Cell type matching in single-cell RNA-sequencing data using FR-Match

por Zhang, Yun, Aevermann, Brian, Gala, Rohan, Scheuermann, Richard H.
Publicado 2022

Machine learning for cell type classification from single nucleus RNA sequencing data

por Le, Huy, Peng, Beverly, Uy, Janelle, Carrillo, Daniel, Zhang, Yun, Aevermann, Brian D., Scheuermann, Richard H.
Publicado 2022

The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness

por Abramson, Bradley W, Novotny, Mark, Hartwick, Nolan T, Colt, Kelly, Aevermann, Brian D, Scheuermann, Richard H, Michael, Todd P
Publicado 2021

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test

por Zhang, Yun, Aevermann, Brian D, Bakken, Trygve E, Miller, Jeremy A, Hodge, Rebecca D, Lein, Ed S, Scheuermann, Richard H
Publicado 2020

A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

por Aevermann, Brian, Zhang, Yun, Novotny, Mark, Keshk, Mohamed, Bakken, Trygve, Miller, Jeremy, Hodge, Rebecca, Lelieveldt, Boudewijn, Lein, Ed, Scheuermann, Richard H.
Publicado 2021

Cell type discovery using single-cell transcriptomics: implications for ontological representation

por 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
Publicado 2018

Cell type discovery and representation in the era of high-content single cell phenotyping

por 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.
Publicado 2017

Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

por 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.
Publicado 2023

Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response

por 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.
Publicado 2021

Author Correction: Brain Data Standards - A method for building data-driven cell-type ontologies

por 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
Publicado 2023

Brain Data Standards - A method for building data-driven cell-type ontologies

por 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
Publicado 2023

Influenza Research Database: An integrated bioinformatics resource for influenza virus research

por 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.
Publicado 2017

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

por Bakken, Trygve E., Hodge, Rebecca D., Miller, Jeremy A., Yao, Zizhen, Nguyen, Thuc Nghi, Aevermann, Brian, Barkan, Eliza, Bertagnolli, Darren, Casper, Tamara, Dee, Nick, Garren, Emma, Goldy, Jeff, Graybuck, Lucas T., Kroll, Matthew, Lasken, Roger S., Lathia, Kanan, Parry, Sheana, Rimorin, Christine, Scheuermann, Richard H., Schork, Nicholas J., Shehata, Soraya I., Tieu, Michael, Phillips, John W., Bernard, Amy, Smith, Kimberly A., Zeng, Hongkui, Lein, Ed S., Tasic, Bosiljka
Publicado 2018

Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons

por 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.
Publicado 2020

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type

por 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
Publicado 2018

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults

por Ben-Othman, Rym, Cai, Bing, Liu, Aaron C., Varankovich, Natallia, He, Daniel, Blimkie, Travis M., Lee, Amy H., Gill, Erin E., Novotny, Mark, Aevermann, Brian, Drissler, Sibyl, Shannon, Casey P., McCann, Sarah, Marty, Kim, Bjornson, Gordean, Edgar, Rachel D., Lin, David Tse Shen, Gladish, Nicole, Maclsaac, Julia, Amenyogbe, Nelly, Chan, Queenie, Llibre, Alba, Collin, Joyce, Landais, Elise, Le, Khoa, Reiss, Samantha M., Koff, Wayne C., Havenar-Daughton, Colin, Heran, Manraj, Sangha, Bippan, Walt, David, Krajden, Mel, Crotty, Shane, Sok, Devin, Briney, Bryan, Burton, Dennis R., Duffy, Darragh, Foster, Leonard J., Mohn, William W., Kobor, Michael S., Tebbutt, Scott J., Brinkman, Ryan R., Scheuermann, Richard H., Hancock, Robert E. W., Kollmann, Tobias R., Sadarangani, Manish
Publicado 2020

Conserved cell types with divergent features in human versus mouse cortex

por Hodge, Rebecca D, Bakken, Trygve E, Miller, Jeremy A, Smith, Kimberly A, Barkan, Eliza R, Graybuck, Lucas T, Close, Jennie L, Long, Brian, Johansen, Nelson, Penn, Osnat, Yao, Zizhen, Eggermont, Jeroen, Hollt, Thomas, Levi, Boaz P, Shehata, Soraya I, Aevermann, Brian, Beller, Allison, Bertagnolli, Darren, Brouner, Krissy, Casper, Tamara, Cobbs, Charles, Dalley, Rachel, Dee, Nick, Ding, Song-Lin, Ellenbogen, Richard G, Fong, Olivia, Garren, Emma, Goldy, Jeff, Gwinn, Ryder P, Hirschstein, Daniel, Keene, C Dirk, Keshk, Mohamed, Ko, Andrew L, Lathia, Kanan, Mahfouz, Ahmed, Maltzer, Zoe, McGraw, Medea, Nguyen, Thuc Nghi, Nyhus, Julie, Ojemann, Jeffrey G, Oldre, Aaron, Parry, Sheana, Reynolds, Shannon, Rimorin, Christine, Shapovalova, Nadiya V, Somasundaram, Saroja, Szafer, Aaron, Thomsen, Elliot R, Tieu, Michael, Quon, Gerald, Scheuermann, Richard H, Yuste, Rafael, Sunkin, Susan M, Lelieveldt, Boudewijn, Feng, David, Ng, Lydia, Bernard, Amy, Hawrylycz, Michael, Phillips, John W., Tasic, Bosiljka, Zeng, Hongkui, Jones, Allan R, Koch, Christof, Lein, Ed S
Publicado 2019

A comprehensive collection of systems biology data characterizing the host response to viral infection

por 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.
Publicado 2014

A guide to the BRAIN Initiative Cell Census Network data ecosystem

por Hawrylycz, Michael, Martone, Maryann E., Ascoli, Giorgio A., Bjaalie, Jan G., Dong, Hong-Wei, Ghosh, Satrajit S., Gillis, Jesse, Hertzano, Ronna, Haynor, David R., Hof, Patrick R., Kim, Yongsoo, Lein, Ed, Liu, Yufeng, Miller, Jeremy A., Mitra, Partha P., Mukamel, Eran, Ng, Lydia, Osumi-Sutherland, David, Peng, Hanchuan, Ray, Patrick L., Sanchez, Raymond, Regev, Aviv, Ropelewski, Alex, Scheuermann, Richard H., Tan, Shawn Zheng Kai, Thompson, Carol L., Tickle, Timothy, Tilgner, Hagen, Varghese, Merina, Wester, Brock, White, Owen, Zeng, Hongkui, Aevermann, Brian, Allemang, David, Ament, Seth, Athey, Thomas L., Baker, Cody, Baker, Katherine S., Baker, Pamela M., Bandrowski, Anita, Banerjee, Samik, Bishwakarma, Prajal, Carr, Ambrose, Chen, Min, Choudhury, Roni, Cool, Jonah, Creasy, Heather, D’Orazi, Florence, Degatano, Kylee, Dichter, Benjamin, Ding, Song-Lin, Dolbeare, Tim, Ecker, Joseph R., Fang, Rongxin, Fillion-Robin, Jean-Christophe, Fliss, Timothy P., Gee, James, Gillespie, Tom, Gouwens, Nathan, Zhang, Guo-Qiang, Halchenko, Yaroslav O., Harris, Nomi L., Herb, Brian R., Hintiryan, Houri, Hood, Gregory, Horvath, Sam, Huo, Bingxing, Jarecka, Dorota, Jiang, Shengdian, Khajouei, Farzaneh, Kiernan, Elizabeth A., Kir, Huseyin, Kruse, Lauren, Lee, Changkyu, Lelieveldt, Boudewijn, Li, Yang, Liu, Hanqing, Liu, Lijuan, Markuhar, Anup, Mathews, James, Mathews, Kaylee L., Mezias, Chris, Miller, Michael I., Mollenkopf, Tyler, Mufti, Shoaib, Mungall, Christopher J., Orvis, Joshua, Puchades, Maja A., Qu, Lei, Receveur, Joseph P., Ren, Bing, Sjoquist, Nathan, Staats, Brian, Tward, Daniel, van Velthoven, Cindy T. J., Wang, Quanxin, Xie, Fangming, Xu, Hua, Yao, Zizhen, Yun, Zhixi, Zhang, Yun Renee, Zheng, W. Jim, Zingg, Brian
Publicado 2023

Comparative cellular analysis of motor cortex in human, marmoset and mouse

por Bakken, Trygve E., Jorstad, Nikolas L., Hu, Qiwen, Lake, Blue B., Tian, Wei, Kalmbach, Brian E., Crow, Megan, Hodge, Rebecca D., Krienen, Fenna M., Sorensen, Staci A., Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian D., Aldridge, Andrew I., Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa G., Crichton, Kirsten, Daigle, Tanya L., Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas T., Herb, Brian R., Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang Eric, Liu, Christine S., Liu, Hanqing, Lucero, Jacinta D., Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy A., Moussa, Marmar, Nery, Joseph R., Nicovich, Philip R., Niu, Sheng-Yong, Orvis, Joshua, Osteen, Julia K., Owen, Scott, Palmer, Carter R., Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora M., Rimorin, Christine, Rivkin, Angeline, Romanow, William J., Sedeño-Cortés, Adriana E., Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna Marie, Zhang, Renee, Ament, Seth A., Behrens, M. Margarita, Bravo, Hector Corrada, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick R., Höllt, Thomas, Horwitz, Gregory D., Keene, C. Dirk, Kharchenko, Peter V., Ko, Andrew L., Lelieveldt, Boudewijn P., Luo, Chongyuan, Mukamel, Eran A., Pinto-Duarte, António, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard H., Smith, Kimberly, Spain, William J., White, Owen R., Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan Z., McCarroll, Steven A., Ting, Jonathan T., Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph R., Linnarsson, Sten, Lein, Ed S.
Publicado 2021