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1. SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain

Author

Bennett, Corbett, Ouellette, Ben, Ramirez, Tamina K., Cahoon, Alex, Cabasco, Hannah, Browning, Yoni, Lakunina, Anna, Lynch, Galen F., McBride, Ethan G., Belski, Hannah, Gillis, Ryan, Grasso, Conor, Howard, Robert, Johnson, Tye, Loeffler, Henry, Smith, Heston, Sullivan, David, Williford, Allison, Caldejon, Shiella, Durand, Severine, Gale, Samuel, Guthrie, Alan, Ha, Vivian, Han, Warren, Hardcastle, Ben, Mochizuki, Chris, Sridhar, Arjun, Suarez, Lucas, Swapp, Jackie, Wilkes, Joshua, Siegle, Joshua H., Farrell, Colin, Groblewski, Peter A., and Olsen, Shawn R.

Published
2024
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2. Responses of pyramidal cell somata and apical dendrites in mouse visual cortex over multiple days

Author

Gillon, Colleen J., Lecoq, Jérôme A., Pina, Jason E., Ahmed, Ruweida, Billeh, Yazan N., Caldejon, Shiella, Groblewski, Peter, Henley, Timothy M., Kato, India, Lee, Eric, Luviano, Jennifer, Mace, Kyla, Nayan, Chelsea, Nguyen, Thuyanh V., North, Kat, Perkins, Jed, Seid, Sam, Valley, Matthew T., Williford, Ali, Bengio, Yoshua, Lillicrap, Timothy P., Zylberberg, Joel, and Richards, Blake A.

Published
2023
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3. A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex

Author

Yao, Shenqin, Wang, Quanxin, Hirokawa, Karla E., Ouellette, Benjamin, Ahmed, Ruweida, Bomben, Jasmin, Brouner, Krissy, Casal, Linzy, Caldejon, Shiella, Cho, Andy, Dotson, Nadezhda I., Daigle, Tanya L., Egdorf, Tom, Enstrom, Rachel, Gary, Amanda, Gelfand, Emily, Gorham, Melissa, Griffin, Fiona, Gu, Hong, Hancock, Nicole, Howard, Robert, Kuan, Leonard, Lambert, Sophie, Lee, Eric Kenji, Luviano, Jennifer, Mace, Kyla, Maxwell, Michelle, Mortrud, Marty T., Naeemi, Maitham, Nayan, Chelsea, Ngo, Nhan-Kiet, Nguyen, Thuyanh, North, Kat, Ransford, Shea, Ruiz, Augustin, Seid, Sam, Swapp, Jackie, Taormina, Michael J., Wakeman, Wayne, Zhou, Thomas, Nicovich, Philip R., Williford, Ali, Potekhina, Lydia, McGraw, Medea, Ng, Lydia, Groblewski, Peter A., Tasic, Bosiljka, Mihalas, Stefan, Harris, Julie A., Cetin, Ali, and Zeng, Hongkui

Published
2023
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4. Survey of spiking in the mouse visual system reveals functional hierarchy

Author

Siegle, Joshua H., Jia, Xiaoxuan, Durand, Séverine, Gale, Sam, Bennett, Corbett, Graddis, Nile, Heller, Greggory, Ramirez, Tamina K., Choi, Hannah, Luviano, Jennifer A., Groblewski, Peter A., Ahmed, Ruweida, Arkhipov, Anton, Bernard, Amy, Billeh, Yazan N., Brown, Dillan, Buice, Michael A., Cain, Nicolas, Caldejon, Shiella, Casal, Linzy, Cho, Andrew, Chvilicek, Maggie, Cox, Timothy C., Dai, Kael, Denman, Daniel J., de Vries, Saskia E. J., Dietzman, Roald, Esposito, Luke, Farrell, Colin, Feng, David, Galbraith, John, Garrett, Marina, Gelfand, Emily C., Hancock, Nicole, Harris, Julie A., Howard, Robert, Hu, Brian, Hytnen, Ross, Iyer, Ramakrishnan, Jessett, Erika, Johnson, Katelyn, Kato, India, Kiggins, Justin, Lambert, Sophie, Lecoq, Jerome, Ledochowitsch, Peter, Lee, Jung Hoon, Leon, Arielle, Li, Yang, Liang, Elizabeth, Long, Fuhui, Mace, Kyla, Melchior, Jose, Millman, Daniel, Mollenkopf, Tyler, Nayan, Chelsea, Ng, Lydia, Ngo, Kiet, Nguyen, Thuyahn, Nicovich, Philip R., North, Kat, Ocker, Gabriel Koch, Ollerenshaw, Doug, Oliver, Michael, Pachitariu, Marius, Perkins, Jed, Reding, Melissa, Reid, David, Robertson, Miranda, Ronellenfitch, Kara, Seid, Sam, Slaughterbeck, Cliff, Stoecklin, Michelle, Sullivan, David, Sutton, Ben, Swapp, Jackie, Thompson, Carol, Turner, Kristen, Wakeman, Wayne, Whitesell, Jennifer D., Williams, Derric, Williford, Ali, Young, Rob, Zeng, Hongkui, Naylor, Sarah, Phillips, John W., Reid, R. Clay, Mihalas, Stefan, Olsen, Shawn R., and Koch, Christof

Published
2021
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5. A comprehensive transcriptional map of primate brain development.

Author

Bakken, Trygve E, Miller, Jeremy A, Ding, Song-Lin, Sunkin, Susan M, Smith, Kimberly A, Ng, Lydia, Szafer, Aaron, Dalley, Rachel A, Royall, Joshua J, Lemon, Tracy, Shapouri, Sheila, Aiona, Kaylynn, Arnold, James, Bennett, Jeffrey L, Bertagnolli, Darren, Bickley, Kristopher, Boe, Andrew, Brouner, Krissy, Butler, Stephanie, Byrnes, Emi, Caldejon, Shiella, Carey, Anita, Cate, Shelby, Chapin, Mike, Chen, Jefferey, Dee, Nick, Desta, Tsega, Dolbeare, Tim A, Dotson, Nadia, Ebbert, Amanda, Fulfs, Erich, Gee, Garrett, Gilbert, Terri L, Goldy, Jeff, Gourley, Lindsey, Gregor, Ben, Gu, Guangyu, Hall, Jon, Haradon, Zeb, Haynor, David R, Hejazinia, Nika, Hoerder-Suabedissen, Anna, Howard, Robert, Jochim, Jay, Kinnunen, Marty, Kriedberg, Ali, Kuan, Chihchau L, Lau, Christopher, Lee, Chang-Kyu, Lee, Felix, Luong, Lon, Mastan, Naveed, May, Ryan, Melchor, Jose, Mosqueda, Nerick, Mott, Erika, Ngo, Kiet, Nyhus, Julie, Oldre, Aaron, Olson, Eric, Parente, Jody, Parker, Patrick D, Parry, Sheana, Pendergraft, Julie, Potekhina, Lydia, Reding, Melissa, Riley, Zackery L, Roberts, Tyson, Rogers, Brandon, Roll, Kate, Rosen, David, Sandman, David, Sarreal, Melaine, Shapovalova, Nadiya, Shi, Shu, Sjoquist, Nathan, Sodt, Andy J, Townsend, Robbie, Velasquez, Lissette, Wagley, Udi, Wakeman, Wayne B, White, Cassandra, Bennett, Crissa, Wu, Jennifer, Young, Rob, Youngstrom, Brian L, Wohnoutka, Paul, Gibbs, Richard A, Rogers, Jeffrey, Hohmann, John G, Hawrylycz, Michael J, Hevner, Robert F, Molnár, Zoltán, Phillips, John W, Dang, Chinh, Jones, Allan R, Amaral, David G, Bernard, Amy, and Lein, Ed S

Subjects
Brain, Neocortex, Animals, Macaca mulatta, Humans, Microcephaly, Risk Factors, Schizophrenia, Cell Adhesion, Species Specificity, Transcription, Genetic, Conserved Sequence, Aging, Female, Male, Neurogenesis, Intellectual Disability, Transcriptome, Spatio-Temporal Analysis, Autism Spectrum Disorder, Neurodevelopmental Disorders, Transcription, Genetic, General Science & Technology
Abstract

The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.

Published
2016

6. A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

Author

de Vries, Saskia E. J., Lecoq, Jerome A., Buice, Michael A., Groblewski, Peter A., Ocker, Gabriel K., Oliver, Michael, Feng, David, Cain, Nicholas, Ledochowitsch, Peter, Millman, Daniel, Roll, Kate, Garrett, Marina, Keenan, Tom, Kuan, Leonard, Mihalas, Stefan, Olsen, Shawn, Thompson, Carol, Wakeman, Wayne, Waters, Jack, Williams, Derric, Barber, Chris, Berbesque, Nathan, Blanchard, Brandon, Bowles, Nicholas, Caldejon, Shiella D., Casal, Linzy, Cho, Andrew, Cross, Sissy, Dang, Chinh, Dolbeare, Tim, Edwards, Melise, Galbraith, John, Gaudreault, Nathalie, Gilbert, Terri L., Griffin, Fiona, Hargrave, Perry, Howard, Robert, Huang, Lawrence, Jewell, Sean, Keller, Nika, Knoblich, Ulf, Larkin, Josh D., Larsen, Rachael, Lau, Chris, Lee, Eric, Lee, Felix, Leon, Arielle, Li, Lu, Long, Fuhui, Luviano, Jennifer, Mace, Kyla, Nguyen, Thuyanh, Perkins, Jed, Robertson, Miranda, Seid, Sam, Shea-Brown, Eric, Shi, Jianghong, Sjoquist, Nathan, Slaughterbeck, Cliff, Sullivan, David, Valenza, Ryan, White, Casey, Williford, Ali, Witten, Daniela M., Zhuang, Jun, Zeng, Hongkui, Farrell, Colin, Ng, Lydia, Bernard, Amy, Phillips, John W., Reid, R. Clay, and Koch, Christof

Published
2020
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7. Transcriptional landscape of the prenatal human brain.

Author

Miller, Jeremy A, Ding, Song-Lin, Sunkin, Susan M, Smith, Kimberly A, Ng, Lydia, Szafer, Aaron, Ebbert, Amanda, Riley, Zackery L, Royall, Joshua J, Aiona, Kaylynn, Arnold, James M, Bennet, Crissa, Bertagnolli, Darren, Brouner, Krissy, Butler, Stephanie, Caldejon, Shiella, Carey, Anita, Cuhaciyan, Christine, Dalley, Rachel A, Dee, Nick, Dolbeare, Tim A, Facer, Benjamin AC, Feng, David, Fliss, Tim P, Gee, Garrett, Goldy, Jeff, Gourley, Lindsey, Gregor, Benjamin W, Gu, Guangyu, Howard, Robert E, Jochim, Jayson M, Kuan, Chihchau L, Lau, Christopher, Lee, Chang-Kyu, Lee, Felix, Lemon, Tracy A, Lesnar, Phil, McMurray, Bergen, Mastan, Naveed, Mosqueda, Nerick, Naluai-Cecchini, Theresa, Ngo, Nhan-Kiet, Nyhus, Julie, Oldre, Aaron, Olson, Eric, Parente, Jody, Parker, Patrick D, Parry, Sheana E, Stevens, Allison, Pletikos, Mihovil, Reding, Melissa, Roll, Kate, Sandman, David, Sarreal, Melaine, Shapouri, Sheila, Shapovalova, Nadiya V, Shen, Elaine H, Sjoquist, Nathan, Slaughterbeck, Clifford R, Smith, Michael, Sodt, Andy J, Williams, Derric, Zöllei, Lilla, Fischl, Bruce, Gerstein, Mark B, Geschwind, Daniel H, Glass, Ian A, Hawrylycz, Michael J, Hevner, Robert F, Huang, Hao, Jones, Allan R, Knowles, James A, Levitt, Pat, Phillips, John W, Sestan, Nenad, Wohnoutka, Paul, Dang, Chinh, Bernard, Amy, Hohmann, John G, and Lein, Ed S

Subjects
Brain, Neocortex, Fetus, Animals, Humans, Mice, Anatomy, Artistic, Species Specificity, Gene Expression Regulation, Developmental, Conserved Sequence, Gene Regulatory Networks, Atlases as Topic, Transcriptome, Anatomy, Artistic, Gene Expression Regulation, Developmental, General Science & Technology
Abstract

The anatomical and functional architecture of the human brain is mainly determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of the mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and post-mitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and outer subventricular zones even though the outer zone is expanded in humans. Both germinal and post-mitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in the frontal lobe. Finally, many neurodevelopmental disorder and human-evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

Published
2014

8. Responses to pattern-violating visual stimuli evolve differently over days in somata and distal apical dendrites

Author

Gillon, Colleen J., primary, Pina, Jason E., additional, Lecoq, Jérôme, additional, Ahmed, Ruweida, additional, Billeh, Yazan N., additional, Caldejon, Shiella, additional, Groblewski, Peter A., additional, Henley, Timothy M., additional, Kato, India, additional, Lee, Eric, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V., additional, North, Kat, additional, Perkins, Jed, additional, Seid, Sam, additional, Valley, Matthew T., additional, Williford, Ali, additional, Bengio, Yoshua, additional, Lillicrap, Timothy P., additional, Richards, Blake A., additional, and Zylberberg, Joel, additional

Published
2023
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9. SHIELD: Skull-shaped hemispheric implants enabling large-scale-electrophysiology datasets in the mouse brain

Author

Bennett, Corbett, primary, Ouellette, Ben, additional, Ramirez, Tamina K, additional, Cahoon, Alex, additional, Cabasco, Hannah, additional, Belski, Hannah, additional, Gillis, Ryan, additional, Grasso, Conor, additional, Howard, Robert, additional, Johnson, Tye, additional, Loeffler, Henry, additional, Smith, Heston, additional, Sullivan, David, additional, Williford, Allison, additional, Caldejon, Shiella, additional, Durand, Severine, additional, Gale, Samuel D, additional, Guthrie, Alan, additional, Ha, Vivian, additional, Han, Warren, additional, Hardcastle, Ben, additional, McBride, Ethan, additional, Mochizuki, Chris, additional, Sridhar, Arjun, additional, Suarez, Lucas, additional, Swapp, Jackie, additional, Wilkes, Josh, additional, Farrell, Colin, additional, Groblewski, Peter, additional, and Olsen, Shawn, additional

Published
2023
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10. An anatomic transcriptional atlas of human glioblastoma

Author

Puchalski, Ralph B., Shah, Nameeta, Miller, Jeremy, Dalley, Rachel, Nomura, Steve R., Yoon, Jae-Guen, Smith, Kimberly A., Lankerovich, Michael, Bertagnolli, Darren, Bickley, Kris, Boe, Andrew F., Brouner, Krissy, Butler, Stephanie, Caldejon, Shiella, Chapin, Mike, Datta, Suvro, Dee, Nick, Desta, Tsega, Dolbeare, Tim, Dotson, Nadezhda, Ebbert, Amanda, Feng, David, Feng, Xu, Fisher, Michael, Gee, Garrett, Goldy, Jeff, Gourley, Lindsey, Gregor, Benjamin W., Gu, Guangyu, Hejazinia, Nika, Hohmann, John, Hothi, Parvinder, Howard, Robert, Joines, Kevin, Kriedberg, Ali, Kuan, Leonard, Lau, Chris, Lee, Felix, Lee, Hwahyung, Lemon, Tracy, Long, Fuhui, Mastan, Naveed, Mott, Erika, Murthy, Chantal, Ngo, Kiet, Olson, Eric, Reding, Melissa, Riley, Zack, Rosen, David, Sandman, David, Shapovalova, Nadiya, Slaughterbeck, Clifford R., Sodt, Andrew, Stockdale, Graham, Szafer, Aaron, Wakeman, Wayne, Wohnoutka, Paul E., White, Steven J., Marsh, Don, Rostomily, Robert C., Ng, Lydia, Dang, Chinh, Jones, Allan, Keogh, Bart, Gittleman, Haley R., Barnholtz-Sloan, Jill S., Cimino, Patrick J., Uppin, Megha S., Keene, C. Dirk, Farrokhi, Farrokh R., Lathia, Justin D., Berens, Michael E., Iavarone, Antonio, Bernard, Amy, Lein, Ed, Phillips, John W., Rostad, Steven W., Cobbs, Charles, Hawrylycz, Michael J., and Foltz, Greg D.

Published
2018

11. Hierarchical organization of cortical and thalamic connectivity

Author

Harris, Julie A., Mihalas, Stefan, Hirokawa, Karla E., Whitesell, Jennifer D., Choi, Hannah, Bernard, Amy, Bohn, Phillip, Caldejon, Shiella, Casal, Linzy, Cho, Andrew, Feiner, Aaron, Feng, David, Gaudreault, Nathalie, Gerfen, Charles R., Graddis, Nile, Groblewski, Peter A., Henry, Alex M., Ho, Anh, Howard, Robert, Knox, Joseph E., Kuan, Leonard, Kuang, Xiuli, Lecoq, Jerome, Lesnar, Phil, Li, Yaoyao, Luviano, Jennifer, McConoughey, Stephen, Mortrud, Marty T., Naeemi, Maitham, Ng, Lydia, Oh, Seung Wook, Ouellette, Benjamin, Shen, Elise, Sorensen, Staci A., Wakeman, Wayne, Wang, Quanxin, Wang, Yun, Williford, Ali, Phillips, John W., Jones, Allan R., Koch, Christof, and Zeng, Hongkui

Published
2019
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12. Classification of electrophysiological and morphological neuron types in the mouse visual cortex

Author

Gouwens, Nathan W., Sorensen, Staci A., Berg, Jim, Lee, Changkyu, Jarsky, Tim, Ting, Jonathan, Sunkin, Susan M., Feng, David, Anastassiou, Costas A., Barkan, Eliza, Bickley, Kris, Blesie, Nicole, Braun, Thomas, Brouner, Krissy, Budzillo, Agata, Caldejon, Shiella, Casper, Tamara, Castelli, Dan, Chong, Peter, Crichton, Kirsten, Cuhaciyan, Christine, Daigle, Tanya L., Dalley, Rachel, Dee, Nick, Desta, Tsega, Ding, Song-Lin, Dingman, Samuel, Doperalski, Alyse, Dotson, Nadezhda, Egdorf, Tom, Fisher, Michael, de Frates, Rebecca A., Garren, Emma, Garwood, Marissa, Gary, Amanda, Gaudreault, Nathalie, Godfrey, Keith, Gorham, Melissa, Gu, Hong, Habel, Caroline, Hadley, Kristen, Harrington, James, Harris, Julie A., Henry, Alex, Hill, DiJon, Josephsen, Sam, Kebede, Sara, Kim, Lisa, Kroll, Matthew, Lee, Brian, Lemon, Tracy, Link, Katherine E., Liu, Xiaoxiao, Long, Brian, Mann, Rusty, McGraw, Medea, Mihalas, Stefan, Mukora, Alice, Murphy, Gabe J., Ng, Lindsay, Ngo, Kiet, Nguyen, Thuc Nghi, Nicovich, Philip R., Oldre, Aaron, Park, Daniel, Parry, Sheana, Perkins, Jed, Potekhina, Lydia, Reid, David, Robertson, Miranda, Sandman, David, Schroedter, Martin, Slaughterbeck, Cliff, Soler-Llavina, Gilberto, Sulc, Josef, Szafer, Aaron, Tasic, Bosiljka, Taskin, Naz, Teeter, Corinne, Thatra, Nivretta, Tung, Herman, Wakeman, Wayne, Williams, Grace, Young, Rob, Zhou, Zhi, Farrell, Colin, Peng, Hanchuan, Hawrylycz, Michael J., Lein, Ed, Ng, Lydia, Arkhipov, Anton, Bernard, Amy, Phillips, John W., Zeng, Hongkui, and Koch, Christof

Published
2019
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13. Responses to Pattern-Violating Visual Stimuli Evolve Differently Over Days in Somata and Distal Apical Dendrites.

Author

Gillon, Colleen J., Pina, Jason E., Lecoq, Jérôme A., Ahmed, Ruweida, Billeh, Yazan N., Caldejon, Shiella, Groblewski, Peter, Henley, Timothy M., Kato, India, Lee, Eric, Luviano, Jennifer, Mace, Kyla, Nayan, Chelsea, Nguyen, Thuyanh V., North, Kat, Perkins, Jed, Seid, Sam, Valley, Matthew T., Williford, Ali, and Bengio, Yoshua

Subjects
VISUAL perception, PYRAMIDAL neurons, VISUAL cortex, NEOCORTEX, NEURONS
Abstract

Scientists have long conjectured that the neocortex learns patterns in sensory data to generate top-down predictions of upcoming stimuli. In line with this conjecture, different responses to pattern-matching vs pattern-violating visual stimuli have been observed in both spiking and somatic calcium imaging data. However, it remains unknown whether these pattern-violation signals are different between the distal apical dendrites, which are heavily targeted by top-down signals, and the somata, where bottom-up information is primarily integrated. Furthermore, it is unknown how responses to pattern-violating stimuli evolve over time as an animal gains more experience with them. Here, we address these unanswered questions by analyzing responses of individual somata and dendritic branches of layer 2/3 and layer 5 pyramidal neurons tracked over multiple days in primary visual cortex of awake, behaving female and male mice. We use sequences of Gabor patches with patterns in their orientations to create pattern-matching and pattern-violating stimuli, and two-photon calcium imaging to record neuronal responses. Many neurons in both layers show large differences between their responses to pattern-matching and pattern-violating stimuli. Interestingly, these responses evolve in opposite directions in the somata and distal apical dendrites, with somata becoming less sensitive to pattern-violating stimuli and distal apical dendrites more sensitive. These differences between the somata and distal apical dendrites may be important for hierarchical computation of sensory predictions and learning, since these two compartments tend to receive bottom-up and top-down information, respectively. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Recurrent pattern completion drives the neocortical representation of sensory inference

Author

Shin, Hyeyoung, primary, Ogando, Mora B., additional, Abdeladim, Lamiae, additional, Durand, Severine, additional, Belski, Hannah, additional, Cabasco, Hannah, additional, Loefler, Henry, additional, Bawany, Ahad, additional, Hardcastle, Ben, additional, Wilkes, Josh, additional, Nguyen, Katrina, additional, Suarez, Lucas, additional, Johnson, Tye, additional, Han, Warren, additional, Ouellette, Ben, additional, Grasso, Connor, additional, Swapp, Jackie, additional, Ha, Vivian, additional, Young, Ahrial, additional, Caldejon, Shiella, additional, Williford, Ali, additional, Groblewski, Peter, additional, Olsen, Shawn, additional, Kiselycznyk, Carly, additional, Lecoq, Jerome, additional, and Adesnik, Hillel, additional

Published
2023
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15. Differential encoding of temporal context and expectation under representational drift across hierarchically connected areas

Author

Wyrick, David G, primary, Cain, Nicholas, additional, Larsen, Rylan S., additional, Lecoq, Jérôme, additional, Valley, Matthew, additional, Ahmed, Ruweida, additional, Bowlus, Jessica, additional, Boyer, Gabriella, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Chvilicek, Maggie, additional, DePartee, Maxwell, additional, Groblewski, Peter A, additional, Huang, Cindy, additional, Johnson, Katelyn, additional, Kato, India, additional, Larkin, Josh, additional, Lee, Eric, additional, Liang, Elizabeth, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nayan, Chelsea, additional, Nguyen, Thuyanhn, additional, Reding, Melissa, additional, Seid, Sam, additional, Sevigny, Joshua, additional, Stoecklin, Michelle, additional, Williford, Ali, additional, Choi, Hannah, additional, Garrett, Marina, additional, and Mazzucato, Luca, additional

Published
2023
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16. Stimulus novelty uncovers coding diversity in visual cortical circuits

Author

Garrett, Marina, primary, Groblewski, Peter, additional, Piet, Alex, additional, Ollerenshaw, Doug, additional, Najafi, Farzaneh, additional, Yavorska, Iryna, additional, Amster, Adam, additional, Bennett, Corbett, additional, Buice, Michael, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, D’Orazi, Florence, additional, Daniel, Scott, additional, de Vries, Saskia EJ, additional, Kapner, Daniel, additional, Kiggins, Justin, additional, Lecoq, Jerome, additional, Ledochowitsch, Peter, additional, Manavi, Sahar, additional, Mei, Nicholas, additional, Morrison, Christopher B., additional, Naylor, Sarah, additional, Orlova, Natalia, additional, Perkins, Jed, additional, Ponvert, Nick, additional, Roll, Clark, additional, Seid, Sam, additional, Williams, Derric, additional, Williford, Allison, additional, Ahmed, Ruweida, additional, Amine, Daniel, additional, Billeh, Yazan, additional, Bowman, Chris, additional, Cain, Nicholas, additional, Cho, Andrew, additional, Dawe, Tim, additional, Departee, Max, additional, Desoto, Marie, additional, Feng, David, additional, Gale, Sam, additional, Gelfand, Emily, additional, Gradis, Nile, additional, Grasso, Conor, additional, Hancock, Nicole, additional, Hu, Brian, additional, Hytnen, Ross, additional, Jia, Xiaoxuan, additional, Johnson, Tye, additional, Kato, India, additional, Kivikas, Sara, additional, Kuan, Leonard, additional, L’Heureux, Quinn, additional, Lambert, Sophie, additional, Leon, Arielle, additional, Liang, Elizabeth, additional, Long, Fuhui, additional, Mace, Kyla, additional, Magrans de Abril, Ildefons, additional, Mochizuki, Chris, additional, Nayan, Chelsea, additional, North, Katherine, additional, Ng, Lydia, additional, Ocker, Gabriel Koch, additional, Oliver, Michael, additional, Rhoads, Paul, additional, Ronellenfitch, Kara, additional, Schelonka, Kathryn, additional, Sevigny, Josh, additional, Sullivan, David, additional, Sutton, Ben, additional, Swapp, Jackie, additional, Nguyen, Thuyanh K, additional, Waughman, Xana, additional, Wilkes, Joshua, additional, Wang, Michael, additional, Farrell, Colin, additional, Wakeman, Wayne, additional, Zeng, Hongkui, additional, Phillips, John, additional, Mihalas, Stefan, additional, Arkhipov, Anton, additional, Koch, Christof, additional, and Olsen, Shawn R, additional

Published
2023
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17. A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex

Author

Yao, Shenqin, primary, Wang, Quanxin, additional, Hirokawa, Karla E., additional, Ouellette, Benjamin, additional, Ahmed, Ruweida, additional, Bomben, Jasmin, additional, Brouner, Krissy, additional, Casal, Linzy, additional, Caldejon, Shiella, additional, Cho, Andy, additional, Dotson, Nadezhda I., additional, Daigle, Tanya L., additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Gary, Amanda, additional, Gelfand, Emily, additional, Gorham, Melissa, additional, Griffin, Fiona, additional, Gu, Hong, additional, Hancock, Nicole, additional, Howard, Robert, additional, Kuan, Leonard, additional, Lambert, Sophie, additional, Lee, Eric Kenji, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Maxwell, Michelle, additional, Mortrud, Marty T., additional, Naeemi, Maitham, additional, Nayan, Chelsea, additional, Ngo, Nhan-Kiet, additional, Nguyen, Thuyanh, additional, North, Kat, additional, Ransford, Shea, additional, Ruiz, Augustin, additional, Seid, Sam, additional, Swapp, Jackie, additional, Taormina, Michael J., additional, Wakeman, Wayne, additional, Zhou, Thomas, additional, Nicovich, Philip R., additional, Williford, Ali, additional, Potekhina, Lydia, additional, McGraw, Medea, additional, Ng, Lydia, additional, Groblewski, Peter A., additional, Tasic, Bosiljka, additional, Mihalas, Stefan, additional, Harris, Julie A., additional, Cetin, Ali, additional, and Zeng, Hongkui, additional

Published
2022
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18. A Standardized Nonvisual Behavioral Event Is Broadcasted Homogeneously across Cortical Visual Areas without Modulating Visual Responses

Author

Ramadan, Mahdi, primary, Lee, Eric Kenji, additional, de Vries, Saskia, additional, Caldejon, Shiella, additional, Kato, India, additional, Roll, Kate, additional, Griffin, Fiona, additional, Nguyen, Thuyanh V., additional, Larkin, Josh, additional, Rhoads, Paul, additional, Mace, Kyla, additional, Kriedberg, Ali, additional, Howard, Robert, additional, Berbesque, Nathan, additional, and Lecoq, Jérôme, additional

Published
2022
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19. Comprehensive cellular‐resolution atlas of the adult human brain

Author

Ding, Song‐Lin, Royall, Joshua J., Sunkin, Susan M., Ng, Lydia, Facer, Benjamin A.C., Lesnar, Phil, Guillozet‐Bongaarts, Angie, McMurray, Bergen, Szafer, Aaron, Dolbeare, Tim A., Stevens, Allison, Tirrell, Lee, Benner, Thomas, Caldejon, Shiella, Dalley, Rachel A., Dee, Nick, Lau, Christopher, Nyhus, Julie, Reding, Melissa, Riley, Zackery L., Sandman, David, Shen, Elaine, van der Kouwe, Andre, Varjabedian, Ani, Write, Michelle, Zollei, Lilla, Dang, Chinh, Knowles, James A., Koch, Christof, Phillips, John W., Sestan, Nenad, Wohnoutka, Paul, Zielke, H. Ronald, Hohmann, John G., Jones, Allan R., Bernard, Amy, Hawrylycz, Michael J., Hof, Patrick R., Fischl, Bruce, and LeinReference, Ed S.

Published
2017
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20. Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex

Author

Mayner, William G. P., primary, Marshall, William, additional, Billeh, Yazan N., additional, Gandhi, Saurabh R., additional, Caldejon, Shiella, additional, Cho, Andrew, additional, Griffin, Fiona, additional, Hancock, Nicole, additional, Lambert, Sophie, additional, Lee, Eric K., additional, Luviano, Jennifer A., additional, Mace, Kyla, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V., additional, North, Kat, additional, Seid, Sam, additional, Williford, Ali, additional, Cirelli, Chiara, additional, Groblewski, Peter A., additional, Lecoq, Jerome, additional, Tononi, Giulio, additional, Koch, Christof, additional, and Arkhipov, Anton, additional

Published
2022
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21. A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex

Author

Yao, Shenqin, primary, Wang, Quanxin, additional, Hirokawa, Karla, additional, Ouellette, Benjamin, additional, Ahmed, Ruweida, additional, Bomben, Jasmin, additional, Brouner, Krissy, additional, Casal, Linzy, additional, Caldejon, Shiella, additional, Cho, Andy, additional, Dotson, Nadezhda, additional, Daigle, Tanya, additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Gary, Amanda, additional, Gelfand, Emily, additional, Gorham, Melissa, additional, Griffin, Fiona, additional, Gu, Hong, additional, Hancock, Nicole, additional, Howard, Robert, additional, Kuan, Leonard, additional, Lambert, Sophie, additional, Lee, Eric, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Maxwell, Michelle, additional, Mortrud, Marty, additional, Naeemi, Maitham, additional, Nayan, Chelsea, additional, Ngo, Nhan-Kiet, additional, Nguyen, Thuyanh, additional, North, Kat, additional, Ransford, Shea, additional, Ruiz, Augustin, additional, Seid, Sam, additional, Swapp, Jackie, additional, Taormina, Michael, additional, Wakeman, Wayne, additional, Zhou, Thomas, additional, Nicovich, Philip, additional, Williford, Ali, additional, Potekhina, Lydia, additional, McGraw, Medea, additional, Ng, Lydia, additional, Groblewski, Peter, additional, Tasic, Bosiljka, additional, Mihalas, Stefan, additional, Harris, Julie, additional, Cetin, Ali, additional, and Zeng, Hongkui, additional

Published
2021
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22. Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

Author

Siegle, Joshua H, primary, Ledochowitsch, Peter, additional, Jia, Xiaoxuan, additional, Millman, Daniel J, additional, Ocker, Gabriel K, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andy, additional, Denman, Daniel J, additional, Durand, Séverine, additional, Groblewski, Peter A, additional, Heller, Gregg, additional, Kato, India, additional, Kivikas, Sara, additional, Lecoq, Jérôme, additional, Nayan, Chelsea, additional, Ngo, Kiet, additional, Nicovich, Philip R, additional, North, Kat, additional, Ramirez, Tamina K, additional, Swapp, Jackie, additional, Waughman, Xana, additional, Williford, Ali, additional, Olsen, Shawn R, additional, Koch, Christof, additional, Buice, Michael A, additional, and de Vries, Saskia EJ, additional

Published
2021
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23. Author response: Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

Author

Siegle, Joshua H, primary, Ledochowitsch, Peter, additional, Jia, Xiaoxuan, additional, Millman, Daniel J, additional, Ocker, Gabriel K, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andy, additional, Denman, Daniel J, additional, Durand, Séverine, additional, Groblewski, Peter A, additional, Heller, Gregg, additional, Kato, India, additional, Kivikas, Sara, additional, Lecoq, Jérôme, additional, Nayan, Chelsea, additional, Ngo, Kiet, additional, Nicovich, Philip R, additional, North, Kat, additional, Ramirez, Tamina K, additional, Swapp, Jackie, additional, Waughman, Xana, additional, Williford, Ali, additional, Olsen, Shawn R, additional, Koch, Christof, additional, Buice, Michael A, additional, and de Vries, Saskia EJ, additional

Published
2021
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25. Learning from unexpected events in the neocortical microcircuit

Author

Gillon, Colleen J., primary, Pina, Jason E., additional, Lecoq, Jérôme A., additional, Ahmed, Ruweida, additional, Billeh, Yazan N., additional, Caldejon, Shiella, additional, Groblewski, Peter, additional, Henley, Timothy M., additional, Kato, India, additional, Lee, Eric, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V., additional, North, Kat, additional, Perkins, Jed, additional, Seid, Sam, additional, Valley, Matthew T., additional, Williford, Ali, additional, Bengio, Yoshua, additional, Lillicrap, Timothy P., additional, Richards, Blake A., additional, and Zylberberg, Joel, additional

Published
2021
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26. A standardized behavioral event equally impacts the activity of cortical visual areas and layers

Author

Ramadan, Mahdi, primary, Lee, Eric Kenji, additional, Caldejon, Shiella, additional, Kato, India, additional, Roll, Kate, additional, Griffin, Fiona, additional, Nguyen, Thuyanh V., additional, Larkin, Josh, additional, Rhoads, Paul, additional, Mace, Kyla, additional, Kriedberg, Ali, additional, Howard, Robert, additional, Berbesque, Nathan, additional, and Lecoq, Jérôme, additional

Published
2020
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27. Measuring stimulus-evoked neurophysiological differentiation in distinct populations of neurons in mouse visual cortex

Author

Mayner, William G. P., primary, Marshall, William, additional, Billeh, Yazan N., additional, Gandhi, Saurabh R., additional, Caldejon, Shiella, additional, Cho, Andrew, additional, Griffin, Fiona, additional, Hancock, Nicole, additional, Lambert, Sophie, additional, Lee, Eric, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nayan, Chelsea, additional, Nguyan, Thuyanh, additional, North, Kat, additional, Seid, Sam, additional, Williford, Ali, additional, Cirelli, Chiara, additional, Groblewski, Peter, additional, Lecoq, Jerome, additional, Tononi, Giulio, additional, Koch, Christof, additional, and Arkhipov, Anton, additional

Published
2020
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28. VIP interneurons in mouse primary visual cortex selectively enhance responses to weak but specific stimuli

Author

Millman, Daniel J, primary, Ocker, Gabriel Koch, additional, Caldejon, Shiella, additional, Kato, India, additional, Larkin, Josh D, additional, Lee, Eric Kenji, additional, Luviano, Jennifer, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V, additional, North, Kat, additional, Seid, Sam, additional, White, Cassandra, additional, Lecoq, Jerome, additional, Reid, Clay, additional, Buice, Michael A, additional, and de Vries, Saskia EJ, additional

Published
2020
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29. Multiplane Mesoscope reveals distinct cortical interactions following expectation violations

Author

Orlova, Natalia, primary, Najafi, Farzaneh, additional, Tsyboulski, Dmitri, additional, Seid, Sam, additional, Kivikas, Sara, additional, Kato, India, additional, Griffin, Fiona, additional, Leon, Arielle, additional, Hytnen, Ross D., additional, L’Heureux, Quinn, additional, North, Kat, additional, Swapp, Jackie, additional, Nayan, Chelsea, additional, Hancock, Nicole, additional, Ahmed, Ruweida, additional, Gelfand, Emily, additional, Cho, Andrew, additional, Mace, Kyla, additional, Howard, Robert, additional, Casal, Linzy, additional, Lambert, Sophie, additional, Lee, Eric Kenji, additional, Caldejon, Shiella, additional, Waughman, Xana, additional, Williford, Allison, additional, Garrett, Marina, additional, Ollerenshaw, Doug, additional, Olsen, Shawn R., additional, Groblewski, Peter A., additional, Saggau, Peter, additional, and Lecoq, Jérôme, additional

Published
2020
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30. Author response: VIP interneurons in mouse primary visual cortex selectively enhance responses to weak but specific stimuli

Author

Millman, Daniel J, primary, Ocker, Gabriel Koch, additional, Caldejon, Shiella, additional, Kato, India, additional, Larkin, Josh D, additional, Lee, Eric Kenji, additional, Luviano, Jennifer, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V, additional, North, Kat, additional, Seid, Sam, additional, White, Cassandra, additional, Lecoq, Jerome, additional, Reid, Clay, additional, Buice, Michael A, additional, and de Vries, Saskia EJ, additional

Published
2020
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31. Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

Author

Siegle, Joshua H., primary, Ledochowitsch, Peter, additional, Jia, Xiaoxuan, additional, Millman, Daniel, additional, Ocker, Gabriel K., additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Denman, Daniel J., additional, Durand, Séverine, additional, Groblewski, Peter A., additional, Heller, Greggory, additional, Kato, India, additional, Kivikas, Sara, additional, Lecoq, Jerome, additional, Nayan, Chelsea, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, North, Kat R., additional, Ramirez, Tamina K., additional, Swapp, Jackie, additional, Waughman, Xana, additional, Williford, Ali, additional, Olsen, Shawn R., additional, Koch, Christof, additional, Buice, Michael A., additional, and de Vries, Saskia E. J., additional

Published
2020
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32. Widespread presence of direction-reversing neurons in the mouse visual system

Author

Billeh, Yazan N., Iyer, Ramakrishnan, Wahle, Iman A., Caldejon, Shiella, Durand, Séverine, Groblewski, Peter A., Larkin, Josh D., Lecoq, Jerome, Williford, Ali, Mihalas, Stefan, Arkhipov, Anton, de Vries, Saskia E. J., Billeh, Yazan N., Iyer, Ramakrishnan, Wahle, Iman A., Caldejon, Shiella, Durand, Séverine, Groblewski, Peter A., Larkin, Josh D., Lecoq, Jerome, Williford, Ali, Mihalas, Stefan, Arkhipov, Anton, and de Vries, Saskia E. J.

Abstract

Direction selectivity, the preference of motion in one direction over the opposite, is a fundamental property of visual neurons across species. We find that a substantial proportion of direction selective neurons in the mouse visual system reverse their preferred direction of motion in response to drifting gratings at different spatiotemporal parameters. A spatiotemporally asymmetric filter model recapitulates our experimental observations.

Published
2019

33. A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

Author

de Vries, Saskia E. J., primary, Lecoq, Jerome A., additional, Buice, Michael A., additional, Groblewski, Peter A., additional, Ocker, Gabriel K., additional, Oliver, Michael, additional, Feng, David, additional, Cain, Nicholas, additional, Ledochowitsch, Peter, additional, Millman, Daniel, additional, Roll, Kate, additional, Garrett, Marina, additional, Keenan, Tom, additional, Kuan, Leonard, additional, Mihalas, Stefan, additional, Olsen, Shawn, additional, Thompson, Carol, additional, Wakeman, Wayne, additional, Waters, Jack, additional, Williams, Derric, additional, Barber, Chris, additional, Berbesque, Nathan, additional, Blanchard, Brandon, additional, Bowles, Nicholas, additional, Caldejon, Shiella D., additional, Casal, Linzy, additional, Cho, Andrew, additional, Cross, Sissy, additional, Dang, Chinh, additional, Dolbeare, Tim, additional, Edwards, Melise, additional, Galbraith, John, additional, Gaudreault, Nathalie, additional, Gilbert, Terri L., additional, Griffin, Fiona, additional, Hargrave, Perry, additional, Howard, Robert, additional, Huang, Lawrence, additional, Jewell, Sean, additional, Keller, Nika, additional, Knoblich, Ulf, additional, Larkin, Josh D., additional, Larsen, Rachael, additional, Lau, Chris, additional, Lee, Eric, additional, Lee, Felix, additional, Leon, Arielle, additional, Li, Lu, additional, Long, Fuhui, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nguyen, Thuyanh, additional, Perkins, Jed, additional, Robertson, Miranda, additional, Seid, Sam, additional, Shea-Brown, Eric, additional, Shi, Jianghong, additional, Sjoquist, Nathan, additional, Slaughterbeck, Cliff, additional, Sullivan, David, additional, Valenza, Ryan, additional, White, Casey, additional, Williford, Ali, additional, Witten, Daniela M., additional, Zhuang, Jun, additional, Zeng, Hongkui, additional, Farrell, Colin, additional, Ng, Lydia, additional, Bernard, Amy, additional, Phillips, John W., additional, Reid, R. Clay, additional, and Koch, Christof, additional

Published
2019
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34. VIP interneurons selectively enhance weak but behaviorally-relevant stimuli

Author

Millman, Daniel J., primary, Ocker, Gabriel Koch, additional, Caldejon, Shiella, additional, Kato, India, additional, Larkin, Josh D., additional, Lee, Eric Kenji, additional, Luviano, Jennifer, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V., additional, North, Kat, additional, Seid, Sam, additional, White, Cassandra, additional, Lecoq, Jerome A., additional, Reid, R. Clay, additional, Buice, Michael A., additional, and de Vries, Saskia E.J., additional

Published
2019
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35. Widespread presence of direction-reversing neurons in the mouse visual system

Author

Billeh, Yazan N., primary, Iyer, Ramakrishnan, additional, Wahle, Iman A., additional, Caldejon, Shiella, additional, Durand, Séverine, additional, Groblewski, Peter A., additional, Larkin, Josh D, additional, Lecoq, Jerome, additional, Williford, Ali, additional, Mihalas, Stefan, additional, Arkhipov, Anton, additional, and de Vries, Saskia E. J., additional

Published
2019
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36. A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas

Author

Siegle, Joshua H., primary, Jia, Xiaoxuan, additional, Durand, Séverine, additional, Gale, Sam, additional, Bennett, Corbett, additional, Graddis, Nile, additional, Heller, Greggory, additional, Ramirez, Tamina K., additional, Choi, Hannah, additional, Luviano, Jennifer A., additional, Groblewski, Peter A., additional, Ahmed, Ruweida, additional, Arkhipov, Anton, additional, Bernard, Amy, additional, Billeh, Yazan N., additional, Brown, Dillan, additional, Buice, Michael A., additional, Cain, Nicolas, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Chvilicek, Maggie, additional, Cox, Timothy C., additional, Dai, Kael, additional, Denman, Daniel J., additional, de Vries, Saskia E. J., additional, Dietzman, Roald, additional, Esposito, Luke, additional, Farrell, Colin, additional, Feng, David, additional, Galbraith, John, additional, Garrett, Marina, additional, Gelfand, Emily C., additional, Hancock, Nicole, additional, Harris, Julie A., additional, Howard, Robert, additional, Hu, Brian, additional, Hytnen, Ross, additional, Iyer, Ramakrishnan, additional, Jessett, Erika, additional, Johnson, Katelyn, additional, Kato, India, additional, Kiggins, Justin, additional, Lambert, Sophie, additional, Lecoq, Jerome, additional, Ledochowitsch, Peter, additional, Lee, Jung Hoon, additional, Leon, Arielle, additional, Li, Yang, additional, Liang, Elizabeth, additional, Long, Fuhui, additional, Mace, Kyla, additional, Melchior, Jose, additional, Millman, Daniel, additional, Mollenkopf, Tyler, additional, Nayan, Chelsea, additional, Ng, Lydia, additional, Ngo, Kiet, additional, Nguyen, Thuyahn, additional, Nicovich, Philip R., additional, North, Kat, additional, Ocker, Gabriel Koch, additional, Ollerenshaw, Doug, additional, Oliver, Michael, additional, Pachitariu, Marius, additional, Perkins, Jed, additional, Reding, Melissa, additional, Reid, David, additional, Robertson, Miranda, additional, Ronellenfitch, Kara, additional, Seid, Sam, additional, Slaughterbeck, Cliff, additional, Stoecklin, Michelle, additional, Sullivan, David, additional, Sutton, Ben, additional, Swapp, Jackie, additional, Thompson, Carol, additional, Turner, Kristen, additional, Wakeman, Wayne, additional, Whitesell, Jennifer D., additional, Williams, Derric, additional, Williford, Ali, additional, Young, Rob, additional, Zeng, Hongkui, additional, Naylor, Sarah, additional, Phillips, John W., additional, Reid, R. Clay, additional, Mihalas, Stefan, additional, Olsen, Shawn R., additional, and Koch, Christof, additional

Published
2019
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37. Classification of electrophysiological and morphological types in mouse visual cortex

Author

Gouwens, Nathan W., primary, Sorensen, Staci A., additional, Berg, Jim, additional, Lee, Changkyu, additional, Jarsky, Tim, additional, Ting, Jonathan, additional, Sunkin, Susan M., additional, Feng, David, additional, Anastassiou, Costas, additional, Barkan, Eliza, additional, Bickley, Kris, additional, Blesie, Nicole, additional, Braun, Thomas, additional, Brouner, Krissy, additional, Budzillo, Agata, additional, Caldejon, Shiella, additional, Casper, Tamara, additional, Casteli, Dan, additional, Chong, Peter, additional, Crichton, Kirsten, additional, Cuhaciyan, Christine, additional, Tanya, L. Daigle, additional, Dalley, Rachel, additional, Dee, Nick, additional, Desta, Tsega, additional, Dingman, Samuel, additional, Doperalski, Alyse, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Fisher, Michael, additional, de Frates, Rebecca A., additional, Garren, Emma, additional, Garwood, Marissa, additional, Gary, Amanda, additional, Gaudreault, Nathalie, additional, Godfrey, Keith, additional, Gorham, Melissa, additional, Gu, Hong, additional, Habel, Caroline, additional, Hadley, Kristen, additional, Harrington, James, additional, Harris, Julie, additional, Henry, Alex, additional, Hill, DiJon, additional, Josephsen, Sam, additional, Kebede, Sara, additional, Kim, Lisa, additional, Kroll, Matthew, additional, Lee, Brian, additional, Lemon, Tracy, additional, Liu, Xiaoxiao, additional, Long, Brian, additional, Mann, Rusty, additional, McGraw, Medea, additional, Mihalas, Stefan, additional, Mukora, Alice, additional, Murphy, Gabe J., additional, Ng, Lindsay, additional, Ngo, Kiet, additional, Nguyen, Thuc Nghi, additional, Nicovich, Philip R., additional, Oldre, Aaron, additional, Park, Daniel, additional, Parry, Sheana, additional, Perkins, Jed, additional, Potekhina, Lydia, additional, Reid, David, additional, Robertson, Miranda, additional, Sandman, David, additional, Schroedter, Martin, additional, Slaughterbeck, Cliff, additional, Soler-Llavina, Gilberto, additional, Sulc, Josef, additional, Szafer, Aaron, additional, Tasic, Bosiljka, additional, Taskin, Naz, additional, Teeter, Corinne, additional, Thatra, Nivretta, additional, Tung, Herman, additional, Wakeman, Wayne, additional, Williams, Grace, additional, Young, Rob, additional, Zhou, Zhi, additional, Farrell, Colin, additional, Peng, Hanchuan, additional, Hawrylycz, Michael J., additional, Lein, Ed, additional, Ng, Lydia, additional, Arkhipov, Anton, additional, Bernard, Amy, additional, Phillips, John W., additional, Zeng, Hongkui, additional, and Koch, Christof, additional

Published
2018
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38. A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

Author

de Vries, Saskia E. J., primary, Lecoq, Jerome, additional, Buice, Michael A., additional, Groblewski, Peter A., additional, Ocker, Gabriel K., additional, Oliver, Michael, additional, Feng, David, additional, Cain, Nicholas, additional, Ledochowitsch, Peter, additional, Millman, Daniel, additional, Roll, Kate, additional, Garrett, Marina, additional, Keenan, Tom, additional, Kuan, Leonard, additional, Mihalas, Stefan, additional, Olsen, Shawn, additional, Thompson, Carol, additional, Wakeman, Wayne, additional, Waters, Jack, additional, Williams, Derric, additional, Barber, Chris, additional, Berbesque, Nathan, additional, Blanchard, Brandon, additional, Bowles, Nicholas, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Cross, Sissy, additional, Dang, Chinh, additional, Dolbeare, Tim, additional, Edwards, Melise, additional, Galbraith, John, additional, Gaudreault, Nathalie, additional, Griffin, Fiona, additional, Hargrave, Perry, additional, Howard, Robert, additional, Huang, Lawrence, additional, Jewell, Sean, additional, Keller, Nika, additional, Knoblich, Ulf, additional, Larkin, Josh, additional, Larsen, Rachael, additional, Lau, Chris, additional, Lee, Eric, additional, Lee, Felix, additional, Leon, Arielle, additional, Li, Lu, additional, Long, Fuhui, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nguyen, Thuyanh, additional, Perkins, Jed, additional, Robertson, Miranda, additional, Seid, Sam, additional, Shea-Brown, Eric, additional, Shi, Jianghong, additional, Sjoquist, Nathan, additional, Slaughterbeck, Cliff, additional, Sullivan, David, additional, Valenza, Ryan, additional, White, Casey, additional, Williford, Ali, additional, Witten, Daniela, additional, Zhuang, Jun, additional, Zeng, Hongkui, additional, Farrell, Colin, additional, Ng, Lydia, additional, Bernard, Amy, additional, Phillips, John W., additional, Reid, R. Clay, additional, and Koch, Christof, additional

Published
2018
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39. The organization of intracortical connections by layer and cell class in the mouse brain

Author

Harris, Julie A., primary, Mihalas, Stefan, additional, Hirokawa, Karla E., additional, Whitesell, Jennifer D., additional, Knox, Joseph E., additional, Bernard, Amy, additional, Bohn, Phillip, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Feng, David, additional, Gaudreault, Nathalie, additional, Gerfen, Charles R., additional, Graddis, Nile, additional, Groblewski, Peter A., additional, Henry, Alex, additional, Ho, Anh, additional, Howard, Robert, additional, Kuan, Leonard, additional, Lecoq, Jerome, additional, Luviano, Jennifer, additional, McConoghy, Stephen, additional, Mortrud, Marty T., additional, Naeemi, Maitham, additional, Ng, Lydia, additional, Oh, Seung W., additional, Ouellette, Benjamin, additional, Sorensen, Staci A., additional, Wakeman, Wayne, additional, Wang, Quanxin, additional, Williford, Ali, additional, Phillips, John W., additional, Jones, Allan, additional, Koch, Christof, additional, and Zeng, Hongkui, additional

Published
2018
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40. Neuropathological and transcriptomic characteristics of the aged brain

Author

Miller, Jeremy A, primary, Guillozet-Bongaarts, Angela, additional, Gibbons, Laura E, additional, Postupna, Nadia, additional, Renz, Anne, additional, Beller, Allison E, additional, Sunkin, Susan M, additional, Ng, Lydia, additional, Rose, Shannon E, additional, Smith, Kimberly A, additional, Szafer, Aaron, additional, Barber, Chris, additional, Bertagnolli, Darren, additional, Bickley, Kristopher, additional, Brouner, Krissy, additional, Caldejon, Shiella, additional, Chapin, Mike, additional, Chua, Mindy L, additional, Coleman, Natalie M, additional, Cudaback, Eiron, additional, Cuhaciyan, Christine, additional, Dalley, Rachel A, additional, Dee, Nick, additional, Desta, Tsega, additional, Dolbeare, Tim A, additional, Dotson, Nadezhda I, additional, Fisher, Michael, additional, Gaudreault, Nathalie, additional, Gee, Garrett, additional, Gilbert, Terri L, additional, Goldy, Jeff, additional, Griffin, Fiona, additional, Habel, Caroline, additional, Haradon, Zeb, additional, Hejazinia, Nika, additional, Hellstern, Leanne L, additional, Horvath, Steve, additional, Howard, Kim, additional, Howard, Robert, additional, Johal, Justin, additional, Jorstad, Nikolas L, additional, Josephsen, Samuel R, additional, Kuan, Chihchau L, additional, Lai, Florence, additional, Lee, Eric, additional, Lee, Felix, additional, Lemon, Tracy, additional, Li, Xianwu, additional, Marshall, Desiree A, additional, Melchor, Jose, additional, Mukherjee, Shubhabrata, additional, Nyhus, Julie, additional, Pendergraft, Julie, additional, Potekhina, Lydia, additional, Rha, Elizabeth Y, additional, Rice, Samantha, additional, Rosen, David, additional, Sapru, Abharika, additional, Schantz, Aimee, additional, Shen, Elaine, additional, Sherfield, Emily, additional, Shi, Shu, additional, Sodt, Andy J, additional, Thatra, Nivretta, additional, Tieu, Michael, additional, Wilson, Angela M, additional, Montine, Thomas J, additional, Larson, Eric B, additional, Bernard, Amy, additional, Crane, Paul K, additional, Ellenbogen, Richard G, additional, Keene, C Dirk, additional, and Lein, Ed, additional

Published
2017
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41. Author response: Neuropathological and transcriptomic characteristics of the aged brain

Author

Miller, Jeremy A, primary, Guillozet-Bongaarts, Angela, additional, Gibbons, Laura E, additional, Postupna, Nadia, additional, Renz, Anne, additional, Beller, Allison E, additional, Sunkin, Susan M, additional, Ng, Lydia, additional, Rose, Shannon E, additional, Smith, Kimberly A, additional, Szafer, Aaron, additional, Barber, Chris, additional, Bertagnolli, Darren, additional, Bickley, Kristopher, additional, Brouner, Krissy, additional, Caldejon, Shiella, additional, Chapin, Mike, additional, Chua, Mindy L, additional, Coleman, Natalie M, additional, Cudaback, Eiron, additional, Cuhaciyan, Christine, additional, Dalley, Rachel A, additional, Dee, Nick, additional, Desta, Tsega, additional, Dolbeare, Tim A, additional, Dotson, Nadezhda I, additional, Fisher, Michael, additional, Gaudreault, Nathalie, additional, Gee, Garrett, additional, Gilbert, Terri L, additional, Goldy, Jeff, additional, Griffin, Fiona, additional, Habel, Caroline, additional, Haradon, Zeb, additional, Hejazinia, Nika, additional, Hellstern, Leanne L, additional, Horvath, Steve, additional, Howard, Kim, additional, Howard, Robert, additional, Johal, Justin, additional, Jorstad, Nikolas L, additional, Josephsen, Samuel R, additional, Kuan, Chihchau L, additional, Lai, Florence, additional, Lee, Eric, additional, Lee, Felix, additional, Lemon, Tracy, additional, Li, Xianwu, additional, Marshall, Desiree A, additional, Melchor, Jose, additional, Mukherjee, Shubhabrata, additional, Nyhus, Julie, additional, Pendergraft, Julie, additional, Potekhina, Lydia, additional, Rha, Elizabeth Y, additional, Rice, Samantha, additional, Rosen, David, additional, Sapru, Abharika, additional, Schantz, Aimee, additional, Shen, Elaine, additional, Sherfield, Emily, additional, Shi, Shu, additional, Sodt, Andy J, additional, Thatra, Nivretta, additional, Tieu, Michael, additional, Wilson, Angela M, additional, Montine, Thomas J, additional, Larson, Eric B, additional, Bernard, Amy, additional, Crane, Paul K, additional, Ellenbogen, Richard G, additional, Keene, C Dirk, additional, and Lein, Ed, additional

Published
2017
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42. Comprehensive cellular-resolution atlas of the adult human brain

Author

Ding, Song-Lin, primary, Royall, Joshua J., additional, Sunkin, Susan M., additional, Ng, Lydia, additional, Facer, Benjamin A.C., additional, Lesnar, Phil, additional, Guillozet-Bongaarts, Angie, additional, McMurray, Bergen, additional, Szafer, Aaron, additional, Dolbeare, Tim A., additional, Stevens, Allison, additional, Tirrell, Lee, additional, Benner, Thomas, additional, Caldejon, Shiella, additional, Dalley, Rachel A., additional, Dee, Nick, additional, Lau, Christopher, additional, Nyhus, Julie, additional, Reding, Melissa, additional, Riley, Zackery L., additional, Sandman, David, additional, Shen, Elaine, additional, van der Kouwe, Andre, additional, Varjabedian, Ani, additional, Write, Michelle, additional, Zollei, Lilla, additional, Dang, Chinh, additional, Knowles, James A., additional, Koch, Christof, additional, Phillips, John W., additional, Sestan, Nenad, additional, Wohnoutka, Paul, additional, Zielke, H. Ronald, additional, Hohmann, John G., additional, Jones, Allan R., additional, Bernard, Amy, additional, Hawrylycz, Michael J., additional, Hof, Patrick R., additional, Fischl, Bruce, additional, and LeinReference, Ed S., additional

Published
2016
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43. Transcriptional Landscape of the Prenatal Human Brain

Author

Miller, Jeremy A., Ding, Song-Lin, Sunkin, Susan M., Smith, Kimberly A, Ng, Lydia, Szafer, Aaron, Ebbert, Amanda, Riley, Zackery L., Aiona, Kaylynn, Arnold, James M., Bennet, Crissa, Bertagnolli, Darren, Brouner, Krissy, Butler, Stephanie, Caldejon, Shiella, Carey, Anita, Cuhaciyan, Christine, Dalley, Rachel A., Dee, Nick, Dolbeare, Tim A., Facer, Benjamin A. C., Feng, David, Fliss, Tim P., Gee, Garrett, Goldy, Jeff, Gourley, Lindsey, Gregor, Benjamin W., Gu, Guangyu, Howard, Robert E., Jochim, Jayson M., Kuan, Chihchau L., Lau, Christopher, Lee, Chang-Kyu, Lee, Felix, Lemon, Tracy A., Lesnar, Phil, McMurray, Bergen, Mastan, Naveed, Mosqueda, Nerick F., Naluai-Cecchini, Theresa, Ngo, Nhan-Kiet, Nyhus, Julie, Oldre, Aaron, Olson, Eric, Parente, Jody, Parker, Patrick D., Parry, Sheana E., Player, Allison Stevens, Pletikos, Mihovil, Reding, Melissa, Royall, Joshua J., Roll, Kate, Sandman, David, Sarreal, Melaine, Shapouri, Sheila, Shapovalova, Nadiya V., Shen, Elaine H., Sjoquist, Nathan, Slaughterbeck, Clifford R., Smith, Michael, Sodt, Andy J., Williams, Derric, Zöllei, Lilla, Fischl, Bruce, Gerstein, Mark B., Geschwind, Daniel H., Glass, Ian A., Hawrylycz, Michael J., Hevner, Robert F., Huang, Hao, Jones, Allan R., Knowles, James A., Levitt, Pat, Phillips, John W., Sestan, Nenad, Wohnoutka, Paul, Dang, Chinh, Bernard, Amy, Hohmann, John G., and Lein, Ed S.

Subjects
Human brain, Transcriptome, Microarray, Development, Gene expression, Evolution
Abstract

Summary The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe. Finally, many neurodevelopmental disorder and human evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

Published
2014
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44. Recurrent pattern completion drives the neocortical representation of sensory inference.

Author

Shin H, Ogando MB, Abdeladim L, Durand S, Belski H, Cabasco H, Loefler H, Bawany A, Hardcastle B, Wilkes J, Nguyen K, Suarez L, Johnson T, Han W, Ouellette B, Grasso C, Swapp J, Ha V, Young A, Caldejon S, Williford A, Groblewski P, Olsen S, Kiselycznyk C, Lecoq J, and Adesnik H

Abstract

When sensory information is incomplete or ambiguous, the brain relies on prior expectations to infer perceptual objects. Despite the centrality of this process to perception, the neural mechanism of sensory inference is not known. Illusory contours (ICs) are key tools to study sensory inference because they contain edges or objects that are implied only by their spatial context. Using cellular resolution, mesoscale two-photon calcium imaging and multi-Neuropixels recordings in the mouse visual cortex, we identified a sparse subset of neurons in the primary visual cortex (V1) and higher visual areas that respond emergently to ICs. We found that these highly selective 'IC-encoders' mediate the neural representation of IC inference. Strikingly, selective activation of these neurons using two-photon holographic optogenetics was sufficient to recreate IC representation in the rest of the V1 network, in the absence of any visual stimulus. This outlines a model in which primary sensory cortex facilitates sensory inference by selectively strengthening input patterns that match prior expectations through local, recurrent circuitry. Our data thus suggest a clear computational purpose for recurrence in the generation of holistic percepts under sensory ambiguity. More generally, selective reinforcement of top-down predictions by pattern-completing recurrent circuits in lower sensory cortices may constitute a key step in sensory inference.

Published
2023
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45. Differential encoding of temporal context and expectation under representational drift across hierarchically connected areas.

Author

Wyrick DG, Cain N, Larsen RS, Lecoq J, Valley M, Ahmed R, Bowlus J, Boyer G, Caldejon S, Casal L, Chvilicek M, DePartee M, Groblewski PA, Huang C, Johnson K, Kato I, Larkin J, Lee E, Liang E, Luviano J, Mace K, Nayan C, Nguyen T, Reding M, Seid S, Sevigny J, Stoecklin M, Williford A, Choi H, Garrett M, and Mazzucato L

Abstract

The classic view that neural populations in sensory cortices preferentially encode responses to incoming stimuli has been strongly challenged by recent experimental studies. Despite the fact that a large fraction of variance of visual responses in rodents can be attributed to behavioral state and movements, trial-history, and salience, the effects of contextual modulations and expectations on sensory-evoked responses in visual and association areas remain elusive. Here, we present a comprehensive experimental and theoretical study showing that hierarchically connected visual and association areas differentially encode the temporal context and expectation of naturalistic visual stimuli, consistent with the theory of hierarchical predictive coding. We measured neural responses to expected and unexpected sequences of natural scenes in the primary visual cortex (V1), the posterior medial higher order visual area (PM), and retrosplenial cortex (RSP) using 2-photon imaging in behaving mice collected through the Allen Institute Mindscope's OpenScope program. We found that information about image identity in neural population activity depended on the temporal context of transitions preceding each scene, and decreased along the hierarchy. Furthermore, our analyses revealed that the conjunctive encoding of temporal context and image identity was modulated by expectations of sequential events. In V1 and PM, we found enhanced and specific responses to unexpected oddball images, signaling stimulus-specific expectation violation. In contrast, in RSP the population response to oddball presentation recapitulated the missing expected image rather than the oddball image. These differential responses along the hierarchy are consistent with classic theories of hierarchical predictive coding whereby higher areas encode predictions and lower areas encode deviations from expectation. We further found evidence for drift in visual responses on the timescale of minutes. Although activity drift was present in all areas, population responses in V1 and PM, but not in RSP, maintained stable encoding of visual information and representational geometry. Instead we found that RSP drift was independent of stimulus information, suggesting a role in generating an internal model of the environment in the temporal domain. Overall, our results establish temporal context and expectation as substantial encoding dimensions in the visual cortex subject to fast representational drift and suggest that hierarchically connected areas instantiate a predictive coding mechanism., Competing Interests: Declaration of interests The authors declare no competing interests.

Published
2023
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