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High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities.
Müller, P. and de la Cuesta-Zuluaga, J. and Kuhn, M. and Baghai Arassi, M. and Treis, T. and Blasche, S. and Zimmermann, M. and Bork, P. and Patil, K.R. and Typas, A. and Garcia-Santamarina, S. and Maier, L.
Nature Protocols 19 (3): 668-699. March 2024

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility.
Lareau, C.A. and Liu, V. and Muus, C. and Praktiknjo, S.D. and Nitsch, L. and Kautz, P. and Sandor, K. and Yin, Y. and Gutierrez, J.C. and Pelka, K. and Satpathy, A.T. and Regev, A. and Sankaran, V.G. and Ludwig, L.S.
Nature Protocols 18 (5): 1416-1440. May 2023

Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.
Malinovska, L. and Cappelletti, V. and Kohler, D. and Piazza, I. and Tsai, T.H. and Pepelnjak, M. and Stalder, P. and Dörig, C. and Sesterhenn, F. and Elsässer, F. and Kralickova, L. and Beaton, N. and Reiter, L. and de Souza, N. and Vitek, O. and Picotti, P.
Nature Protocols 18 : 659-682. 16 March 2023

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Moriel, N. and Senel, E. and Friedman, N. and Rajewsky, N. and Karaiskos, N. and Nitzan, M.
Nature Protocols 16 (9): 4177-4200. September 2021

Determination of G-protein-coupled receptor oligomerization by molecular brightness analyses in single cells.
Işbilir, A. and Serfling, R. and Möller, J. and Thomas, R. and De Faveri, C. and Zabel, U. and Scarselli, M. and Beck-Sickinger, A.G. and Bock, A. and Coin, I. and Lohse, M.J. and Annibale, P.
Nature Protocols 16 (3): 1419-1451. March 2021

Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques.
Uroda, T. and Chillón, I. and Annibale, P. and Teulon, J.M. and Pessey, O. and Karuppasamy, M. and Pellequer, J.L. and Marcia, M.
Nature Protocols 15 (6): 2107-2139. June 2020

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.
Pedersen, H.K. and Forslund, S.K. and Gudmundsdottir, V. and Petersen, A.Ø. and Hildebrand, F. and Hyötyläinen, T. and Nielsen, T. and Hansen, T. and Bork, P. and Ehrlich, S.D. and Brunak, S. and Oresic, M. and Pedersen, O. and Nielsen, H.B.
Nature Protocols 13 (12): 2781-2800. December 2018

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry.
Mertins, P. and Tang, L.C. and Krug, K. and Clark, D.J. and Gritsenko, M.A. and Chen, L. and Clauser, K.R. and Clauss, T.R. and Shah, P. and Gillette, M.A. and Petyuk, V.A. and Thomas, S.N. and Mani, D.R. and Mundt, F. and Moore, R.J. and Hu, Y. and Zhao, R. and Schnaubelt, M. and Keshishian, H. and Monroe, M.E. and Zhang, Z. and Udeshi, N.D. and Mani, D. and Davies, S.R. and Townsend, R.R. and Chan, D.W. and Smith, R.D. and Zhang, H. and Liu, T. and Carr, S.A.
Nature Protocols 13 (7): 1632-1661. July 2018

Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry.
Schopper, S. and Kahraman, A. and Leuenberger, P. and Feng, Y. and Piazza, I. and Müller, O. and Boersema, P.J. and Picotti, P.
Nature Protocols 12 (11): 2391-2410. November 2017

Single-cell template strand sequencing by strand-seq enables the characterization of individual homologs.
Sanders, A.D. and Falconer, E. and Hills, M. and Spierings, D.C.J. and Lansdorp, P.M.
Nature Protocols 12 (6): 1151-1176. June 2017

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.
Sugimoto, Y. and Chakrabarti, A.M. and Luscombe, N.M. and Ule, J.
Nature Protocols 12 (3): 611-637. March 2017

Self-organization of human embryonic stem cells on micropatterns.
Deglincerti, A. and Etoc, F. and Guerra, M.C. and Martyn, I. and Metzger, J. and Ruzo, A. and Simunovic, M. and Yoney, A. and Brivanlou, A.H. and Siggia, E. and Warmflash, A.
Nature Protocols 11 (11): 2223-2232. November 2016

Isolation and cultivation of naive-like human pluripotent stem cells based on HERVH expression.
Wang, J. and Singh, M. and Sun, C. and Besser, D. and Prigione, A. and Ivics, Z. and Hurst, L.D. and Izsvák, Z.
Nature Protocols 11 (2): 327-346. February 2016

Quantitative assessment of angiogenesis, perfused blood vessels and endothelial tip cells in the postnatal mouse brain.
Wälchli, T. and Mateos, J.M. and Weinman, O. and Babic, D. and Regli, L. and Hoerstrup, S.P. and Gerhardt, H. and Schwab, M.E. and Vogel, J.
Nature Protocols 10 (1): 53-74. January 2015

In vivo shRNA screens in solid tumors.
Gargiulo, G. and Serresi, M. and Cesaroni, M. and Hulsman, D. and van Lohuizen, M.
Nature Protocols 9 (12): 2880-2902. December 2014

Germline transgenesis in pigs by cytoplasmic microinjection of Sleeping Beauty transposons.
Ivics, Z. and Garrels, W. and Mátés, L. and Yau, T.Y. and Bashir, S. and Zidek, V. and Landa, V. and Geurts, A. and Pravenec, M. and Rülicke, T. and Kues, W.A. and Izsvák, Z.
Nature Protocols 9 (4): 810-827. April 2014

Germline transgenesis in rabbits by pronuclear microinjection of Sleeping Beauty transposons.
Ivics, Z. and Hiripi, L. and Hoffmann, O.I. and Mátés, L. and Yau, T.Y. and Bashir, S. and Zidek, V. and Landa, V. and Geurts, A. and Pravenec, M. and Rülicke, T. and Bösze, Z. and Izsvák, Z.
Nature Protocols 9 (4): 794-809. April 2014

Germline transgenesis in rodents by pronuclear microinjection of Sleeping Beauty transposons.
Ivics, Z. and Mátés, L. and Yau, T.Y. and Landa, V. and Zidek, V. and Bashir, S. and Hoffmann, O.I. and Hiripi, L. and Garrels, W. and Kues, W.A. and Boesze, Z. and Geurts, A. and Pravenec, M. and Rülicke, T. and Izsvák, Z.
Nature Protocols 9 (4): 773-793. April 2014

Generation of targeted mouse mutants by embryo microinjection of TALEN mRNA.
Wefers, B. and Panda, S.K. and Ortiz, O. and Brandl, C. and Hensler, S. and Hansen, J. and Wurst, W. and Kühn, R.
Nature Protocols 8 (12): 2355-2379. December 2013

Large-scale identification of ubiquitination sites by mass spectrometry.
Udeshi, N.D. and Mertins, P. and Svinkina, T. and Carr, S.A.
Nature Protocols 8 (10): 1950-1960. October 2013

Single-molecule mRNA detection and counting in mammalian tissue.
Lyubimova, A. and Itzkovitz, S. and Junker, J.P. and Fan, Z.P. and Wu, X. and van Oudenaarden, A.
Nature Protocols 8 (9): 1743-1758. September 2013

Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast-embryonic stem cell fusion.
Li, L. and Blankenstein, T.
Nature Protocols 8 (8): 1567-1582. August 2013

Elucidating membrane structure and protein behavior using giant plasma membrane vesicles.
Sezgin, E. and Kaiser, H.J. and Baumgart, T. and Schwille, P. and Simons, K. and Levental, I.
Nature Protocols 7 (6): 1042-1051. June 2012

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
Bonn, S. and Zinzen, R.P. and Perez-Gonzalez, A. and Riddell, A. and Gavin, A.C. and Furlong, E.E.
Nature Protocols 7 (5): 978-994. May 2012

Sleeping Beauty transposon mutagenesis in rat spermatogonial stem cells.
Ivics, Z. and Izsvak, Z. and Medrano, G. and Chapman, K.M. and Hamra, F.K.
Nature Protocols 6 (10): 1521-1535. October 2011

A differential proteome screening system for post-translational modification-dependent transcription factor interactions.
Pless, O. and Kowenz-Leutz, E. and Dittmar, G. and Leutz, A.
Nature Protocols 6 (3): 359-364. February 2011

Preparation of retinal explant cultures to study ex vivo tip endothelial cell responses.
Sawamiphak, S. and Ritter, M. and Acker-Palmer, A.
Nature Protocols 5 (10): 1659-1665. October 2010

Phylogenetic classification and identification of bacteria by mass spectrometry.
Freiwald, A. and Sauer, S.
Nature Protocols 4 (5): 732-742. 23 April 2009

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics.
Cox, J. and Matic, I. and Hilger, M. and Nagaraj, N. and Selbach, M. and Olsen, J.V. and Mann, M.
Nature Protocols 4 (5): 698-705. 2009

Single-nucleotide polymorphisms: analysis by mass spectrometry.
Sauer, S. and Reinhardt, R. and Lehrach, H. and Gut, I.G.
Nature Protocols 1 (4): 1761-1771. 22 November 2006

Analysis of translation initiation using a translation control reporter system.
Wiesenthal, V. and Leutz, A. and Calkhoven, C.F.
Nature Protocols 1 (3): 1531-1537. 9 November 2006

Cysteine engineering of polyproteins for single-molecule force spectroscopy.
Dietz, H. and Bertz, M. and Schlierf, M. and Berkemeier, F. and Bornschloegl, T. and Junker, J.P. and Rief, M.
Nature Protocols 1 (1): 80-84. 2006

Review

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.
Müller, A. and Schmidt, D. and Albrecht, J.P. and Rieckert, L. and Otto, M. and Galicia Garcia, L.E. and Fabig, G. and Solimena, M. and Weigert, M.
Nature Protocols 29 February 2024 (In Press)