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Fast and accurate protein structure search with Foldseek
van Kempen, Michel, Kim, Stephanie S., Tumescheit, Charlotte, Mirdita, Milot, Lee, Jeongjae, Gilchrist, Cameron L. M., Söding, Johannes, Steinegger, Martin
Published in Nature biotechnology (01.02.2024)
Published in Nature biotechnology (01.02.2024)
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Nextflow enables reproducible computational workflows
Di Tommaso, Paolo, Chatzou, Maria, Floden, Evan W, Barja, Pablo Prieto, Palumbo, Emilio, Notredame, Cedric
Published in Nature biotechnology (01.04.2017)
Published in Nature biotechnology (01.04.2017)
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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Blanco-Míguez, Aitor, Beghini, Francesco, Cumbo, Fabio, McIver, Lauren J., Thompson, Kelsey N., Zolfo, Moreno, Manghi, Paolo, Dubois, Leonard, Huang, Kun D., Thomas, Andrew Maltez, Nickols, William A., Piccinno, Gianmarco, Piperni, Elisa, Punčochář, Michal, Valles-Colomer, Mireia, Tett, Adrian, Giordano, Francesca, Davies, Richard, Wolf, Jonathan, Berry, Sarah E., Spector, Tim D., Franzosa, Eric A., Pasolli, Edoardo, Asnicar, Francesco, Huttenhower, Curtis, Segata, Nicola
Published in Nature biotechnology (01.11.2023)
Published in Nature biotechnology (01.11.2023)
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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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PICRUSt2 for prediction of metagenome functions
Douglas, Gavin M., Maffei, Vincent J., Zaneveld, Jesse R., Yurgel, Svetlana N., Brown, James R., Taylor, Christopher M., Huttenhower, Curtis, Langille, Morgan G. I.
Published in Nature biotechnology (01.06.2020)
Published in Nature biotechnology (01.06.2020)
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Dictionary learning for integrative, multimodal and scalable single-cell analysis
Hao, Yuhan, Stuart, Tim, Kowalski, Madeline H., Choudhary, Saket, Hoffman, Paul, Hartman, Austin, Srivastava, Avi, Molla, Gesmira, Madad, Shaista, Fernandez-Granda, Carlos, Satija, Rahul
Published in Nature biotechnology (01.02.2024)
Published in Nature biotechnology (01.02.2024)
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Integrative analysis of multimodal mass spectrometry data in MZmine 3
Schmid, Robin, Heuckeroth, Steffen, Korf, Ansgar, Smirnov, Aleksandr, Myers, Owen, Dyrlund, Thomas S., Bushuiev, Roman, Murray, Kevin J., Hoffmann, Nils, Lu, Miaoshan, Sarvepalli, Abinesh, Zhang, Zheng, Fleischauer, Markus, Dührkop, Kai, Wesner, Mark, Hoogstra, Shawn J., Rudt, Edward, Mokshyna, Olena, Brungs, Corinna, Ponomarov, Kirill, Mutabdžija, Lana, Damiani, Tito, Pudney, Chris J., Earll, Mark, Helmer, Patrick O., Fallon, Timothy R., Schulze, Tobias, Rivas-Ubach, Albert, Bilbao, Aivett, Richter, Henning, Nothias, Louis-Félix, Wang, Mingxun, Orešič, Matej, Weng, Jing-Ke, Böcker, Sebastian, Jeibmann, Astrid, Hayen, Heiko, Karst, Uwe, Dorrestein, Pieter C., Petras, Daniel, Du, Xiuxia, Pluskal, Tomáš
Published in Nature biotechnology (01.04.2023)
Published in Nature biotechnology (01.04.2023)
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Visualizing and interpreting cancer genomics data via the Xena platform
Goldman, Mary J., Craft, Brian, Hastie, Mim, Repečka, Kristupas, McDade, Fran, Kamath, Akhil, Banerjee, Ayan, Luo, Yunhai, Rogers, Dave, Brooks, Angela N., Zhu, Jingchun, Haussler, David
Published in Nature biotechnology (01.06.2020)
Published in Nature biotechnology (01.06.2020)
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CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Nayfach, Stephen, Camargo, Antonio Pedro, Schulz, Frederik, Eloe-Fadrosh, Emiley, Roux, Simon, Kyrpides, Nikos C.
Published in Nature biotechnology (01.05.2021)
Published in Nature biotechnology (01.05.2021)
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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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Robust decomposition of cell type mixtures in spatial transcriptomics
Cable, Dylan M., Murray, Evan, Zou, Luli S., Goeva, Aleksandrina, Macosko, Evan Z., Chen, Fei, Irizarry, Rafael A.
Published in Nature biotechnology (01.04.2022)
Published in Nature biotechnology (01.04.2022)
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The nf-core framework for community-curated bioinformatics pipelines
Ewels, Philip A., Peltzer, Alexander, Fillinger, Sven, Patel, Harshil, Alneberg, Johannes, Wilm, Andreas, Garcia, Maxime Ulysse, Di Tommaso, Paolo, Nahnsen, Sven
Published in Nature biotechnology (01.03.2020)
Published in Nature biotechnology (01.03.2020)
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Cell2location maps fine-grained cell types in spatial transcriptomics
Kleshchevnikov, Vitalii, Shmatko, Artem, Dann, Emma, Aivazidis, Alexander, King, Hamish W., Li, Tong, Elmentaite, Rasa, Lomakin, Artem, Kedlian, Veronika, Gayoso, Adam, Jain, Mika Sarkin, Park, Jun Sung, Ramona, Lauma, Tuck, Elizabeth, Arutyunyan, Anna, Vento-Tormo, Roser, Gerstung, Moritz, James, Louisa, Stegle, Oliver, Bayraktar, Omer Ali
Published in Nature biotechnology (01.05.2022)
Published in Nature biotechnology (01.05.2022)
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Greengenes2 unifies microbial data in a single reference tree
McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash, Knight, Rob
Published in Nature biotechnology (01.05.2024)
Published in Nature biotechnology (01.05.2024)
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SignalP 6.0 predicts all five types of signal peptides using protein language models
Teufel, Felix, Almagro Armenteros, José Juan, Johansen, Alexander Rosenberg, Gíslason, Magnús Halldór, Pihl, Silas Irby, Tsirigos, Konstantinos D., Winther, Ole, Brunak, Søren, von Heijne, Gunnar, Nielsen, Henrik
Published in Nature biotechnology (01.07.2022)
Published in Nature biotechnology (01.07.2022)
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Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
Li, Bin, Zhang, Wen, Guo, Chuang, Xu, Hao, Li, Longfei, Fang, Minghao, Hu, Yinlei, Zhang, Xinye, Yao, Xinfeng, Tang, Meifang, Liu, Ke, Zhao, Xuetong, Lin, Jun, Cheng, Linzhao, Chen, Falai, Xue, Tian, Qu, Kun
Published in Nature methods (01.06.2022)
Published in Nature methods (01.06.2022)
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Dimensionality reduction for visualizing single-cell data using UMAP
Becht, Etienne, McInnes, Leland, Healy, John, Dutertre, Charles-Antoine, Kwok, Immanuel W H, Ng, Lai Guan, Ginhoux, Florent, Newell, Evan W
Published in Nature biotechnology (01.01.2019)
Published in Nature biotechnology (01.01.2019)
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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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