Author: "Ding, Song‐Lin" / Publication Year Range: Last 10 years - Searchworks@Jio Institute Digital Library Search Results

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233 results on '"Ding, Song‐Lin"'

1. 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.
Published: 2024
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2. Single-cell DNA methylation and 3D genome architecture in the human brain.

Author: Lucero, Jacinta, Osteen, Julia, Emerson, Nora, Rink, Jon, Lee, Jasper, Li, Yang, Siletti, Kimberly, Liem, Michelle, Claffey, Naomi, OConnor, Carolyn, Yanny, Anna, Nyhus, Julie, Dee, Nick, Casper, Tamara, Shapovalova, Nadiya, Hirschstein, Daniel, Ding, Song-Lin, Hodge, Rebecca, Levi, Boaz, Keene, C, Linnarsson, Sten, Lein, Ed, Ren, Bing, Behrens, M, Ecker, Joseph, Liu, Hanqing, Castanon, Rosa, Kenworthy, Mia, Altshul, Jordan, Valadon, Cynthia, Aldridge, Andrew, Nery, Joseph, Chen, Huaming, Xu, Jiaying, Tian, Wei, Zhou, Jingtian, Bartlett, Anna, Zeng, Qiurui, and Johnson, Nicholas
Abstract: Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.
Published: 2023

3. A guide to the BRAIN Initiative Cell Census Network data ecosystem

Author: Hawrylycz, Michael, Martone, Maryann E, Ascoli, Giorgio A, Bjaalie, Jan G, Dong, Hong-Wei, Ghosh, Satrajit S, Gillis, Jesse, Hertzano, Ronna, Haynor, David R, Hof, Patrick R, Kim, Yongsoo, Lein, Ed, Liu, Yufeng, Miller, Jeremy A, Mitra, Partha P, Mukamel, Eran, Ng, Lydia, Osumi-Sutherland, David, Peng, Hanchuan, Ray, Patrick L, Sanchez, Raymond, Regev, Aviv, Ropelewski, Alex, Scheuermann, Richard H, Tan, Shawn Zheng Kai, Thompson, Carol L, Tickle, Timothy, Tilgner, Hagen, Varghese, Merina, Wester, Brock, White, Owen, Zeng, Hongkui, Aevermann, Brian, Allemang, David, Ament, Seth, Athey, Thomas L, Baker, Cody, Baker, Katherine S, Baker, Pamela M, Bandrowski, Anita, Banerjee, Samik, Bishwakarma, Prajal, Carr, Ambrose, Chen, Min, Choudhury, Roni, Cool, Jonah, Creasy, Heather, D’Orazi, Florence, Degatano, Kylee, Dichter, Benjamin, Ding, Song-Lin, Dolbeare, Tim, Ecker, Joseph R, Fang, Rongxin, Fillion-Robin, Jean-Christophe, Fliss, Timothy P, Gee, James, Gillespie, Tom, Gouwens, Nathan, Zhang, Guo-Qiang, Halchenko, Yaroslav O, Harris, Nomi L, Herb, Brian R, Hintiryan, Houri, Hood, Gregory, Horvath, Sam, Huo, Bingxing, Jarecka, Dorota, Jiang, Shengdian, Khajouei, Farzaneh, Kiernan, Elizabeth A, Kir, Huseyin, Kruse, Lauren, Lee, Changkyu, Lelieveldt, Boudewijn, Li, Yang, Liu, Hanqing, Liu, Lijuan, Markuhar, Anup, Mathews, James, Mathews, Kaylee L, Mezias, Chris, Miller, Michael I, Mollenkopf, Tyler, Mufti, Shoaib, Mungall, Christopher J, Orvis, Joshua, Puchades, Maja A, Qu, Lei, Receveur, Joseph P, Ren, Bing, Sjoquist, Nathan, Staats, Brian, Tward, Daniel, van Velthoven, Cindy TJ, Wang, Quanxin, Xie, Fangming, Xu, Hua, Yao, Zizhen, and Yun, Zhixi
Subjects: Biological Sciences, Genetics, Neurosciences, Mental Health, Data Science, 1.1 Normal biological development and functioning, Neurological, Animals, Humans, Mice, Brain, Ecosystem, Neurons, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract: Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.
Published: 2023

4. 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

5. 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

6. 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

7. Progress update from the hippocampal subfields group

Author: Olsen, Rosanna K, Carr, Valerie A, Daugherty, Ana M, La Joie, Renaud, Amaral, Robert SC, Amunts, Katrin, Augustinack, Jean C, Bakker, Arnold, Bender, Andrew R, Berron, David, Boccardi, Marina, Bocchetta, Martina, Burggren, Alison C, Chakravarty, M Mallar, Chételat, Gaël, de Flores, Robin, DeKraker, Jordan, Ding, Song‐Lin, Geerlings, Mirjam I, Huang, Yushan, Insausti, Ricardo, Johnson, Elliott G, Kanel, Prabesh, Kedo, Olga, Kennedy, Kristen M, Keresztes, Attila, Lee, Joshua K, Lindenberger, Ulman, Mueller, Susanne G, Mulligan, Elizabeth M, Ofen, Noa, Palombo, Daniela J, Pasquini, Lorenzo, Pluta, John, Raz, Naftali, Rodrigue, Karen M, Schlichting, Margaret L, Shing, Yee Lee, Stark, Craig EL, Steve, Trevor A, Suthana, Nanthia A, Wang, Lei, Werkle‐Bergner, Markus, Yushkevich, Paul A, Yu, Qijing, Wisse, Laura EM, and Group, Hippocampal Subfields
Subjects: Biological Psychology, Biomedical and Clinical Sciences, Neurosciences, Psychology, Hippocampus, Volumetry, Human, Neuroimaging, Structural imaging, Neuroanatomy, Histology, Cytoarchitecture, ex vivo, Hippocampal Subfields Group, ex vivo, Genetics, Biological psychology
Abstract: IntroductionHeterogeneity of segmentation protocols for medial temporal lobe regions and hippocampal subfields on in vivo magnetic resonance imaging hinders the ability to integrate findings across studies. We aim to develop a harmonized protocol based on expert consensus and histological evidence.MethodsOur international working group, funded by the EU Joint Programme-Neurodegenerative Disease Research (JPND), is working toward the production of a reliable, validated, harmonized protocol for segmentation of medial temporal lobe regions. The working group uses a novel postmortem data set and online consensus procedures to ensure validity and facilitate adoption.ResultsThis progress report describes the initial results and milestones that we have achieved to date, including the development of a draft protocol and results from the initial reliability tests and consensus procedures.DiscussionA harmonized protocol will enable the standardization of segmentation methods across laboratories interested in medial temporal lobe research worldwide.
Published: 2019

8. Conserved cell types with divergent features in human versus mouse cortex.

Author: Hodge, Rebecca D, Bakken, Trygve E, Miller, Jeremy A, Smith, Kimberly A, Barkan, Eliza R, Graybuck, Lucas T, Close, Jennie L, Long, Brian, Johansen, Nelson, Penn, Osnat, Yao, Zizhen, Eggermont, Jeroen, Höllt, Thomas, Levi, Boaz P, Shehata, Soraya I, Aevermann, Brian, Beller, Allison, Bertagnolli, Darren, Brouner, Krissy, Casper, Tamara, Cobbs, Charles, Dalley, Rachel, Dee, Nick, Ding, Song-Lin, Ellenbogen, Richard G, Fong, Olivia, Garren, Emma, Goldy, Jeff, Gwinn, Ryder P, Hirschstein, Daniel, Keene, C Dirk, Keshk, Mohamed, Ko, Andrew L, Lathia, Kanan, Mahfouz, Ahmed, Maltzer, Zoe, McGraw, Medea, Nguyen, Thuc Nghi, Nyhus, Julie, Ojemann, Jeffrey G, Oldre, Aaron, Parry, Sheana, Reynolds, Shannon, Rimorin, Christine, Shapovalova, Nadiya V, Somasundaram, Saroja, Szafer, Aaron, Thomsen, Elliot R, Tieu, Michael, Quon, Gerald, Scheuermann, Richard H, Yuste, Rafael, Sunkin, Susan M, Lelieveldt, Boudewijn, Feng, David, Ng, Lydia, Bernard, Amy, Hawrylycz, Michael, Phillips, John W, Tasic, Bosiljka, Zeng, Hongkui, Jones, Allan R, Koch, Christof, and Lein, Ed S
Subjects: Cerebral Cortex, Astrocytes, Neurons, Animals, Humans, Mice, Species Specificity, Neural Inhibition, Principal Component Analysis, Adolescent, Adult, Aged, Middle Aged, Female, Male, Young Adult, Biological Evolution, Single-Cell Analysis, Transcriptome, RNA-Seq, Genetics, Neurosciences, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Aetiology, Underpinning research, Neurological, General Science & Technology
Abstract: Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease. Here we used single-nucleus RNA-sequencing analysis to perform a comprehensive study of cell types in the middle temporal gyrus of human cortex. We identified a highly diverse set of excitatory and inhibitory neuron types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to similar mouse cortex single-cell RNA-sequencing datasets revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of properties of human cell types. Despite this general conservation, we also found extensive differences between homologous human and mouse cell types, including marked alterations in proportions, laminar distributions, gene expression and morphology. These species-specific features emphasize the importance of directly studying human brain.
Published: 2019

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

Author: Boldog, Eszter, Bakken, Trygve E, Hodge, Rebecca D, Novotny, Mark, Aevermann, Brian D, Baka, Judith, Bordé, Sándor, Close, Jennie L, Diez-Fuertes, Francisco, Ding, Song-Lin, Faragó, Nóra, Kocsis, Ágnes K, Kovács, Balázs, Maltzer, Zoe, McCorrison, Jamison M, Miller, Jeremy A, Molnár, Gábor, Oláh, Gáspár, Ozsvár, Attila, Rózsa, Márton, Shehata, Soraya I, Smith, Kimberly A, Sunkin, Susan M, Tran, Danny N, Venepally, Pratap, Wall, Abby, Puskás, László G, Barzó, Pál, Steemers, Frank J, Schork, Nicholas J, Scheuermann, Richard H, Lasken, Roger S, Lein, Ed S, and Tamás, Gábor
Subjects: Biomedical and Clinical Sciences, Neurosciences, Genetics, Brain Disorders, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Adult, Aged, Axons, Cerebral Cortex, Dendritic Spines, GABAergic Neurons, Gap Junctions, Gene Library, Humans, Male, Polymerase Chain Reaction, Presynaptic Terminals, Pyramidal Cells, RNA, Sequence Analysis, RNA, Transcriptome, Psychology, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract: We describe convergent evidence from transcriptomics, morphology, and physiology for a specialized GABAergic neuron subtype in human cortex. Using unbiased single-nucleus RNA sequencing, we identify ten GABAergic interneuron subtypes with combinatorial gene signatures in human cortical layer 1 and characterize a group of human interneurons with anatomical features never described in rodents, having large 'rosehip'-like axonal boutons and compact arborization. These rosehip cells show an immunohistochemical profile (GAD1+CCK+, CNR1-SST-CALB2-PVALB-) matching a single transcriptomically defined cell type whose specific molecular marker signature is not seen in mouse cortex. Rosehip cells in layer 1 make homotypic gap junctions, predominantly target apical dendritic shafts of layer 3 pyramidal neurons, and inhibit backpropagating pyramidal action potentials in microdomains of the dendritic tuft. These cells are therefore positioned for potent local control of distal dendritic computation in cortical pyramidal neurons.
Published: 2018

10. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Author: Yao, Zizhen, van Velthoven, Cindy T.J., Nguyen, Thuc Nghi, Goldy, Jeff, Sedeno-Cortes, Adriana E., Baftizadeh, Fahimeh, Bertagnolli, Darren, Casper, Tamara, Chiang, Megan, Crichton, Kirsten, Ding, Song-Lin, Fong, Olivia, Garren, Emma, Glandon, Alexandra, Gouwens, Nathan W., Gray, James, Graybuck, Lucas T., Hawrylycz, Michael J., Hirschstein, Daniel, Kroll, Matthew, Lathia, Kanan, Lee, Changkyu, Levi, Boaz, McMillen, Delissa, Mok, Stephanie, Pham, Thanh, Ren, Qingzhong, Rimorin, Christine, Shapovalova, Nadiya, Sulc, Josef, Sunkin, Susan M., Tieu, Michael, Torkelson, Amy, Tung, Herman, Ward, Katelyn, Dee, Nick, Smith, Kimberly A., Tasic, Bosiljka, and Zeng, Hongkui
Published: 2021
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11. Anatomical structures, cell types and biomarkers of the Human Reference Atlas

Author: Börner, Katy, Teichmann, Sarah A., Quardokus, Ellen M., Gee, James C., Browne, Kristen, Osumi-Sutherland, David, Herr, II, Bruce W., Bueckle, Andreas, Paul, Hrishikesh, Haniffa, Muzlifah, Jardine, Laura, Bernard, Amy, Ding, Song-Lin, Miller, Jeremy A., Lin, Shin, Halushka, Marc K., Boppana, Avinash, Longacre, Teri A., Hickey, John, Lin, Yiing, Valerius, M. Todd, He, Yongqun, Pryhuber, Gloria, Sun, Xin, Jorgensen, Marda, Radtke, Andrea J., Wasserfall, Clive, Ginty, Fiona, Ho, Jonhan, Sunshine, Joel, Beuschel, Rebecca T., Brusko, Maigan, Lee, Sujin, Malhotra, Rajeev, Jain, Sanjay, and Weber, Griffin
Published: 2021
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12. 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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13. Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis

Author: Ding, Song-Lin, Yao, Zizhen, Hirokawa, Karla E., Nguyen, Thuc Nghi, Graybuck, Lucas T., Fong, Olivia, Bohn, Phillip, Ngo, Kiet, Smith, Kimberly A., Koch, Christof, Phillips, John W., Lein, Ed S., Harris, Julie A., Tasic, Bosiljka, and Zeng, Hongkui
Published: 2020
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14. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

Author: Wang, Quanxin, Ding, Song-Lin, Li, Yang, Royall, Josh, Feng, David, Lesnar, Phil, Graddis, Nile, Naeemi, Maitham, Facer, Benjamin, Ho, Anh, Dolbeare, Tim, Blanchard, Brandon, Dee, Nick, Wakeman, Wayne, Hirokawa, Karla E., Szafer, Aaron, Sunkin, Susan M., Oh, Seung Wook, Bernard, Amy, Phillips, John W., Hawrylycz, Michael, Koch, Christof, Zeng, Hongkui, Harris, Julie A., and Ng, Lydia
Published: 2020
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15. Comparison of the connectivity of the posterior intralaminar thalamic nucleus and peripeduncular nucleus in rats and mice

Author: Cai, Hui-Ru, primary, Chen, Sheng-Qiang, additional, Xiang, Xiao-Jun, additional, Zhang, Xue-Qin, additional, Ma, Run-Zhe, additional, Zhu, Ge, additional, and Ding, Song-Lin, additional
Published: 2024
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16. Lamination, Borders, and Thalamic Projections of the Primary Visual Cortex in Human, Non-Human Primate, and Rodent Brains

Author: Ding, Song-Lin, primary
Published: 2024
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17. A comprehensive transcriptional map of primate brain development.

Author: Bakken, Trygve E, Miller, Jeremy A, Ding, Song-Lin, Sunkin, Susan M, Smith, Kimberly A, Ng, Lydia, Szafer, Aaron, Dalley, Rachel A, Royall, Joshua J, Lemon, Tracy, Shapouri, Sheila, Aiona, Kaylynn, Arnold, James, Bennett, Jeffrey L, Bertagnolli, Darren, Bickley, Kristopher, Boe, Andrew, Brouner, Krissy, Butler, Stephanie, Byrnes, Emi, Caldejon, Shiella, Carey, Anita, Cate, Shelby, Chapin, Mike, Chen, Jefferey, Dee, Nick, Desta, Tsega, Dolbeare, Tim A, Dotson, Nadia, Ebbert, Amanda, Fulfs, Erich, Gee, Garrett, Gilbert, Terri L, Goldy, Jeff, Gourley, Lindsey, Gregor, Ben, Gu, Guangyu, Hall, Jon, Haradon, Zeb, Haynor, David R, Hejazinia, Nika, Hoerder-Suabedissen, Anna, Howard, Robert, Jochim, Jay, Kinnunen, Marty, Kriedberg, Ali, Kuan, Chihchau L, Lau, Christopher, Lee, Chang-Kyu, Lee, Felix, Luong, Lon, Mastan, Naveed, May, Ryan, Melchor, Jose, Mosqueda, Nerick, Mott, Erika, Ngo, Kiet, Nyhus, Julie, Oldre, Aaron, Olson, Eric, Parente, Jody, Parker, Patrick D, Parry, Sheana, Pendergraft, Julie, Potekhina, Lydia, Reding, Melissa, Riley, Zackery L, Roberts, Tyson, Rogers, Brandon, Roll, Kate, Rosen, David, Sandman, David, Sarreal, Melaine, Shapovalova, Nadiya, Shi, Shu, Sjoquist, Nathan, Sodt, Andy J, Townsend, Robbie, Velasquez, Lissette, Wagley, Udi, Wakeman, Wayne B, White, Cassandra, Bennett, Crissa, Wu, Jennifer, Young, Rob, Youngstrom, Brian L, Wohnoutka, Paul, Gibbs, Richard A, Rogers, Jeffrey, Hohmann, John G, Hawrylycz, Michael J, Hevner, Robert F, Molnár, Zoltán, Phillips, John W, Dang, Chinh, Jones, Allan R, Amaral, David G, Bernard, Amy, and Lein, Ed S
Subjects: Brain, Neocortex, Animals, Macaca mulatta, Humans, Microcephaly, Risk Factors, Schizophrenia, Cell Adhesion, Species Specificity, Transcription, Genetic, Conserved Sequence, Aging, Female, Male, Neurogenesis, Intellectual Disability, Transcriptome, Spatio-Temporal Analysis, Autism Spectrum Disorder, Neurodevelopmental Disorders, Transcription, Genetic, General Science & Technology
Abstract: The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.
Published: 2016

18. Quantitative comparison of 21 protocols for labeling hippocampal subfields and parahippocampal subregions in in vivo MRI: Towards a harmonized segmentation protocol

Author: Yushkevich, Paul A, Amaral, Robert SC, Augustinack, Jean C, Bender, Andrew R, Bernstein, Jeffrey D, Boccardi, Marina, Bocchetta, Martina, Burggren, Alison C, Carr, Valerie A, Chakravarty, M Mallar, Chételat, Gaël, Daugherty, Ana M, Davachi, Lila, Ding, Song-Lin, Ekstrom, Arne, Geerlings, Mirjam I, Hassan, Abdul, Huang, Yushan, Iglesias, J Eugenio, La Joie, Renaud, Kerchner, Geoffrey A, LaRocque, Karen F, Libby, Laura A, Malykhin, Nikolai, Mueller, Susanne G, Olsen, Rosanna K, Palombo, Daniela J, Parekh, Mansi B, Pluta, John B, Preston, Alison R, Pruessner, Jens C, Ranganath, Charan, Raz, Naftali, Schlichting, Margaret L, Schoemaker, Dorothee, Singh, Sachi, Stark, Craig EL, Suthana, Nanthia, Tompary, Alexa, Turowski, Marta M, Van Leemput, Koen, Wagner, Anthony D, Wang, Lei, Winterburn, Julie L, Wisse, Laura EM, Yassa, Michael A, Zeineh, Michael M, and Group, for the Hippocampal Subfields
Subjects: Biomedical and Clinical Sciences, Biomedical Imaging, Neurosciences, Adult, Clinical Protocols, Hippocampus, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Parahippocampal Gyrus, Medial temporal lobe, Hippocampal subfields, CA1, CA2, CA3, Dentate gyrus, Subiculum, Entorhinal cortex, Perirhinal cortex, Parahippocampal gyrus, Magnetic resonance imaging, Segmentation, Unified protocol, Hippocampal Subfields Group, Medical and Health Sciences, Psychology and Cognitive Sciences, Neurology & Neurosurgery, Biomedical and clinical sciences, Health sciences
Abstract: ObjectiveAn increasing number of human in vivo magnetic resonance imaging (MRI) studies have focused on examining the structure and function of the subfields of the hippocampal formation (the dentate gyrus, CA fields 1-3, and the subiculum) and subregions of the parahippocampal gyrus (entorhinal, perirhinal, and parahippocampal cortices). The ability to interpret the results of such studies and to relate them to each other would be improved if a common standard existed for labeling hippocampal subfields and parahippocampal subregions. Currently, research groups label different subsets of structures and use different rules, landmarks, and cues to define their anatomical extents. This paper characterizes, both qualitatively and quantitatively, the variability in the existing manual segmentation protocols for labeling hippocampal and parahippocampal substructures in MRI, with the goal of guiding subsequent work on developing a harmonized substructure segmentation protocol.MethodMRI scans of a single healthy adult human subject were acquired both at 3 T and 7 T. Representatives from 21 research groups applied their respective manual segmentation protocols to the MRI modalities of their choice. The resulting set of 21 segmentations was analyzed in a common anatomical space to quantify similarity and identify areas of agreement.ResultsThe differences between the 21 protocols include the region within which segmentation is performed, the set of anatomical labels used, and the extents of specific anatomical labels. The greatest overall disagreement among the protocols is at the CA1/subiculum boundary, and disagreement across all structures is greatest in the anterior portion of the hippocampal formation relative to the body and tail.ConclusionsThe combined examination of the 21 protocols in the same dataset suggests possible strategies towards developing a harmonized subfield segmentation protocol and facilitates comparison between published studies.
Published: 2015

19. Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories

Author: Wuestefeld, Anika, primary, Baumeister, Hannah, additional, Adams, Jenna N., additional, de Flores, Robin, additional, Hodgetts, Carl J., additional, Mazloum‐Farzaghi, Negar, additional, Olsen, Rosanna K., additional, Puliyadi, Vyash, additional, Tran, Tammy T., additional, Bakker, Arnold, additional, Canada, Kelsey L., additional, Dalton, Marshall A., additional, Daugherty, Ana M., additional, La Joie, Renaud, additional, Wang, Lei, additional, Bedard, Madigan L., additional, Buendia, Esther, additional, Chung, Eunice, additional, Denning, Amanda, additional, del Mar Arroyo‐Jiménez, María, additional, Artacho‐Pérula, Emilio, additional, Irwin, David J., additional, Ittyerah, Ranjit, additional, Lee, Edward B., additional, Lim, Sydney, additional, del Pilar Marcos‐Rabal, María, additional, Iñiguez de Onzoño Martin, Maria Mercedes, additional, Lopez, Monica Munoz, additional, de la Rosa Prieto, Carlos, additional, Schuck, Theresa, additional, Trotman, Winifred, additional, Vela, Alicia, additional, Yushkevich, Paul, additional, Amunts, Katrin, additional, Augustinack, Jean C., additional, Ding, Song‐Lin, additional, Insausti, Ricardo, additional, Kedo, Olga, additional, Berron, David, additional, and Wisse, Laura E. M., additional
Published: 2024
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20. Comparison of histological delineation of the entorhinal, perirhinal, ectorhinal, and parahippocampal cortices by different neuroanatomy laboratories

Author: Baumeister, Hannah, primary, Wuestefeld, Anika, additional, Adams, Jenna N., additional, Bakker, Arnold, additional, Daugherty, Ana M., additional, de Flores, Robin, additional, Hodgetts, Carl J, additional, La Joie, Renaud, additional, Mazloum‐Farzaghi, Negar, additional, Olsen, Rosanna K, additional, Puliyadi, Vyash, additional, Stark, Craig E.L., additional, Tran, Tammy T, additional, Wang, Lei, additional, Yushkevich, Paul A., additional, Amunts, Katrin, additional, Augustinack, Jean, additional, Ding, Song‐Lin, additional, Insausti, Ricardo, additional, Kedo, Olga, additional, Berron, David, additional, and Wisse, Laura EM, additional
Published: 2023
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21. Characterizing the human hippocampus in aging and Alzheimer’s disease using a computational atlas derived from ex vivo MRI and histology

Author: Adler, Daniel H., Wisse, Laura E. M., Ittyerah, Ranjit, Pluta, John B., Ding, Song-Lin, Xie, Long, Wang, Jiancong, Kadivar, Salmon, Robinson, John L., Schuck, Theresa, Trojanowski, John Q., Grossman, Murray, Detre, John A., Elliott, Mark A., Toledo, Jon B., Liu, Weixia, Pickup, Stephen, Miller, Michael I., Das, Sandhitsu R., Wolk, David A., and Yushkevich, Paul A.
Published: 2018

22. Classification of electrophysiological and morphological neuron types in the mouse visual cortex

Author: Gouwens, Nathan W., Sorensen, Staci A., Berg, Jim, Lee, Changkyu, Jarsky, Tim, Ting, Jonathan, Sunkin, Susan M., Feng, David, Anastassiou, Costas A., Barkan, Eliza, Bickley, Kris, Blesie, Nicole, Braun, Thomas, Brouner, Krissy, Budzillo, Agata, Caldejon, Shiella, Casper, Tamara, Castelli, Dan, Chong, Peter, Crichton, Kirsten, Cuhaciyan, Christine, Daigle, Tanya L., Dalley, Rachel, Dee, Nick, Desta, Tsega, Ding, Song-Lin, Dingman, Samuel, Doperalski, Alyse, Dotson, Nadezhda, Egdorf, Tom, Fisher, Michael, de Frates, Rebecca A., Garren, Emma, Garwood, Marissa, Gary, Amanda, Gaudreault, Nathalie, Godfrey, Keith, Gorham, Melissa, Gu, Hong, Habel, Caroline, Hadley, Kristen, Harrington, James, Harris, Julie A., Henry, Alex, Hill, DiJon, Josephsen, Sam, Kebede, Sara, Kim, Lisa, Kroll, Matthew, Lee, Brian, Lemon, Tracy, Link, Katherine E., Liu, Xiaoxiao, Long, Brian, Mann, Rusty, McGraw, Medea, Mihalas, Stefan, Mukora, Alice, Murphy, Gabe J., Ng, Lindsay, Ngo, Kiet, Nguyen, Thuc Nghi, Nicovich, Philip R., Oldre, Aaron, Park, Daniel, Parry, Sheana, Perkins, Jed, Potekhina, Lydia, Reid, David, Robertson, Miranda, Sandman, David, Schroedter, Martin, Slaughterbeck, Cliff, Soler-Llavina, Gilberto, Sulc, Josef, Szafer, Aaron, Tasic, Bosiljka, Taskin, Naz, Teeter, Corinne, Thatra, Nivretta, Tung, Herman, Wakeman, Wayne, Williams, Grace, Young, Rob, Zhou, Zhi, Farrell, Colin, Peng, Hanchuan, Hawrylycz, Michael J., Lein, Ed, Ng, Lydia, Arkhipov, Anton, Bernard, Amy, Phillips, John W., Zeng, Hongkui, and Koch, Christof
Published: 2019
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23. 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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24. Single-cell DNA methylation and 3D genome architecture in the human brain

Author: Tian, Wei, primary, Zhou, Jingtian, additional, Bartlett, Anna, additional, Zeng, Qiurui, additional, Liu, Hanqing, additional, Castanon, Rosa G., additional, Kenworthy, Mia, additional, Altshul, Jordan, additional, Valadon, Cynthia, additional, Aldridge, Andrew, additional, Nery, Joseph R., additional, Chen, Huaming, additional, Xu, Jiaying, additional, Johnson, Nicholas D., additional, Lucero, Jacinta, additional, Osteen, Julia K., additional, Emerson, Nora, additional, Rink, Jon, additional, Lee, Jasper, additional, Li, Yang E., additional, Siletti, Kimberly, additional, Liem, Michelle, additional, Claffey, Naomi, additional, O’Connor, Carolyn, additional, Yanny, Anna Marie, additional, Nyhus, Julie, additional, Dee, Nick, additional, Casper, Tamara, additional, Shapovalova, Nadiya, additional, Hirschstein, Daniel, additional, Ding, Song-Lin, additional, Hodge, Rebecca, additional, Levi, Boaz P., additional, Keene, C. Dirk, additional, Linnarsson, Sten, additional, Lein, Ed, additional, Ren, Bing, additional, Behrens, M. Margarita, additional, and Ecker, Joseph R., additional
Published: 2023
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25. Transcriptomic cytoarchitecture reveals principles of human neocortex organization

Author: Jorstad, Nikolas L., primary, Close, Jennie, additional, Johansen, Nelson, additional, Yanny, Anna Marie, additional, Barkan, Eliza R., additional, Travaglini, Kyle J., additional, Bertagnolli, Darren, additional, Campos, Jazmin, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Dee, Nick, additional, Ding, Song-Lin, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hirschstein, Daniel, additional, Kiick, Katelyn, additional, Kroll, Matthew, additional, Kunst, Michael, additional, Lathia, Kanan, additional, Long, Brian, additional, Martin, Naomi, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Shapovalova, Nadiya, additional, Shehata, Soraya, additional, Siletti, Kimberly, additional, Somasundaram, Saroja, additional, Sulc, Josef, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Callaway, Edward M., additional, Hof, Patrick R., additional, Keene, C. Dirk, additional, Levi, Boaz P., additional, Linnarsson, Sten, additional, Mitra, Partha P., additional, Smith, Kimberly, additional, Hodge, Rebecca D., additional, Bakken, Trygve E., additional, and Lein, Ed S, additional
Published: 2023
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26. Transcriptomic diversity of cell types across the adult human brain

Author: Siletti, Kimberly, primary, Hodge, Rebecca, additional, Mossi Albiach, Alejandro, additional, Lee, Ka Wai, additional, Ding, Song-Lin, additional, Hu, Lijuan, additional, Lönnerberg, Peter, additional, Bakken, Trygve, additional, Casper, Tamara, additional, Clark, Michael, additional, Dee, Nick, additional, Gloe, Jessica, additional, Hirschstein, Daniel, additional, Shapovalova, Nadiya V., additional, Keene, C. Dirk, additional, Nyhus, Julie, additional, Tung, Herman, additional, Yanny, Anna Marie, additional, Arenas, Ernest, additional, Lein, Ed S., additional, and Linnarsson, Sten, additional
Published: 2023
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27. 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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28. Multi-template analysis of human perirhinal cortex in brain MRI: Explicitly accounting for anatomical variability

Author: Xie, Long, Pluta, John B., Das, Sandhitsu R., Wisse, Laura E.M., Wang, Hongzhi, Mancuso, Lauren, Kliot, Dasha, Avants, Brian B., Ding, Song-Lin, Manjón, José V., Wolk, David A., and Yushkevich, Paul A.
Published: 2017
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29. A novel subdivision of the bed nucleus of stria terminalis in monkey, rat, and mouse brains.

Author: Ding, Song‐Lin
Abstract: The bed nucleus of stria terminalis (BST) is a critical structure that mediates sustained vigilant responses to contextual, diffuse, and unpredictable threats. Dysfunction of the BST could lead to excessive anxiety and hypervigilance, which are often observed in posttraumatic stress disorder and anxiety disorders. Vigilance of potential future threats from the external environment is a basic brain function and probably requires rapid and/or short neural circuits, which enable both quick detection of the potential threats and fast adaptive responses. However, the BST in literature does not appear to receive spatial information directly from earlier visual or spatial processing structures. In this study, a novel subdivision of the BST is uncovered in monkey, rat, and mouse brains based on the human equivalent and is found in mouse to receive direct inputs from the ventral lateral geniculate nucleus and pretectal nucleus as well as from the spatial processing structures such as subiculum, presubiculum, and medial entorhinal cortex. This new subdivision, termed spindle‐shaped small cell subdivision (BSTsc), is located between the known BST and the anterior thalamus. In addition to the unique afferent connections and cell morphology, the BSTsc also displays unique molecular signature (e.g., positive for excitatory markers) compared with other BST subdivisions, which are mostly composed of inhibitory GABAergic neurons. The BSTsc appears to have largely overlapping efferent projections with other BST subdivisions such as the projections to the amygdala, hypothalamus, nucleus accumbens, septum, and brainstem. Together, the present study suggests that the BSTsc is poised to serve as a shortcut bridge directly linking spatial information from the environment to vigilant adaptive internal responses. [ABSTRACT FROM AUTHOR]
Published: 2023
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30. Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories

Author: Wuestefeld, Anika, primary, Baumeister, Hannah, additional, Adams, Jenna N, additional, de Flores, Robin, additional, Hodgetts, Carl, additional, Mazloum-Farzaghi, Negar, additional, Olsen, Rosanna K, additional, Puliyadi, Vyash, additional, Tran, Tammy T, additional, Bakker, Arnold, additional, Canada, Kelsey L, additional, Dalton, Marshall A, additional, Daugherty, Ana M, additional, La Joie, Renaud, additional, Wang, Lei, additional, Bedard, Madigan, additional, Buendia, Esther, additional, Denning, Amanda, additional, Irwin, David J, additional, Ittyerah, Ranjit, additional, Lee, Edward B, additional, Lim, Sydney, additional, Iniguez de Onzono Martin, Maria Mercedes, additional, Munoz Lopez, Monica, additional, Schuck, Theresa, additional, Trotman, Winifred, additional, Vela, Alicia, additional, Yushkevich, Paul, additional, Amunts, Karin, additional, Augustinack, Jean C, additional, Ding, Song-Lin, additional, Insausti, Ricardo, additional, Kedo, Olga, additional, Berron, David, additional, and Wisse, Laura E M, additional
Published: 2023
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31. 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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32. 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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33. Quantitative comparison of 21 protocols for labeling hippocampal subfields and parahippocampal subregions in in vivo MRI: Towards a harmonized segmentation protocol

Author: Yushkevich, Paul A., Amaral, Robert S.C., Augustinack, Jean C., Bender, Andrew R., Bernstein, Jeffrey D., Boccardi, Marina, Bocchetta, Martina, Burggren, Alison C., Carr, Valerie A., Chakravarty, M. Mallar, Chételat, Gaël, Daugherty, Ana M., Davachi, Lila, Ding, Song-Lin, Ekstrom, Arne, Geerlings, Mirjam I., Hassan, Abdul, Huang, Yushan, Iglesias, J. Eugenio, La Joie, Renaud, Kerchner, Geoffrey A., LaRocque, Karen F., Libby, Laura A., Malykhin, Nikolai, Mueller, Susanne G., Olsen, Rosanna K., Palombo, Daniela J., Parekh, Mansi B., Pluta, John B., Preston, Alison R., Pruessner, Jens C., Ranganath, Charan, Raz, Naftali, Schlichting, Margaret L., Schoemaker, Dorothee, Singh, Sachi, Stark, Craig E.L., Suthana, Nanthia, Tompary, Alexa, Turowski, Marta M., Van Leemput, Koen, Wagner, Anthony D., Wang, Lei, Winterburn, Julie L., Wisse, Laura E.M., Yassa, Michael A., and Zeineh, Michael M.
Published: 2015
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34. Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories

Author: Wuestefeld, Anika, Baumeister, Hannah, Canada, Kelsey L., Dalton, Marshall A., Daugherty, Ana M., Joie, Renaud La, Wang, Lei, Bedard, Madigan, Buendia, Esther, Denning, Amanda, del Mar Arroyo-Jiménez, María, Artacho-Pérula, Emilio, Adams, Jenna N., Irwin, David J., Ittyerah, Ranjit, Lee, Edward B., Lim, Sydney, del Pilar Marcos-Rabal, María, de Onzoño Martin, Maria Mercedes Iñiguez, Lopez, Monica Munoz, de la Rosa Prieto, Carlos, Schuck, Theresa, Trotman, Winifred, de Flores, Robin, Vela, Alicia, Yushkevich, Paul, Amunts, Katrin, Augustinack, Jean C., Ding, Song-Lin, Insausti, Ricardo, Kedo, Olga, Berron, David, Wisse, Laura E. M., Hodgetts, Carl, Mazloum-Farzaghi, Negar, Olsen, Rosanna K., Puliyadi, Vyash, Tran, Tammy T., and Bakker, Arnold
Subjects: ddc:570, Article
Abstract: The medial temporal lobe (MTL) cortex, located adjacent to the hippocampus, is crucial for memory and prone to the accumulation of certain neuropathologies such as Alzheimer’s disease neurofibrillary tau tangles. The MTL cortex is composed of several subregions which differ in their functional and cytoarchitectonic features. As neuroanatomical schools rely on different cytoarchitectonic definitions of these subregions, it is unclear to what extent their delineations of MTL cortex subregions overlap. Here, we provide an overview of cytoarchitectonic definitions of the cortices that make up the parahippocampal gyrus (entorhinal and parahippocampal cortices) and the adjacent Brodmann areas (BA) 35 and 36, as provided by four neuroanatomists from different laboratories, aiming to identify the rationale for overlapping and diverging delineations.Nissl-stained series were acquired from the temporal lobes of three human specimens (two right and one left hemisphere). Slices (50 µm thick) were prepared perpendicular to the long axis of the hippocampus spanning the entire longitudinal extent of the MTL cortex. Four neuroanatomists annotated MTL cortex subregions on digitized (20X resolution) slices with 5 mm spacing. Parcellations, terminology, and border placement were compared among neuroanatomists. Cytoarchitectonic features of each subregion are described in detail.Qualitative analysis of the annotations showed higher agreement in the definitions of the entorhinal cortex and BA35, while definitions of BA36 and the parahippocampal cortex exhibited less overlap among neuroanatomists. The degree of overlap of cytoarchitectonic definitions was partially reflected in the neuroanatomists’ agreement on the respective delineations. Lower agreement in annotations was observed in transitional zones between structures where seminal cytoarchitectonic features are expressed more gradually.The results highlight that definitions and parcellations of the MTL cortex differ among neuroanatomical schools and thereby increase understanding of why these differences may arise. This work sets a crucial foundation to further advance anatomically-informed human neuroimaging research on the MTL cortex.
Published: 2023
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35. Localization and connectivity of rodent equivalent of the primate posterior cingulate cortex (area 23)

Author: Xiang, Xiao-Jun, primary, Chen, Sheng-Qiang, additional, Zhang, Xue-Qin, additional, Chen, Chang-Hui, additional, Zhang, Shun-Yu, additional, Cai, Hui-Ru, additional, and Ding, Song-Lin, additional
Published: 2023
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36. A novel subdivision of the bed nucleus of stria terminalis in monkey, rat, and mouse brains

Author: Ding, Song‐Lin, primary
Published: 2022
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37. The effects of bilateral prostriata lesions on spatial learning and memory in the rat

Author: Zhang, Shun-Yu, primary, Chen, Sheng-Qiang, additional, Zhang, Jin-Yuan, additional, Chen, Chang-Hui, additional, Xiang, Xiao-Jun, additional, Cai, Hui-Ru, additional, and Ding, Song-Lin, additional
Published: 2022
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38. Transcriptomic cytoarchitecture reveals principles of human neocortex organization

Author: Jorstad, Nikolas L., primary, Close, Jennie, additional, Johansen, Nelson, additional, Yanny, Anna Marie, additional, Barkan, Eliza R., additional, Travaglini, Kyle J., additional, Bertagnolli, Darren, additional, Campos, Jazmin, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Dee, Nick, additional, Ding, Song-Lin, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hirschstein, Daniel, additional, Kroll, Matthew, additional, Kunst, Michael, additional, Lathia, Kanan, additional, Long, Brian, additional, Martin, Naomi, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Rimorin, Christine, additional, Ruiz, Augustin, additional, Shapovalova, Nadiya, additional, Shehata, Soraya, additional, Siletti, Kimberly, additional, Somasundaram, Saroja, additional, Sulc, Josef, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Tung, Herman, additional, Ward, Katelyn, additional, Callaway, Edward M., additional, Hof, Patrick R., additional, Keene, C. Dirk, additional, Levi, Boaz P., additional, Linnarsson, Sten, additional, Mitra, Partha P., additional, Smith, Kimberly, additional, Hodge, Rebecca D., additional, Bakken, Trygve E., additional, and Lein, Ed S., additional
Published: 2022
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39. Transcriptomic diversity of cell types across the adult human brain

Author: Siletti, Kimberly, primary, Hodge, Rebecca, additional, Mossi Albiach, Alejandro, additional, Hu, Lijuan, additional, Lee, Ka Wai, additional, Lönnerberg, Peter, additional, Bakken, Trygve, additional, Ding, Song-Lin, additional, Clark, Michael, additional, Casper, Tamara, additional, Dee, Nick, additional, Gloe, Jessica, additional, Keene, C. Dirk, additional, Nyhus, Julie, additional, Tung, Herman, additional, Yanny, Anna Marie, additional, Arenas, Ernest, additional, Lein, Ed S., additional, and Linnarsson, Sten, additional
Published: 2022
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40. Comparative transcriptomics reveals human-specific cortical features

Author: Jorstad, Nikolas L., primary, Song, Janet H.T., additional, Exposito-Alonso, David, additional, Suresh, Hamsini, additional, Castro, Nathan, additional, Krienen, Fenna M., additional, Yanny, Anna Marie, additional, Close, Jennie, additional, Gelfand, Emily, additional, Travaglini, Kyle J., additional, Basu, Soumyadeep, additional, Beaudin, Marc, additional, Bertagnolli, Darren, additional, Crow, Megan, additional, Ding, Song-Lin, additional, Eggermont, Jeroen, additional, Glandon, Alexandra, additional, Goldy, Jeff, additional, Kroes, Thomas, additional, Long, Brian, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Rimorin, Christine, additional, Siletti, Kimberly, additional, Somasundaram, Saroja, additional, Tieu, Michael, additional, Torkelson, Amy, additional, Ward, Katelyn, additional, Feng, Guoping, additional, Hopkins, William D., additional, Höllt, Thomas, additional, Keene, C. Dirk, additional, Linnarsson, Sten, additional, McCarroll, Steven A., additional, Lelieveldt, Boudewijn P., additional, Sherwood, Chet C., additional, Smith, Kimberly, additional, Walsh, Christopher A., additional, Dobin, Alexander, additional, Gillis, Jesse, additional, Lein, Ed S., additional, Hodge, Rebecca D., additional, and Bakken, Trygve E., additional
Published: 2022
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41. 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

42. Editorial: 15 years of frontiers in neuroanatomy: the circuits behind the visual cortex.

Author: Takahata, Toru and Ding, Song-Lin
Subjects: VISUAL cortex, CORPUS callosum, OPTICAL information processing, VISUAL pathways, MOTOR cortex, SUPERIOR colliculus, NEUROANATOMY
Abstract: The editorial "15 years of frontiers in neuroanatomy: the circuits behind the visual cortex" presents four original research articles focusing on novel neuroanatomical concepts related to the visual system. The studies explore how the brain in mice connects visual information to movement, how fibers in the brain's corpus callosum are organized, how the primary visual cortex connects to different types of cells in the superior colliculus, and how different areas of the brain in macaques process visual information from the fovea. These findings deepen our understanding of how visual information is processed in the brain and offer insights into potential disruptions in disease. The research contributes to advancing the field of neuroanatomy and visual neuroscience. [Extracted from the article]
Published: 2024
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43. Chemoarchitecture of area prostriata in adult and developing mice: Comparison with presubiculum and parasubiculum

Author: Chen, Sheng‐Qiang, primary, Chen, Chang‐Hui, additional, Xiang, Xiao‐Jun, additional, Zhang, Shun‐Yu, additional, and Ding, Song‐Lin, additional
Published: 2022
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44. Chemo-architecture of area prostriata in adult and developing mice: comparison with presubiculum and parasubiculum

Author: Chen, Sheng-Qiang, primary, Chen, Chang-Hui, additional, Xiang, Xiao-Jun, additional, Zhang, Shun-Yu, additional, and Ding, Song-Lin, additional
Published: 2022
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45. 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
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46. Comprehensive cellular‐resolution atlas of the adult human brain

Author: Ding, Song‐Lin, Royall, Joshua J., Sunkin, Susan M., Ng, Lydia, Facer, Benjamin A.C., Lesnar, Phil, Guillozet‐Bongaarts, Angie, McMurray, Bergen, Szafer, Aaron, Dolbeare, Tim A., Stevens, Allison, Tirrell, Lee, Benner, Thomas, Caldejon, Shiella, Dalley, Rachel A., Dee, Nick, Lau, Christopher, Nyhus, Julie, Reding, Melissa, Riley, Zackery L., Sandman, David, Shen, Elaine, van der Kouwe, Andre, Varjabedian, Ani, Write, Michelle, Zollei, Lilla, Dang, Chinh, Knowles, James A., Koch, Christof, Phillips, John W., Sestan, Nenad, Wohnoutka, Paul, Zielke, H. Ronald, Hohmann, John G., Jones, Allan R., Bernard, Amy, Hawrylycz, Michael J., Hof, Patrick R., Fischl, Bruce, and LeinReference, Ed S.
Published: 2017
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47. 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

48. Cover Image, Volume 530, Issue 1

Author: Ding, Song‐Lin, primary, Royall, Joshua J., additional, Lesnar, Phil, additional, Facer, Benjamin A.C., additional, Smith, Kimberly A., additional, Wei, Yina, additional, Brouner, Kristina, additional, Dalley, Rachel A., additional, Dee, Nick, additional, Dolbeare, Tim A., additional, Ebbert, Amanda, additional, Glass, Ian A., additional, Keller, Nika H., additional, Lee, Felix, additional, Lemon, Tracy A., additional, Nyhus, Julie, additional, Pendergraft, Julie, additional, Reid, Robert, additional, Sarreal, Melaine, additional, Shapovalova, Nadiya V., additional, Szafer, Aaron, additional, Phillips, John W., additional, Sunkin, Susan M., additional, Hohmann, John G., additional, Jones, Allan R., additional, Hawrylycz, Michael J., additional, Hof, Patrick R., additional, Ng, Lydia, additional, Bernard, Amy, additional, and Lein, Ed S., additional
Published: 2021
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49. Cellular resolution anatomical and molecular atlases for prenatal human brains

Author: Ding, Song‐Lin, primary, Royall, Joshua J., additional, Lesnar, Phil, additional, Facer, Benjamin A.C., additional, Smith, Kimberly A., additional, Wei, Yina, additional, Brouner, Kristina, additional, Dalley, Rachel A., additional, Dee, Nick, additional, Dolbeare, Tim A., additional, Ebbert, Amanda, additional, Glass, Ian A., additional, Keller, Nika H., additional, Lee, Felix, additional, Lemon, Tracy A., additional, Nyhus, Julie, additional, Pendergraft, Julie, additional, Reid, Robert, additional, Sarreal, Melaine, additional, Shapovalova, Nadiya V., additional, Szafer, Aaron, additional, Phillips, John W., additional, Sunkin, Susan M., additional, Hohmann, John G., additional, Jones, Allan R., additional, Hawrylycz, Michael J., additional, Hof, Patrick R., additional, Ng, Lydia, additional, Bernard, Amy, additional, and Lein, Ed S., additional
Published: 2021
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50. Experimental investigation on the performance and mechanism of graphene oxide nanofluids in turning Ti-6Al-4V

Author: Ding Song-lin, Yi Shuang, and Mo John
Subjects: 0209 industrial biotechnology, Materials science, Scanning electron microscope, Graphene, Strategy and Management, Chip formation, 02 engineering and technology, Management Science and Operations Research, 021001 nanoscience & nanotechnology, Industrial and Manufacturing Engineering, law.invention, Coolant, chemistry.chemical_compound, 020901 industrial engineering & automation, Nanofluid, Machining, chemistry, law, Boron nitride, Surface roughness, Composite material, 0210 nano-technology
Abstract: This paper investigated the working mechanism of a new type of graphene based nanofluids in turning Ti-6Al-4 V. Comparative study was conducted to analyse chip formation, cutting temperature and surface roughness in turning Ti-6Al-4 V with graphene oxide (GO) nanofluids. Surface topography and chip morphology were examined when turning with polycrystalline cubic boron nitride (PCBN) inserts by scanning electron microscope (SEM). Influences of coolant pressure, concentration and machining parameters such as cutting speed, feed rate and cutting depth were investigated. The results showed that the surface roughness was reduced by about 34.34% when using GO nanofluids as compared with conventional coolant. The cutting temperature was reduced by 27.16 ℃ , 30.42 ℃ , and 31.8 ℃ , respectively when lower velocity, lower feed and higher coolant pressure were applied whereas the cutting temperature decreased by 50.53 ℃ when the pressure of the GO nanofluids was 10 bar.
Published: 2019
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