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Crow, Megan, Suresh, Hamsini, Lee, John, Gillis, Jesse (April 2022) Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. Nucleic Acids Research. ISSN 0305-1048
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 (October 2021) Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature, 598 (7879). pp. 111-119. ISSN 0028-0836
Yao, Zizhen, Liu, Hanqing, Xie, Fangming, Fischer, Stephan, Adkins, Ricky S, Aldridge, Andrew I, Ament, Seth A, Bartlett, Anna, Behrens, M Margarita, Van den Berge, Koen, Bertagnolli, Darren, de Bézieux, Hector Roux, Biancalani, Tommaso, Booeshaghi, A Sina, Bravo, Héctor Corrada, Casper, Tamara, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Crichton, Kirsten, Crow, Megan, Dee, Nick, Dougherty, Elizabeth L, Doyle, Wayne I, Dudoit, Sandrine, Fang, Rongxin, Felix, Victor, Fong, Olivia, Giglio, Michelle, Goldy, Jeff, Hawrylycz, Mike, Herb, Brian R, Hertzano, Ronna, Hou, Xiaomeng, Hu, Qiwen, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, Li, Yang Eric, Lucero, Jacinta D, Luo, Chongyuan, Mahurkar, Anup, McMillen, Delissa, Nadaf, Naeem M, Nery, Joseph R, Nguyen, Thuc Nghi, Niu, Sheng-Yong, Ntranos, Vasilis, Orvis, Joshua, Osteen, Julia K, Pham, Thanh, Pinto-Duarte, Antonio, Poirion, Olivier, Preissl, Sebastian, Purdom, Elizabeth, Rimorin, Christine, Risso, Davide, Rivkin, Angeline C, Smith, Kimberly, Street, Kelly, Sulc, Josef, Svensson, Valentine, Tieu, Michael, Torkelson, Amy, Tung, Herman, Vaishnav, Eeshit Dhaval, Vanderburg, Charles R, van Velthoven, Cindy, Wang, Xinxin, White, Owen R, Huang, Z Josh, Kharchenko, Peter V, Pachter, Lior, Ngai, John, Regev, Aviv, Tasic, Bosiljka, Welch, Joshua D, Gillis, Jesse, Macosko, Evan Z, Ren, Bing, Ecker, Joseph R, Zeng, Hongkui, Mukamel, Eran A (October 2021) A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature, 598 (7879). pp. 103-110. ISSN 0028-0836
BRAIN Initiative Cell Census Network (BICCN), (October 2021) A multimodal cell census and atlas of the mammalian primary motor cortex. Nature, 598 (7879). pp. 86-102. ISSN 0028-0836
Fischer, Stephan, Crow, Megan, Harris, Benjamin D, Gillis, Jesse (July 2021) Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. Nature Protocols. ISSN 1754-2189
Harris, Benjamin D, Crow, Megan, Fischer, Stephan, Gillis, Jesse (May 2021) Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. Cell Systems. ISSN 2405-4712
Xu, X., Crow, M., Rice, B. R., Li, F., Harris, B., Liu, L., Demesa-Arevalo, E., Lu, Z., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S. N., Yang, B., Sylvester, A. W., Gingeras, T. R., Schmitz, R. J., Ware, D., Lipka, A. E., Gillis, J., Jackson, D. (December 2020) Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell, S1534- (20). pp. 31021-31022. ISSN 1534-5807
Crow, Megan, Suresh, Hamsini, Lee, John, Gillis, Jesse (November 2020) Coexpression reveals conserved mechanisms of transcriptional cell identity. BioRxiv. (Unpublished)
BRAIN Initiative Cell Census Network (BICCN), , Adkins, Ricky, Aldridge, Andrew, Allen, Shona, Ament, Seth, An, Xu, Armand, Ethan, Ascoli, Giorgio, Bakken, Trygve, Bandrowski, Anita, Banerjee, Samik, Barkas, Nikolaos, Bartlett, Anna, Bateup, Helen, Behrens, Margarita, Berens, Philipp, Berg, Jim, Bernabucci, Matteo, Bernaerts, Yves, Bertagnolli, Darren, Biancalani, Tommaso, Boggeman, Lara, Booeshaghi, Sina, Bowman, Ian, Bravo, Héctor Corrada, Cadwell, Cathryn René, Callaway, Edward, Carlin, Benjamin, O'Connor, Carolyn, Carter, Robert, Casper, Tamara, Castanon, Rosa, Castro, Jesus Ramon, Chance, Rebecca, Chatterjee, Apaala, Chen, Huaming, Chun, Jerold, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Crichton, Kirsten, Crow, Megan, D'Orazi, Florence, Daigle, Tanya, Dalley, Rachel, Dee, Nick, Degatano, Kylee, Dichter, Benjamin, Diep, Dinh, Ding, Liya, Ding, Song-Lin, Dominguez, Bertha, Dong, Hong-Wei, Dong, Weixiu, Dougherty, Elizabeth, Dudoit, Sandrine, Ecker, Joseph, Eichhorn, Stephen, Fang, Rongxin, Felix, Victor, Feng, Guoping, Feng, Zhao, Fischer, Stephan, Fitzpatrick, Conor, Fong, Olivia, Foster, Nicholas, Galbavy, William, Gee, James, Ghosh, Satrajit, Giglio, Michelle, Gillespie, Thomas, Gillis, Jesse, Goldman, Melissa, Goldy, Jeff, Gong, Hui, Gou, Lin, Grauer, Michael, Halchenko, Yaroslav, Harris, Julie, Hartmanis, Leonard, Hatfield, Joshua, Hawrylycz, Mike, Helba, Brian, Herb, Brian, Hertzano, Ronna, Hintiryan, Houri, Hirokawa, Karla, Hockemeyer, Dirk, Hodge, Rebecca, Hood, Greg, Horwitz, Gregory, Hou, Xiaomeng, Hu, Lijuan, Hu, Qiwen, Huang, Josh, Huo, Bingxing, Ito-Cole, Tony, Jacobs, Matthew, Jia, Xueyan, Jiang, Shengdian, Jiang, Tao, Jiang, Xiaolong, Jin, Xin, Jorstad, Nikolas, Kalmbach, Brian, Kancherla, Jayaram, Keene, Dirk, Kelly, Kathleen, Khajouei, Farzaneh, Kharchenko, Peter, Kim, Gukhan, Ko, Andrew, Kobak, Dmitry, Konwar, Kishori, Kramer, Daniel, Krienen, Fenna, Kroll, Matthew, Kuang, Xiuli, Kuo, Hsien-Chi, Lake, Blue, Larsen, Rachael, Lathia, Kanan, Laturnus, Sophie, Lee, Angus, Lee, Cheng-Ta, Lee, Kuo-Fen, Lein, Ed, Lesnar, Phil, Li, Anan, Li, Xiangning, Li, Xu, Li, Yang Eric, Li, Yaoyao, Li, Yuanyuan, Lim, Byungkook, Linnarsson, Sten, Liu, Christine, Liu, Hanqing, Liu, Lijuan, Lucero, Jacinta, Luo, Chongyuan, Luo, Qingming, Macosko, Evan, Mahurkar, Anup, Martone, Maryann, Matho, Katherine, McCarroll, Steven, McCracken, Carrie, McMillen, Delissa, Miranda, Elanine, Mitra, Partha, Miyazaki, Paula Assakura, Mizrachi, Judith, Mok, Stephanie, Mukamel, Eran, Mulherkar, Shalaka, Nadaf, Naeem, Naeemi, Maitham, Narasimhan, Arun, Nery, Joseph, Ng, Lydia, Ngai, John, Nguyen, Thuc Nghi, Nickel, Lance, Nicovich, Philip, Niu, Sheng-Yong, Ntranos, Vasilis, Nunn, Michael, Olley, Dustin, Orvis, Joshua, Osteen, Julia, Osten, Pavel, Owen, Scott, Pachter, Lior, Palaniswamy, Ramesh, Palmer, Carter, Pang, Yan, Peng, Hanchuan, Pham, Thanh, Pinto-Duarte, Antonio, Plongthongkum, Nongluk, Poirion, Olivier, Preissl, Sebastian, Purdom, Elizabeth, Qu, Lei, Rashid, Mohammad, Reed, Nora, Regev, Aviv, Ren, Bing, Ren, Miao, Rimorin, Christine, Risso, Davide, Rivkin, Angeline, Muñoz-Castañeda, Rodrigo, Romanow, William, Ropelewski, Alexander, Roux de Bézieux, Hector, Ruan, Zongcai, Sandberg, Rickard, Savoia, Steven, Scala, Federico, Schor, Michael, Shen, Elise, Siletti, Kimberly, Smith, Jared, Smith, Kimberly, Somasundaram, Saroja, Song, Yuanyuan, Sorensen, Staci, Stafford, David, Street, Kelly, Sulc, Josef, Sunkin, Susan, Svensson, Valentine, Tan, Pengcheng, Tan, Zheng Huan, Tasic, Bosiljka, Thompson, Carol, Tian, Wei, Tickle, Timothy, Tieu, Michael, Ting, Jonathan, Tolias, Andreas Savas, Torkelson, Amy, Tung, Herman, Vaishnav, Eeshit Dhaval, Van den Berge, Koen, van Velthoven, Cindy TJ, Vanderburg, Charles, Veldman, Matthew, Vu, Minh, Wakeman, Wayne, Wang, Peng, Wang, Quanxin, Wang, Xinxin, Wang, Yimin, Wang, Yun, Welch, Joshua, White, Owen, Williams, Elora, Xie, Fangming, Xie, Peng, Xiong, Feng, Yang, William, Yanny, Anna Marie, Yao, Zizhen, Yin, Lulu, Yu, Yang, Yuan, Jing, Z, Hongkui (October 2020) A multimodal cell census and atlas of the mammalian primary motor cortex. BioRxiv. (Unpublished)
Lee, J., Shah, M., Ballouz, S., Crow, M., Gillis, J. (May 2020) CoCoCoNet: conserved and comparative co-expression across a diverse set of species. Nucleic Acids Research. ISSN 0305-1048
Lee, John, Shah, Manthan, Ballouz, Sara, Crow, Megan, Gillis, Jesse (April 2020) CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species. BioRxiv. (Unpublished)
Bakken, Trygve, Jorstad, Nikolas, Hu, Qiwen, Lake, Blue, Tian, Wei, Kalmbach, Brian, Crow, Megan, Hodge, Rebecca, Krienen, Fenna, Sorensen, Staci, Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian, Aldridge, Andrew, Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa, Crichton, Kirsten, Daigle, Tanya, Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas, Herb, Brian, Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang Eric, Liu, Christine, Liu, Hanqing, Lucero, Jacinta, Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy, Moussa, Marmar, Nery, Joseph, Nicovich, Philip, Orvis, Joshua, Osteen, Julia, Owen, Scott, Palmer, Carter, Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora, Rimorin, Christine, Rivkin, Angeline, Romanow, William, Sedeño-Cortés, Adriana, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna Marie, Zhang, Renee, Ament, Seth, Behrens, Margarita, Bravo, Hector Corrada, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick, Höllt, Thomas, Horwitz, Gregory, Keene, Dirk, Kharchenko, Peter, Ko, Andrew, Lelieveldt, Boudewijn, Luo, Chongyuan, Mukamel, Eran, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard, Smith, Kimberly, Spain, William, White, Owen, Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan, McCarroll, Steven, Ting, Jonathan, Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph, Linnarsson, Sten, Lein, Ed (April 2020) Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse. BioRxiv. (Unpublished)
Crow, M., Denk, F. (July 2019) RNA-seq data in pain research-an illustrated guide. Pain, 160 (7). pp. 1502-1504. ISSN 0304-3959
Crow, M., Gillis, J. (June 2019) Single cell RNA-sequencing: replicability of cell types. Current Opinion in Neurobiology, 56. pp. 69-77. ISSN 09594388 (ISSN)
Crow, M., Lim, N., Ballouz, S., Pavlidis, P., Gillis, J. (March 2019) Predictability of human differential gene expression. Proc Natl Acad Sci U S A. ISSN 0027-8424
Crow, M., Gillis, J. (August 2018) Co-expression in Single-Cell Analysis: Saving Grace or Original Sin? Trends Genet, 34 (11). pp. 823-831. ISSN 0168-9525 (Print)0168-9525
Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (February 2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun, 9 (1). p. 884. ISSN 2041-1723
Kalish, B. T., Cheadle, L., Hrvatin, S., Nagy, M. A., Rivera, S., Crow, M., Gillis, J., Kirchner, R., Greenberg, M. E. (January 2018) Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement. Proc Natl Acad Sci U S A, 115 (5). E1051-E1060. ISSN 0027-8424
Crow, M., Paul, A., Huang, J., Gillis, J. (October 2017) USING SINGLE CELL RNA-SEQ TO EXPLORE CELL-TYPE SPECIFIC CO-EXPRESSION OF NEUROPSYCHIATRIC DISEASE GENES. European Neuropsychopharmacology, 27. abstract S350-S350. ISSN 0924-977X
Paul, A., Crow, M., Raudales, R., He, M., Gillis, J., Huang, Z. J. (2017) Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity. Cell.
Zai, G., Alberry, B., Arloth, J., Banlaki, Z., Bares, C., Boot, E., Camilo, C., Chadha, K., Chen, Q., Cole, C. B., Cost, K. T., Crow, M., Ekpor, I., Fischer, S. B., Flatau, L., Gagliano, S., Kirli, U., Kukshal, P., Labrie, V., Lang, M., Lett, T. A., Maffioletti, E., Maier, R., Mihaljevic, M., Mittal, K., Monson, E. T., O'Brien, N. L., Ostergaard, S. D., Ovenden, E., Patel, S., Peterson, R. E., Pouget, J. G., Rovaris, D. L., Seaman, L., Shankarappa, B., Tsetsos, F., Vereczkei, A., Wang, C., Xulu, K., Yuen, R. K., Zhao, J., Zai, C. C., Kennedy, J. L. (December 2016) Rapporteur summaries of plenary, symposia, and oral sessions from the XXIIIrd World Congress of Psychiatric Genetics Meeting in Toronto, Canada, 16-20 October 2015. Psychiatr Genet, 26 (6). pp. 229-257. ISSN 1473-5873 (Electronic)0955-8829 (Linking)
Zai, G., Alberry, B., Arloth, J., Banlaki, Z., Bares, C., Boot, E., Camilo, C., Chadha, K., Chen, Q., Cole, C. B., Cost, K. T., Crow, M., Ekpor, I., Fischer, S. B., Flatau, L., Gagliano, S., Kirli, U., Kukshal, P., Labrie, V., Lang, M., Lett, T. A., Maffioletti, E., Maier, R., Mihaljevic, M., Mittal, K., Monson, E. T., O'Brien, N. L., Ostergaard, S. D., Ovenden, E., Patel, S., Peterson, R. E., Pouget, J. G., Rovaris, D. L., Seaman, L., Shankarappa, B., Tsetsos, F., Vereczkei, A., Wang, C., Xulu, K., Yuen, R. K., Zhao, J., Zai, C. C., Kennedy, J. L. (September 2016) Rapporteur summaries of plenary, symposia, and oral sessions from the XXIIIrd World Congress of Psychiatric Genetics Meeting in Toronto, Canada, 16-20 October 2015. Psychiatr Genet. ISSN 1473-5873 (Electronic)0955-8829 (Linking)
Denk, Franziska, Crow, Megan, Didangelos, Athanasios, Lopes, Douglas M, McMahon, Stephen B (May 2016) Persistent Alterations in Microglial Enhancers in a Model of Chronic Pain. Cell Reports, 15 (8). pp. 1771-81. ISSN 2211-1247
Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (May 2016) Exploiting single-cell expression to characterize co-expression replicability. Genome Biol, 17 (1). p. 101. ISSN 1474-760X (Electronic)1474-7596 (Linking) (Public Dataset)
