Výsledky vyhľadávania - "Nature biotechnology"

Dictionary learning for integrative, multimodal and scalable single-cell analysis Autor Hao, Yuhan, Stuart, Tim, Kowalski, Madeline H., Choudhary, Saket, Hoffman, Paul, Hartman, Austin, Srivastava, Avi, Molla, Gesmira, Madad, Shaista, Fernandez-Granda, Carlos, Satija, Rahul

“…Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference…”
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Fast and accurate protein structure search with Foldseek Autor van Kempen, Michel, Kim, Stephanie S., Tumescheit, Charlotte, Mirdita, Milot, Lee, Jeongjae, Gilchrist, Cameron L. M., Söding, Johannes, Steinegger, Martin

“…As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck. Foldseek…”
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SignalP 6.0 predicts all five types of signal peptides using protein language models Autor 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

“…Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from…”
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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 Autor 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

“…Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we…”
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Large language models generate functional protein sequences across diverse families Autor Madani, Ali, Krause, Ben, Greene, Eric R., Subramanian, Subu, Mohr, Benjamin P., Holton, James M., Olmos, Jose Luis, Xiong, Caiming, Sun, Zachary Z., Socher, Richard, Fraser, James S., Naik, Nikhil

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Integrative analysis of multimodal mass spectrometry data in MZmine 3 Autor 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

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Large language models generate functional protein sequences across diverse families Autor Madani, Ali, Krause, Ben, Greene, Eric R., Subramanian, Subu, Mohr, Benjamin P., Holton, James M., Olmos, Jose Luis, Xiong, Caiming, Sun, Zachary Z., Socher, Richard, Fraser, James S., Naik, Nikhil

“…Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here we describe ProGen, a…”
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Nanopore sequencing technology, bioinformatics and applications Autor Wang, Yunhao, Zhao, Yue, Bollas, Audrey, Wang, Yuru, Au, Kin Fai

“…Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and…”
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Identification of mobile genetic elements with geNomad Autor Camargo, Antonio Pedro, Roux, Simon, Schulz, Frederik, Babinski, Michal, Xu, Yan, Hu, Bin, Chain, Patrick S. G., Nayfach, Stephen, Kyrpides, Nikos C.

“…Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological…”
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PICRUSt2 for prediction of metagenome functions Autor Douglas, Gavin M, Maffei, Vincent J, Zaneveld, Jesse R, Yurgel, Svetlana N, Brown, James R, Taylor, Christopher M, Huttenhower, Curtis, Langille, Morgan G I

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Visualizing and interpreting cancer genomics data via the Xena platform Autor 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

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Generalizing RNA velocity to transient cell states through dynamical modeling Autor Bergen, Volker, Lange, Marius, Peidli, Stefan, Wolf, F Alexander, Theis, Fabian J

“…RNA velocity has opened up new ways of studying cellular differentiation in single-cell RNA-sequencing data. It describes the rate of gene expression change…”
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CRISPR-Cas12-based detection of SARS-CoV-2 Autor Broughton, James P, Deng, Xianding, Yu, Guixia, Fasching, Clare L, Servellita, Venice, Singh, Jasmeet, Miao, Xin, Streithorst, Jessica A, Granados, Andrea, Sotomayor-Gonzalez, Alicia, Zorn, Kelsey, Gopez, Allan, Hsu, Elaine, Gu, Wei, Miller, Steve, Pan, Chao-Yang, Guevara, Hugo, Wadford, Debra A, Chen, Janice S, Chiu, Charles Y

“…An outbreak of betacoronavirus severe acute respiratory syndrome (SARS)-CoV-2 began in Wuhan, China in December 2019. COVID-19, the disease associated with…”
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CheckV assesses the quality and completeness of metagenome-assembled viral genomes Autor Nayfach, Stephen, Camargo, Antonio Pedro, Schulz, Frederik, Eloe-Fadrosh, Emiley, Roux, Simon, Kyrpides, Nikos C.

“…Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present…”
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Robust decomposition of cell type mixtures in spatial transcriptomics Autor Cable, Dylan M., Murray, Evan, Zou, Luli S., Goeva, Aleksandrina, Macosko, Evan Z., Chen, Fei, Irizarry, Rafael A.

“…A limitation of spatial transcriptomics technologies is that individual measurements may contain contributions from multiple cells, hindering the discovery of…”
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Autor Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R, Bokulich, Nicholas A, Abnet, Christian C, Al-Ghalith, Gabriel A, Alexander, Harriet, Alm, Eric J, Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E, Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J, Brown, C Titus, Callahan, Benjamin J, Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K, Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C, Douglas, Gavin M, Durall, Daniel M, Duvallet, Claire, Edwardson, Christian F, Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M, Gibbons, Sean M, Gibson, Deanna L, Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A, Janssen, Stefan, Jarmusch, Alan K, Jiang, Lingjing, Kaehler, Benjamin D, Kang, Kyo Bin, Keefe, Christopher R, Keim, Paul, Kelley, Scott T, Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G I, Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D, McDonald, Daniel, McIver, Lauren J, Melnik, Alexey V, Metcalf, Jessica L, Morgan, Sydney C, Morton, Jamie T, Naimey, Ahmad Turan, Navas-Molina, Jose A, Nothias, Louis Felix, Orchanian, Stephanie B, Pearson, Talima, Peoples, Samuel L, Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, 2nd, Michael S, Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R, Swafford, Austin D, Thompson, Luke R, Torres, Pedro J, Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J, Ul-Hasan, Sabah, van der Hooft, Justin J J, Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William

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Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning Autor Greenwald, Noah F., Miller, Geneva, Moen, Erick, Kong, Alex, Kagel, Adam, Dougherty, Thomas, Fullaway, Christine Camacho, McIntosh, Brianna J., Leow, Ke Xuan, Schwartz, Morgan Sarah, Pavelchek, Cole, Cui, Sunny, Camplisson, Isabella, Bar-Tal, Omer, Singh, Jaiveer, Fong, Mara, Chaudhry, Gautam, Abraham, Zion, Moseley, Jackson, Warshawsky, Shiri, Soon, Erin, Greenbaum, Shirley, Risom, Tyler, Hollmann, Travis, Bendall, Sean C., Keren, Leeat, Graf, William, Angelo, Michael, Van Valen, David

“…A principal challenge in the analysis of tissue imaging data is cell segmentation—the task of identifying the precise boundary of every cell in an image. To…”
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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Autor Kim, Daehwan, Paggi, Joseph M, Park, Chanhee, Bennett, Christopher, Salzberg, Steven L

“…The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2…”
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Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors Autor Anzalone, Andrew V, Koblan, Luke W, Liu, David R

“…The development of new CRISPR-Cas genome editing tools continues to drive major advances in the life sciences. Four classes of CRISPR-Cas-derived genome…”
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Cell2location maps fine-grained cell types in spatial transcriptomics Autor 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

“…Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in health and disease, but comprehensive mapping of cell types in…”
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