ColabFold: making protein folding accessible to all
Mirdita, Milot, Schütze, Konstantin, Moriwaki, Yoshitaka, Heo, Lim, Ovchinnikov, Sergey, Steinegger, Martin
Published in Nature methods (01.06.2022)
Published in Nature methods (01.06.2022)
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nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation
Isensee, Fabian, Jaeger, Paul F., Kohl, Simon A. A., Petersen, Jens, Maier-Hein, Klaus H.
Published in Nature methods (01.02.2021)
Published in Nature methods (01.02.2021)
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SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, Pauli, Gommers, Ralf, Oliphant, Travis E., Haberland, Matt, Reddy, Tyler, Cournapeau, David, Burovski, Evgeni, Peterson, Pearu, Weckesser, Warren, Bright, Jonathan, van der Walt, Stéfan J., Brett, Matthew, Wilson, Joshua, Millman, K. Jarrod, Mayorov, Nikolay, Nelson, Andrew R. J., Jones, Eric, Kern, Robert, Larson, Eric, Carey, C J, Polat, İlhan, Feng, Yu, Moore, Eric W., VanderPlas, Jake, Laxalde, Denis, Perktold, Josef, Cimrman, Robert, Henriksen, Ian, Quintero, E. A., Harris, Charles R., Archibald, Anne M., Ribeiro, Antônio H., Pedregosa, Fabian, van Mulbregt, Paul
Published in Nature methods (01.03.2020)
Published in Nature methods (01.03.2020)
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Cellpose: a generalist algorithm for cellular segmentation
Stringer, Carsen, Wang, Tim, Michaelos, Michalis, Pachitariu, Marius
Published in Nature methods (01.01.2021)
Published in Nature methods (01.01.2021)
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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, Haoyu, Concepcion, Gregory T., Feng, Xiaowen, Zhang, Haowen, Li, Heng
Published in Nature methods (01.02.2021)
Published in Nature methods (01.02.2021)
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Fast, sensitive and accurate integration of single-cell data with Harmony
Korsunsky, Ilya, Millard, Nghia, Fan, Jean, Slowikowski, Kamil, Zhang, Fan, Wei, Kevin, Baglaenko, Yuriy, Brenner, Michael, Loh, Po-ru, Raychaudhuri, Soumya
Published in Nature methods (01.12.2019)
Published in Nature methods (01.12.2019)
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ilastik: interactive machine learning for (bio)image analysis
Berg, Stuart, Kutra, Dominik, Kroeger, Thorben, Straehle, Christoph N., Kausler, Bernhard X., Haubold, Carsten, Schiegg, Martin, Ales, Janez, Beier, Thorsten, Rudy, Markus, Eren, Kemal, Cervantes, Jaime I, Xu, Buote, Beuttenmueller, Fynn, Wolny, Adrian, Zhang, Chong, Koethe, Ullrich, Hamprecht, Fred A., Kreshuk, Anna
Published in Nature methods (01.12.2019)
Published in Nature methods (01.12.2019)
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Martini 3: a general purpose force field for coarse-grained molecular dynamics
Souza, Paulo C. T., Alessandri, Riccardo, Barnoud, Jonathan, Thallmair, Sebastian, Faustino, Ignacio, Grünewald, Fabian, Patmanidis, Ilias, Abdizadeh, Haleh, Bruininks, Bart M. H., Wassenaar, Tsjerk A., Kroon, Peter C., Melcr, Josef, Nieto, Vincent, Corradi, Valentina, Khan, Hanif M., Domański, Jan, Javanainen, Matti, Martinez-Seara, Hector, Reuter, Nathalie, Best, Robert B., Vattulainen, Ilpo, Monticelli, Luca, Periole, Xavier, Tieleman, D. Peter, de Vries, Alex H., Marrink, Siewert J.
Published in Nature methods (01.04.2021)
Published in Nature methods (01.04.2021)
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Single-cell chromatin state analysis with Signac
Stuart, Tim, Srivastava, Avi, Madad, Shaista, Lareau, Caleb A., Satija, Rahul
Published in Nature methods (01.11.2021)
Published in Nature methods (01.11.2021)
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Feature-based molecular networking in the GNPS analysis environment
Nothias, Louis-Félix, Petras, Daniel, Schmid, Robin, Dührkop, Kai, Rainer, Johannes, Sarvepalli, Abinesh, Protsyuk, Ivan, Ernst, Madeleine, Tsugawa, Hiroshi, Fleischauer, Markus, Aicheler, Fabian, Aksenov, Alexander A., Alka, Oliver, Allard, Pierre-Marie, Barsch, Aiko, Cachet, Xavier, Caraballo-Rodriguez, Andres Mauricio, Da Silva, Ricardo R., Dang, Tam, Garg, Neha, Gauglitz, Julia M., Gurevich, Alexey, Isaac, Giorgis, Jarmusch, Alan K., Kameník, Zdeněk, Kang, Kyo Bin, Kessler, Nikolas, Koester, Irina, Korf, Ansgar, Le Gouellec, Audrey, Ludwig, Marcus, Martin H., Christian, McCall, Laura-Isobel, McSayles, Jonathan, Meyer, Sven W., Mohimani, Hosein, Morsy, Mustafa, Moyne, Oriane, Neumann, Steffen, Neuweger, Heiko, Nguyen, Ngoc Hung, Nothias-Esposito, Melissa, Paolini, Julien, Phelan, Vanessa V., Pluskal, Tomáš, Quinn, Robert A., Rogers, Simon, Shrestha, Bindesh, Tripathi, Anupriya, van der Hooft, Justin J. J., Vargas, Fernando, Weldon, Kelly C., Witting, Michael, Yang, Heejung, Zhang, Zheng, Zubeil, Florian, Kohlbacher, Oliver, Böcker, Sebastian, Alexandrov, Theodore, Bandeira, Nuno, Wang, Mingxun, Dorrestein, Pieter C.
Published in Nature methods (01.09.2020)
Published in Nature methods (01.09.2020)
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Benchmarking atlas-level data integration in single-cell genomics
Luecken, Malte D., Büttner, M., Chaichoompu, K., Danese, A., Interlandi, M., Mueller, M. F., Strobl, D. C., Zappia, L., Dugas, M., Colomé-Tatché, M., Theis, Fabian J.
Published in Nature methods (01.01.2022)
Published in Nature methods (01.01.2022)
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Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices
Alseekh, Saleh, Aharoni, Asaph, Brotman, Yariv, Contrepois, Kévin, D’Auria, John, Ewald, Jan, C. Ewald, Jennifer, Fraser, Paul D., Giavalisco, Patrick, Hall, Robert D., Heinemann, Matthias, Link, Hannes, Luo, Jie, Neumann, Steffen, Nielsen, Jens, Perez de Souza, Leonardo, Saito, Kazuki, Sauer, Uwe, Schroeder, Frank C., Schuster, Stefan, Siuzdak, Gary, Skirycz, Aleksandra, Sumner, Lloyd W., Snyder, Michael P., Tang, Huiru, Tohge, Takayuki, Wang, Yulan, Wen, Weiwei, Wu, Si, Xu, Guowang, Zamboni, Nicola, Fernie, Alisdair R.
Published in Nature methods (01.07.2021)
Published in Nature methods (01.07.2021)
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fMRIPrep: a robust preprocessing pipeline for functional MRI
Esteban, Oscar, Markiewicz, Christopher J., Blair, Ross W., Moodie, Craig A., Isik, A. Ilkay, Erramuzpe, Asier, Kent, James D., Goncalves, Mathias, DuPre, Elizabeth, Snyder, Madeleine, Oya, Hiroyuki, Ghosh, Satrajit S., Wright, Jessey, Durnez, Joke, Poldrack, Russell A., Gorgolewski, Krzysztof J.
Published in Nature methods (01.01.2019)
Published in Nature methods (01.01.2019)
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U-Net: deep learning for cell counting, detection, and morphometry
Falk, Thorsten, Mai, Dominic, Bensch, Robert, Çiçek, Özgün, Abdulkadir, Ahmed, Marrakchi, Yassine, Böhm, Anton, Deubner, Jan, Jäckel, Zoe, Seiwald, Katharina, Dovzhenko, Alexander, Tietz, Olaf, Dal Bosco, Cristina, Walsh, Sean, Saltukoglu, Deniz, Tay, Tuan Leng, Prinz, Marco, Palme, Klaus, Simons, Matias, Diester, Ilka, Brox, Thomas, Ronneberger, Olaf
Published in Nature methods (01.01.2019)
Published in Nature methods (01.01.2019)
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