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C-COMPASS: a user-friendly neural network tool profiles cell compartments at protein and lipid levels.
Haas, Daniel T., Weindl, Daniel ORCID: https://orcid.org/0000-0001-9963-6057, Kakimoto, Pamela, Trautmann, Eva-Maria ORCID: https://orcid.org/0009-0002-0691-0489, Schessner, Julia P., Mao, Xia, Gerl, Mathias J. ORCID: https://orcid.org/0000-0002-8074-7221, Gerwien, Maximilian ORCID: https://orcid.org/0000-0002-2884-4155, Müller, Timo D., Klose, Christian, Cheng, Xiping, Hasenauer, Jan ORCID: https://orcid.org/0000-0002-4935-3312 and Krahmer, Natalie ORCID: https://orcid.org/0000-0003-4063-7367
Nature Methods 23 (1): 118-130. January 2026

Automated classification of cellular expression in multiplexed imaging data with Nimbus.
Rumberger, Josef Lorenz ORCID: https://orcid.org/0000-0002-7225-7011, Greenwald, Noah F. ORCID: https://orcid.org/0000-0002-7836-4379, Ranek, Jolene S., Boonrat, Potchara, Walker, Cameron, Franzen, Jannik ORCID: https://orcid.org/0000-0002-0761-641X, Varra, Sricharan Reddy ORCID: https://orcid.org/0009-0000-5757-6818, Kong, Alex, Sowers, Cameron, Liu, Candace C., Averbukh, Inna, Piyadasa, Hadeesha, Vanguri, Rami, Nederlof, Iris ORCID: https://orcid.org/0000-0001-7608-6515, Wang, Xuefei Julie ORCID: https://orcid.org/0000-0002-9327-9543, Van Valen, David ORCID: https://orcid.org/0000-0001-7534-7621, Kok, Marleen, Bendall, Sean C. ORCID: https://orcid.org/0000-0003-1341-2453, Hollmann, Travis J., Kainmueller, Dagmar ORCID: https://orcid.org/0000-0002-9830-2415 and Angelo, Michael ORCID: https://orcid.org/0000-0003-1531-5067
Nature Methods 22 (10): 2161-2170. October 2025

Ultra-high-scale cytometry-based cellular interaction mapping.
Vonficht, Dominik ORCID: https://orcid.org/0000-0002-5579-7083, Jopp-Saile, Lea ORCID: https://orcid.org/0000-0002-7032-3003, Yousefian, Schayan ORCID: https://orcid.org/0000-0003-0902-0369, Flore, Viktoria ORCID: https://orcid.org/0009-0001-3023-433X, Simó Vesperinas, Inés, Teuber, Ruth, Avanesyan, Bogdan ORCID: https://orcid.org/0009-0004-2547-6598, Luo, Yanjiang ORCID: https://orcid.org/0009-0003-0401-467X, Röthemeier, Caroline, Grünschläger, Florian ORCID: https://orcid.org/0000-0003-0021-6912, Fernandez-Vaquero, Mirian, Fregona, Vincent ORCID: https://orcid.org/0000-0003-4857-1737, Ordoñez-Rueda, Diana ORCID: https://orcid.org/0000-0002-8387-6707, Schmalbrock, Laura K. ORCID: https://orcid.org/0000-0002-6080-6175, Deininger, Luca ORCID: https://orcid.org/0009-0005-5125-6422, Yamachui Sitcheu, Angelo Jovin ORCID: https://orcid.org/0009-0002-9384-6496, Gu, Zuguang, Funk, Maja C. ORCID: https://orcid.org/0000-0002-6007-1164, Mikut, Ralf ORCID: https://orcid.org/0000-0001-9100-5496, Heikenwälder, Mathias, Eggert, Angelika, von Stackelberg, Arend, Kobold, Sebastian ORCID: https://orcid.org/0000-0002-5612-4673, Krönke, Jan, Keller, Ulrich ORCID: https://orcid.org/0000-0002-8485-1958, Trumpp, Andreas, Hegazy, Ahmed N., Eckert, Cornelia ORCID: https://orcid.org/0000-0003-1039-2872, Hübschmann, Daniel ORCID: https://orcid.org/0000-0002-6041-7049 and Haas, Simon ORCID: https://orcid.org/0000-0001-9227-2051
Nature Methods 22 (9): 1887-1899. September 2025

Segment anything for microscopy.
Archit, A. ORCID: https://orcid.org/0009-0002-9533-8620, Freckmann, L., Nair, S., Khalid, N. ORCID: https://orcid.org/0000-0001-9274-3757, Hilt, P., Rajashekar, V., Freitag, M. ORCID: https://orcid.org/0009-0005-0920-2535, Teuber, C. ORCID: https://orcid.org/0009-0004-3866-191X, Spitzner, M., Tapia Contreras, C., Buckley, G. ORCID: https://orcid.org/0000-0003-2763-492X, von Haaren, S., Gupta, S., Grade, M., Wirth, M. ORCID: https://orcid.org/0000-0002-8340-0872, Schneider, G., Dengel, A., Ahmed, S. and Pape, C. ORCID: https://orcid.org/0000-0001-6562-7187
Nature Methods 22 (3): 579-591. March 2025

A bistable inhibitory optoGPCR for multiplexed optogenetic control of neural circuits.
Wietek, J. ORCID: https://orcid.org/0000-0002-8079-7042, Nozownik, A., Pulin, M. ORCID: https://orcid.org/0000-0001-6255-0276, Saraf-Sinik, I., Matosevich, N., Gowrishankar, R., Gat, A. ORCID: https://orcid.org/0009-0005-3336-2096, Malan, D., Brown, B.J., Dine, J., Imambocus, B.N., Levy, R., Sauter, K., Litvin, A. ORCID: https://orcid.org/0000-0002-0420-0216, Regev, N., Subramaniam, S., Abrera, K., Summarli, D. ORCID: https://orcid.org/0009-0003-6637-0805, Goren, E.M., Mizrachi, G., Bitton, E., Benjamin, A. ORCID: https://orcid.org/0000-0003-3031-2008, Copits, B.A. ORCID: https://orcid.org/0000-0003-3732-890X, Sasse, P. ORCID: https://orcid.org/0000-0002-8502-9472, Rost, B.R. ORCID: https://orcid.org/0000-0003-1906-0081, Schmitz, D. ORCID: https://orcid.org/0000-0003-2741-5241, Bruchas, M.R. ORCID: https://orcid.org/0000-0003-4713-7816, Soba, P. ORCID: https://orcid.org/0000-0002-6163-4686, Oren-Suissa, M. ORCID: https://orcid.org/0000-0001-9937-8326, Nir, Y. ORCID: https://orcid.org/0000-0002-5433-6349, Wiegert, J.S. ORCID: https://orcid.org/0000-0003-0893-9349 and Yizhar, O. ORCID: https://orcid.org/0000-0003-4228-1448
Nature Methods 21 (7): 1275-1287. July 2024

Metrics reloaded: recommendations for image analysis validation.
Maier-Hein, L. ORCID: https://orcid.org/0000-0003-4910-9368, Reinke, A. ORCID: https://orcid.org/0000-0003-4363-1876, Godau, P. ORCID: https://orcid.org/0000-0002-0365-7265, Tizabi, M.D., Buettner, F., Christodoulou, E., Glocker, B. ORCID: https://orcid.org/0000-0002-4897-9356, Isensee, F., Kleesiek, J., Kozubek, M., Reyes, M., Riegler, M.A. ORCID: https://orcid.org/0000-0002-3153-2064, Wiesenfarth, M., Kavur, A.E., Sudre, C.H., Baumgartner, M., Eisenmann, M. ORCID: https://orcid.org/0000-0002-0713-8761, Heckmann-Nötzel, D., Rädsch, T. ORCID: https://orcid.org/0000-0003-3518-0315, Acion, L. ORCID: https://orcid.org/0000-0001-5213-6012, Antonelli, M. ORCID: https://orcid.org/0000-0002-3005-4523, Arbel, T. ORCID: https://orcid.org/0000-0001-8870-3007, Bakas, S. ORCID: https://orcid.org/0000-0001-8734-6482, Benis, A. ORCID: https://orcid.org/0000-0002-9125-8300, Blaschko, M.B., Cardoso, M.J. ORCID: https://orcid.org/0000-0003-1284-2558, Cheplygina, V. ORCID: https://orcid.org/0000-0003-0176-9324, Cimini, B.A. ORCID: https://orcid.org/0000-0001-9640-9318, Collins, G.S. ORCID: https://orcid.org/0000-0002-2772-2316, Farahani, K., Ferrer, L., Galdran, A., van Ginneken, B., Haase, R. ORCID: https://orcid.org/0000-0001-5949-2327, Hashimoto, D.A. ORCID: https://orcid.org/0000-0003-4725-3104, Hoffman, M.M. ORCID: https://orcid.org/0000-0002-4517-1562, Huisman, M., Jannin, P. ORCID: https://orcid.org/0000-0002-7415-071X, Kahn, C.E. ORCID: https://orcid.org/0000-0002-6654-7434, Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Kainz, B., Karargyris, A. ORCID: https://orcid.org/0000-0002-1930-3410, Karthikesalingam, A., Kofler, F., Kopp-Schneider, A. ORCID: https://orcid.org/0000-0002-1810-0267, Kreshuk, A. ORCID: https://orcid.org/0000-0003-1334-6388, Kurc, T., Landman, B.A. ORCID: https://orcid.org/0000-0001-5733-2127, Litjens, G. ORCID: https://orcid.org/0000-0003-1554-1291, Madani, A., Maier-Hein, K., Martel, A.L. ORCID: https://orcid.org/0000-0003-1375-5501, Mattson, P. ORCID: https://orcid.org/0000-0002-5984-238X, Meijering, E. ORCID: https://orcid.org/0000-0001-8015-8358, Menze, B. ORCID: https://orcid.org/0000-0003-4136-5690, Moons, K.G.M., Müller, H. ORCID: https://orcid.org/0000-0001-6800-9878, Nichyporuk, B. ORCID: https://orcid.org/0009-0006-8087-6089, Nickel, F., Petersen, J., Rajpoot, N. ORCID: https://orcid.org/0000-0002-4706-1308, Rieke, N. ORCID: https://orcid.org/0000-0003-0241-9334, Saez-Rodriguez, J. ORCID: https://orcid.org/0000-0002-8552-8976, Sánchez, C.I., Shetty, S., van Smeden, M., Summers, R.M. ORCID: https://orcid.org/0000-0001-8081-7376, Taha, A.A. ORCID: https://orcid.org/0000-0002-7604-9041, Tiulpin, A. ORCID: https://orcid.org/0000-0002-7852-4141, Tsaftaris, S.A., Van Calster, B., Varoquaux, G. ORCID: https://orcid.org/0000-0003-1076-5122 and Jäger, P.F. ORCID: https://orcid.org/0000-0002-6243-2568
Nature Methods 21 (2): 195-212. 12 February 2024

Understanding metric-related pitfalls in image analysis validation.
Reinke, A. ORCID: https://orcid.org/0000-0003-4363-1876, Tizabi, M.D. ORCID: https://orcid.org/0000-0003-3687-6381, Baumgartner, M. ORCID: https://orcid.org/0000-0003-4455-9917, Eisenmann, M., Heckmann-Nötzel, D., Kavur, A.E. ORCID: https://orcid.org/0000-0002-9328-8140, Rädsch, T. ORCID: https://orcid.org/0000-0003-3518-0315, Sudre, C.H., Acion, L. ORCID: https://orcid.org/0000-0001-5213-6012, Antonelli, M. ORCID: https://orcid.org/0000-0002-3005-4523, Arbel, T., Bakas, S. ORCID: https://orcid.org/0000-0001-8734-6482, Benis, A. ORCID: https://orcid.org/0000-0002-9125-8300, Buettner, F., Cardoso, M.J. ORCID: https://orcid.org/0000-0003-1284-2558, Cheplygina, V. ORCID: https://orcid.org/0000-0003-0176-9324, Chen, J. ORCID: https://orcid.org/0000-0002-8500-1357, Christodoulou, E., Cimini, B.A. ORCID: https://orcid.org/0000-0001-9640-9318, Farahani, K., Ferrer, L., Galdran, A., van Ginneken, B., Glocker, B. ORCID: https://orcid.org/0000-0002-4897-9356, Godau, P. ORCID: https://orcid.org/0000-0002-0365-7265, Hashimoto, D.A. ORCID: https://orcid.org/0000-0003-4725-3104, Hoffman, M.M. ORCID: https://orcid.org/0000-0002-4517-1562, Huisman, M., Isensee, F., Jannin, P. ORCID: https://orcid.org/0000-0002-7415-071X, Kahn, C.E. ORCID: https://orcid.org/0000-0002-6654-7434, Kainmueller, D. ORCID: https://orcid.org/0000-0002-9830-2415, Kainz, B., Karargyris, A. ORCID: https://orcid.org/0000-0002-1930-3410, Kleesiek, J. ORCID: https://orcid.org/0000-0001-8686-0682, Kofler, F., Kooi, T., Kopp-Schneider, A. ORCID: https://orcid.org/0000-0002-1810-0267, Kozubek, M. ORCID: https://orcid.org/0000-0001-7902-589X, Kreshuk, A. ORCID: https://orcid.org/0000-0003-1334-6388, Kurc, T., Landman, B.A. ORCID: https://orcid.org/0000-0001-5733-2127, Litjens, G. ORCID: https://orcid.org/0000-0003-1554-1291, Madani, A., Maier-Hein, K., Martel, A.L. ORCID: https://orcid.org/0000-0003-1375-5501, Meijering, E. ORCID: https://orcid.org/0000-0001-8015-8358, Menze, B. ORCID: https://orcid.org/0000-0003-4136-5690, Moons, K.G.M., Müller, H. ORCID: https://orcid.org/0000-0001-6800-9878, Nichyporuk, B. ORCID: https://orcid.org/0009-0006-8087-6089, Nickel, F., Petersen, J., Rafelski, S.M. ORCID: https://orcid.org/0000-0002-1399-5970, Rajpoot, N. ORCID: https://orcid.org/0000-0002-4706-1308, Reyes, M., Riegler, M.A. ORCID: https://orcid.org/0000-0002-3153-2064, Rieke, N. ORCID: https://orcid.org/0000-0003-0241-9334, Saez-Rodriguez, J. ORCID: https://orcid.org/0000-0002-8552-8976, Sánchez, C.I., Shetty, S., Summers, R.M. ORCID: https://orcid.org/0000-0001-8081-7376, Taha, A.A., Tiulpin, A. ORCID: https://orcid.org/0000-0002-7852-4141, Tsaftaris, S.A., Van Calster, B., Varoquaux, G. ORCID: https://orcid.org/0000-0003-1076-5122, Yaniv, Z.R. ORCID: https://orcid.org/0000-0003-0315-7727, Jäger, P.F. ORCID: https://orcid.org/0000-0002-6243-2568 and Maier-Hein, L. ORCID: https://orcid.org/0000-0003-4910-9368
Nature Methods 21 (2): 182-194. February 2024

Spatiotemporal, optogenetic control of gene expression in organoids.
Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Emmenegger, L. ORCID: https://orcid.org/0000-0003-2165-7944, Zappulo, A., Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Oliveras Martinez, A. ORCID: https://orcid.org/0000-0002-5880-5245, Cerda Jara, C. ORCID: https://orcid.org/0000-0003-1783-5533, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Hessler, T., Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Zinzen, R. ORCID: https://orcid.org/0000-0002-8638-5102, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
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. ORCID: https://orcid.org/0000-0003-1076-5595, Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971, Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Li, Y. ORCID: https://orcid.org/0000-0001-5791-096X, Davis, T., Scialdone, A. ORCID: https://orcid.org/0000-0002-4956-2843, Welch, L.R. ORCID: https://orcid.org/0000-0001-6419-9416, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature Methods 20 (7): 1037-1047. July 2023

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Breimann, L. ORCID: https://orcid.org/0000-0001-7702-5749, Zouinkhi, M. ORCID: https://orcid.org/0000-0002-9441-2908, Epstein, L., Kolyvanov, K., Mamrak, N., King, B., Long, Xi, Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973, Lionnet, T. ORCID: https://orcid.org/0000-0003-1508-0202 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
Nature Methods 19 (12): 1563-1567. December 2022

Best practice standards for circular RNA research.
Nielsen, A.F. ORCID: https://orcid.org/0000-0003-2653-4863, Bindereif, A., Bozzoni, I. ORCID: https://orcid.org/0000-0002-3485-8537, Hanan, M., Hansen, T.B., Irimia, M., Kadener, S., Kristensen, L.S. ORCID: https://orcid.org/0000-0002-5980-7939, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Morlando, M., Jarlstad Olesen, M.T., Pasterkamp, R.J. ORCID: https://orcid.org/0000-0003-1631-6440, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Suenkel, C. ORCID: https://orcid.org/0000-0002-5326-6043 and Kjems, J. ORCID: https://orcid.org/0000-0003-4128-9317
Nature Methods 19 (10): 1208-1220. October 2022

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
Fiorillo, L. ORCID: https://orcid.org/0000-0003-2967-0123, Musella, F., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Irastorza-Azcarate, I. ORCID: https://orcid.org/0000-0001-5245-2322, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Abraham, A. ORCID: https://orcid.org/0000-0003-3533-6543, Prisco, A., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Nature Methods 18 (5): 482-490. May 2021

SNT: a unifying toolbox for quantification of neuronal anatomy.
Arshadi, C. ORCID: https://orcid.org/0000-0002-1885-080X, Günther, U. ORCID: https://orcid.org/0000-0002-1179-8228, Eddison, M., Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973 and Ferreira, T.A. ORCID: https://orcid.org/0000-0001-6866-1540
Nature Methods 18 : 374-377. April 2021

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.
Hörl, D. ORCID: https://orcid.org/0000-0003-1710-1708, Rojas Rusak, F. ORCID: https://orcid.org/0000-0002-0637-9467, Preusser, F. ORCID: https://orcid.org/0000-0001-8231-2195, Tillberg, P. ORCID: https://orcid.org/0000-0002-2568-2365, Randel, N. ORCID: https://orcid.org/0000-0002-7817-4137, Chhetri, R.K. ORCID: https://orcid.org/0000-0001-6039-4505, Cardona, A. ORCID: https://orcid.org/0000-0001-6039-4505, Keller, P.J. ORCID: https://orcid.org/0000-0003-2896-4920, Harz, H., Leonhardt, H. ORCID: https://orcid.org/0000-0002-5086-6449, Treier, M. ORCID: https://orcid.org/0000-0002-8751-1246 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
Nature Methods 16 (9): 870-874. September 2019

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control.
Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature Methods 16 (9): 879-886. September 2019

Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.
Vladimirov, N. ORCID: https://orcid.org/0000-0002-1159-0689, Wang, C., Höckendorf, B., Pujala, A., Tanimoto, M., Mu, Y. ORCID: https://orcid.org/0000-0001-9297-4854, Yang, C.T., Wittenbach, J.D., Freeman, J., Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Koyama, M., Keller, P.J. ORCID: https://orcid.org/0000-0003-2896-4920 and Ahrens, M.B. ORCID: https://orcid.org/0000-0002-3457-4462
Nature Methods 15 (12): 1117-1125. December 2018

Content-aware image restoration: pushing the limits of fluorescence microscopy.
Weigert, M. ORCID: https://orcid.org/0000-0002-7780-9057, Schmidt, U., Boothe, T. ORCID: https://orcid.org/0000-0003-1925-0213, Müller, A. ORCID: https://orcid.org/0000-0002-3560-5769, Dibrov, A., Jain, A. ORCID: https://orcid.org/0000-0003-4704-7992, Wilhelm, B. ORCID: https://orcid.org/0000-0003-1608-5267, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Broaddus, C., Culley, S. ORCID: https://orcid.org/0000-0003-2112-0143, Rocha-Martins, M., Segovia-Miranda, F., Norden, C. ORCID: https://orcid.org/0000-0001-8835-1451, Henriques, R., Zerial, M., Solimena, M., Rink, J., Tomancak, P. ORCID: https://orcid.org/0000-0002-2222-9370, Royer, L. ORCID: https://orcid.org/0000-0002-9991-9724, Jug, F. ORCID: https://orcid.org/0000-0002-8499-5812 and Myers, E.W.
Nature Methods 15 (12): 1090-1097. December 2018

Diffusion pseudotime robustly reconstructs lineage branching.
Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170, Büttner, M., Wolf, F.A., 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., Sachsenberg, T., Aiche, S., Bielow, C. ORCID: https://orcid.org/0000-0001-5756-3988, Weisser, H., Aicheler, F., Andreotti, S., Ehrlich, H.C., Gutenbrunner, P., Kenar, E., Liang, X., Nahnsen, S., Nilse, L., Pfeuffer, J., Rosenberger, G., Rurik, M., Schmitt, U., Veit, J., Walzer, M., Wojnar, D., Wolski, W.E., Schilling, O., Choudhary, J.S., Malmstroem, L., Aebersold, R., Reinert, K. and Kohlbacher, O.
Nature Methods 13 (9): 741-748. September 2016

Standardized benchmarking in the quest for orthologs.
Altenhoff, A.M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D.A., DeLuca, T., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L.P., Schreiber, F., da Silva, A.S., Szklarczyk, D., Train, C.M., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Lecompte, O., von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102, Xenarios, I., Sjölander, K., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, Martin, M.J., Muffato, M., Gabaldón, T., Lewis, S.E., Thomas, P.D., 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. ORCID: https://orcid.org/0000-0002-5600-0988, Mukherjee, N. ORCID: https://orcid.org/0000-0003-0017-1400, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Zauber, H. ORCID: https://orcid.org/0000-0003-2595-1147, Hirsekorn, A., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Nature Methods 13 (2): 165-170. February 2016

Efficient set tests for the genetic analysis of correlated traits.
Casale, F.P., Rakitsch, B., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556 and Stegle, O.
Nature Methods 12 (8): 755-758. August 2015

De novo protein structure determination from near-atomic-resolution cryo-EM maps.
Wang, R.Y.R., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Li, X., Egelman, E.H., Basler, M., Cheng, Y., 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., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Geiger, D. and Heckerman, D.
Nature Methods 12 (4): 332-334. April 2015

Chemically defined generation of human cardiomyocytes.
Burridge, P.W., Matsa, E., Shukla, P., Lin, Z.C., Churko, J.M., Ebert, A.D., Lan, F., Diecke, S. ORCID: https://orcid.org/0000-0002-5219-5992, Huber, B., Mordwinkin, N.M., Plews, J.R., Abilez, O.J., Cui, B., Gold, J.D. and Wu, J.C.
Nature Methods 11 (8): 855-60. August 2014

Efficient Bayesian-based multiview deconvolution.
Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Amat, F., Stamataki, E., Sarov, M., Singer, R.H., 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., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Heckerman, D., Aryee, M. ORCID: https://orcid.org/0000-0002-6848-1344 and Listgarten, J.
Nature Methods 11 (3): 309-311. March 2014

Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., de Vos, W.M., Wang, J., Li, J., Dore, J., Ehrlich, S.D., Stamatakis, A. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nature Methods 10 (12): 1196-1199. December 2013

Accurate and universal delineation of prokaryotic species.
Mende, D.R., Sunagawa, S., Zeller, G. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nature Methods 10 (9): 881-884. September 2013

MicroRNA target site identification by integrating sequence and binding information.
Majoros, W.H., Lekprasert, P., Mukherjee, N. ORCID: https://orcid.org/0000-0003-0017-1400, Skalsky, R.L., Corcoran, D.L., Cullen, B.R. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Nature Methods 10 (7): 630-633. July 2013

Integrated proteomic analysis of post-translational modifications by serial enrichment.
Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Qiao, J.W., Patel, J., Udeshi, N.D., Clauser, K.R., Mani, D.R., Burgess, M.W., Gillette, M.A., Jaffe, J.D. and Carr, S.A.
Nature Methods 10 (7): 634-637. July 2013

A Y2H-seq approach defines the human protein methyltransferase interactome.
Weimann, M., Grossmann, A., Woodsmith, J., Özkan, Z., Birth, P., Meierhofer, D., Benlasfer, N., Valovka, T., Timmermann, B., Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630, Sauer, S. ORCID: https://orcid.org/0000-0002-4794-3693 and Stelzl, U. ORCID: https://orcid.org/0000-0003-2500-3585
Nature Methods 10 (4): 339-342. April 2013

A microfluidic device and computational platform for high-throughput live imaging of gene expression.
Busch, W., Moore, B.T., Martsberger, B., Mace, D.L., Twigg, R.W., Jung, J., Pruteanu-Malinici, I., Kennedy, S.J., Fricke, G.K., Clark, R.L., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 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., Hills, M., Naumann, U., Poon, S.S.S., Chavez, E.A., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Zhao, Y., 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., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J.Y., White, D.J., Hartenstein, V., Eliceiri, K., Tomancak, P. and Cardona, A.
Nature Methods 9 (7): 676-682. July 2012

Combined RNAi and localization for functionally dissecting long noncoding RNAs.
Chakraborty, D., Kappei, D., Theis, M., Nitzsche, A., Ding, L., Paszkowski-Rogacz, M., Surendranath, V., Berger, N., Schulz, H. ORCID: https://orcid.org/0000-0002-0226-964X, Saar, K. ORCID: https://orcid.org/0000-0002-4483-1569, Hubner, N. ORCID: https://orcid.org/0000-0002-1218-6223 and Buchholz, F.
Nature Methods 9 (4): 360-362. 12 February 2012

FaST linear mixed models for genome-wide association studies.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Listgarten, J., Liu, Y., Kadie, C.M., 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

A paired-end sequencing strategy to map the complex landscape of transcription initiation.
Ni, T., Corcoran, D.L., Rach, E.A., Song, S., Spana, E.P., Gao, Y., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Zhu, J.
Nature Methods 7 (7): 521-527. July 2010

Generating knockout rats by transposon mutagenesis in spermatogonial stem cells.
Izsvak, Z. ORCID: https://orcid.org/0000-0002-2053-2384, Froehlich, J., Grabundzija, I., Shirley, J.R., Powell, H.M., Chapman, K.M., Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658 and Hamra, F.K.
Nature Methods 7 (6): 443-445. June 2010

Silencing neurotransmission with membrane-tethered toxins.
Auer, S., Stuerzebecher, A.S., Juettner, R. ORCID: https://orcid.org/0000-0003-3565-0698, Santos-Torres, J., Hanack, C., Frahm, S. ORCID: https://orcid.org/0000-0001-5645-2557, Liehl, B. and Ibanez-Tallon, I.
Nature Methods 7 (3): 229-236. March 2010

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.
Stoeckius, M. ORCID: https://orcid.org/0000-0002-5658-029X, Maaskola, J., Colombo, T. ORCID: https://orcid.org/0000-0003-2415-7507, Rahn, H.P. ORCID: https://orcid.org/0000-0002-5233-3937, Friedlaender, M.R. ORCID: https://orcid.org/0000-0001-6577-4363, Li, N., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Piano, F. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature Methods 6 (10): 745-751. October 2009

An empirical framework for binary interactome mapping.
Venkatesan, K., Rual, J.F., Vazquez, A., Stelzl, U., Lemmens, I., Hirozane-Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K.I., Yildirim, M.A., Simonis, N., Heinzmann, K., Gebreab, F., Sahalie, J.M., Cevik, S., Simon, C., de Smet, A.S., Dann, E., Smolyar, A., Vinayagam, A., Yu, H., Szeto, D., Borick, H., Dricot, A., Klitgord, N., Murray, R.R., Lin, C., Lalowski, M., Timm, J., Rau, K., Boone, C., Braun, P., Cusick, M.E., Roth, F.P., Hill, D.E., Tavernier, J., Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630, Barabasi, A.L. and Vidal, M.
Nature Methods 6 (1): 83-90. January 2009

Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK).
Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751 and Mann, M.
Nature Methods 3 (12): 981-983. December 2006

Targeting and tracing antigens in live cells with fluorescent nanobodies.
Rothbauer, U., Zolghadr, K., Tillib, S., Nowak, D., Schermelleh, L., Gahl, A., Backmann, N., Conrath, K., Muyldermans, S., Cardoso, M.C. ORCID: https://orcid.org/0000-0001-8427-8859 and Leonhardt, H. ORCID: https://orcid.org/0000-0002-5086-6449
Nature Methods 3 (11): 887-889. November 2006

Trapped in action: direct visualization of DNA methyltransferase activity in living cells.
Schermelleh, L., Spada, F., Easwaran, H.P., Zolghadr, K., Margot, J.B., Cardoso, M.C. ORCID: https://orcid.org/0000-0001-8427-8859 and Leonhardt, H. ORCID: https://orcid.org/0000-0002-5086-6449
Nature Methods 2 (10): 751-756. 1 October 2005

Review

Transposon-mediated genome manipulation in vertebrates.
Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658, Li, M.A., Mates, L. ORCID: https://orcid.org/0000-0002-0058-470X, Boeke, J.D., Nagy, A., Bradley, A. and Izsvak, Z. ORCID: https://orcid.org/0000-0002-2053-2384
Nature Methods 6 (6): 415-422. June 2009

Protein production and purification.
Gräslund, S., Nordlund, P., Weigelt, J., Hallberg, M., Bray, J., Gileadi, O., Knapp, S., Oppermann, U., Arrowsmith, C., Hui, R., Ming, J., dhe-Paganon, S., Park, H.W., Savchenko, A., Yee, A., Edwards, A., Vincentelli, R., Cambillau, C., Kim, R., Kim, S.H., Rao, Z., Shi, Y., Terwilliger, T.C., Kim, C.Y., Hung, L.W., Waldo, G.S., Peleg, Y., Albeck, S., Unger, T., Dym, O., Prilusky, J., Sussman, J.L., Stevens, R.C., Lesley, S.A., Wilson, I.A., Joachimiak, A., Collart, F., Dementieva, I., Donnelly, M.I., Eschenfeldt, W.H., Kim, Y.M., Stols, L., Wu, R., Zhou, M., Burley, S.K., Emtage, J.S., Sauder, J.M., Thompson, D., Bain, K., Luz, J., Gheyi, T., Zhang, F., Atwell, S., Almo, S.C., Bonanno, J.B., Fiser, A., Swaminathan, S., Studier, F.W., Chance, M.R., Sali, A., Acton, T.B., Xiao, R., Zhao, L., Ma, L.C., Hunt, J.F., Tong, L., Cunningham, K., Inouye, M., Anderson, S., Janjua, H., Shastry, R., Ho, C.K., Wang, D., Wang, H., Jiang, M., Montelione, G.T., Stuart, D.I., Owens, R.J., Daenke, S., Schütz, A. ORCID: https://orcid.org/0000-0002-0606-2574, Heinemann, U. ORCID: https://orcid.org/0000-0002-8191-3850, Yokoyama, S., Büssow, K. and Gunsalus, K.C.
Nature Methods 5 (2): 135-146. February 2008

Letter

Translon: a single term for translated regions.
Świrski, Michał I., Tierney, Jack A.S., Albà, M. Mar, Andreev, Dmitry E., Aspden, Julie L., Atkins, John F., Bassani-Sternberg, Michal, Berry, Marla J., Biffo, Stefano, Boris-Lawrie, Kathleen, Borodovsky, Mark, Brierley, Ian, Brook, Matthew, Brunet, Marie A., Bujnicki, Janusz M., Caliskan, Neva, Calviello, Lorenzo ORCID: https://orcid.org/0000-0002-5600-0988, Carvunis, Anne-Ruxandra, Cate, Jamie H.D., Cenik, Can, Chang, Kung Yao, Chen, Yiwen, Chothani, Sonia, Choudhary, Jyoti S., Clark, Patricia L., Clauwaert, Jim, Cooley, Lynn, Dassi, Erik, Dean, Kellie, Diaz, Jean-Jacques, Dieterich, Christop ORCID: https://orcid.org/0000-0001-9468-6311, Dikstein, Rivka, Dinman, Jonathan D., Dmitriev, Sergey E., Dontsova, Olga A., Dunham, Christine M., Eswarappa, Sandeep M., Farabaugh, Philip J., Faridi, Pouya, Fierro-Monti, Ivo, Firth, Andrew E., Gatfield, David, Gebauer, Fátima, Gelfand, Mikhail S., Gray, Nicola K., Green, Rachel, Hill, Chris H., Hou, Ya-Ming, Hübner, Norbert ORCID: https://orcid.org/0000-0002-1218-6223, Ignatova, Zoya, Ivanov, Pavel, Iwasaki, Shintaro, Johnson, Rory, Jomaa, Ahmad, Jovanovic, Marko, Jungreis, Irwin, Kellis, Manolis, Kieft, Jeffrey S., Kochetov, Alex V., Koonin, Eugene V., Korostelev, Andrei A., Kufel, Joanna, Kulakovskiy, Ivan V., Kurian, Leo, Lafontaine, Denis L.J., Larsson, Ola, Loughran, Gary, Lukeš, Julius, Mariotti, Marco, Martens-Uzunova, Elena S., Martinez, Thomas F., Matsumoto, Akinobu, McManus, Joel, Medenbach, Jan, Melnikov, Sergey V., Menschaert, Gerben, Merchante, Catharina, Mikl, Martin, Miller, W. Allen, Mühlemann, Oliver, Namy, Olivier, Nedialkova, Danny D., Nosek, Jozef, Orchard, Sandra, Ozretić, Petar, Pertea, Mihaela, Pervouchine, Dmitri D., Romão, Luísa, Ron, David, Roucou, Xavier, Rubtsova, Maria P., Ruiz-Orera, Jorge ORCID: https://orcid.org/0000-0002-8317-0034, Saghatelian, Alan, Salzberg, Steven L., Seale, Lucia A., Seoighe, Cathal, Sergiev, Petr V., Shah, Premal, Shirokikh, Nikolay, Slavoff, Sarah A., Sonenberg, Nahum, Stasevich, Timothy J., Szczesny, Roman J., Tamm, Tiina, Tchórzewski, Marek, Topisirovic, Ivan, Tremblay, Michel L., Tuller, Tamir, Ulitsky, Igor ORCID: https://orcid.org/0000-0003-0555-6561, Valášek, Leoš Shivaya, Van Damme, Petra, Viero, Gabriella, Vizcaino, Juan Antonio, Vogel, Christine, Wallace, Edward W.J., Weissman, Jonathan S., Westhof, Eric, Whiffin, Nicola, Wilson, Daniel N., Xie, Zhi, Yewdell, Jonathan W., Yordanova, Martina M., Yu, Chien-Hung, Yurchenko, Vyacheslav, Zagrovic, Bojan, Valen, Eivind and Baranov, Pavel V.
Nature Methods 22 (10): 2002-2006. October 2025

CLIJ: GPU-accelerated image processing for everyone.
Haase, R., Royer, L.A., Steinbach, P., Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Dibrov, A., Schmidt, U., Weigert, M., Maghelli, N., Tomancak, P., Jug, F. and Myers, E.W.
Nature Methods 17 (1): 5-6. January 2020

Picky: a simple online PRM and SRM method designer for targeted proteomics.
Zauber, H. ORCID: https://orcid.org/0000-0003-2595-1147, Kirchner, M. ORCID: https://orcid.org/0000-0002-7049-534X and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
Nature Methods 15 (3): 156-157. 28 February 2018

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations.
van den Brink, S.C. ORCID: https://orcid.org/0000-0003-3683-7737, Sage, F., Vertesy, A. ORCID: https://orcid.org/0000-0001-6075-5702, Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Peterson-Maduro, J., Baron, C.S., Robin, C. and van Oudenaarden, A.
Nature Methods 14 (10): 935-936. 29 September 2017

BigDataViewer: visualization and processing for large image data sets.
Pietzsch, T., Saalfeld, S., Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X and Tomancak, P.
Nature Methods 12 (6): 481-483. 28 May 2015

OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone, P.G., Schindelin, J., Stuyvenberg, L., Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Weber, M., Eliceiri, K.W., Huisken, J. and Tomancak, P.
Nature Methods 10 (7): 598-599. July 2013

Improved linear mixed models for genome-wide association studies.
Listgarten, J., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Kadie, C.M., Davidson, R.I., Eskin, E. and Heckerman, D.
Nature Methods 9 (6): 525-526. 30 May 2012

Software for bead-based registration of selective plane illumination microscopy data.
Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Saalfeld, S., Schindelin, J. and Tomancak, P.
Nature Methods 7 (6): 418-419. June 2010

Editorial

The next generation of in situ multi-omics.
Salla, M. ORCID: https://orcid.org/0009-0003-8453-2935, Penkert, K. ORCID: https://orcid.org/0000-0002-9948-533X and Ludwig, L.S. ORCID: https://orcid.org/0000-0002-2916-2164
Nature Methods 22 (3): 461-462. March 2025

Genome architecture mapping detects transcriptionally active, multiway chromatin contacts.
Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature Methods 20 (7): 993-994. July 2023

Spatial heterogeneity in molecular brightness.
Annibale, P. ORCID: https://orcid.org/0000-0003-3208-5347 and Lohse, M.J. ORCID: https://orcid.org/0000-0002-0599-3510
Nature Methods 17 (3): 273-275. March 2020

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

Laser microdissection of a colon cancer specimen with subsequent RNA isolation, mRNA amplification and microarray hybridization.
Stoinski-Bungs, E., Seeger, S., Kemmner, W. ORCID: https://orcid.org/0000-0002-1494-7225, Scheinert, P. and Krupp, G.
Nature Methods Application Notes : an10-an11. 1 January 2006

Sleeping Beauty hits them all: transposon-mediated saturation mutagenesis in the mouse germline.
Izsvak, Z. ORCID: https://orcid.org/0000-0002-2053-2384 and Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658
Nature Methods 2 (10): 735-736. October 2005