Machine learning for cell type classification from single nucleus RNA sequencing data von Le, Huy, Peng, Beverly, Uy, Janelle, Carrillo, Daniel, Zhang, Yun, Aevermann, Brian D, Scheuermann, Richard H

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Cell type discovery and representation in the era of high-content single cell phenotyping von Bakken, Trygve, Cowell, Lindsay, Aevermann, Brian D, Novotny, Mark, Hodge, Rebecca, Miller, Jeremy A, Lee, Alexandra, Chang, Ivan, McCorrison, Jamison, Pulendran, Bali, Qian, Yu, Schork, Nicholas J, Lasken, Roger S, Lein, Ed S, Scheuermann, Richard H

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Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain von Zhang, Yun, Miller, Jeremy A., Park, Jeongbin, Lelieveldt, Boudewijn P., Long, Brian, Abdelaal, Tamim, Aevermann, Brian D., Biancalani, Tommaso, Comiter, Charles, Dzyubachyk, Oleh, Eggermont, Jeroen, Langseth, Christoffer Mattsson, Petukhov, Viktor, Scalia, Gabriele, Vaishnav, Eeshit Dhaval, Zhao, Yilin, Lein, Ed S., Scheuermann, Richard H.

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Comparative Analysis of the Small Heat Shock Proteins in Three Angiosperm Genomes Identifies New Subfamilies and Reveals Diverse Evolutionary Patterns von Waters, Elizabeth R., Aevermann, Brian D., Sanders-Reed, Zipporah

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Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response von Aevermann, Brian D., Shannon, Casey P., Novotny, Mark, Ben-Othman, Rym, Cai, Bing, Zhang, Yun, Ye, Jamie C., Kobor, Michael S., Gladish, Nicole, Lee, Amy Huei-Yi, Blimkie, Travis M., Hancock, Robert E., Llibre, Alba, Duffy, Darragh, Koff, Wayne C., Sadarangani, Manish, Tebbutt, Scott J., Kollmann, Tobias R., Scheuermann, Richard H.

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Brain Data Standards - A method for building data-driven cell-type ontologies von Tan, Shawn Zheng Kai, Kir, Huseyin, Aevermann, Brian D., Gillespie, Tom, Harris, Nomi, Hawrylycz, Michael J., Jorstad, Nikolas L., Lein, Ed S., Matentzoglu, Nicolas, Miller, Jeremy A., Mollenkopf, Tyler S., Mungall, Christopher J., Ray, Patrick L., Sanchez, Raymond E. A., Staats, Brian, Vermillion, Jim, Yadav, Ambika, Zhang, Yun, Scheuermann, Richard H., Osumi-Sutherland, David

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Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans von Lee, Alexandra J, Das, Suman R, Wang, Wei, Fitzgerald, Theresa, Pickett, Brett E, Aevermann, Brian D, Topham, David J, Falsey, Ann R, Scheuermann, Richard H

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Influenza Research Database: An integrated bioinformatics resource for influenza virus research von Zhang, Yun, Aevermann, Brian D, Anderson, Tavis K, Burke, David F, Dauphin, Gwenaelle, Gu, Zhiping, He, Sherry, Kumar, Sanjeev, Larsen, Christopher N, Lee, Alexandra J, Li, Xiaomei, Macken, Catherine, Mahaffey, Colin, Pickett, Brett E, Reardon, Brian, Smith, Thomas, Stewart, Lucy, Suloway, Christian, Sun, Guangyu, Tong, Lei, Vincent, Amy L, Walters, Bryan, Zaremba, Sam, Zhao, Hongtao, Zhou, Liwei, Zmasek, Christian, Klem, Edward B, Scheuermann, Richard H

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Author Correction: Brain Data Standards - A method for building data-driven cell-type ontologies von Tan, Shawn Zheng Kai, Kir, Huseyin, Aevermann, Brian D., Gillespie, Tom, Harris, Nomi, Hawrylycz, Michael J., Jorstad, Nikolas L., Lein, Ed S., Matentzoglu, Nicolas, Miller, Jeremy A., Mollenkopf, Tyler S., Mungall, Christopher J., Ray, Patrick L., Sanchez, Raymond E. A., Staats, Brian, Vermillion, Jim, Yadav, Ambika, Zhang, Yun, Scheuermann, Richard H., Osumi-Sutherland, David

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Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons von Krishnaswami, Suguna Rani, Grindberg, Rashel V, Novotny, Mark, Venepally, Pratap, Lacar, Benjamin, Bhutani, Kunal, Linker, Sara B, Pham, Son, Erwin, Jennifer A, Miller, Jeremy A, Hodge, Rebecca, McCarthy, James K, Kelder, Martijn, McCorrison, Jamison, Aevermann, Brian D, Fuertes, Francisco Diez, Scheuermann, Richard H, Lee, Jun, Lein, Ed S, Schork, Nicholas, McConnell, Michael J, Gage, Fred H, Lasken, Roger S

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FastMix: a versatile data integration pipeline for cell type-specific biomarker inference von Zhang, Yun, Sun, Hao, Mandava, Aishwarya, Aevermann, Brian D, Kollmann, Tobias R, Scheuermann, Richard H, Qiu, Xing, Qian, Yu

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The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness von Abramson, Bradley W, Novotny, Mark, Hartwick, Nolan T, Colt, Kelly, Aevermann, Brian D, Scheuermann, Richard H, Michael, Todd P

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Cell type discovery using single-cell transcriptomics: implications for ontological representation von Aevermann, Brian D, Novotny, Mark, Bakken, Trygve, Miller, Jeremy A, Diehl, Alexander D, Osumi-Sutherland, David, Lasken, Roger S, Lein, Ed S, Scheuermann, Richard H

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Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons von Hodge, Rebecca D., Miller, Jeremy A., Novotny, Mark, Kalmbach, Brian E., Ting, Jonathan T., Bakken, Trygve E., Aevermann, Brian D., Barkan, Eliza R., Berkowitz-Cerasano, Madeline L., Cobbs, Charles, Diez-Fuertes, Francisco, Ding, Song-Lin, McCorrison, Jamison, Schork, Nicholas J., Shehata, Soraya I., Smith, Kimberly A., Sunkin, Susan M., Tran, Danny N., Venepally, Pratap, Yanny, Anna Marie, Steemers, Frank J., Phillips, John W., Bernard, Amy, Koch, Christof, Lasken, Roger S., Scheuermann, Richard H., Lein, Ed S.

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FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test von Zhang, Yun, Aevermann, Brian D, Bakken, Trygve E, Miller, Jeremy A, Hodge, Rebecca D, Lein, Ed S, Scheuermann, Richard H

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Cross-Comparison of Inflammatory Skin Disease Transcriptomics Identifies PTEN as a Pathogenic Disease Classifier in Cutaneous Lupus Erythematosus von Aevermann, Brian D, Di Domizio, Jeremy, Olah, Peter, Saidoune, Fanny, Armstrong, John M, Bachelez, Hervé, Barker, Jonathan, Haniffa, Muzlifah, Julia, Valerie, Juul, Kasper, Krishnaswamy, Jayendra Kumar, Litman, Thomas, Parsons, Ian, Sarin, Kavita Y, Schmuth, Matthias, Sierra, Michael, Simpson, Michael, Homey, Bernhard, Griffiths, Christopher E M, Scheuermann, Richard H, Gilliet, Michel

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comparative genomic analysis of the small heat shock proteins in Caenorhabditis elegans and briggsae von Aevermann, Brian D, Waters, Elizabeth R

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Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type von Boldog, Eszter, Bakken, Trygve E., Hodge, Rebecca D., Novotny, Mark, Aevermann, Brian D., Baka, Judith, Bordé, Sándor, Close, Jennie L., Diez-Fuertes, Francisco, Ding, Song-Lin, Faragó, Nóra, Kocsis, Ágnes K., Kovács, Balázs, Maltzer, Zoe, McCorrison, Jamison M., Miller, Jeremy A., Molnár, Gábor, Oláh, Gáspár, Ozsvár, Attila, Rózsa, Márton, Shehata, Soraya I., Smith, Kimberly A., Sunkin, Susan M., Tran, Danny N., Venepally, Pratap, Wall, Abby, Puskás, László G., Barzó, Pál, Steemers, Frank J., Schork, Nicholas J., Scheuermann, Richard H., Lasken, Roger S., Lein, Ed S., Tamás, Gábor

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A comprehensive collection of systems biology data characterizing the host response to viral infection von Aevermann, Brian D., Pickett, Brett E., Kumar, Sanjeev, Klem, Edward B., Agnihothram, Sudhakar, Askovich, Peter S., Bankhead, Armand, Bolles, Meagen, Carter, Victoria, Chang, Jean, Clauss, Therese R.W., Dash, Pradyot, Diercks, Alan H., Eisfeld, Amie J., Ellis, Amy, Fan, Shufang, Ferris, Martin T., Gralinski, Lisa E., Green, Richard R., Gritsenko, Marina A., Hatta, Masato, Heegel, Robert A., Jacobs, Jon M., Jeng, Sophia, Josset, Laurence, Kaiser, Shari M., Kelly, Sara, Law, G. Lynn, Li, Chengjun, Li, Jiangning, Long, Casey, Luna, Maria L., Matzke, Melissa, McDermott, Jason, Menachery, Vineet, Metz, Thomas O., Mitchell, Hugh, Monroe, Matthew E., Navarro, Garnet, Neumann, Gabriele, Podyminogin, Rebecca L., Purvine, Samuel O., Rosenberger, Carrie M., Sanders, Catherine J., Schepmoes, Athena A., Shukla, Anil K., Sims, Amy, Sova, Pavel, Tam, Vincent C., Tchitchek, Nicolas, Thomas, Paul G., Tilton, Susan C., Totura, Allison, Wang, Jing, Webb-Robertson, Bobbie-Jo, Wen, Ji, Weiss, Jeffrey M., Yang, Feng, Yount, Boyd, Zhang, Qibin, McWeeney, Shannon, Smith, Richard D., Waters, Katrina M., Kawaoka, Yoshihiro, Baric, Ralph, Aderem, Alan, Katze, Michael G., Scheuermann, Richard H.

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A comparative genomic analysis of the small heat shock proteins in Caenorhabditiselegans and briggsae von Aevermann, Brian D., Waters, Elizabeth R.

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