, T.H. Mouhieddine, S.J. Chavda, C. Boehner, L. Elagina, C.J. Neuse, J. Cha, M. Rahmat, A. Taylor-Weiner, E. Van Allen, S. Kumar, E. Kastritis, I. Leshchiner, E.A. Morgan, J. Laubach, T. Casneuf, P. Richardson, N.C. Munshi, K.C. Anderson, L. Trippa, F. Aguet, C. Stewart, M.-A. Dimopoulos, K. Yong, P.L. Bergsagel, S. Manier, G. Getz, I.M. Ghobrial, "Genomic profiling of smoldering multiple myeloma identifies patients at a high risk of disease progression," J. Clin. Oncol. 38(21), 2380-2389, 2020.

A. Taylor-Weiner*, F. Aguet*, N. Haradhvala, S. Gosai, J. Kim, K.G. Ardlie, E. Van Allen, G. Getz, "Scaling computational genomics to millions of individuals with GPUs," Genome Biol 20, 228, 2019.

K. Yizhak, F. Aguet, J. Kim, J.M. Hess, K. Kübler, J. Grimsby, R. Frazer, H. Zhang, N.J. Haradhvala, D. Rosebrock, D. Livitz, X. Li, E. Arich-Landkof, N. Shoresh, C. Stewart, A.V. Segrè, P.A. Branton, P. Polak, K.G. Ardlie, G. Getz, "RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues," Science 364, 10.1126/science.aaw0726, 2019. [Science Perspective]

M. Ghandi, F.W. Huang, J. Jané-Valbuena, G.V. Kryukov, C.C. Lo, E.R. McDonald III, J. Barretina, E.T. Gelfand, C.M. Bielski, H. Li, K. Hu, A.Y. Andreev-Drakhlin, J. Kim, J.M. Hess, B.J. Haas, F. Aguet, B.A. Weir, M.V. Rothberg, B.R. Paolella, M.S. Lawrence, R. Akbani, Y. Lu, H.L. Tiv, P.C. Gokhale, A. de Weck, A.A. Mansour, C. Oh, J. Shih, K. Hadi, Y. Rosen, J. Bistline, K. Venkatesan, A. Reddy, D. Sonkin, M. Liu, J. Lehar, J.M. Korn, D.A. Porter, M.D. Jones, J. Golji, G. Caponigro, J.E. Taylor, C.M. Dunning, A.L. Creech, A.C. Warren, J.M. McFarland, M. Zamanighomi, A. Kauffmann, N. Stransky, M. Imielinski, Y.E. Maruvka, A.D. Cherniack, A. Tsherniak, F. Vazquez, J.D. Jaffe, A.A. Lane, D.M. Weinstock, C.M. Johannessen, M.P. Morrissey, F. Stegmeier, R. Schlegel, W.C. Hahn, G. Getz, G.B. Mills, J.S. Boehm, T.R. Golub, L.A. Garraway, W.R. Sellers, "Next-generation characterization of the Cancer Cell Line Encyclopedia," Nature 569, 503-508, 2019.

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 (co-first author), "Genetic effects on gene expression across human tissues," Nature 550, 204-213, 2017. Coverage: [Nature News & Views] [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]

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]

T. Böcking, F. Aguet, I. Rapoport, M. Banzhaf, A. Yu, J.C. Zeeh, T. Kirchhausen, "Key Interactions for Clathrin Coat Stability," Structure 22(6), 819-829, 2014. [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]

A. Bourquard, F. Aguet, and M. Unser, "Optical imaging using binary sensors," Opt. Express 18(5), 4876-4888, 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]

Reviews & book chapters

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.

C. Vonesch, F. Aguet, J.-L. Vonesch, M. Unser, "The Colored Revolution of Bioimaging," IEEE Signal Process. Mag. 23(3), 20-31, 2006. [pdf].

Ph.D. dissertation

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]

International conference proceedings (peer-reviewed)

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.