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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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Journal Article
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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Journal Article
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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Journal Article
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
Chklovski, Alex, Parks, Donovan H., Woodcroft, Ben J., Tyson, Gene W.
Published in Nature methods (01.08.2023)
Published in Nature methods (01.08.2023)
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Journal Article
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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Journal Article
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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Journal Article
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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Journal Article
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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Journal Article
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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Journal Article
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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Journal Article
scGPT: toward building a foundation model for single-cell multi-omics using generative AI
Cui, Haotian, Wang, Chloe, Maan, Hassaan, Pang, Kuan, Luo, Fengning, Duan, Nan, Wang, Bo
Published in Nature methods (01.08.2024)
Published in Nature methods (01.08.2024)
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Journal Article
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines
Ershov, Dmitry, Phan, Minh-Son, Pylvänäinen, Joanna W., Rigaud, Stéphane U., Le Blanc, Laure, Charles-Orszag, Arthur, Conway, James R. W., Laine, Romain F., Roy, Nathan H., Bonazzi, Daria, Duménil, Guillaume, Jacquemet, Guillaume, Tinevez, Jean-Yves
Published in Nature methods (01.07.2022)
Published in Nature methods (01.07.2022)
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Journal Article
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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Journal Article
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
Hu, Jian, Li, Xiangjie, Coleman, Kyle, Schroeder, Amelia, Ma, Nan, Irwin, David J., Lee, Edward B., Shinohara, Russell T., Li, Mingyao
Published in Nature methods (01.11.2021)
Published in Nature methods (01.11.2021)
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Journal Article
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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Journal Article