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183 results on '"Kalmbach, Brian"'

1. Areal specializations in the morpho-electric and transcriptomic properties of primate layer 5 extratelencephalic projection neurons

Author: Dembrow, Nikolai C., Sawchuk, Scott, Dalley, Rachel, Opitz-Araya, Ximena, Hudson, Mark, Radaelli, Cristina, Alfiler, Lauren, Walling-Bell, Sarah, Bertagnolli, Darren, Goldy, Jeff, Johansen, Nelson, Miller, Jeremy A., Nasirova, Kamiliam, Owen, Scott F., Parga-Becerra, Alejandro, Taskin, Naz, Tieu, Michael, Vumbaco, David, Weed, Natalie, Wilson, Julia, Lee, Brian R., Smith, Kimberly A., Sorensen, Staci A., Spain, William J., Lein, Ed S., Perlmutter, Steve I., Ting, Jonathan T., and Kalmbach, Brian E.
Published: 2024
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2. Comparative cellular analysis of motor cortex in human, marmoset and mouse

Author: 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, and Ting, Jonathan T
Subjects: Human Genome, Neurosciences, Genetics, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Atlases as Topic, Callithrix, Epigenesis, Genetic, Epigenomics, Female, GABAergic Neurons, Gene Expression Profiling, Glutamates, Humans, In Situ Hybridization, Fluorescence, Male, Mice, Middle Aged, Motor Cortex, Neurons, Organ Specificity, Phylogeny, Single-Cell Analysis, Species Specificity, Transcriptome, General Science & Technology
Abstract: The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
Published: 2021

3. A multimodal cell census and atlas of the mammalian primary motor cortex

Author: Callaway, Edward M, Dong, Hong-Wei, Ecker, Joseph R, Hawrylycz, Michael J, Huang, Z Josh, Lein, Ed S, Ngai, John, Osten, Pavel, Ren, Bing, Tolias, Andreas Savas, White, Owen, Zeng, Hongkui, Zhuang, Xiaowei, Ascoli, Giorgio A, Behrens, M Margarita, Chun, Jerold, Feng, Guoping, Gee, James C, Ghosh, Satrajit S, Halchenko, Yaroslav O, Hertzano, Ronna, Lim, Byung Kook, Martone, Maryann E, Ng, Lydia, Pachter, Lior, Ropelewski, Alexander J, Tickle, Timothy L, Yang, X William, Zhang, Kun, Bakken, Trygve E, Berens, Philipp, Daigle, Tanya L, Harris, Julie A, Jorstad, Nikolas L, Kalmbach, Brian E, Kobak, Dmitry, Li, Yang Eric, Liu, Hanqing, Matho, Katherine S, Mukamel, Eran A, Naeemi, Maitham, Scala, Federico, Tan, Pengcheng, Ting, Jonathan T, Xie, Fangming, Zhang, Meng, Zhang, Zhuzhu, Zhou, Jingtian, Zingg, Brian, Armand, Ethan, Yao, Zizhen, Bertagnolli, Darren, Casper, Tamara, Crichton, Kirsten, Dee, Nick, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Dougherty, Elizabeth L, Fong, Olivia, Goldman, Melissa, Goldy, Jeff, Hodge, Rebecca D, Hu, Lijuan, Keene, C Dirk, Krienen, Fenna M, Kroll, Matthew, Lake, Blue B, Lathia, Kanan, Linnarsson, Sten, Liu, Christine S, Macosko, Evan Z, McCarroll, Steven A, McMillen, Delissa, Nadaf, Naeem M, Nguyen, Thuc Nghi, Palmer, Carter R, Pham, Thanh, Plongthongkum, Nongluk, Reed, Nora M, Regev, Aviv, Rimorin, Christine, Romanow, William J, Savoia, Steven, Siletti, Kimberly, Smith, Kimberly, Sulc, Josef, Tasic, Bosiljka, Tieu, Michael, Torkelson, Amy, Tung, Herman, van Velthoven, Cindy TJ, Vanderburg, Charles R, Yanny, Anna Marie, Fang, Rongxin, Hou, Xiaomeng, Lucero, Jacinta D, Osteen, Julia K, Pinto-Duarte, Antonio, and Poirion, Olivier
Subjects: Genetics, Neurosciences, Human Genome, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Atlases as Topic, Callithrix, Epigenomics, Female, Gene Expression Profiling, Glutamates, Humans, In Situ Hybridization, Fluorescence, Male, Mice, Motor Cortex, Neurons, Organ Specificity, Phylogeny, Single-Cell Analysis, Species Specificity, Transcriptome, BRAIN Initiative Cell Census Network, General Science & Technology
Abstract: Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
Published: 2021

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

Author: 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, and Lein, Ed S
Subjects: Biological Sciences, Biomedical and Clinical Sciences, Neurosciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Brain, Electrophysiology, Gene Expression Profiling, Humans, In Situ Hybridization, Fluorescence, Mice, Neurons, Pyramidal Cells, Telencephalon, Temporal Lobe, Transcriptome
Abstract: von Economo neurons (VENs) are bipolar, spindle-shaped neurons restricted to layer 5 of human frontoinsula and anterior cingulate cortex that appear to be selectively vulnerable to neuropsychiatric and neurodegenerative diseases, although little is known about other VEN cellular phenotypes. Single nucleus RNA-sequencing of frontoinsula layer 5 identifies a transcriptomically-defined cell cluster that contained VENs, but also fork cells and a subset of pyramidal neurons. Cross-species alignment of this cell cluster with a well-annotated mouse classification shows strong homology to extratelencephalic (ET) excitatory neurons that project to subcerebral targets. This cluster also shows strong homology to a putative ET cluster in human temporal cortex, but with a strikingly specific regional signature. Together these results suggest that VENs are a regionally distinctive type of ET neuron. Additionally, we describe the first patch clamp recordings of VENs from neurosurgically-resected tissue that show distinctive intrinsic membrane properties relative to neighboring pyramidal neurons.
Published: 2020

5. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

Author: Ben-Simon, Yoav, primary, Hooper, Marcus, additional, Narayan, Sujatha, additional, Daigle, Tanya, additional, Dwivedi, Deepanjali, additional, Way, Sharon W, additional, Oster, Aaron, additional, Stafford, David A, additional, Mich, John K, additional, Taormina, Michael J, additional, Martinez, Refugio A, additional, Opitz-Araya, Ximena, additional, Roth, Jada R, additional, Allen, Shona, additional, Ayala, Angela, additional, Bakken, Trygve E, additional, Barcelli, Tyler, additional, Barta, Stuard, additional, Bendrick, Jacqueline, additional, Bertagnolli, Darren, additional, Bowlus, Jessica, additional, Boyer, Gabriella, additional, Brouner, Krissy, additional, Casian, Brittny, additional, Casper, Tamara, additional, Chakka, Anish B, additional, Chakrabarty, Rushil, additional, Chance, Rebecca K, additional, Chavan, Sakshi, additional, Departee, Maxwell, additional, Donadio, Nicholas, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Gabitto, Mariano, additional, Gary, Amanda, additional, Gasperini, Molly, additional, Goldy, Jeff, additional, Gore, Bryan B, additional, Graybuck, Lucas, additional, Greisman, Noah, additional, Haeseleer, Francoise, additional, Halterman, Carliana, additional, Helback, Olivia, additional, Hockmeyer, Dirk, additional, Huang, Cindy, additional, Huff, Sydney, additional, Hunker, Avery, additional, Johansen, Nelson, additional, Juneau, Zoe, additional, Kalmbach, Brian, additional, Khem, Shannon, additional, Kutsal, Rana, additional, Larsen, Rachael, additional, Lee, Changkyu, additional, Lee, Angus Y, additional, Leibly, Madison, additional, Lenz, Garreck H, additional, Liang, Elizabeth, additional, Lusk, Nicholas, additional, Malone, Jocelin, additional, Mollenkopf, Tyler, additional, Morin, Elyse, additional, Newman, Dakota, additional, Ng, Lydia, additional, Ngo, Kiet, additional, Omstead, Victoria, additional, Oyama, Alana, additional, Pham, Trangthanh, additional, Pom, Christina A, additional, Potekhina, Lydia, additional, Ransford, Shea, additional, Rette, Dean, additional, Rimorin, Christine, additional, Rocha, Dana, additional, Ruiz, Augustin, additional, Sanchez, Raymond E.A., additional, Sedeno-Cortes, Adriana, additional, Sevigny, Joshua P, additional, Shapovalova, Nadiya, additional, Shulga, Lyudmila, additional, Sigler, Ana R, additional, Siverts, La Akea, additional, Somasundaram, Saroja, additional, Stewart, Kaiya, additional, Tieu, Michael, additional, Trader, Cameron, additional, van Velthoven, Cindy T.J., additional, Walker, Miranda, additional, Weed, Natalie, additional, Wirthlin, Morgan, additional, Wood, Toren, additional, Wynalda, Brooke, additional, Yao, Zizhen, additional, Zhou, Thomas, additional, Ariza, Jeanelle, additional, Dee, Nick, additional, Reding, Melissa, additional, Ronellenfitch, Kara, additional, Mufti, Shoaib, additional, Sunkin, Susan M, additional, Smith, Kimberly A, additional, Esposito, Luke, additional, Waters, Jack, additional, Thyagarajan, Bargavi, additional, Yao, Shenqin, additional, Lein, Ed, additional, Zeng, Hongkui, additional, Levi, Boaz P, additional, Ngai, John, additional, Ting, Jonathan T, additional, and Tasic, Bosiljka, additional
Published: 2024
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6. Multi-modal characterization and simulation of human epileptic circuitry

Author: Buchin, Anatoly, de Frates, Rebecca, Nandi, Anirban, Mann, Rusty, Chong, Peter, Ng, Lindsay, Miller, Jeremy, Hodge, Rebecca, Kalmbach, Brian, Bose, Soumita, Rutishauser, Ueli, McConoughey, Stephen, Lein, Ed, Berg, Jim, Sorensen, Staci, Gwinn, Ryder, Koch, Christof, Ting, Jonathan, and Anastassiou, Costas A.
Published: 2022
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7. Morpho-electric diversity of human hippocampal CA1 pyramidal neurons

Author: Mertens, Eline J., primary, Leibner, Yoni, additional, Pie, Jean, additional, Galakhova, Anna A., additional, Waleboer, Femke, additional, Meijer, Julia, additional, Heistek, Tim S., additional, Wilbers, René, additional, Heyer, Djai, additional, Goriounova, Natalia A., additional, Idema, Sander, additional, Verhoog, Matthijs B., additional, Kalmbach, Brian E., additional, Lee, Brian R., additional, Gwinn, Ryder P., additional, Lein, Ed S., additional, Aronica, Eleonora, additional, Ting, Jonathan, additional, Mansvelder, Huibert D., additional, Segev, Idan, additional, and de Kock, Christiaan P.J., additional
Published: 2024
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8. Human neocortical expansion involves glutamatergic neuron diversification

Author: Berg, Jim, Sorensen, Staci A., Ting, Jonathan T., Miller, Jeremy A., Chartrand, Thomas, Buchin, Anatoly, Bakken, Trygve E., Budzillo, Agata, Dee, Nick, Ding, Song-Lin, Gouwens, Nathan W., Hodge, Rebecca D., Kalmbach, Brian, Lee, Changkyu, Lee, Brian R., Alfiler, Lauren, Baker, Katherine, Barkan, Eliza, Beller, Allison, Berry, Kyla, Bertagnolli, Darren, Bickley, Kris, Bomben, Jasmine, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Chong, Peter, Crichton, Kirsten, Dalley, Rachel, de Frates, Rebecca, Desta, Tsega, Lee, Samuel Dingman, D’Orazi, Florence, Dotson, Nadezhda, Egdorf, Tom, Enstrom, Rachel, Farrell, Colin, Feng, David, Fong, Olivia, Furdan, Szabina, Galakhova, Anna A., Gamlin, Clare, Gary, Amanda, Glandon, Alexandra, Goldy, Jeff, Gorham, Melissa, Goriounova, Natalia A., Gratiy, Sergey, Graybuck, Lucas, Gu, Hong, Hadley, Kristen, Hansen, Nathan, Heistek, Tim S., Henry, Alex M., Heyer, Djai B., Hill, DiJon, Hill, Chris, Hupp, Madie, Jarsky, Tim, Kebede, Sara, Keene, Lisa, Kim, Lisa, Kim, Mean-Hwan, Kroll, Matthew, Latimer, Caitlin, Levi, Boaz P., Link, Katherine E., Mallory, Matthew, Mann, Rusty, Marshall, Desiree, Maxwell, Michelle, McGraw, Medea, McMillen, Delissa, Melief, Erica, Mertens, Eline J., Mezei, Leona, Mihut, Norbert, Mok, Stephanie, Molnar, Gabor, Mukora, Alice, Ng, Lindsay, Ngo, Kiet, Nicovich, Philip R., Nyhus, Julie, Olah, Gaspar, Oldre, Aaron, Omstead, Victoria, Ozsvar, Attila, Park, Daniel, Peng, Hanchuan, Pham, Trangthanh, Pom, Christina A., Potekhina, Lydia, Rajanbabu, Ramkumar, Ransford, Shea, Reid, David, Rimorin, Christine, Ruiz, Augustin, Sandman, David, Sulc, Josef, Sunkin, Susan M., Szafer, Aaron, Szemenyei, Viktor, Thomsen, Elliot R., Tieu, Michael, Torkelson, Amy, Trinh, Jessica, Tung, Herman, Wakeman, Wayne, Waleboer, Femke, Ward, Katelyn, Wilbers, René, Williams, Grace, Yao, Zizhen, Yoon, Jae-Geun, Anastassiou, Costas, Arkhipov, Anton, Barzo, Pal, Bernard, Amy, Cobbs, Charles, de Witt Hamer, Philip C., Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gwinn, Ryder P., Hawrylycz, Michael J., Hof, Patrick R., Idema, Sander, Jones, Allan R., Keene, C. Dirk, Ko, Andrew L., Murphy, Gabe J., Ng, Lydia, Ojemann, Jeffrey G., Patel, Anoop P., Phillips, John W., Silbergeld, Daniel L., Smith, Kimberly, Tasic, Bosiljka, Yuste, Rafael, Segev, Idan, de Kock, Christiaan P. J., Mansvelder, Huibert D., Tamas, Gabor, Zeng, Hongkui, Koch, Christof, and Lein, Ed S.
Published: 2021
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9. Connecting single-cell transcriptomes to projectomes in mouse visual cortex

Author: Sorensen, Staci A., primary, Gouwens, Nathan W., additional, Wang, Yun, additional, Mallory, Matt, additional, Budzillo, Agata, additional, Dalley, Rachel, additional, Lee, Brian, additional, Gliko, Olga, additional, Kuo, Hsien-chi, additional, Kuang, Xiuli, additional, Mann, Rusty, additional, Ahmadinia, Leila, additional, Alfiler, Lauren, additional, Baftizadeh, Fahimeh, additional, Baker, Katherine, additional, Bannick, Sarah, additional, Bertagnolli, Darren, additional, Bickley, Kris, additional, Bohn, Phil, additional, Brown, Dillan, additional, Bomben, Jasmine, additional, Brouner, Krissy, additional, Chen, Chao, additional, Chen, Kai, additional, Chvilicek, Maggie, additional, Collman, Forrest, additional, Daigle, Tanya, additional, Dawes, Tim, additional, de Frates, Rebecca, additional, Dee, Nick, additional, DePartee, Maxwell, additional, Egdorf, Tom, additional, El-Hifnawi, Laila, additional, Enstrom, Rachel, additional, Esposito, Luke, additional, Farrell, Colin, additional, Gala, Rohan, additional, Glomb, Andrew, additional, Gamlin, Clare, additional, Gary, Amanda, additional, Goldy, Jeff, additional, Gu, Hong, additional, Hadley, Kristen, additional, Hawrylycz, Mike, additional, Henry, Alex, additional, Hill, Dijon, additional, Hirokawa, Karla E., additional, Huang, Zili, additional, Johnson, Katelyn, additional, Juneau, Zoe, additional, Kebede, Sara, additional, Kim, Lisa, additional, Lee, Changkyu, additional, Lesnar, Phil, additional, Li, Anan, additional, Li, Yaoyao, additional, Liang, Elizabeth, additional, Link, Katie, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa A., additional, Mukora, Alice, additional, Ng, Lindsay, additional, Ochoa, Thomas, additional, Oldre, Aaron, additional, Park, Daniel, additional, Pom, Christina Alice, additional, Popovich, Zoran, additional, Potekhina, Lydia, additional, Rajanbabu, Ram, additional, Ransford, Shea, additional, Reding, Melissa, additional, Ruiz, Augustin, additional, Sandman, David, additional, Siverts, La’Akea, additional, Smith, Kimberly A., additional, Stoecklin, Michelle, additional, Sulc, Josef, additional, Tieu, Michael, additional, Ting, Jonathan, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, Dave, additional, Walker, Miranda, additional, Wang, Micheal, additional, Wanner, Adrian, additional, Waters, Jack, additional, Williams, Grace, additional, Wilson, Julia, additional, Xiong, Wei, additional, Lein, Ed, additional, Berg, Jim, additional, Kalmbach, Brian, additional, Yao, Shenqin, additional, Gong, Hui, additional, Luo, Qingming, additional, Ng, Lydia, additional, Sümbül, Uygar, additional, Jarsky, Tim, additional, Yao, Zizhen, additional, Tasic, Bosiljka, additional, and Zeng, Hongkui, additional
Published: 2023
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10. Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues

Author: Glaser, Adam, primary, Chandrashekar, Jayaram, additional, Vasquez, Joshua, additional, Arshadi, Cameron, additional, Ouellette, Naveen, additional, Jiang, Xiaoyun, additional, Baka, Judith, additional, Kovacs, Gabor, additional, Woodard, Micah, additional, Seshamani, Sharmishtaa, additional, Cao, Kevin, additional, Clack, Nathan, additional, Recknagel, Andrew, additional, Grim, Anna, additional, Balaram, Pooja, additional, Turschak, Emily, additional, Liddell, Alan, additional, Rohde, John, additional, Hellevik, Ayana, additional, Takasaki, Kevin, additional, Barner, Lindsey Erion, additional, Logsdon, Molly, additional, Chronopoulos, Chris, additional, de Vries, Saskia, additional, Ting, Jonathan, additional, Perlmutter, Steve, additional, Kalmbach, Brian, additional, Dembrow, Nikolai, additional, Reid, R. Clay, additional, Feng, David, additional, and Svoboda, Karel, additional
Published: 2023
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11. Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex

Author: Lee, Brian R., primary, Dalley, Rachel, additional, Miller, Jeremy A., additional, Chartrand, Thomas, additional, Close, Jennie, additional, Mann, Rusty, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Bertagnolli, Darren, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Csajbok, Eva, additional, Donadio, Nicholas, additional, Driessens, Stan L.W., additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Galakhova, Anna A., additional, Gary, Amanda, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hadley, Kristen, additional, Heistek, Tim S., additional, Hill, Dijon, additional, Hou, Wen-Hsien, additional, Johansen, Nelson, additional, Jorstad, Nik, additional, Kim, Lisa, additional, Kocsis, Agnes Katalin, additional, Kruse, Lauren, additional, Kunst, Michael, additional, León, Gabriela, additional, Long, Brian, additional, Mallory, Matthew, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica J., additional, Molnar, Gabor, additional, Mortrud, Marty T., additional, Newman, Dakota, additional, Nyhus, Julie, additional, Opitz-Araya, Ximena, additional, Ozsvár, Attila, additional, Pham, Trangthanh, additional, Pom, Alice, additional, Potekhina, Lydia, additional, Rajanbabu, Ram, additional, Ruiz, Augustin, additional, Sunkin, Susan M., additional, Szöts, Ildikó, additional, Taskin, Naz, additional, Thyagarajan, Bargavi, additional, Tieu, Michael, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, David, additional, Waleboer, Femke, additional, Walling-Bell, Sarah, additional, Weed, Natalie, additional, Williams, Grace, additional, Wilson, Julia, additional, Yao, Shenqin, additional, Zhou, Thomas, additional, Barzó, Pál, additional, Bakken, Trygve, additional, Cobbs, Charles, additional, Dee, Nick, additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gouwens, Nathan W., additional, Grannan, Benjamin, additional, Gwinn, Ryder P., additional, Hauptman, Jason S., additional, Hodge, Rebecca, additional, Jarsky, Tim, additional, Keene, C. Dirk, additional, Ko, Andrew L., additional, Korshoej, Anders Rosendal, additional, Levi, Boaz P., additional, Meier, Kaare, additional, Ojemann, Jeffrey G., additional, Patel, Anoop, additional, Ruzevick, Jacob, additional, Silbergeld, Daniel L., additional, Smith, Kimberly, additional, Sørensen, Jens Christian, additional, Waters, Jack, additional, Zeng, Hongkui, additional, Berg, Jim, additional, Capogna, Marco, additional, Goriounova, Natalia A., additional, Kalmbach, Brian, additional, de Kock, Christiaan P.J., additional, Mansvelder, Huib D., additional, Sorensen, Staci A., additional, Tamas, Gabor, additional, Lein, Ed S., additional, and Ting, Jonathan T., additional
Published: 2023
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12. Morpho-electric and computational properties of three types of human hippocampal CA1 pyramidal neurons

Author: Mertens, Eline, primary, Leibner, Yoni, additional, Pie, Jean, additional, Galakhova, Anna, additional, Waleboer, Femke, additional, Meijer, Julia, additional, Heistek, Tim, additional, Wilbers, Rene, additional, Heyer, Djai, additional, Goriounova, Natalia, additional, Idema, Sander, additional, Verhoog, Matthijs, additional, Kalmbach, Brian, additional, Lee, Brian, additional, Gwinn, Ryder, additional, Lein, Ed, additional, Aronica, Eleonora, additional, Ting, Jonathan, additional, Mansvelder, Huib, additional, Segev, Idan, additional, and de Kock, Christiaan, additional
Published: 2023
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13. Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse

Author: 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, Preiss, 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, and Lein, Ed S.
Published: 2022
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14. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification

Author: Berg, Jim, Sorensen, Staci A., Ting, Jonathan T., Miller, Jeremy A., Chartrand, Thomas, Buchin, Anatoly, Bakken, Trygve E., Budzillo, Agata, Dee, Nick, Ding, Song-Lin, Gouwens, Nathan W., Hodge, Rebecca D., Kalmbach, Brian, Lee, Changkyu, Lee, Brian R., Alfiler, Lauren, Baker, Katherine, Barkan, Eliza, Beller, Allison, Berry, Kyla, Bertagnolli, Darren, Bickley, Kris, Bomben, Jasmine, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Chong, Peter, Crichton, Kirsten, Dalley, Rachel, de Frates, Rebecca, Desta, Tsega, Lee, Samuel Dingman, D’Orazi, Florence, Dotson, Nadezhda, Egdorf, Tom, Enstrom, Rachel, Farrell, Colin, Feng, David, Fong, Olivia, Furdan, Szabina, Galakhova, Anna A., Gamlin, Clare, Gary, Amanda, Glandon, Alexandra, Goldy, Jeff, Gorham, Melissa, Goriounova, Natalia A., Gratiy, Sergey, Graybuck, Lucas, Gu, Hong, Hadley, Kristen, Hansen, Nathan, Heistek, Tim S., Henry, Alex M., Heyer, Djai B., Hill, DiJon, Hill, Chris, Hupp, Madie, Jarsky, Tim, Kebede, Sara, Keene, Lisa, Kim, Lisa, Kim, Mean-Hwan, Kroll, Matthew, Latimer, Caitlin, Levi, Boaz P., Link, Katherine E., Mallory, Matthew, Mann, Rusty, Marshall, Desiree, Maxwell, Michelle, McGraw, Medea, McMillen, Delissa, Melief, Erica, Mertens, Eline J., Mezei, Leona, Mihut, Norbert, Mok, Stephanie, Molnar, Gabor, Mukora, Alice, Ng, Lindsay, Ngo, Kiet, Nicovich, Philip R., Nyhus, Julie, Olah, Gaspar, Oldre, Aaron, Omstead, Victoria, Ozsvar, Attila, Park, Daniel, Peng, Hanchuan, Pham, Trangthanh, Pom, Christina A., Potekhina, Lydia, Rajanbabu, Ramkumar, Ransford, Shea, Reid, David, Rimorin, Christine, Ruiz, Augustin, Sandman, David, Sulc, Josef, Sunkin, Susan M., Szafer, Aaron, Szemenyei, Viktor, Thomsen, Elliot R., Tieu, Michael, Torkelson, Amy, Trinh, Jessica, Tung, Herman, Wakeman, Wayne, Waleboer, Femke, Ward, Katelyn, Wilbers, René, Williams, Grace, Yao, Zizhen, Yoon, Jae-Geun, Anastassiou, Costas, Arkhipov, Anton, Barzo, Pal, Bernard, Amy, Cobbs, Charles, de Witt Hamer, Philip C., Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gwinn, Ryder P., Hawrylycz, Michael J., Hof, Patrick R., Idema, Sander, Jones, Allan R., Keene, C. Dirk, Ko, Andrew L., Murphy, Gabe J., Ng, Lydia, Ojemann, Jeffrey G., Patel, Anoop P., Phillips, John W., Silbergeld, Daniel L., Smith, Kimberly, Tasic, Bosiljka, Yuste, Rafael, Segev, Idan, de Kock, Christiaan P. J., Mansvelder, Huibert D., Tamas, Gabor, Zeng, Hongkui, Koch, Christof, and Lein, Ed S.
Published: 2022
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15. Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex

Author: Kim, Mean-Hwan, primary, Radaelli, Cristina, additional, Thomsen, Elliot R, additional, Monet, Deja, additional, Chartrand, Thomas, additional, Jorstad, Nikolas L, additional, Mahoney, Joseph T, additional, Taormina, Michael J, additional, Long, Brian, additional, Baker, Katherine, additional, Bakken, Trygve E, additional, Campagnola, Luke, additional, Casper, Tamara, additional, Clark, Michael, additional, Dee, Nick, additional, D'Orazi, Florence, additional, Gamlin, Clare, additional, Kalmbach, Brian E, additional, Kebede, Sara, additional, Lee, Brian R, additional, Ng, Lindsay, additional, Trinh, Jessica, additional, Cobbs, Charles, additional, Gwinn, Ryder P, additional, Keene, C Dirk, additional, Ko, Andrew L, additional, Ojemann, Jeffrey G, additional, Silbergeld, Daniel L, additional, Sorensen, Staci A, additional, Berg, Jim, additional, Smith, Kimberly A, additional, Nicovich, Philip R, additional, Jarsky, Tim, additional, Zeng, Hongkui, additional, Ting, Jonathan T, additional, Levi, Boaz P, additional, and Lein, Ed, additional
Published: 2023
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16. Integrated multimodal cell atlas of Alzheimer’s disease

Author: Gabitto, Mariano, primary, Travaglini, Kyle, additional, Ariza, Jeannelle, additional, Kaplan, Eitan, additional, Long, Brian, additional, Rachleff, Victoria, additional, Ding, Yi, additional, Mahoney, Joseph, additional, Dee, Nick, additional, Goldy, Jeff, additional, Melief, Erica, additional, Brouner, Krissy, additional, Compos, Jazmin, additional, Campos, John, additional, Carr, Ambrose, additional, Casper, Tamara, additional, Chakrabarty, Rushil, additional, Clark, Michael, additional, Cool, Jonah, additional, Dalley, Rachel, additional, Darvas, Martin, additional, Dolbeare, Tim, additional, Ding, Song-Lin, additional, Egdorf, Tom, additional, Esposito, Luke, additional, Ferrer, Rebecca, additional, Gala, Rohan, additional, Gary, Amanda, additional, Gloe, Jessica, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Ho, Windy, additional, Jarsky, Tim, additional, Johansen, Nelson, additional, Kalmbach, Brian, additional, Keene, Lisa, additional, Khawand, Sarah, additional, Kilgore, Mitchell, additional, Kirkland, Amanda, additional, Kunst, Michael, additional, Lee, Brian, additional, Donald, Christine Mac, additional, Malone, Jocelin, additional, Maltzer, Zoe, additional, Martin, Naomi, additional, McCue, Rachel, additional, McMillen, Delissa, additional, Meyerdierks, Emma, additional, Meyers, Kelly, additional, Mollenkopf, Tyler, additional, Montine, Mark, additional, Nolan, Amber, additional, Nyhus, Julie, additional, Olsen, Paul, additional, Pacleb, Maiya, additional, Pham, Trangthanh, additional, Pom, Christina, additional, Postupna, Nadia, additional, Ruiz, Augustin, additional, Schantz, Aimee, additional, Sorensen, Staci, additional, Staats, Brian, additional, Sullivan, Matt, additional, Sunkin, Susan, additional, Thompson, Carol, additional, Tieu, Michael, additional, Ting, Jonathan, additional, Torkelson, Amy, additional, Tran, Tracy, additional, Cuevas, Nasmil Valera, additional, Wang, Ming-Qiang, additional, Waters, Jack, additional, Wilson, Angela, additional, Haynor, David, additional, Gatto, Nicole, additional, Jayadev, Suman, additional, Mufti, Shoaib, additional, Ng, Lydia, additional, Mukherjee, Shubhabrata, additional, Crane, Paul, additional, Latimer, Caitlin, additional, Levi, Boaz, additional, Smith, Kimberly, additional, Close, Jennie, additional, Miller, Jeremy, additional, Hodge, Rebecca, additional, Larson, Eric, additional, Grabowski, Thomas, additional, Hawrylycz, Michael, additional, Keene, C., additional, and Lein, Ed, additional
Published: 2023
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17. Integrated multimodal cell atlas of Alzheimer’s disease

Author: Gabitto, Mariano I., primary, Travaglini, Kyle J., additional, Rachleff, Victoria M., additional, Kaplan, Eitan S., additional, Long, Brian, additional, Ariza, Jeanelle, additional, Ding, Yi, additional, Mahoney, Joseph T., additional, Dee, Nick, additional, Goldy, Jeff, additional, Melief, Erica J., additional, Brouner, Krissy, additional, Campos, Jazmin, additional, Campos, John, additional, Carr, Ambrose J., additional, Casper, Tamara, additional, Chakrabarty, Rushil, additional, Clark, Michael, additional, Cool, Jonah, additional, Valera Cuevas, Nasmil J., additional, Dalley, Rachel, additional, Darvas, Martin, additional, Ding, Song-Lin, additional, Dolbeare, Tim, additional, Mac Donald, Christine L., additional, Egdorf, Tom, additional, Esposito, Luke, additional, Ferrer, Rebecca, additional, Gala, Rohan, additional, Gary, Amanda, additional, Gloe, Jessica, additional, Guilford, Nathan, additional, Guzman, Junitta, additional, Hirschstein, Daniel, additional, Ho, Windy, additional, Jarksy, Tim, additional, Johansen, Nelson, additional, Kalmbach, Brian E., additional, Keene, Lisa M., additional, Khawand, Sarah, additional, Kilgore, Mitch, additional, Kirkland, Amanda, additional, Kunst, Michael, additional, Lee, Brian R., additional, Malone, Jocelin, additional, Maltzer, Zoe, additional, Martin, Naomi, additional, McCue, Rachel, additional, McMillen, Delissa, additional, Meyerdierks, Emma, additional, Meyers, Kelly P., additional, Mollenkopf, Tyler, additional, Montine, Mark, additional, Nolan, Amber L., additional, Nyhus, Julie, additional, Olsen, Paul A., additional, Pacleb, Maiya, additional, Peña, Nicholas, additional, Pham, Thanh, additional, Pom, Christina Alice, additional, Postupna, Nadia, additional, Ruiz, Augustin, additional, Schantz, Aimee M., additional, Shapovalova, Nadiya V., additional, Sorensen, Staci A., additional, Staats, Brian, additional, Sullivan, Matt, additional, Sunkin, Susan M., additional, Thompson, Carol, additional, Tieu, Michael, additional, Ting, Jonathan, additional, Torkelson, Amy, additional, Tran, Tracy, additional, Wang, Ming-Qiang, additional, Waters, Jack, additional, Wilson, Angela M., additional, Haynor, David, additional, Gatto, Nicole, additional, Jayadev, Suman, additional, Mufti, Shoaib, additional, Ng, Lydia, additional, Mukherjee, Shubhabrata, additional, Crane, Paul K., additional, Latimer, Caitlin S., additional, Levi, Boaz P., additional, Smith, Kimberly, additional, Close, Jennie L., additional, Miller, Jeremy A., additional, Hodge, Rebecca D., additional, Larson, Eric B., additional, Grabowski, Thomas J., additional, Hawrylycz, Michael, additional, Dirk Keene, C., additional, and Lein, Ed S., additional
Published: 2023
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18. Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

Author: Chartrand, Thomas, Dalley, Rachel, Close, Jennie, Goriounova, Natalia A., Lee, Brian R., Mann, Rusty, Miller, Jeremy A., Molnar, Gabor, Mukora, Alice, Alfiler, Lauren, Baker, Katherine, Bakken, Trygve E., Berg, Jim, Bertagnolli, Darren, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Csajbok, Eva Adrienn, Dee, Nick, Egdorf, Tom, Enstrom, Rachel, Galakhova, Anna A., Gary, Amanda, Gelfand, Emily, Goldy, Jeff, Hadley, Kristen, Heistek, Tim S., Hill, Di Jon, Jorstad, Nik, Kim, Lisa, Kocsis, Agnes Katalin, Kruse, Lauren, Kunst, Michael, Leon, Gabriela, Long, Brian, Mallory, Matthew, McGraw, Medea, McMillen, Delissa, Melief, Erica J., Mihut, Norbert, Ng, Lindsay, Nyhus, Julie, Oláh, Gáspár, Ozsvár, Attila, Omstead, Victoria, Peterfi, Zoltan, Pom, Alice, Potekhina, Lydia, Rajanbabu, Ramkumar, Rozsa, Marton, Ruiz, Augustin, Sandle, Joanna, Sunkin, Susan M., Szots, Ildiko, Tieu, Michael, Toth, Martin, Trinh, Jessica, Vargas, Sara, Vumbaco, David, Williams, Grace, Wilson, Julia, Yao, Zizhen, Barzo, Pal, Cobbs, Charles, Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gouwens, Nathan W., Grannan, Benjamin, Gwinn, Ryder P., Hauptman, Jason S., Jarsky, Tim, Keene, C. Dirk, Ko, Andrew L., Koch, Christof, Ojemann, Jeffrey G., Patel, Anoop, Ruzevick, Jacob, Silbergeld, Daniel L., Smith, Kimberly, Sorensen, Staci A., Tasic, Bosiljka, Ting, Jonathan T., Waters, Jack, de Kock, Christiaan P.J., Mansvelder, Huib D., Tamas, Gabor, Zeng, Hongkui, Kalmbach, Brian, Lein, Ed S., Chartrand, Thomas, Dalley, Rachel, Close, Jennie, Goriounova, Natalia A., Lee, Brian R., Mann, Rusty, Miller, Jeremy A., Molnar, Gabor, Mukora, Alice, Alfiler, Lauren, Baker, Katherine, Bakken, Trygve E., Berg, Jim, Bertagnolli, Darren, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Csajbok, Eva Adrienn, Dee, Nick, Egdorf, Tom, Enstrom, Rachel, Galakhova, Anna A., Gary, Amanda, Gelfand, Emily, Goldy, Jeff, Hadley, Kristen, Heistek, Tim S., Hill, Di Jon, Jorstad, Nik, Kim, Lisa, Kocsis, Agnes Katalin, Kruse, Lauren, Kunst, Michael, Leon, Gabriela, Long, Brian, Mallory, Matthew, McGraw, Medea, McMillen, Delissa, Melief, Erica J., Mihut, Norbert, Ng, Lindsay, Nyhus, Julie, Oláh, Gáspár, Ozsvár, Attila, Omstead, Victoria, Peterfi, Zoltan, Pom, Alice, Potekhina, Lydia, Rajanbabu, Ramkumar, Rozsa, Marton, Ruiz, Augustin, Sandle, Joanna, Sunkin, Susan M., Szots, Ildiko, Tieu, Michael, Toth, Martin, Trinh, Jessica, Vargas, Sara, Vumbaco, David, Williams, Grace, Wilson, Julia, Yao, Zizhen, Barzo, Pal, Cobbs, Charles, Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gouwens, Nathan W., Grannan, Benjamin, Gwinn, Ryder P., Hauptman, Jason S., Jarsky, Tim, Keene, C. Dirk, Ko, Andrew L., Koch, Christof, Ojemann, Jeffrey G., Patel, Anoop, Ruzevick, Jacob, Silbergeld, Daniel L., Smith, Kimberly, Sorensen, Staci A., Tasic, Bosiljka, Ting, Jonathan T., Waters, Jack, de Kock, Christiaan P.J., Mansvelder, Huib D., Tamas, Gabor, Zeng, Hongkui, Kalmbach, Brian, and Lein, Ed S.
Abstract: Neocortical layer 1 (L1) is a site of convergence between pyramidal-neuron dendrites and feedback axons where local inhibitory signaling can profoundly shape cortical processing. Evolutionary expansion of human neocortex is marked by distinctive pyramidal neurons with extensive L1 branching, but whether L1 interneurons are similarly diverse is underexplored. Using Patch-seq recordings from human neurosurgical tissue, we identified four transcriptomic subclasses with mouse L1 homologs, along with distinct subtypes and types unmatched in mouse L1. Subclass and subtype comparisons showed stronger transcriptomic differences in human L1 and were correlated with strong morphoelectric variability along dimensions distinct from mouse L1 variability. Accompanied by greater layer thickness and other cytoarchitecture changes, these findings suggest that L1 has diverged in evolution, reflecting the demands of regulating the expanded human neocortical circuit.
Published: 2023
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19. Integrated multimodal cell atlas of Alzheimer’s disease

Author: Gabitto, Mariano I., Travaglini, Kyle J., Rachleff, Victoria M., Kaplan, Eitan S., Long, Brian, Ariza, Jeanelle, Ding, Yi, Mahoney, Joseph T., Dee, Nick, Goldy, Jeff, Melief, Erica J., Agrawal, Anamika, Kana, Omar, Zhen, Xingjian, Barlow, Samuel T., Brouner, Krissy, Campos, Jazmin, Campos, John, Carr, Ambrose J., Casper, Tamara, Chakrabarty, Rushil, Clark, Michael, Cool, Jonah, Dalley, Rachel, Darvas, Martin, Ding, Song-Lin, Dolbeare, Tim, Egdorf, Tom, Esposito, Luke, Ferrer, Rebecca, Fleckenstein, Lynn E., Gala, Rohan, Gary, Amanda, Gelfand, Emily, Gloe, Jessica, Guilford, Nathan, Guzman, Junitta, Hirschstein, Daniel, Ho, Windy, Hupp, Madison, Jarsky, Tim, Johansen, Nelson, Kalmbach, Brian E., Keene, Lisa M., Khawand, Sarah, Kilgore, Mitchell D., Kirkland, Amanda, Kunst, Michael, Lee, Brian R., Leytze, Mckaila, Mac Donald, Christine L., Malone, Jocelin, Maltzer, Zoe, Martin, Naomi, McCue, Rachel, McMillen, Delissa, Mena, Gonzalo, Meyerdierks, Emma, Meyers, Kelly P., Mollenkopf, Tyler, Montine, Mark, Nolan, Amber L., Nyhus, Julie K., Olsen, Paul A., Pacleb, Maiya, Pagan, Chelsea M., Peña, Nicholas, Pham, Trangthanh, Pom, Christina Alice, Postupna, Nadia, Rimorin, Christine, Ruiz, Augustin, Saldi, Giuseppe A., Schantz, Aimee M., Shapovalova, Nadiya V., Sorensen, Staci A., Staats, Brian, Sullivan, Matt, Sunkin, Susan M., Thompson, Carol, Tieu, Michael, Ting, Jonathan T., Torkelson, Amy, Tran, Tracy, Valera Cuevas, Nasmil J., Walling-Bell, Sarah, Wang, Ming-Qiang, Waters, Jack, Wilson, Angela M., Xiao, Ming, Haynor, David, Gatto, Nicole M., Jayadev, Suman, Mufti, Shoaib, Ng, Lydia, Mukherjee, Shubhabrata, Crane, Paul K., Latimer, Caitlin S., Levi, Boaz P., Smith, Kimberly A., Close, Jennie L., Miller, Jeremy A., Hodge, Rebecca D., Larson, Eric B., Grabowski, Thomas J., Hawrylycz, Michael, Keene, C. Dirk, and Lein, Ed S.
Abstract: Alzheimer’s disease (AD) is the leading cause of dementia in older adults. Although AD progression is characterized by stereotyped accumulation of proteinopathies, the affected cellular populations remain understudied. Here we use multiomics, spatial genomics and reference atlases from the BRAIN Initiative to study middle temporal gyrus cell types in 84 donors with varying AD pathologies. This cohort includes 33 male donors and 51 female donors, with an average age at time of death of 88 years. We used quantitative neuropathology to place donors along a disease pseudoprogression score. Pseudoprogression analysis revealed two disease phases: an early phase with a slow increase in pathology, presence of inflammatory microglia, reactive astrocytes, loss of somatostatin+inhibitory neurons, and a remyelination response by oligodendrocyte precursor cells; and a later phase with exponential increase in pathology, loss of excitatory neurons and Pvalb+and Vip+inhibitory neuron subtypes. These findings were replicated in other major AD studies.
Published: 2024
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20. Impaired dendritic spike generation in the Fragile X prefrontal cortex is due to loss of dendritic sodium channels

Author: Brandalise, Federico, primary, Kalmbach, Brian E., additional, Cook, Erik P., additional, and Brager, Darrin H., additional
Published: 2023
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21. Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex

Author: Lee, Brian, primary, Dalley, Rachel, additional, Miller, Jeremy A, additional, Chartrand, Thomas, additional, Close, Jennie, additional, Mann, Rusty, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Bertagnolli, Darren, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Csajbok, Eva, additional, Dee, Nick, additional, Donadio, Nicholas, additional, Driessens, Stan L.W., additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Galakhova, Anna A, additional, Gary, Amanda, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hadley, Kristen, additional, Heistek, Tim S., additional, Hill, Dijon, additional, Johansen, Nelson, additional, Jorstad, Nik, additional, Kim, Lisa, additional, Kocsis, Agnes Katalin, additional, Kruse, Lauren, additional, Kunst, Michael, additional, Leon, Gabriela, additional, Long, Brian, additional, Mallory, Matthew, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica J, additional, Molnar, Gabor, additional, Mortrud, Marty T, additional, Newman, Dakota, additional, Nyhus, Julie, additional, Opitz-Araya, Ximena, additional, Pham, Trangthanh, additional, Pom, Alice, additional, Potekhina, Lydia, additional, Rajanbabu, Ram, additional, Ruiz, Augustin, additional, Sunkin, Susan M, additional, Szots, Ildiko, additional, Taskin, Naz, additional, Thyagarajan, Bargavi, additional, Tieu, Michael, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, David, additional, Waleboer, Femke, additional, Weed, Natalie, additional, Williams, Grace, additional, Wilson, Julia, additional, Yao, Shenqin, additional, Zhou, Thomas, additional, Barzo, Pal, additional, Bakken, Trygve, additional, Cobbs, Charles, additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gouwens, Nathan W, additional, Grannan, Benjamin, additional, Gwinn, Ryder P., additional, Hauptman, Jason S., additional, Hodge, Rebecca, additional, Jarsky, Tim, additional, Keene, C.Dirk, additional, Ko, Andrew L., additional, Levi, Boaz, additional, Ojemann, Jeffrey G., additional, Patel, Anoop, additional, Ruzevick, Jacob, additional, Silbergeld, Daniel L., additional, Smith, Kim, additional, Waters, Jack, additional, Zeng, Hongkui, additional, Berg, Jim, additional, Goriounova, Natalia A., additional, Kalmbach, Brian, additional, de Kock, Christiaan P.J., additional, Mansvelder, Huib D, additional, Sorensen, Staci A, additional, Tamas, Gabor, additional, Lein, Ed S., additional, and Ting, Jonathan T, additional
Published: 2022
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22. Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types

Author: Nandi, Anirban, primary, Chartrand, Thomas, additional, Van Geit, Werner, additional, Buchin, Anatoly, additional, Yao, Zizhen, additional, Lee, Soo Yeun, additional, Wei, Yina, additional, Kalmbach, Brian, additional, Lee, Brian, additional, Lein, Ed, additional, Berg, Jim, additional, Sümbül, Uygar, additional, Koch, Christof, additional, Tasic, Bosiljka, additional, and Anastassiou, Costas A., additional
Published: 2022
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23. Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

Author: Chartrand, Thomas, primary, Dalley, Rachel, additional, Close, Jennie, additional, Goriounova, Natalia A., additional, Lee, Brian R., additional, Mann, Rusty, additional, Miller, Jeremy A., additional, Molnar, Gabor, additional, Mukora, Alice, additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Bakken, Trygve E., additional, Berg, Jim, additional, Bertagnolli, Darren, additional, Braun, Thomas, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Csajbok, Eva Adrienn, additional, Dee, Nick, additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Galakhova, Anna A., additional, Gary, Amanda, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hadley, Kristen, additional, Heistek, Tim S., additional, Hill, DiJon, additional, Jorstad, Nik, additional, Kim, Lisa, additional, Kocsis, Agnes Katalin, additional, Kruse, Lauren, additional, Kunst, Michael, additional, Leon, Gabriela, additional, Long, Brian, additional, Mallory, Matthew, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica J., additional, Mihut, Norbert, additional, Ng, Lindsay, additional, Nyhus, Julie, additional, Omstead, Victoria, additional, Peterfi, Zoltan, additional, Pom, Alice, additional, Potekhina, Lydia, additional, Rajanbabu, Ramkumar, additional, Rozsa, Marton, additional, Ruiz, Augustin, additional, Sandle, Joanna, additional, Sunkin, Susan M., additional, Szots, Ildiko, additional, Tieu, Michael, additional, Toth, Martin, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, David, additional, Williams, Grace, additional, Wilson, Julia, additional, Yao, Zizhen, additional, Barzo, Pal, additional, Cobbs, Charles, additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gouwens, Nathan W., additional, Grannan, Benjamin, additional, Gwinn, Ryder P., additional, Hauptman, Jason S., additional, Jarsky, Tim, additional, Keene, C.Dirk, additional, Ko, Andrew L., additional, Koch, Christof, additional, Ojemann, Jeffrey G., additional, Patel, Anoop, additional, Ruzevick, Jacob, additional, Silberberg, Daniel L., additional, Smith, Kimberly, additional, Sorensen, Staci A., additional, Tasic, Bosiljka, additional, Ting, Jonathan T., additional, Waters, Jack, additional, de Kock, Christiaan P.J., additional, Mansvelder, Huib D., additional, Tamas, Gabor, additional, Zeng, Hongkui, additional, Kalmbach, Brian, additional, and Lein, Ed S., additional
Published: 2022
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24. A robust ex vivo experimental platform for molecular-genetic dissection of adult human neocortical cell types and circuits

Author: Ting, Jonathan T., Kalmbach, Brian, Chong, Peter, de Frates, Rebecca, Keene, C. Dirk, Gwinn, Ryder P., Cobbs, Charles, Ko, Andrew L., Ojemann, Jeffrey G., Ellenbogen, Richard G., Koch, Christof, and Lein, Ed
Published: 2018
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25. Interactions between Prefrontal Cortex and Cerebellum Revealed by Trace Eyelid Conditioning

Author: Kalmbach, Brian E., Ohyama, Tatsuya, and Kreider, Joy C.
Abstract: Eyelid conditioning has proven useful for analysis of learning and computation in the cerebellum. Two variants, delay and trace conditioning, differ only by the relative timing of the training stimuli. Despite the subtlety of this difference, trace eyelid conditioning is prevented by lesions of the cerebellum, hippocampus, or medial prefrontal cortex (mPFC), whereas delay eyelid conditioning is prevented by cerebellar lesions and is largely unaffected by forebrain lesions. Here we test whether these lesion results can be explained by two assertions: (1) Cerebellar learning requires temporal overlap between the mossy fiber inputs activated by the tone conditioned stimulus (CS) and the climbing fiber inputs activated by the reinforcing unconditioned stimulus (US), and therefore (2) trace conditioning requires activity that outlasts the presentation of the CS in a subset of mossy fibers separate from those activated directly by the CS. By use of electrical stimulation of mossy fibers as a CS, we show that cerebellar learning during trace eyelid conditioning requires an input that persists during the stimulus-free trace interval. By use of reversible inactivation experiments, we provide evidence that this input arises from the mPFC and arrives at the cerebellum via a previously unidentified site in the pontine nuclei. In light of previous PFC recordings in various species, we suggest that trace eyelid conditioning involves an interaction between the persistent activity of delay cells in mPFC-a putative mechanism of working memory-and motor learning in the cerebellum.
Published: 2009
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26. Comparative cellular analysis of motor cortex in human, marmoset and mouse

Author: 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., 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, and Lein, Ed S.
Abstract: AbstractThe primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
Published: 2022

27. Impaired dendritic spike generation in the Fragile X prefrontal cortex is due to loss of dendritic sodium channels

Author: Brandalise, Federico, primary, Kalmbach, Brian E., additional, Cook, Erik P., additional, and Brager, Darrin H., additional
Published: 2022
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28. Author Correction:Human neocortical expansion involves glutamatergic neuron diversification (Nature, (2021), 598, 7879, (151-158), 10.1038/s41586-021-03813-8)

Author: Berg, Jim, Sorensen, Staci A., Ting, Jonathan T., Miller, Jeremy A., Chartrand, Thomas, Buchin, Anatoly, Bakken, Trygve E., Budzillo, Agata, Dee, Nick, Ding, Song-Lin, Gouwens, Nathan W., Hodge, Rebecca D., Kalmbach, Brian, Lee, Changkyu, Lee, Brian R., Alfiler, Lauren, Baker, Katherine, Barkan, Eliza, Beller, Allison, Berry, Kyla, Bertagnolli, Darren, Bickley, Kris, Bomben, Jasmine, Braun, Thomas, Brouner, Krissy, Casper, Tamara, Chong, Peter, Crichton, Kirsten, Dalley, Rachel, de Frates, Rebecca, Desta, Tsega, Lee, Samuel Dingman, D’Orazi, Florence, Dotson, Nadezhda, Egdorf, Tom, Enstrom, Rachel, Farrell, Colin, Feng, David, Fong, Olivia, Furdan, Szabina, Galakhova, Anna A., Gamlin, Clare, Gary, Amanda, Glandon, Alexandra, Goldy, Jeff, Gorham, Melissa, Goriounova, Natalia A., Gratiy, Sergey, Graybuck, Lucas, Gu, Hong, Hadley, Kristen, Hansen, Nathan, Heistek, Tim S., Henry, Alex M., Heyer, Djai B., Hill, DiJon, Hill, Chris, Hupp, Madie, Jarsky, Tim, Kebede, Sara, Keene, Lisa, Kim, Lisa, Kim, Mean-Hwan, Kroll, Matthew, Latimer, Caitlin, Levi, Boaz P., Link, Katherine E., Mallory, Matthew, Mann, Rusty, Marshall, Desiree, Maxwell, Michelle, McGraw, Medea, McMillen, Delissa, Melief, Erica, Mertens, Eline J., Mezei, Leona, Mihut, Norbert, Mok, Stephanie, Molnar, Gabor, Mukora, Alice, Ng, Lindsay, Ngo, Kiet, Nicovich, Philip R., Nyhus, Julie, Olah, Gaspar, Oldre, Aaron, Omstead, Victoria, Ozsvar, Attila, Park, Daniel, Peng, Hanchuan, Pham, Trangthanh, Pom, Christina A., Potekhina, Lydia, Rajanbabu, Ramkumar, Ransford, Shea, Reid, David, Rimorin, Christine, Ruiz, Augustin, Sandman, David, Sulc, Josef, Sunkin, Susan M., Szafer, Aaron, Szemenyei, Viktor, Thomsen, Elliot R., Tieu, Michael, Torkelson, Amy, Trinh, Jessica, Tung, Herman, Wakeman, Wayne, Waleboer, Femke, Ward, Katelyn, Wilbers, René, Williams, Grace, Yao, Zizhen, Yoon, Jae-Geun, Anastassiou, Costas, Arkhipov, Anton, Barzo, Pal, Bernard, Amy, Cobbs, Charles, de Witt Hamer, Philip C., Ellenbogen, Richard G., Esposito, Luke, Ferreira, Manuel, Gwinn, Ryder P., Hawrylycz, Michael J., Hof, Patrick R., Idema, Sander, Jones, Allan R., Keene, C. Dirk, Ko, Andrew L., Murphy, Gabe J., Ng, Lydia, Ojemann, Jeffrey G., Patel, Anoop P., Phillips, John W., Silbergeld, Daniel L., Smith, Kimberly, Tasic, Bosiljka, Yuste, Rafael, Segev, Idan, de Kock, Christiaan P. J., Mansvelder, Huibert D., Tamas, Gabor, Zeng, Hongkui, Koch, Christof, and Lein, Ed S.
Abstract: In the version of this Article initially published, the Acknowledgements statement contained an error. Originally appearing with thanks for support given in part as follows, “R01EY023173 from The National Eye Institute, U01MH105982 from the National Institute of Mental Health and Eunice Kennedy Shriver National Institute of Child Health and Human Development, and R011EY023173 from The National Institute of Allergy and Infectious Disease,” the last number (R011EY023173) was mistakenly added and is not in fact a grant or one provided by the NIAID. The mention has been removed. The changes have been made to the online version of the Article.
Published: 2022

29. A multimodal cell census and atlas of the mammalian primary motor cortex

Author: Callaway, Edward M., Dong, Hong-Wei, Ecker, Joseph R., Hawrylycz, Michael J., Huang, Z. Josh, Lein, Ed S., Ngai, John, Osten, Pavel, Ren, Bing, Tolias, Andreas Savas, White, Owen, Zeng, Hongkui, Zhuang, Xiaowei, Ascoli, Giorgio A., Behrens, M. Margarita, Chun, Jerold, Feng, Guoping, Gee, James C., Ghosh, Satrajit S., Halchenko, Yaroslav O., Hertzano, Ronna, Lim, Byung Kook, Martone, Maryann E., Ng, Lydia, Pachter, Lior, Ropelewski, Alexander J., Tickle, Timothy L., Yang, X. William, Zhang, Kun, Bakken, Trygve E., Berens, Philipp, Daigle, Tanya L., Harris, Julie A., Jorstad, Nikolas L., Kalmbach, Brian E., Kobak, Dmitry, Li, Yang Eric, Liu, Hanqing, Matho, Katherine S., Mukamel, Eran A., Naeemi, Maitham, Scala, Federico, Tan, Pengcheng, Ting, Jonathan T., Xie, Fangming, Zhang, Meng, Zhang, Zhuzhu, Zhou, Jingtian, Zingg, Brian, Armand, Ethan, Yao, Zizhen, Bertagnolli, Darren, Casper, Tamara, Crichton, Kirsten, Dee, Nick, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Dougherty, Elizabeth L., Fong, Olivia, Goldman, Melissa, Goldy, Jeff, Hodge, Rebecca D., Hu, Lijuan, Keene, C. Dirk, Krienen, Fenna M., Kroll, Matthew, Lake, Blue B., Lathia, Kanan, Linnarsson, Sten, Liu, Christine S., Macosko, Evan Z., McCarroll, Steven A., McMillen, Delissa, Nadaf, Naeem M., Nguyen, Thuc Nghi, Palmer, Carter R., Pham, Thanh, Plongthongkum, Nongluk, Reed, Nora M., Regev, Aviv, Rimorin, Christine, Romanow, William J., Savoia, Steven, Siletti, Kimberly, Smith, Kimberly, Sulc, Josef, Tasic, Bosiljka, Tieu, Michael, Torkelson, Amy, Tung, Herman, van Velthoven, Cindy T. J., Vanderburg, Charles R., Yanny, Anna Marie, Fang, Rongxin, Hou, Xiaomeng, Lucero, Jacinta D., Osteen, Julia K., Pinto-Duarte, Antonio, Poirion, Olivier, Preissl, Sebastian, Wang, Xinxin, Aldridge, Andrew I., Bartlett, Anna, Boggeman, Lara, O’Connor, Carolyn, Castanon, Rosa G., Chen, Huaming, Fitzpatrick, Conor, Luo, Chongyuan, Nery, Joseph R., Nunn, Michael, Rivkin, Angeline C., Tian, Wei, Dominguez, Bertha, Ito-Cole, Tony, Jacobs, Matthew, Jin, Xin, Lee, Cheng-Ta, Lee, Kuo-Fen, Miyazaki, Paula Assakura, Pang, Yan, Rashid, Mohammad, Smith, Jared B., Vu, Minh, Williams, Elora, Biancalani, Tommaso, Booeshaghi, A. Sina, Crow, Megan, Dudoit, Sandrine, Fischer, Stephan, Gillis, Jesse, Hu, Qiwen, Kharchenko, Peter V., Niu, Sheng-Yong, Ntranos, Vasilis, Purdom, Elizabeth, Risso, Davide, de Bézieux, Hector Roux, Somasundaram, Saroja, Street, Kelly, Svensson, Valentine, Vaishnav, Eeshit Dhaval, Van den Berge, Koen, Welch, Joshua D., An, Xu, Bateup, Helen S., Bowman, Ian, Chance, Rebecca K., Foster, Nicholas N., Galbavy, William, Gong, Hui, Gou, Lin, Hatfield, Joshua T., Hintiryan, Houri, Hirokawa, Karla E., Kim, Gukhan, Kramer, Daniel J., Li, Anan, Li, Xiangning, Luo, Qingming, Muñoz-Castañeda, Rodrigo, Stafford, David A., Feng, Zhao, Jia, Xueyan, Jiang, Shengdian, Jiang, Tao, Kuang, Xiuli, Larsen, Rachael, Lesnar, Phil, Li, Yaoyao, Li, Yuanyuan, Liu, Lijuan, Peng, Hanchuan, Qu, Lei, Ren, Miao, Ruan, Zongcai, Shen, Elise, Song, Yuanyuan, Wakeman, Wayne, Wang, Peng, Wang, Yimin, Wang, Yun, Yin, Lulu, Yuan, Jing, Zhao, Sujun, Zhao, Xuan, Narasimhan, Arun, Palaniswamy, Ramesh, Banerjee, Samik, Ding, Liya, Huilgol, Dhananjay, Huo, Bingxing, Kuo, Hsien-Chi, Laturnus, Sophie, Li, Xu, Mitra, Partha P., Mizrachi, Judith, Wang, Quanxin, Xie, Peng, Xiong, Feng, Yu, Yang, Eichhorn, Stephen W., Berg, Jim, Bernabucci, Matteo, Bernaerts, Yves, Cadwell, Cathryn René, Castro, Jesus Ramon, Dalley, Rachel, Hartmanis, Leonard, Horwitz, Gregory D., Jiang, Xiaolong, Ko, Andrew L., Miranda, Elanine, Mulherkar, Shalaka, Nicovich, Philip R., Owen, Scott F., Sandberg, Rickard, Sorensen, Staci A., Tan, Zheng Huan, Allen, Shona, Hockemeyer, Dirk, Lee, Angus Y., Veldman, Matthew B., Adkins, Ricky S., Ament, Seth A., Bravo, Héctor Corrada, Carter, Robert, Chatterjee, Apaala, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Felix, Victor, Giglio, Michelle, Herb, Brian R., Kancherla, Jayaram, Mahurkar, Anup, McCracken, Carrie, Nickel, Lance, Olley, Dustin, Orvis, Joshua, Schor, Michael, Hood, Greg, Dichter, Benjamin, Grauer, Michael, Helba, Brian, Bandrowski, Anita, Barkas, Nikolaos, Carlin, Benjamin, D’Orazi, Florence D., Degatano, Kylee, Gillespie, Thomas H., Khajouei, Farzaneh, Konwar, Kishori, Thompson, Carol, Kelly, Kathleen, Mok, Stephanie, Sunkin, Susan, BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, [missing], BICCN contributing principal investigators, [missing], Principal manuscript editors, [missing], Manuscript writing and figure generation, [missing], Analysis coordination, [missing], Integrated data analysis, [missing], scRNA-seq and snRNA-seq data generation and processing, [missing], ATAC-seq data generation and processing, [missing], Methylcytosine data production and analysis, [missing], Epi-retro-seq data generation and processing, [missing], ‘Omics data analysis, [missing], Tracing and connectivity data generation, [missing], Morphology data generation and reconstruction, [missing], OLST/STPT and other data generation, [missing], Morphology, connectivity and imaging analysis, [missing], Spatially resolved single-cell transcriptomics (MERFISH), [missing], Multimodal profiling (Patch-seq), [missing], Transgenic tools, [missing], NeMO archive and analytics, [missing], Brain Image Library (BIL) archive, [missing], DANDI archive, [missing], Brain Cell Data Center (BCDC), [missing], Project management, [missing], and BRAIN Initiative Cell Census Network (BICCN), [missing]
Subjects: Epigenomics, Male, INTERNEURONS, ORGANIZATION, MOUSE, Molecular neuroscience, Neural circuits, CLASSIFICATION, Article, Mice, Atlases as Topic, Glutamates, Species Specificity, Animals, Humans, TRANSCRIPTOMICS, SPECIFICATION, NEURONS, In Situ Hybridization, Fluorescence, Phylogeny, Neurons, Multidisciplinary, Gene Expression Profiling, Biology and Life Sciences, PATHWAYS, Brain, Callithrix, Censuses, Cellular neuroscience, Mathematics and Statistics, SINGLE, Organ Specificity, MORPHOLOGY, Motor cortex, Female, Single-Cell Analysis, Transcriptome
Abstract: Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties., The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.
Published: 2021

30. Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons

Author: Kalmbach,Brian
Subjects: food and beverages
Abstract: R based code and physiological/morphological features related to Kalmbach et al.,Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons.&nbsp
Published: 2021
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31. Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons

Author: Kalmbach, Brian E., primary, Hodge, Rebecca D., additional, Jorstad, Nikolas L., additional, Owen, Scott, additional, de Frates, Rebecca, additional, Yanny, Anna Marie, additional, Dalley, Rachel, additional, Mallory, Matt, additional, Graybuck, Lucas T., additional, Radaelli, Cristina, additional, Keene, C. Dirk, additional, Gwinn, Ryder P., additional, Silbergeld, Daniel L., additional, Cobbs, Charles, additional, Ojemann, Jeffrey G., additional, Ko, Andrew L., additional, Patel, Anoop P., additional, Ellenbogen, Richard G., additional, Bakken, Trygve E., additional, Daigle, Tanya L., additional, Dee, Nick, additional, Lee, Brian R., additional, McGraw, Medea, additional, Nicovich, Philip R., additional, Smith, Kimberly, additional, Sorensen, Staci A., additional, Tasic, Bosiljka, additional, Zeng, Hongkui, additional, Koch, Christof, additional, Lein, Ed S., additional, and Ting, Jonathan T., additional
Published: 2021
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32. Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

Author: Lee, Brian R, primary, Budzillo, Agata, primary, Hadley, Kristen, additional, Miller, Jeremy A, additional, Jarsky, Tim, additional, Baker, Katherine, additional, Hill, DiJon, additional, Kim, Lisa, additional, Mann, Rusty, additional, Ng, Lindsay, additional, Oldre, Aaron, additional, Rajanbabu, Ram, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Braun, Thomas, additional, Dalley, Rachel A, additional, Gouwens, Nathan W, additional, Kalmbach, Brian E, additional, Kim, Tae Kyung, additional, Smith, Kimberly A, additional, Soler-Llavina, Gilberto, additional, Sorensen, Staci, additional, Tasic, Bosiljka, additional, Ting, Jonathan T, additional, Lein, Ed, additional, Zeng, Hongkui, additional, Murphy, Gabe J, additional, and Berg, Jim, additional
Published: 2021
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33. Author response: Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

Author: Lee, Brian R, primary, Budzillo, Agata, additional, Hadley, Kristen, additional, Miller, Jeremy A, additional, Jarsky, Tim, additional, Baker, Katherine, additional, Hill, DiJon, additional, Kim, Lisa, additional, Mann, Rusty, additional, Ng, Lindsay, additional, Oldre, Aaron, additional, Rajanbabu, Ram, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Braun, Thomas, additional, Dalley, Rachel A, additional, Gouwens, Nathan W, additional, Kalmbach, Brian E, additional, Kim, Tae Kyung, additional, Smith, Kimberly A, additional, Soler-Llavina, Gilberto, additional, Sorensen, Staci, additional, Tasic, Bosiljka, additional, Ting, Jonathan T, additional, Lein, Ed, additional, Zeng, Hongkui, additional, Murphy, Gabe J, additional, and Berg, Jim, additional
Published: 2021
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34. Comparative cellular analysis of motor cortex in human, marmoset and mouse

Author: Bakken, Trygve E. (author), Jorstad, Nikolas L. (author), Hu, Qiwen (author), Tian, Wei (author), Kalmbach, Brian E. (author), Eggermont, Jeroen (author), Aevermann, Brian D. (author), Höllt, T. (author), Lelieveldt, B.P.F. (author), Bakken, Trygve E. (author), Jorstad, Nikolas L. (author), Hu, Qiwen (author), Tian, Wei (author), Kalmbach, Brian E. (author), Eggermont, Jeroen (author), Aevermann, Brian D. (author), Höllt, T. (author), and Lelieveldt, B.P.F. (author)
Abstract: The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations., Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse Download PDF Author Correction Open Access Published: 22 March 2022 Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse Trygve E. Bakken, Nikolas L. Jorstad, …Ed S. Lein Nature (2022)Cite this article 399 Accesses 1 Altmetric Metrics details The Original Article was published on 06 October 2021 Correction to: Nature https://doi-org.tudelft.idm.oclc.org/10.1038/s41586-021-03465-8 Published online 6 October 2021 In the version of this article initially published, the Acknowledgements section was incomplete and has now been amended to include the following: “NIH BRAIN Initiative awards U01 MH121282 to J.R.E and M.M.B, U19 MH114831 to J.R.E. and E.M.C., U19 MH114830 to H.Z., U01 MH114819 to G.F., 1U01MH114828 to K.Z. and J.C., RF1MH123220 to M.H. and R.H.S., and U19 MH114821. NIH awards R01DC019370 to R.H., R24MH114815 to R.H. and O.R.W., and R24 MH114788 to O.R.W. Nancy and Buster Alvord Endowment to C.D.K.” The changes have been made to the HTML and PDF versions of the article, Comp Graphics & Visualisation, Pattern Recognition and Bioinformatics
Published: 2021
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35. Species-Specific Differences in the Medial Prefrontal Projections to the Pons Between Rat and Rabbit

Author: Moya, Maria V., Siegel, Jennifer J., McCord, Eedann D., Kalmbach, Brian E., Dembrow, Nikolai, Johnston, Daniel, and Chitwood, Raymond A.
Published: 2014
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36. Enhancer viruses for combinatorial cell-subclass-specific labeling

Author: Graybuck, Lucas T., primary, Daigle, Tanya L., additional, Sedeño-Cortés, Adriana E., additional, Walker, Miranda, additional, Kalmbach, Brian, additional, Lenz, Garreck H., additional, Morin, Elyse, additional, Nguyen, Thuc Nghi, additional, Garren, Emma, additional, Bendrick, Jacqueline L., additional, Kim, Tae Kyung, additional, Zhou, Thomas, additional, Mortrud, Marty, additional, Yao, Shenqin, additional, Siverts, La’ Akea, additional, Larsen, Rachael, additional, Gore, Bryan B., additional, Szelenyi, Eric R., additional, Trader, Cameron, additional, Balaram, Pooja, additional, van Velthoven, Cindy T.J., additional, Chiang, Megan, additional, Mich, John K., additional, Dee, Nick, additional, Goldy, Jeff, additional, Cetin, Ali H., additional, Smith, Kimberly, additional, Way, Sharon W., additional, Esposito, Luke, additional, Yao, Zizhen, additional, Gradinaru, Viviana, additional, Sunkin, Susan M., additional, Lein, Ed, additional, Levi, Boaz P., additional, Ting, Jonathan T., additional, Zeng, Hongkui, additional, and Tasic, Bosiljka, additional
Published: 2021
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37. Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Author: Mich, John K., primary, Graybuck, Lucas T., additional, Hess, Erik E., additional, Mahoney, Joseph T., additional, Kojima, Yoshiko, additional, Ding, Yi, additional, Somasundaram, Saroja, additional, Miller, Jeremy A., additional, Kalmbach, Brian E., additional, Radaelli, Cristina, additional, Gore, Bryan B., additional, Weed, Natalie, additional, Omstead, Victoria, additional, Bishaw, Yemeserach, additional, Shapovalova, Nadiya V., additional, Martinez, Refugio A., additional, Fong, Olivia, additional, Yao, Shenqin, additional, Mortrud, Marty, additional, Chong, Peter, additional, Loftus, Luke, additional, Bertagnolli, Darren, additional, Goldy, Jeff, additional, Casper, Tamara, additional, Dee, Nick, additional, Opitz-Araya, Ximena, additional, Cetin, Ali, additional, Smith, Kimberly A., additional, Gwinn, Ryder P., additional, Cobbs, Charles, additional, Ko, Andrew L., additional, Ojemann, Jeffrey G., additional, Keene, C. Dirk, additional, Silbergeld, Daniel L., additional, Sunkin, Susan M., additional, Gradinaru, Viviana, additional, Horwitz, Gregory D., additional, Zeng, Hongkui, additional, Tasic, Bosiljka, additional, Lein, Ed S., additional, Ting, Jonathan T., additional, and Levi, Boaz P., additional
Published: 2021
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38. Multi-modal characterization and simulation of human epileptic circuitry

Author: Buchin, Anatoly, de Frates, Rebecca, Nandi, Anirban, Mann, Rusty, Chong, Peter, Ng, Lindsay, Miller, Jeremy, Hodge, Rebecca, Kalmbach, Brian, Bose, Soumita, Rutishauser, Ueli, McConoughey, Stephen, Lein, Ed, Berg, Jim, Sorensen, Staci, Gwinn, Ryder, Koch, Christof, Ting, Jonathan, Anastassiou, Costas A., Buchin, Anatoly, de Frates, Rebecca, Nandi, Anirban, Mann, Rusty, Chong, Peter, Ng, Lindsay, Miller, Jeremy, Hodge, Rebecca, Kalmbach, Brian, Bose, Soumita, Rutishauser, Ueli, McConoughey, Stephen, Lein, Ed, Berg, Jim, Sorensen, Staci, Gwinn, Ryder, Koch, Christof, Ting, Jonathan, and Anastassiou, Costas A.
Abstract: Temporal lobe epilepsy is the fourth most common neurological disorder with about 40% of patients not responding to pharmacological treatment. Increased cellular loss in the hippocampus is linked to disease severity and pathological phenotypes such as heightened seizure propensity. While the hippocampus is the target of therapeutic interventions such as temporal lobe resection, the impact of the disease at the cellular level remains unclear in humans. Here we show that properties of hippocampal granule cells change with disease progression as measured in living, resected hippocampal tissue excised from epilepsy patients. We show that granule cells increase excitability and shorten response latency while also enlarging in cellular volume, surface area and spine density. Single-cell RNA sequencing combined with simulations ascribe the observed electrophysiological changes to gradual modification in three key ion channel conductances: BK, Cav2.2 and Kir2.1. In a bio-realistic computational network model, we show that the changes related to disease progression bring the circuit into a more excitable state. In turn, we observe that by reversing these changes in the three key conductances produces a less excitable, early disease-like state. These results provide mechanistic understanding of epilepsy in humans and will inform future therapies such as viral gene delivery to reverse the course of the disorder.
Published: 2020

39. Fragile X mental retardation protein modulates somatic D-type K+ channels and action potential threshold in the mouse prefrontal cortex

Author: Kalmbach, Brian E., primary and Brager, Darrin H., additional
Published: 2020
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40. Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

Author: Lee, Brian R., primary, Budzillo, Agata, additional, Hadley, Kristen, additional, Miller, Jeremy A., additional, Jarsky, Tim, additional, Baker, Katherine, additional, Hill, DiJon, additional, Kim, Lisa, additional, Mann, Rusty, additional, Ng, Lindsay, additional, Oldre, Aaron, additional, Rajanbabu, Ram, additional, Trinh, Jessica, additional, Braun, Thomas, additional, Dalley, Rachel, additional, Gouwens, Nathan W., additional, Kalmbach, Brian E., additional, Kim, Tae Kyung, additional, Smith, Kimberly, additional, Soler-Llavina, Gilberto J., additional, Sorensen, Staci A., additional, Tasic, Bosiljka, additional, Ting, Jonathan T., additional, Lein, Ed S., additional, Zeng, Hongkui, additional, Murphy, Gabe J., additional, and Berg, Jim, additional
Published: 2020
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41. Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex

Author: Kim, Mean-Hwan, primary, Radaelli, Cristina, additional, Thomsen, Elliot R., additional, Machen, Deja, additional, Chartrand, Tom, additional, Jorstad, Nikolas L., additional, Mahoney, Joseph T., additional, Taormina, Michael J., additional, Long, Brian, additional, Baker, Katherine, additional, Campagnola, Luke, additional, Casper, Tamara, additional, Clark, Michael, additional, Dee, Nick, additional, D’Orazi, Florence, additional, Gamlin, Clare, additional, Kalmbach, Brian, additional, Kebede, Sara, additional, Lee, Brian R., additional, Ng, Lindsay, additional, Trinh, Jessica, additional, Cobbs, Charles, additional, Gwinn, Ryder P., additional, Keene, C. Dirk, additional, Ko, Andrew L., additional, Ojemann, Jeffrey G., additional, Silbergeld, Daniel L., additional, Sorensen, Staci A., additional, Berg, Jim, additional, Smith, Kimberly, additional, Nicovich, Philip R., additional, Jarsky, Tim, additional, Murphy, Gabe, additional, Zeng, Hongkui, additional, Ting, Jonathan T., additional, Levi, Boaz P., additional, and Lein, Ed S., additional
Published: 2020
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42. Fragile X Mental Retardation Protein Bidirectionally Controls Dendritic Ih in a Cell Type-Specific Manner between Mouse Hippocampus and Prefrontal Cortex

Author: Brandalise, Federico, primary, Kalmbach, Brian E., additional, Mehta, Preeti, additional, Thornton, Olivia, additional, Johnston, Daniel, additional, Zemelman, Boris V., additional, and Brager, Darrin H., additional
Published: 2020
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43. Multi-modal characterization and simulation of human epileptic circuitry

Author: Buchin, Anatoly, primary, de Frates, Rebecca, additional, Nandi, Anirban, additional, Mann, Rusty, additional, Chong, Peter, additional, Ng, Lindsay, additional, Miller, Jeremy, additional, Hodge, Rebecca, additional, Kalmbach, Brian, additional, Bose, Soumita, additional, Rutishauser, Ueli, additional, McConoughey, Stephen, additional, Lein, Ed, additional, Berg, Jim, additional, Sorensen, Staci, additional, Gwinn, Ryder, additional, Koch, Christof, additional, Ting, Jonathan, additional, and Anastassiou, Costas A., additional
Published: 2020
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44. Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types

Author: Nandi, Anirban, primary, Chartrand, Tom, additional, Geit, Werner Van, additional, Buchin, Anatoly, additional, Yao, Zizhen, additional, Lee, Soo Yeun, additional, Wei, Yina, additional, Kalmbach, Brian, additional, Lee, Brian, additional, Lein, Ed, additional, Berg, Jim, additional, Sümbül, Uygar, additional, Koch, Christof, additional, Tasic, Bosiljka, additional, and Anastassiou, Costas A., additional
Published: 2020
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45. Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons

Author: Berg, Jim, primary, Sorensen, Staci A., additional, Ting, Jonathan T., additional, Miller, Jeremy A., additional, Chartrand, Thomas, additional, Buchin, Anatoly, additional, Bakken, Trygve E., additional, Budzillo, Agata, additional, Dee, Nick, additional, Ding, Song-Lin, additional, Gouwens, Nathan W., additional, Hodge, Rebecca D., additional, Kalmbach, Brian, additional, Lee, Changkyu, additional, Lee, Brian R., additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Barkan, Eliza, additional, Beller, Allison, additional, Berry, Kyla, additional, Bertagnolli, Darren, additional, Bickley, Kris, additional, Bomben, Jasmine, additional, Braun, Thomas, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Chong, Peter, additional, Crichton, Kirsten, additional, Dalley, Rachel, additional, de Frates, Rebecca, additional, Desta, Tsega, additional, Dingman Lee, Samuel, additional, D’Orazi, Florence, additional, Dotson, Nadezhda, additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Farrell, Colin, additional, Feng, David, additional, Fong, Olivia, additional, Furdan, Szabina, additional, Galakhova, Anna A., additional, Gamlin, Clare, additional, Gary, Amanda, additional, Glandon, Alexandra, additional, Goldy, Jeff, additional, Gorham, Melissa, additional, Goriounova, Natalia A., additional, Gratiy, Sergey, additional, Graybuck, Lucas, additional, Gu, Hong, additional, Hadley, Kristen, additional, Hansen, Nathan, additional, Heistek, Tim S., additional, Henry, Alex M., additional, Heyer, Djai B., additional, Hill, DiJon, additional, Hill, Chris, additional, Hupp, Madie, additional, Jarsky, Tim, additional, Kebede, Sara, additional, Keene, Lisa, additional, Kim, Lisa, additional, Kim, Mean-Hwan, additional, Kroll, Matthew, additional, Latimer, Caitlin, additional, Levi, Boaz P., additional, Link, Katherine E., additional, Mallory, Matthew, additional, Mann, Rusty, additional, Marshall, Desiree, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica, additional, Mertens, Eline J., additional, Mezei, Leona, additional, Mihut, Norbert, additional, Mok, Stephanie, additional, Molnar, Gabor, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, Nyhus, Julie, additional, Olah, Gaspar, additional, Oldre, Aaron, additional, Omstead, Victoria, additional, Ozsvar, Attila, additional, Park, Daniel, additional, Peng, Hanchuan, additional, Pham, Trangthanh, additional, Pom, Christina A., additional, Potekhina, Lydia, additional, Rajanbabu, Ramkumar, additional, Ransford, Shea, additional, Reid, David, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Sandman, David, additional, Sulc, Josef, additional, Sunkin, Susan M., additional, Szafer, Aaron, additional, Szemenyei, Viktor, additional, Thomsen, Elliot R., additional, Tieu, Michael, additional, Torkelson, Amy, additional, Trinh, Jessica, additional, Tung, Herman, additional, Wakeman, Wayne, additional, Ward, Katelyn, additional, Wilbers, René, additional, Williams, Grace, additional, Yao, Zizhen, additional, Yoon, Jae-Geun, additional, Anastassiou, Costas, additional, Arkhipov, Anton, additional, Barzo, Pal, additional, Bernard, Amy, additional, Cobbs, Charles, additional, de Witt Hamer, Philip C., additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gwinn, Ryder P., additional, Hawrylycz, Michael J., additional, Hof, Patrick R., additional, Idema, Sander, additional, Jones, Allan R., additional, Keene, C.Dirk, additional, Ko, Andrew L., additional, Murphy, Gabe J., additional, Ng, Lydia, additional, Ojemann, Jeffrey G., additional, Patel, Anoop P., additional, Phillips, John W., additional, Silbergeld, Daniel L., additional, Smith, Kimberly, additional, Tasic, Bosiljka, additional, Yuste, Rafael, additional, Segev, Idan, additional, de Kock, Christiaan P.J., additional, Mansvelder, Huibert D., additional, Tamas, Gabor, additional, Zeng, Hongkui, additional, Koch, Christof, additional, and Lein, Ed S., additional
Published: 2020
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46. Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

Author: Bakken, Trygve E., primary, Jorstad, Nikolas L., additional, Hu, Qiwen, additional, Lake, Blue B., additional, Tian, Wei, additional, Kalmbach, Brian E., additional, Crow, Megan, additional, Hodge, Rebecca D., additional, Krienen, Fenna M., additional, Sorensen, Staci A., additional, Eggermont, Jeroen, additional, Yao, Zizhen, additional, Aevermann, Brian D., additional, Aldridge, Andrew I., additional, Bartlett, Anna, additional, Bertagnolli, Darren, additional, Casper, Tamara, additional, Castanon, Rosa G., additional, Crichton, Kirsten, additional, Daigle, Tanya L., additional, Dalley, Rachel, additional, Dee, Nick, additional, Dembrow, Nikolai, additional, Diep, Dinh, additional, Ding, Song-Lin, additional, Dong, Weixiu, additional, Fang, Rongxin, additional, Fischer, Stephan, additional, Goldman, Melissa, additional, Goldy, Jeff, additional, Graybuck, Lucas T., additional, Herb, Brian R., additional, Hou, Xiaomeng, additional, Kancherla, Jayaram, additional, Kroll, Matthew, additional, Lathia, Kanan, additional, van Lew, Baldur, additional, Li, Yang Eric, additional, Liu, Christine S., additional, Liu, Hanqing, additional, Lucero, Jacinta D., additional, Mahurkar, Anup, additional, McMillen, Delissa, additional, Miller, Jeremy A., additional, Moussa, Marmar, additional, Nery, Joseph R., additional, Nicovich, Philip R., additional, Orvis, Joshua, additional, Osteen, Julia K., additional, Owen, Scott, additional, Palmer, Carter R., additional, Pham, Thanh, additional, Plongthongkum, Nongluk, additional, Poirion, Olivier, additional, Reed, Nora M., additional, Rimorin, Christine, additional, Rivkin, Angeline, additional, Romanow, William J., additional, Sedeño-Cortés, Adriana E., additional, Siletti, Kimberly, additional, Somasundaram, Saroja, additional, Sulc, Josef, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Wang, Xinxin, additional, Xie, Fangming, additional, Yanny, Anna Marie, additional, Zhang, Renee, additional, Ament, Seth A., additional, Behrens, M. Margarita, additional, Bravo, Hector Corrada, additional, Chun, Jerold, additional, Dobin, Alexander, additional, Gillis, Jesse, additional, Hertzano, Ronna, additional, Hof, Patrick R., additional, Höllt, Thomas, additional, Horwitz, Gregory D., additional, Keene, C. Dirk, additional, Kharchenko, Peter V., additional, Ko, Andrew L., additional, Lelieveldt, Boudewijn P., additional, Luo, Chongyuan, additional, Mukamel, Eran A., additional, Preissl, Sebastian, additional, Regev, Aviv, additional, Ren, Bing, additional, Scheuermann, Richard H., additional, Smith, Kimberly, additional, Spain, William J., additional, White, Owen R., additional, Koch, Christof, additional, Hawrylycz, Michael, additional, Tasic, Bosiljka, additional, Macosko, Evan Z., additional, McCarroll, Steven A., additional, Ting, Jonathan T., additional, Zeng, Hongkui, additional, Zhang, Kun, additional, Feng, Guoping, additional, Ecker, Joseph R., additional, Linnarsson, Sten, additional, and Lein, Ed S., additional
Published: 2020
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47. Differences in Potassium Channel Composition Underlie Distinct Action Potential Kinetics in Transcriptomically Identified Neocortical Mouse Cell Types

Author: Berg, Jim, primary, Lee, Brian, additional, Mann, Rusty, additional, Ng, Lindsay, additional, Budzillo, Agata, additional, Kalmbach, Brian, additional, Baker, Katherine, additional, Zeng, Hongkui, additional, and Murphy, Gabe, additional
Published: 2020
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48. Prospective, brain-wide labeling of neuronal subclasses with enhancer-driven AAVs

Author: Graybuck, Lucas T., Sedeño-Cortés, Adriana E., Nguyen, Thuc Nghi, Walker, Miranda, Szelenyi, Eric, Lenz, Garreck, Sieverts, La’Akea, Kim, Tae Kyung, Garren, Emma, Kalmbach, Brian, Yao, Shenqin, Mortrud, Marty, Mich, John, Goldy, Jeff, Smith, Kimberly, Dee, Nick, Yao, Zizhen, Cetin, Ali, Levi, Boaz, Lein, Ed, Ting, Jonathan, Zeng, Hongkui, Daigle, Tanya, and Tasic, Bosiljka
Abstract: Labeling and perturbation of specific cell types in multicellular systems has transformed our ability to understand them. The rapid pace of cell type identification by new single-cell analysis methods has not been met with efficient access to these newly discovered types. To enable access to specific neural populations in the mouse cortex, we have collected single cell chromatin accessibility data from select cell types. We clustered the single cell data and mapped them to single cell transcriptomics to identify highly specific enhancers for cell subclasses. These enhancers, when cloned into AAVs and delivered to the brain by retro orbital injections, transgene expression in specific cell subclasses throughout the mouse brain. This approach will enable functional investigation of cell types in the mouse cortex and beyond. One sentence Summary Combining scATAC-seq and scRNA-seq identifies subclass-specific enhancers to label cells in mouse cortex at high resolution
Published: 2019
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49. h-channels contribute to divergent electrophysiological properties of supragranular pyramidal neurons in human versus mouse cerebral cortex

Author: Kalmbach, Brian E, Buchin, Anatoly, Long, Brian, Close, Jennie, Nandi, Anirban, Miller, Jeremy A, Bakken, Trygve E, Hodge, Rebecca D, Chong, Peter, de Frates, Rebecca, Dai, Kael, Maltzer, Zoe, Nicovich, Philip R, Keene, C Dirk, Silbergeld, Daniel L, Gwinn, Ryder P, Cobbs, Charles, Ko, Andrew L, Ojemann, Jeffrey G, Koch, Christof, Anastassiou, Costas A, Lein, Ed S, and Ting, Jonathan T
Subjects: Adult, Cerebral Cortex, Male, Potassium Channels, Pyramidal Cells, Cell Membrane, Models, Neurological, food and beverages, Mice, Transgenic, Article, Membrane Potentials, Mice, Inbred C57BL, nervous system, Species Specificity, Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels, Animals, Humans, Female
Abstract: Gene expression studies suggest that differential ion channel expression contributes to differences in rodent versus human neuronal physiology. We tested whether h-channels more prominently contribute to the physiological properties of human compared to mouse supragranular pyramidal neurons. Single-cell/nucleus RNA sequencing revealed ubiquitous HCN1-subunit expression in excitatory neurons in human, but not mouse, supragranular layers. Using patch-clamp recordings, we found stronger h-channel-related membrane properties in supragranular pyramidal neurons in human temporal cortex, compared to mouse supragranular pyramidal neurons in temporal association area. The magnitude of these differences depended upon cortical depth and was largest in pyramidal neurons in deep L3. Additionally, pharmacologically blocking h-channels produced a larger change in membrane properties in human compared to mouse neurons. Finally, using biophysical modeling, we provide evidence that h-channels promote the transfer of theta frequencies from dendrite-to-soma in human L3 pyramidal neurons. Thus, h-channels contribute to between-species differences in a fundamental neuronal property.
Published: 2018

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

Author: Miller, Jeremy, primary, Hodge, Rebecca, additional, Novotny, Mark, additional, Ting, Jonathan, additional, Kalmbach, Brian, additional, Bakken, Trygve, additional, Aevermann, Brian, additional, Barkan, Eliza, additional, Berkowitz-Cerasano, Madeline, additional, Cobbs, Charles, additional, Diez-Fuertes, Francisco, additional, Ding, Song-Lin, additional, Mccorrison, Jamison, additional, Schork, Nicholas, additional, Shehata, Soraya, additional, Smith, Kimberly, additional, Sunkin, Susan, additional, Tran, Danny, additional, Venepally, Pratap, additional, Yanny, Anna Marie, additional, Steemers, Frank, additional, Phillips, John, additional, Bernard, Amy, additional, Koch, Christof, additional, Lasken, Roger, additional, Scheuermann, Richard, additional, and Lein, Ed, additional
Published: 2019
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