Browse by Journal Title

2024

Metrics reloaded: recommendations for image analysis validation.
Maier-Hein, L. and Reinke, A. and Godau, P. and Tizabi, M.D. and Buettner, F. and Christodoulou, E. and Glocker, B. and Isensee, F. and Kleesiek, J. and Kozubek, M. and Reyes, M. and Riegler, M.A. and Wiesenfarth, M. and Kavur, A.E. and Sudre, C.H. and Baumgartner, M. and Eisenmann, M. and Heckmann-Nötzel, D. and Rädsch, T. and Acion, L. and Antonelli, M. and Arbel, T. and Bakas, S. and Benis, A. and Blaschko, M.B. and Cardoso, M.J. and Cheplygina, V. and Cimini, B.A. and Collins, G.S. and Farahani, K. and Ferrer, L. and Galdran, A. and van Ginneken, B. and Haase, R. and Hashimoto, D.A. and Hoffman, M.M. and Huisman, M. and Jannin, P. and Kahn, C.E. and Kainmueller, D. and Kainz, B. and Karargyris, A. and Karthikesalingam, A. and Kofler, F. and Kopp-Schneider, A. and Kreshuk, A. and Kurc, T. and Landman, B.A. and Litjens, G. and Madani, A. and Maier-Hein, K. and Martel, A.L. and Mattson, P. and Meijering, E. and Menze, B. and Moons, K.G.M. and Müller, H. and Nichyporuk, B. and Nickel, F. and Petersen, J. and Rajpoot, N. and Rieke, N. and Saez-Rodriguez, J. and Sánchez, C.I. and Shetty, S. and van Smeden, M. and Summers, R.M. and Taha, A.A. and Tiulpin, A. and Tsaftaris, S.A. and Van Calster, B. and Varoquaux, G. and Jäger, P.F.
Nature Methods 21 (2): 195-212. 12 February 2024

Understanding metric-related pitfalls in image analysis validation.
Reinke, A. and Tizabi, M.D. and Baumgartner, M. and Eisenmann, M. and Heckmann-Nötzel, D. and Kavur, A.E. and Rädsch, T. and Sudre, C.H. and Acion, L. and Antonelli, M. and Arbel, T. and Bakas, S. and Benis, A. and Buettner, F. and Cardoso, M.J. and Cheplygina, V. and Chen, J. and Christodoulou, E. and Cimini, B.A. and Farahani, K. and Ferrer, L. and Galdran, A. and van Ginneken, B. and Glocker, B. and Godau, P. and Hashimoto, D.A. and Hoffman, M.M. and Huisman, M. and Isensee, F. and Jannin, P. and Kahn, C.E. and Kainmueller, D. and Kainz, B. and Karargyris, A. and Kleesiek, J. and Kofler, F. and Kooi, T. and Kopp-Schneider, A. and Kozubek, M. and Kreshuk, A. and Kurc, T. and Landman, B.A. and Litjens, G. and Madani, A. and Maier-Hein, K. and Martel, A.L. and Meijering, E. and Menze, B. and Moons, K.G.M. and Müller, H. and Nichyporuk, B. and Nickel, F. and Petersen, J. and Rafelski, S.M. and Rajpoot, N. and Reyes, M. and Riegler, M.A. and Rieke, N. and Saez-Rodriguez, J. and Sánchez, C.I. and Shetty, S. and Summers, R.M. and Taha, A.A. and Tiulpin, A. and Tsaftaris, S.A. and Van Calster, B. and Varoquaux, G. and Yaniv, Z.R. and Jäger, P.F. and Maier-Hein, L.
Nature Methods 21 (2): 182–194. February 2024

2023

Spatiotemporal, optogenetic control of gene expression in organoids.
Legnini, I. and Emmenegger, L. and Zappulo, A. and Rybak-Wolf, A. and Wurmus, R. and Oliveras Martinez, A. and Cerda Jara, C. and Boltengagen, A. and Hessler, T. and Mastrobuoni, G. and Kempa, S. and Zinzen, R. and Woehler, A. and Rajewsky, N.
Nature Methods 20 (10): 1544-1552. October 2023

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
Beagrie, R.A. and Thieme, C.J. and Annunziatella, C. and Baugher, C. and Zhang, Y. and Schueler, M. and Kukalev, A. and Kempfer, R. and Chiariello, A.M. and Bianco, S. and Li, Y. and Davis, T. and Scialdone, A. and Welch, L.R. and Nicodemi, M. and Pombo, A.
Nature Methods 20 (7): 1037-1047. July 2023

Genome architecture mapping detects transcriptionally active, multiway chromatin contacts.
Thieme, C.J. and Pombo, A.
Nature Methods 20 (7): 993-994. July 2023

2022

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Mamrak, N. and King, B. and Long, Xi and Harrington, K.I.S. and Lionnet, T. and Preibisch, S.
Nature Methods 19 (12): 1563-1567. December 2022

Best practice standards for circular RNA research.
Nielsen, A.F. and Bindereif, A. and Bozzoni, I. and Hanan, M. and Hansen, T.B. and Irimia, M. and Kadener, S. and Kristensen, L.S. and Legnini, I. and Morlando, M. and Jarlstad Olesen, M.T. and Pasterkamp, R.J. and Preibisch, S. and Rajewsky, N. and Suenkel, C. and Kjems, J.
Nature Methods 19 (10): 1208-1220. October 2022

2021

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
Fiorillo, L. and Musella, F. and Conte, M. and Kempfer, R. and Chiariello, A.M. and Bianco, S. and Kukalev, A. and Irastorza-Azcarate, I. and Esposito, A. and Abraham, A. and Prisco, A. and Pombo, A. and Nicodemi, M.
Nature Methods 18 (5): 482-490. May 2021

SNT: a unifying toolbox for quantification of neuronal anatomy.
Arshadi, C. and Günther, U. and Eddison, M. and Harrington, K.I.S. and Ferreira, T.A.
Nature Methods 18 : 374-377. April 2021

2020

Spatial heterogeneity in molecular brightness.
Annibale, P. and Lohse, M.J.
Nature Methods 17 (3): 273-275. March 2020

CLIJ: GPU-accelerated image processing for everyone.
Haase, R. and Royer, L.A. and Steinbach, P. and Schmidt, D. and Dibrov, A. and Schmidt, U. and Weigert, M. and Maghelli, N. and Tomancak, P. and Jug, F. and Myers, E.W.
Nature Methods 17 (1): 5-6. January 2020

2019

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.
Hörl, D. and Rojas Rusak, F. and Preusser, F. and Tillberg, P. and Randel, N. and Chhetri, R.K. and Cardona, A. and Keller, P.J. and Harz, H. and Leonhardt, H. and Treier, M. and Preibisch, S.
Nature Methods 16 (9): 870-874. September 2019

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control.
Legnini, I. and Alles, J. and Karaiskos, N. and Ayoub, S. and Rajewsky, N.
Nature Methods 16 (9): 879-886. September 2019

The author file: Stephan Preibisch.
Marx, V.
Nature Methods 16 (9): 793. September 2019

2018

Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.
Vladimirov, N. and Wang, C. and Höckendorf, B. and Pujala, A. and Tanimoto, M. and Mu, Y. and Yang, C.T. and Wittenbach, J.D. and Freeman, J. and Preibisch, S. and Koyama, M. and Keller, P.J. and Ahrens, M.B.
Nature Methods 15 (12): 1117-1125. December 2018

Content-aware image restoration: pushing the limits of fluorescence microscopy.
Weigert, M. and Schmidt, U. and Boothe, T. and Müller, A. and Dibrov, A. and Jain, A. and Wilhelm, B. and Schmidt, D. and Broaddus, C. and Culley, S. and Rocha-Martins, M. and Segovia-Miranda, F. and Norden, C. and Henriques, R. and Zerial, M. and Solimena, M. and Rink, J. and Tomancak, P. and Royer, L. and Jug, F. and Myers, E.W.
Nature Methods 15 (12): 1090-1097. December 2018

Picky: a simple online PRM and SRM method designer for targeted proteomics.
Zauber, H. and Kirchner, M. and Selbach, M.
Nature Methods 15 (3): 156-157. 28 February 2018

2017

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations.
van den Brink, S.C. and Sage, F. and Vertesy, A. and Spanjaard, B. and Peterson-Maduro, J. and Baron, C.S. and Robin, C. and van Oudenaarden, A.
Nature Methods 14 (10): 935-936. 29 September 2017

2016

Diffusion pseudotime robustly reconstructs lineage branching.
Haghverdi, L. and Büttner, M. and Wolf, F.A. and Buettner, F. and Theis, F.J.
Nature Methods 13 (10): 845-848. October 2016

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
Roest, H.L. and Sachsenberg, T. and Aiche, S. and Bielow, C. and Weisser, H. and Aicheler, F. and Andreotti, S. and Ehrlich, H.C. and Gutenbrunner, P. and Kenar, E. and Liang, X. and Nahnsen, S. and Nilse, L. and Pfeuffer, J. and Rosenberger, G. and Rurik, M. and Schmitt, U. and Veit, J. and Walzer, M. and Wojnar, D. and Wolski, W.E. and Schilling, O. and Choudhary, J.S. and Malmstroem, L. and Aebersold, R. and Reinert, K. and Kohlbacher, O.
Nature Methods 13 (9): 741-748. September 2016

Standardized benchmarking in the quest for orthologs.
Altenhoff, A.M. and Boeckmann, B. and Capella-Gutierrez, S. and Dalquen, D.A. and DeLuca, T. and Forslund, K. and Huerta-Cepas, J. and Linard, B. and Pereira, C. and Pryszcz, L.P. and Schreiber, F. and da Silva, A.S. and Szklarczyk, D. and Train, C.M. and Bork, P. and Lecompte, O. and von Mering, C. and Xenarios, I. and Sjölander, K. and Jensen, L.J. and Martin, M.J. and Muffato, M. and Gabaldón, T. and Lewis, S.E. and Thomas, P.D. and Sonnhammer, E. and Dessimoz, C.
Nature Methods 13 (5): 425-430. May 2016

Detecting actively translated open reading frames in ribosome profiling data.
Calviello, L. and Mukherjee, N. and Wyler, E. and Zauber, H. and Hirsekorn, A. and Selbach, M. and Landthaler, M. and Obermayer, B. and Ohler, U.
Nature Methods 13 (2): 165-170. February 2016

2015

Efficient set tests for the genetic analysis of correlated traits.
Casale, F.P. and Rakitsch, B. and Lippert, C. and Stegle, O.
Nature Methods 12 (8): 755-758. August 2015

BigDataViewer: visualization and processing for large image data sets.
Pietzsch, T. and Saalfeld, S. and Preibisch, S. and Tomancak, P.
Nature Methods 12 (6): 481-483. 28 May 2015

De novo protein structure determination from near-atomic-resolution cryo-EM maps.
Wang, R.Y.R. and Kudryashev, M. and Li, X. and Egelman, E.H. and Basler, M. and Cheng, Y. and Baker, D. and DiMaio, F.
Nature Methods 12 (4): 335-338. April 2015

Accurate liability estimation improves power in ascertained case-control studies.
Weissbrod, O. and Lippert, C. and Geiger, D. and Heckerman, D.
Nature Methods 12 (4): 332-334. April 2015

2014

Chemically defined generation of human cardiomyocytes.
Burridge, P.W. and Matsa, E. and Shukla, P. and Lin, Z.C. and Churko, J.M. and Ebert, A.D. and Lan, F. and Diecke, S. and Huber, B. and Mordwinkin, N.M. and Plews, J.R. and Abilez, O.J. and Cui, B. and Gold, J.D. and Wu, J.C.
Nature Methods 11 (8): 855-60. August 2014

Efficient Bayesian-based multiview deconvolution.
Preibisch, S. and Amat, F. and Stamataki, E. and Sarov, M. and Singer, R.H. and Myers, E. and Tomancak, P.
Nature Methods 11 (6): 645-648. June 2014

Epigenome-wide association studies without the need for cell-type composition.
Zou, J. and Lippert, C. and Heckerman, D. and Aryee, M. and Listgarten, J.
Nature Methods 11 (3): 309-311. March 2014

2013

Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa, S. and Mende, D.R. and Zeller, G. and Izquierdo-Carrasco, F. and Berger, S.A. and Kultima, J.R. and Coelho, L.P. and Arumugam, M. and Tap, J. and Nielsen, H.B. and Rasmussen, S. and Brunak, S. and Pedersen, O. and Guarner, F. and de Vos, W.M. and Wang, J. and Li, J. and Dore, J. and Ehrlich, S.D. and Stamatakis, A. and Bork, P.
Nature Methods 10 (12): 1196-1199. December 2013

Accurate and universal delineation of prokaryotic species.
Mende, D.R. and Sunagawa, S. and Zeller, G. and Bork, P.
Nature Methods 10 (9): 881-884. September 2013

MicroRNA target site identification by integrating sequence and binding information.
Majoros, W.H. and Lekprasert, P. and Mukherjee, N. and Skalsky, R.L. and Corcoran, D.L. and Cullen, B.R. and Ohler, U.
Nature Methods 10 (7): 630-633. July 2013

Integrated proteomic analysis of post-translational modifications by serial enrichment.
Mertins, P. and Qiao, J.W. and Patel, J. and Udeshi, N.D. and Clauser, K.R. and Mani, D.R. and Burgess, M.W. and Gillette, M.A. and Jaffe, J.D. and Carr, S.A.
Nature Methods 10 (7): 634-637. July 2013

OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone, P.G. and Schindelin, J. and Stuyvenberg, L. and Preibisch, S. and Weber, M. and Eliceiri, K.W. and Huisken, J. and Tomancak, P.
Nature Methods 10 (7): 598-599. July 2013

A Y2H-seq approach defines the human protein methyltransferase interactome.
Weimann, M. and Grossmann, A. and Woodsmith, J. and Özkan, Z. and Birth, P. and Meierhofer, D. and Benlasfer, N. and Valovka, T. and Timmermann, B. and Wanker, E.E. and Sauer, S. and Stelzl, U.
Nature Methods 10 (4): 339-342. April 2013

2012

A microfluidic device and computational platform for high-throughput live imaging of gene expression.
Busch, W. and Moore, B.T. and Martsberger, B. and Mace, D.L. and Twigg, R.W. and Jung, J. and Pruteanu-Malinici, I. and Kennedy, S.J. and Fricke, G.K. and Clark, R.L. and Ohler, U. and Benfey, P.N.
Nature Methods 9 (11): 1101-1106. November 2012

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
Falconer, E. and Hills, M. and Naumann, U. and Poon, S.S.S. and Chavez, E.A. and Sanders, A.D. and Zhao, Y. and Hirst, M. and Lansdorp, P.M.
Nature Methods 9 (11): 1107-1112. November 2012

Fiji: an open-source platform for biological-image analysis.
Schindelin, J. and Arganda-Carreras, I. and Frise, E. and Kaynig, V. and Longair, M. and Pietzsch, T. and Preibisch, S. and Rueden, C. and Saalfeld, S. and Schmid, B. and Tinevez, J.Y. and White, D.J. and Hartenstein, V. and Eliceiri, K. and Tomancak, P. and Cardona, A.
Nature Methods 9 (7): 676-682. July 2012

Improved linear mixed models for genome-wide association studies.
Listgarten, J. and Lippert, C. and Kadie, C.M. and Davidson, R.I. and Eskin, E. and Heckerman, D.
Nature Methods 9 (6): 525-526. 30 May 2012

Combined RNAi and localization for functionally dissecting long noncoding RNAs.
Chakraborty, D. and Kappei, D. and Theis, M. and Nitzsche, A. and Ding, L. and Paszkowski-Rogacz, M. and Surendranath, V. and Berger, N. and Schulz, H. and Saar, K. and Hubner, N. and Buchholz, F.
Nature Methods 9 (4): 360-362. 12 February 2012

2011

FaST linear mixed models for genome-wide association studies.
Lippert, C. and Listgarten, J. and Liu, Y. and Kadie, C.M. and Davidson, R.I. and Heckerman, .
Nature Methods 8 (10): 833-835. 4 September 2011

A roadmap to generate renewable protein binders to the human proteome.
Colwill, K. and Graeslund, S.
Nature Methods 8 (7): 551-558. 15 May 2011

2010

A paired-end sequencing strategy to map the complex landscape of transcription initiation.
Ni, T. and Corcoran, D.L. and Rach, E.A. and Song, S. and Spana, E.P. and Gao, Y. and Ohler, U. and Zhu, J.
Nature Methods 7 (7): 521-527. July 2010

Generating knockout rats by transposon mutagenesis in spermatogonial stem cells.
Izsvak, Z. and Froehlich, J. and Grabundzija, I. and Shirley, J.R. and Powell, H.M. and Chapman, K.M. and Ivics, Z. and Hamra, F.K.
Nature Methods 7 (6): 443-445. June 2010

Software for bead-based registration of selective plane illumination microscopy data.
Preibisch, S. and Saalfeld, S. and Schindelin, J. and Tomancak, P.
Nature Methods 7 (6): 418-419. June 2010

Silencing neurotransmission with membrane-tethered toxins.
Auer, S. and Stuerzebecher, A.S. and Juettner, R. and Santos-Torres, J. and Hanack, C. and Frahm, S. and Liehl, B. and Ibanez-Tallon, I.
Nature Methods 7 (3): 229-236. March 2010

2009

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.
Stoeckius, M. and Maaskola, J. and Colombo, T. and Rahn, H.P. and Friedlaender, M.R. and Li, N. and Chen, W. and Piano, F. and Rajewsky, N.
Nature Methods 6 (10): 745-751. October 2009

Transposon-mediated genome manipulation in vertebrates.
Ivics, Z. and Li, M.A. and Mates, L. and Boeke, J.D. and Nagy, A. and Bradley, A. and Izsvak, Z.
Nature Methods 6 (6): 415-422. June 2009

An empirical framework for binary interactome mapping.
Venkatesan, K. and Rual, J.F. and Vazquez, A. and Stelzl, U. and Lemmens, I. and Hirozane-Kishikawa, T. and Hao, T. and Zenkner, M. and Xin, X. and Goh, K.I. and Yildirim, M.A. and Simonis, N. and Heinzmann, K. and Gebreab, F. and Sahalie, J.M. and Cevik, S. and Simon, C. and de Smet, A.S. and Dann, E. and Smolyar, A. and Vinayagam, A. and Yu, H. and Szeto, D. and Borick, H. and Dricot, A. and Klitgord, N. and Murray, R.R. and Lin, C. and Lalowski, M. and Timm, J. and Rau, K. and Boone, C. and Braun, P. and Cusick, M.E. and Roth, F.P. and Hill, D.E. and Tavernier, J. and Wanker, E.E. and Barabasi, A.L. and Vidal, M.
Nature Methods 6 (1): 83-90. January 2009

2008

Protein production and purification.
Gräslund, S. and Nordlund, P. and Weigelt, J. and Hallberg, M. and Bray, J. and Gileadi, O. and Knapp, S. and Oppermann, U. and Arrowsmith, C. and Hui, R. and Ming, J. and dhe-Paganon, S. and Park, H.W. and Savchenko, A. and Yee, A. and Edwards, A. and Vincentelli, R. and Cambillau, C. and Kim, R. and Kim, S.H. and Rao, Z. and Shi, Y. and Terwilliger, T.C. and Kim, C.Y. and Hung, L.W. and Waldo, G.S. and Peleg, Y. and Albeck, S. and Unger, T. and Dym, O. and Prilusky, J. and Sussman, J.L. and Stevens, R.C. and Lesley, S.A. and Wilson, I.A. and Joachimiak, A. and Collart, F. and Dementieva, I. and Donnelly, M.I. and Eschenfeldt, W.H. and Kim, Y.M. and Stols, L. and Wu, R. and Zhou, M. and Burley, S.K. and Emtage, J.S. and Sauder, J.M. and Thompson, D. and Bain, K. and Luz, J. and Gheyi, T. and Zhang, F. and Atwell, S. and Almo, S.C. and Bonanno, J.B. and Fiser, A. and Swaminathan, S. and Studier, F.W. and Chance, M.R. and Sali, A. and Acton, T.B. and Xiao, R. and Zhao, L. and Ma, L.C. and Hunt, J.F. and Tong, L. and Cunningham, K. and Inouye, M. and Anderson, S. and Janjua, H. and Shastry, R. and Ho, C.K. and Wang, D. and Wang, H. and Jiang, M. and Montelione, G.T. and Stuart, D.I. and Owens, R.J. and Daenke, S. and Schütz, A. and Heinemann, U. and Yokoyama, S. and Büssow, K. and Gunsalus, K.C.
Nature Methods 5 (2): 135-146. February 2008

2006

Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK).
Selbach, M. and Mann, M.
Nature Methods 3 (12): 981-983. December 2006

Targeting and tracing antigens in live cells with fluorescent nanobodies.
Rothbauer, U. and Zolghadr, K. and Tillib, S. and Nowak, D. and Schermelleh, L. and Gahl, A. and Backmann, N. and Conrath, K. and Muyldermans, S. and Cardoso, M.C. and Leonhardt, H.
Nature Methods 3 (11): 887-889. November 2006

Laser microdissection of a colon cancer specimen with subsequent RNA isolation, mRNA amplification and microarray hybridization.
Stoinski-Bungs, E. and Seeger, S. and Kemmner, W. and Scheinert, P. and Krupp, G.
Nature Methods Application Notes : an10-an11. 1 January 2006

2005

Trapped in action: direct visualization of DNA methyltransferase activity in living cells.
Schermelleh, L. and Spada, F. and Easwaran, H.P. and Zolghadr, K. and Margot, J.B. and Cardoso, M.C. and Leonhardt, H.
Nature Methods 2 (10): 751-756. 1 October 2005

Sleeping Beauty hits them all: transposon-mediated saturation mutagenesis in the mouse germline.
Izsvak, Z. and Ivics, Z.
Nature Methods 2 (10): 735-736. October 2005