Search Results - "Nature biotechnology"

SignalP 6.0 predicts all five types of signal peptides using protein language models by 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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PICRUSt2 for prediction of metagenome functions by 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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Fast and accurate protein structure search with Foldseek by 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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Visualizing and interpreting cancer genomics data via the Xena platform by 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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CRISPR–Cas12-based detection of SARS-CoV-2 by 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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Generalizing RNA velocity to transient cell states through dynamical modeling by 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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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype by 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 by 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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Dictionary learning for integrative, multimodal and scalable single-cell analysis by 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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Determining cell type abundance and expression from bulk tissues with digital cytometry by Newman, Aaron M., Steen, Chloé B., Liu, Chih Long, Gentles, Andrew J., Chaudhuri, Aadel A., Scherer, Florian, Khodadoust, Michael S., Esfahani, Mohammad S., Luca, Bogdan A., Steiner, David, Diehn, Maximilian, Alizadeh, Ash A.

“…Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular heterogeneity, but it is currently impractical on large sample…”
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A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2–spike protein–protein interaction by Tan, Chee Wah, Chia, Wan Ni, Qin, Xijian, Liu, Pei, Chen, Mark I.-C., Tiu, Charles, Hu, Zhiliang, Chen, Vivian Chih-Wei, Young, Barnaby E., Sia, Wan Rong, Tan, Yee-Joo, Foo, Randy, Yi, Yongxiang, Lye, David C., Anderson, Danielle E., Wang, Lin-Fa

“…A robust serological test to detect neutralizing antibodies to SARS-CoV-2 is urgently needed to determine not only the infection rate, herd immunity and…”
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CheckV assesses the quality and completeness of metagenome-assembled viral genomes by 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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Large language models generate functional protein sequences across diverse families by 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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SignalP 5.0 improves signal peptide predictions using deep neural networks by Almagro Armenteros, José Juan, Tsirigos, Konstantinos D., Sønderby, Casper Kaae, Petersen, Thomas Nordahl, Winther, Ole, Brunak, Søren, von Heijne, Gunnar, Nielsen, Henrik

“…Signal peptides (SPs) are short amino acid sequences in the amino terminus of many newly synthesized proteins that target proteins into, or across, membranes…”
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Assembly of long, error-prone reads using repeat graphs by Kolmogorov, Mikhail, Yuan, Jeffrey, Lin, Yu, Pevzner, Pavel A.

“…Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than…”
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The nf-core framework for community-curated bioinformatics pipelines by Ewels, Philip A., Peltzer, Alexander, Fillinger, Sven, Patel, Harshil, Alneberg, Johannes, Wilm, Andreas, Garcia, Maxime Ulysse, Di Tommaso, Paolo, Nahnsen, Sven

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COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis by Chua, Robert Lorenz, Lukassen, Soeren, Trump, Saskia, Hennig, Bianca P., Wendisch, Daniel, Pott, Fabian, Debnath, Olivia, Thürmann, Loreen, Kurth, Florian, Völker, Maria Theresa, Kazmierski, Julia, Timmermann, Bernd, Twardziok, Sven, Schneider, Stefan, Machleidt, Felix, Müller-Redetzky, Holger, Maier, Melanie, Krannich, Alexander, Schmidt, Sein, Balzer, Felix, Liebig, Johannes, Loske, Jennifer, Suttorp, Norbert, Eils, Jürgen, Ishaque, Naveed, Liebert, Uwe Gerd, von Kalle, Christof, Hocke, Andreas, Witzenrath, Martin, Goffinet, Christine, Drosten, Christian, Laudi, Sven, Lehmann, Irina, Conrad, Christian, Sander, Leif-Erik, Eils, Roland

“…To investigate the immune response and mechanisms associated with severe coronavirus disease 2019 (COVID-19), we performed single-cell RNA sequencing on…”
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A unified catalog of 204,938 reference genomes from the human gut microbiome by Almeida, Alexandre, Nayfach, Stephen, Boland, Miguel, Strozzi, Francesco, Beracochea, Martin, Shi, Zhou Jason, Pollard, Katherine S., Sakharova, Ekaterina, Parks, Donovan H., Hugenholtz, Philip, Segata, Nicola, Kyrpides, Nikos C., Finn, Robert D.

“…Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the…”
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Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics by Peccia, Jordan, Zulli, Alessandro, Brackney, Doug E., Grubaugh, Nathan D., Kaplan, Edward H., Casanovas-Massana, Arnau, Ko, Albert I., Malik, Amyn A., Wang, Dennis, Wang, Mike, Warren, Joshua L., Weinberger, Daniel M., Arnold, Wyatt, Omer, Saad B.

“…We measured severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in primary sewage sludge in the New Haven, Connecticut, USA,…”
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Human chimeric antigen receptor macrophages for cancer immunotherapy by Klichinsky, Michael, Ruella, Marco, Shestova, Olga, Lu, Xueqing Maggie, Best, Andrew, Zeeman, Martha, Schmierer, Maggie, Gabrusiewicz, Konrad, Anderson, Nicholas R., Petty, Nicholas E., Cummins, Katherine D., Shen, Feng, Shan, Xinhe, Veliz, Kimberly, Blouch, Kristin, Yashiro-Ohtani, Yumi, Kenderian, Saad S., Kim, Miriam Y., O’Connor, Roddy S., Wallace, Stephen R., Kozlowski, Miroslaw S., Marchione, Dylan M., Shestov, Maksim, Garcia, Benjamin A., June, Carl H., Gill, Saar

“…Chimeric antigen receptor (CAR) T cell therapy has shown promise in hematologic malignancies, but its application to solid tumors has been challenging 1 – 4 …”
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