Search Results - "Gayoso, Adam"

Interpretable factor models of single-cell RNA-seq via variational autoencoders by Svensson, Valentine, Gayoso, Adam, Yosef, Nir, Pachter, Lior

“…Abstract Motivation Single-cell RNA-seq makes possible the investigation of variability in gene expression among cells, and dependence of variation on cell…”
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Joint probabilistic modeling of single-cell multi-omic data with totalVI by Gayoso, Adam, Steier, Zoë, Lopez, Romain, Regier, Jeffrey, Nazor, Kristopher L., Streets, Aaron, Yosef, Nir

“…The paired measurement of RNA and surface proteins in single cells with cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) is a…”
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Cell2location maps fine-grained cell types in spatial transcriptomics by 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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Characterization of cell fate probabilities in single-cell data with Palantir by Setty, Manu, Kiseliovas, Vaidotas, Levine, Jacob, Gayoso, Adam, Mazutis, Linas, Pe’er, Dana

“…Single-cell RNA sequencing studies of differentiating systems have raised fundamental questions regarding the discrete versus continuous nature of both…”
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Mapping single-cell data to reference atlases by transfer learning by Lotfollahi, Mohammad, Naghipourfar, Mohsen, Luecken, Malte D., Khajavi, Matin, Büttner, Maren, Wagenstetter, Marco, Avsec, Žiga, Gayoso, Adam, Yosef, Nir, Interlandi, Marta, Rybakov, Sergei, Misharin, Alexander V., Theis, Fabian J.

“…Large single-cell atlases are now routinely generated to serve as references for analysis of smaller-scale studies. Yet learning from reference data is…”
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Enhancing scientific discoveries in molecular biology with deep generative models by Lopez, Romain, Gayoso, Adam, Yosef, Nir

“…Generative models provide a well‐established statistical framework for evaluating uncertainty and deriving conclusions from large data sets especially in the…”
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A Python library for probabilistic analysis of single-cell omics data by Gayoso, Adam, Lopez, Romain, Xing, Galen, Boyeau, Pierre, Valiollah Pour Amiri, Valeh, Hong, Justin, Wu, Katherine, Jayasuriya, Michael, Mehlman, Edouard, Langevin, Maxime, Liu, Yining, Samaran, Jules, Misrachi, Gabriel, Nazaret, Achille, Clivio, Oscar, Xu, Chenling, Ashuach, Tal, Gabitto, Mariano, Lotfollahi, Mohammad, Svensson, Valentine, da Veiga Beltrame, Eduardo, Kleshchevnikov, Vitalii, Talavera-López, Carlos, Pachter, Lior, Theis, Fabian J., Streets, Aaron, Jordan, Michael I., Regier, Jeffrey, Yosef, Nir

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Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-Producing Klebsiella pneumoniae by Adams-Sapper, Sheila, Riley, Lee W., Gayoso, Adam

“…Carbapenem-resistant Enterobacteriaceae (CRE) organisms have emerged to become a major global public health threat among antimicrobial resistant bacterial…”
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An empirical Bayes method for differential expression analysis of single cells with deep generative models by Boyeau, Pierre, Regier, Jeffrey, Gayoso, Adam, Jordan, Michael I, Lopez, Romain, Yosef, Nir

“…Detecting differentially expressed genes is important for characterizing subpopulations of cells. In scRNA-seq data, however, nuisance variation due to…”
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Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells by Gayoso, Adam, Weiler, Philipp, Lotfollahi, Mohammad, Klein, Dominik, Hong, Justin, Streets, Aaron, Theis, Fabian J., Yosef, Nir

“…RNA velocity has been rapidly adopted to guide interpretation of transcriptional dynamics in snapshot single-cell data; however, current approaches for…”
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The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans by Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles K F, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Vorperian, Sevahn K, Wang, Wanxin

“…Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the…”
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PeakVI: A deep generative model for single-cell chromatin accessibility analysis by Ashuach, Tal, Reidenbach, Daniel A., Gayoso, Adam, Yosef, Nir

“…Single-cell ATAC sequencing (scATAC-seq) is a powerful and increasingly popular technique to explore the regulatory landscape of heterogeneous cellular…”
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Author Correction: Characterization of cell fate probabilities in single-cell data with Palantir by Setty, Manu, Kiseliovas, Vaidotas, Levine, Jacob, Gayoso, Adam, Mazutis, Linas, Pe’er, Dana

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
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Cell types of origin of the cell-free transcriptome by Vorperian, Sevahn K., Moufarrej, Mira N., Quake, Stephen R.

“…Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the…”
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Deep Generative Modeling for Single-Cell Omics Data by Gayoso, Adam J

“…Single-cell omics technologies have transformed our ability to take high-throughput measurements of the molecular contents of individual cells. Applications of…”
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The scverse project provides a computational ecosystem for single-cell omics data analysis by Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe’er, Dana, Regev, Aviv, Teichmann, Sarah A., Finotello, Francesca, Wolf, F. Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J.

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Publisher Correction: Cell types of origin of the cell-free transcriptome by Vorperian, Sevahn K., Moufarrej, Mira N., Quake, Stephen R.

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The scverse project provides a computational ecosystem for single-cell omics data analysis by Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe'er, Dana, Regev, Aviv, Teichmann, Sarah A, Finotello, Francesca, Wolf, F Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J

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