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8. Veganism and Capitalism

Author

Jones, Robert C., Sanbonmatsu, John, Athanassakis, Yanoula, editor, Larue, Renan, editor, and O’Donohue, William, editor

Published
2024
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10. Cell types of origin of the cell-free transcriptome

Author

Jones, Robert C, Karkanias, Jim, Krasnow, Mark, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D’Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Vorperian, Sevahn K, Wang, Wanxin, Weinstein, Hannah NW, Winkler, Juliane, Wu, Timothy TH, Xie, Jamie, and Yung, Andrea R

Subjects
Human Genome, Genetics, Cell-Free Nucleic Acids, Humans, Transcriptome, Tabula Sapiens Consortium
Abstract

Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases.

Published
2022

12. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Author

Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Vorperian, Sevahn K, Wang, Wanxin, Weinstein, Hannah NW, Winkler, Juliane, Wu, Timothy TH, Xie, Jamie, Yung, Andrea R, Zhang, Yue, and Detweiler, Angela M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Atlases as Topic, B-Lymphocytes, Cells, Humans, Organ Specificity, RNA Splicing, Single-Cell Analysis, T-Lymphocytes, Transcriptome, Tabula Sapiens Consortium*, General Science & Technology
Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

13. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

Author

Li, Hongjie, Janssens, Jasper, De Waegeneer, Maxime, Kolluru, Sai Saroja, Davie, Kristofer, Gardeux, Vincent, Saelens, Wouter, David, Fabrice PA, Brbić, Maria, Spanier, Katina, Leskovec, Jure, McLaughlin, Colleen N, Xie, Qijing, Jones, Robert C, Brueckner, Katja, Shim, Jiwon, Tattikota, Sudhir Gopal, Schnorrer, Frank, Rust, Katja, Nystul, Todd G, Carvalho-Santos, Zita, Ribeiro, Carlos, Pal, Soumitra, Mahadevaraju, Sharvani, Przytycka, Teresa M, Allen, Aaron M, Goodwin, Stephen F, Berry, Cameron W, Fuller, Margaret T, White-Cooper, Helen, Matunis, Erika L, DiNardo, Stephen, Galenza, Anthony, O'Brien, Lucy Erin, Dow, Julian AT, FCA Consortium§, Jasper, Heinrich, Oliver, Brian, Perrimon, Norbert, Deplancke, Bart, Quake, Stephen R, Luo, Liqun, Aerts, Stein, Agarwal, Devika, Ahmed-Braimah, Yasir, Arbeitman, Michelle, Ariss, Majd M, Augsburger, Jordan, Ayush, Kumar, Baker, Catherine C, Banisch, Torsten, Birker, Katja, Bodmer, Rolf, Bolival, Benjamin, Brantley, Susanna E, Brill, Julie A, Brown, Nora C, Buehner, Norene A, Cai, Xiaoyu Tracy, Cardoso-Figueiredo, Rita, Casares, Fernando, Chang, Amy, Clandinin, Thomas R, Crasta, Sheela, Desplan, Claude, Detweiler, Angela M, Dhakan, Darshan B, Donà, Erika, Engert, Stefanie, Floc'hlay, Swann, George, Nancy, González-Segarra, Amanda J, Groves, Andrew K, Gumbin, Samantha, Guo, Yanmeng, Harris, Devon E, Heifetz, Yael, Holtz, Stephen L, Horns, Felix, Hudry, Bruno, Hung, Ruei-Jiun, Jan, Yuh Nung, Jaszczak, Jacob S, Jefferis, Gregory SXE, Karkanias, Jim, Karr, Timothy L, Katheder, Nadja Sandra, Kezos, James, Kim, Anna A, Kim, Seung K, Kockel, Lutz, Konstantinides, Nikolaos, Kornberg, Thomas B, Krause, Henry M, Labott, Andrew Thomas, Laturney, Meghan, Lehmann, Ruth, Leinwand, Sarah, Li, Jiefu, and Li, Joshua Shing Shun

Subjects
FCA Consortium§, Cell Nucleus, Animals, Drosophila melanogaster, Drosophila Proteins, Transcription Factors, Gene Expression Regulation, Sex Characteristics, Genes, Insect, Databases, Genetic, Female, Male, Gene Regulatory Networks, Single-Cell Analysis, Transcriptome, RNA-Seq, Biotechnology, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, General Science & Technology
Abstract

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

Published
2022

14. Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer’s model

Author

Reinitz, Felicia, Chen, Elizabeth Y, di Robilant, Benedetta Nicolis, Chuluun, Bayarsaikhan, Antony, Jane, Jones, Robert C, Gubbi, Neha, Lee, Karen, Ho, William Hai Dang, Kolluru, Sai Saroja, Qian, Dalong, Adorno, Maddalena, Piltti, Katja, Anderson, Aileen, Monje, Michelle, Heller, H Craig, Quake, Stephen R, and Clarke, Michael F

Subjects
Biochemistry and Cell Biology, Biological Sciences, Regenerative Medicine, Genetics, Stem Cell Research, Alzheimer's Disease, Neurosciences, Neurodegenerative, Acquired Cognitive Impairment, Dementia, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Aging, Brain Disorders, Aetiology, 2.1 Biological and endogenous factors, Neurological, Alzheimer Disease, Amyloid beta-Peptides, Amyloid beta-Protein Precursor, Animals, Cellular Senescence, Disease Models, Animal, Inflammation, Mice, Mice, Transgenic, Neurodegenerative Diseases, Plaque, Amyloid, Ubiquitin Thiolesterase, neural stem cells, Alzheimer's, neurodegeneration, Mouse, mouse, regenerative medicine, stem cells, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Alzheimer's disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify a potential earlier targetable phenotype. Utilizing a mouse model of AD and human fetal cells harboring mutant amyloid precursor protein, we show cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it the earliest defect in the evolution of the disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. Reduction of USP16 led to decreased expression of senescence gene Cdkn2a and mitigated aberrant regulation of the Bone Morphogenetic Signaling (BMP) pathway, a previously unknown function of USP16. Thus, we reveal USP16 as a novel target in an AD model that can both ameliorate the NPC defect and rescue memory and learning through its regulation of both Cdkn2a and BMP signaling.

Published
2022

15. Cerebellar nuclei evolved by repeatedly duplicating a conserved cell-type set

Author

Kebschull, Justus M, Richman, Ethan B, Ringach, Noam, Friedmann, Drew, Albarran, Eddy, Kolluru, Sai Saroja, Jones, Robert C, Allen, William E, Wang, Ying, Cho, Seung Woo, Zhou, Huaijun, Ding, Jun B, Chang, Howard Y, Deisseroth, Karl, Quake, Stephen R, and Luo, Liqun

Subjects
Biotechnology, Neurosciences, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Animals, Biological Evolution, Cerebellar Nuclei, Chickens, Female, Humans, Male, Mice, Mice, Inbred C57BL, Neurons, RNA-Seq, General Science & Technology
Abstract

How have complex brains evolved from simple circuits? Here we investigated brain region evolution at cell-type resolution in the cerebellar nuclei, the output structures of the cerebellum. Using single-nucleus RNA sequencing in mice, chickens, and humans, as well as STARmap spatial transcriptomic analysis and whole-central nervous system projection tracing, we identified a conserved cell-type set containing two region-specific excitatory neuron classes and three region-invariant inhibitory neuron classes. This set constitutes an archetypal cerebellar nucleus that was repeatedly duplicated to form new regions. The excitatory cell class that preferentially funnels information to lateral frontal cortices in mice becomes predominant in the massively expanded human lateral nucleus. Our data suggest a model of brain region evolution by duplication and divergence of entire cell-type sets.

Published
2020

16. A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

Author

Almanzar, Nicole, Antony, Jane, Baghel, Ankit S, Bakerman, Isaac, Bansal, Ishita, Barres, Ben A, Beachy, Philip A, Berdnik, Daniela, Bilen, Biter, Brownfield, Douglas, Cain, Corey, Chan, Charles KF, Chen, Michelle B, Clarke, Michael F, Conley, Stephanie D, Darmanis, Spyros, Demers, Aaron, Demir, Kubilay, De Morree, Antoine, du Bois, Tessa Divita Haley, Ebadi, Hamid, Espinoza, F Hernan, Fish, Matt, Gan, Qiang, George, Benson M, Gillich, Astrid, Gomez-Sjoberg, Rafael, Green, Foad, Genetiano, Geraldine, Gu, Xueying, Gulati, Gunsagar S, Hahn, Oliver, Haney, Michael Seamus, Hang, Yan, Harris, Lincoln, He, Mu, Hosseinzadeh, Shayan, Huang, Albin, Huang, Kerwyn Casey, Iram, Tal, Isobe, Taichi, Ives, Feather, Jones, Robert C, Kao, Kevin S, Karkanias, Jim, Karnam, Guruswamy, Keller, Andreas, Kershner, Aaron M, Khoury, Nathalie, Kim, Seung K, Kiss, Bernhard M, Kong, William, Krasnow, Mark A, Kumar, Maya E, Kuo, Christin S, Lam, Jonathan, Lee, Davis P, Lee, Song E, Lehallier, Benoit, Leventhal, Olivia, Li, Guang, Li, Qingyun, Liu, Ling, Lo, Annie, Lu, Wan-Jin, Lugo-Fagundo, Maria F, Manjunath, Anoop, May, Andrew P, Maynard, Ashley, McGeever, Aaron, Mckay, Marina, McNerney, M Windy, Merrill, Bryan, Metzger, Ross J, Mignardi, Marco, Min, Dullei, Nabhan, Ahmad N, Neff, Norma F, Ng, Katharine M, Nguyen, Patricia K, Noh, Joseph, Nusse, Roel, Palovics, Robert, Patkar, Rasika, Peng, Weng Chuan, Penland, Lolita, Pisco, Angela Oliveira, Pollard, Katherine, Puccinelli, Robert, Qi, Zhen, Quake, Stephen R, Rando, Thomas A, Rulifson, Eric J, Schaum, Nicholas, Segal, Joe M, Sikandar, Shaheen S, Sinha, Rahul, Sit, Rene V, Sonnenburg, Justin, and Staehli, Daniel

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Aging, Animals, Cellular Senescence, DNA Mutational Analysis, Female, Gene Expression Regulation, Developmental, Genomic Instability, Immunity, Liver, Male, Mice, Models, Animal, Organ Specificity, Single-Cell Analysis, T-Lymphocytes, Transcriptome, Tabula Muris Consortium, General Science & Technology
Abstract

Ageing is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death1. Despite rapid advances over recent years, many of the molecular and cellular processes that underlie the progressive loss of healthy physiology are poorly understood2. To gain a better insight into these processes, here we generate a single-cell transcriptomic atlas across the lifespan of Mus musculus that includes data from 23 tissues and organs. We found cell-specific changes occurring across multiple cell types and organs, as well as age-related changes in the cellular composition of different organs. Using single-cell transcriptomic data, we assessed cell-type-specific manifestations of different hallmarks of ageing-such as senescence3, genomic instability4 and changes in the immune system2. This transcriptomic atlas-which we denote Tabula Muris Senis, or 'Mouse Ageing Cell Atlas'-provides molecular information about how the most important hallmarks of ageing are reflected in a broad range of tissues and cell types.

Published
2020

20. Heterogenous impairment of α cell function in type 2 diabetes is linked to cell maturation state

Author

Dai, Xiao-Qing, Camunas-Soler, Joan, Briant, Linford J.B., dos Santos, Theodore, Spigelman, Aliya F., Walker, Emily M., Arrojo e Drigo, Rafael, Bautista, Austin, Jones, Robert C., Avrahami, Dana, Lyon, James, Nie, Aifang, Smith, Nancy, Zhang, Yongneng, Johnson, Janyne, Manning Fox, Jocelyn E., Michelakis, Evangelos D., Light, Peter E., Kaestner, Klaus H., Kim, Seung K., Rorsman, Patrik, Stein, Roland W., Quake, Stephen R., and MacDonald, Patrick E.

Published
2022
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21. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

Author

Schaum, Nicholas, Karkanias, Jim, Neff, Norma F, May, Andrew P, Quake, Stephen R, Wyss-Coray, Tony, Darmanis, Spyros, Batson, Joshua, Botvinnik, Olga, Chen, Michelle B, Chen, Steven, Green, Foad, Jones, Robert C, Maynard, Ashley, Penland, Lolita, Pisco, Angela Oliveira, Sit, Rene V, Stanley, Geoffrey M, Webber, James T, Zanini, Fabio, Baghel, Ankit S, Bakerman, Isaac, Bansal, Ishita, Berdnik, Daniela, Bilen, Biter, Brownfield, Douglas, Cain, Corey, Cho, Min, Cirolia, Giana, Conley, Stephanie D, Demers, Aaron, Demir, Kubilay, de Morree, Antoine, Divita, Tessa, du Bois, Haley, Dulgeroff, Laughing Bear Torrez, Ebadi, Hamid, Espinoza, F Hernan, Fish, Matt, Gan, Qiang, George, Benson M, Gillich, Astrid, Genetiano, Geraldine, Gu, Xueying, Gulati, Gunsagar S, Hang, Yan, Hosseinzadeh, Shayan, Huang, Albin, Iram, Tal, Isobe, Taichi, Ives, Feather, Kao, Kevin S, Karnam, Guruswamy, Kershner, Aaron M, Kiss, Bernhard M, Kong, William, Kumar, Maya E, Lam, Jonathan Y, Lee, Davis P, Lee, Song E, Li, Guang, Li, Qingyun, Liu, Ling, Lo, Annie, Lu, Wan-Jin, Manjunath, Anoop, May, Kaia L, May, Oliver L, McKay, Marina, Metzger, Ross J, Mignardi, Marco, Min, Dullei, Nabhan, Ahmad N, Ng, Katharine M, Noh, Joseph, Patkar, Rasika, Peng, Weng Chuan, Puccinelli, Robert, Sikandar, Shaheen S, Sinha, Rahul, Szade, Krzysztof, Tan, Weilun, Tato, Cristina, Tellez, Krissie, Travaglini, Kyle J, Tropini, Carolina, Waldburger, Lucas, van Weele, Linda J, Wosczyna, Michael N, Xiang, Jinyi, Xue, Soso, Youngyunpipatkul, Justin, Zardeneta, Macy E, Zhang, Fan, Zhou, Lu, Castro, Paola, Croote, Derek, DeRisi, Joseph L, Kuo, Christin S, and Lehallier, Benoit

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Animals, Cell Biology, Endothelial Cells, Female, Flow Cytometry, Gene Expression Profiling, Male, Mice, Mice, Inbred C57BL, Microfluidics, Organ Specificity, Single-Cell Analysis, T-Lymphocytes, Transcription Factors, Transcriptome, Tabula Muris Consortium, Overall coordination, Logistical coordination, Organ collection and processing, Library preparation and sequencing, Computational data analysis, Cell type annotation, Writing group, Supplemental text writing group, Principal investigators, General Science & Technology
Abstract

Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3'-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

Published
2018

24. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

Author

Mereu, Elisabetta, Lafzi, Atefeh, Moutinho, Catia, Ziegenhain, Christoph, McCarthy, Davis J., Álvarez-Varela, Adrián, Batlle, Eduard, Sagar, Grün, Dominic, Lau, Julia K., Boutet, Stéphane C., Sanada, Chad, Ooi, Aik, Jones, Robert C., Kaihara, Kelly, Brampton, Chris, Talaga, Yasha, Sasagawa, Yohei, Tanaka, Kaori, Hayashi, Tetsutaro, Braeuning, Caroline, Fischer, Cornelius, Sauer, Sascha, Trefzer, Timo, Conrad, Christian, Adiconis, Xian, Nguyen, Lan T., Regev, Aviv, Levin, Joshua Z., Parekh, Swati, Janjic, Aleksandar, Wange, Lucas E., Bagnoli, Johannes W., Enard, Wolfgang, Gut, Marta, Sandberg, Rickard, Nikaido, Itoshi, Gut, Ivo, Stegle, Oliver, and Heyn, Holger

Published
2020
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26. Contributors

Author

Basch, Gottlieb, primary, Bristor, Doug, additional, Carbonell-Bojollo, Rosa, additional, Chambers, Robert, additional, Gil-Ribes, Jesús A., additional, Gomez-Ariza, Manuel R., additional, Gonzalez-Sanchez, Emilio J., additional, Herren, Hans R., additional, Jenkins, David, additional, Jones, Robert C., additional, Juniper, Tony, additional, Kassam, Amir, additional, Kassam, Laila, additional, Kassam, Shireen, additional, Kassam, Zahra, additional, Langan, Mark, additional, Latham, Jonathan, additional, Mason, Jim, additional, McMichael, Philip, additional, Montgomery, David R., additional, Moreno-Garcia, Manuel, additional, Mulvany, Patrick, additional, Nobari, Nassim, additional, Norberg-Hodge, Helena, additional, Ordoñez-Fernandez, Rafaela, additional, Price, Sophia, additional, Sheldrake, Rupert, additional, Shiva, Vandana, additional, Trivino-Tarradas, Paula, additional, Tudge, Colin, additional, Veroz-Gonzalez, Oscar, additional, and Wilson, Allison K., additional

Published
2021
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27. Computation of Maximal Resolution of Copy Number Variation on a Nanofluidic Device using Digital PCR

Author

Dube, Simant, Mir, Alain, Jones, Robert C., Ramakrishnan, Ramesh, and Sun, Gang

Subjects
Quantitative Biology - Genomics
Abstract

Copy Number Variations (CNVs) of regions of the human genome are important in disease association studies.The digital array is a nanofluidic biochip which utilizes integrated channels and valves that partition mixtures of sample and reagents into 765 nanovolume reaction chambers. It was recently shown how one can perform statistical analysis of CNV in a DNA sample the digital array. In particular, it was shown how one can accurately estimate the true concentration of the molecules in the DNA sample and then determine the ratios of different sequences along with statistical confidence intervals on these estimations. In this paper we perform computation of maximum number of copies which can be distinguished using the digital array which gives its resolution in terms of its ability to determine CNV. Then, we demonstrate the usefulness of the mathematical analysis to solve an important real-world problem of determination of the copy number of X chromosome as our example application., Comment: Preliminary draft. Ongoing work to be submitted in refereed conferences and/or journals

Published
2008

30. Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution

Author

Lu, Tzu-Chiao, primary, Brbić, Maria, additional, Park, Ye-Jin, additional, Jackson, Tyler, additional, Chen, Jiaye, additional, Kolluru, Sai Saroja, additional, Qi, Yanyan, additional, Katheder, Nadja Sandra, additional, Cai, Xiaoyu Tracy, additional, Lee, Seungjae, additional, Chen, Yen-Chung, additional, Auld, Niccole, additional, Liang, Chung-Yi, additional, Ding, Sophia H., additional, Welsch, Doug, additional, D’Souza, Samuel, additional, Pisco, Angela Oliveira, additional, Jones, Robert C., additional, Leskovec, Jure, additional, Lai, Eric C., additional, Bellen, Hugo J., additional, Luo, Liqun, additional, Jasper, Heinrich, additional, Quake, Stephen R., additional, and Li, Hongjie, additional

Published
2023
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31. Veganisms

Author

Jones, Robert C., Castricano, Jodey, editor, and Simonsen, Rasmus R., editor

Published
2016
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33. Molecular hallmarks of heterochronic parabiosis at single-cell resolution

Author

Pálovics, Róbert, Keller, Andreas, Schaum, Nicholas, Tan, Weilun, Fehlmann, Tobias, Borja, Michael, Kern, Fabian, Bonanno, Liana, Calcuttawala, Kruti, Webber, James, McGeever, Aaron, Almanzar, Nicole, Antony, Jane, Baghel, Ankit S., Bakerman, Isaac, Bansal, Ishita, Barres, Ben A., Beachy, Philip A., Berdnik, Daniela, Bilen, Biter, Brownfield, Douglas, Cain, Corey, Chan, Charles K. F., Chen, Michelle B., Clarke, Michael F., Conley, Stephanie D., Demers, Aaron, Demir, Kubilay, de Morree, Antoine, Divita, Tessa, du Bois, Haley, Ebadi, Hamid, Espinoza, F. Hernán, Fish, Matt, Gan, Qiang, George, Benson M., Gillich, Astrid, Gòmez-Sjöberg, Rafael, Green, Foad, Genetiano, Geraldine, Gu, Xueying, Gulati, Gunsagar S., Hahn, Oliver, Haney, Michael Seamus, Hang, Yan, Harris, Lincoln, He, Mu, Hosseinzadeh, Shayan, Huang, Albin, Huang, Kerwyn Casey, Iram, Tal, Isobe, Taichi, Ives, Feather, Jones, Robert C., Kao, Kevin S., Karnam, Guruswamy, Kershner, Aaron M., Khoury, Nathalie, Kim, Seung K., Kiss, Bernhard M., Kong, William, Krasnow, Mark A., Kumar, Maya E., Kuo, Christin S., Lam, Jonathan, Lee, Davis P., Lee, Song E., Lehallier, Benoit, Leventhal, Olivia, Li, Guang, Li, Qingyun, Liu, Ling, Lo, Annie, Lu, Wan-Jin, Lugo-Fagundo, Maria F., Manjunath, Anoop, May, Andrew P., Maynard, Ashley, McKay, Marina, McNerney, M. Windy, Merrill, Bryan, Metzger, Ross J., Mignardi, Marco, Min, Dullei, Nabhan, Ahmad N., Ng, Katharine M., Nguyen, Patricia K., Noh, Joseph, Nusse, Roel, Patkar, Rasika, Peng, Weng Chuan, Penland, Lolita, Pollard, Katherine, Puccinelli, Robert, Qi, Zhen, Rando, Thomas A., Rulifson, Eric J., Segal, Joe M., Sikandar, Shaheen S., Sinha, Rahul, Sit, Rene V., Sonnenburg, Justin, Staehli, Daniel, Szade, Krzysztof, Tan, Michelle, Tato, Cristina, Tellez, Krissie, Torrez Dulgeroff, Laughing Bear, Travaglini, Kyle J., Tropini, Carolina, Tsui, Margaret, Waldburger, Lucas, Wang, Bruce M., van Weele, Linda J., Weinberg, Kenneth, Weissman, Irving L., Wosczyna, Michael N., Wu, Sean M., Xiang, Jinyi, Xue, Soso, Yamauchi, Kevin A., Yang, Andrew C., Yerra, Lakshmi P., Youngyunpipatkul, Justin, Yu, Brian, Zanini, Fabio, Zardeneta, Macy E., Zee, Alexander, Zhao, Chunyu, Zhang, Fan, Zhang, Hui, Zhang, Martin Jinye, Zhou, Lu, Zou, James, Luo, Jian, Pisco, Angela Oliveira, Karkanias, Jim, Neff, Norma F., Darmanis, Spyros, Quake, Stephen R., and Wyss-Coray, Tony

Subjects
Aging, Multidisciplinary, Parabiosis, Mesenchymal Stem Cells, Hematopoietic Stem Cells, Article, Organ Specificity/genetics, Mitochondria, Electron Transport, Electron Transport/genetics, Organ Specificity, Aging/genetics, Adipocytes, Hepatocytes, Rejuvenation, RNA-Seq, Single-Cell Analysis
Abstract

The ability to slow or reverse biological ageing would have major implications for mitigating disease risk and maintaining vitality1. Although an increasing number of interventions show promise for rejuvenation2, their effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplored. Here we performed single-cell RNA sequencing on 20 organs to reveal cell-type-specific responses to young and aged blood in heterochronic parabiosis. Adipose mesenchymal stromal cells, haematopoietic stem cells and hepatocytes are among those cell types that are especially responsive. On the pathway level, young blood invokes new gene sets in addition to reversing established ageing patterns, with the global rescue of genes encoding electron transport chain subunits pinpointing a prominent role of mitochondrial function in parabiosis-mediated rejuvenation. We observed an almost universal loss of gene expression with age that is largely mimicked by parabiosis: aged blood reduces global gene expression, and young blood restores it in select cell types. Together, these data lay the groundwork for a systemic understanding of the interplay between blood-borne factors and cellular integrity.

Published
2022

34. The capacities conception

Author

Andrews, Kristin, primary, Comstock, Gary, additional, Crozier, G.K.D., additional, Donaldson, Sue, additional, Fenton, Andrew, additional, John, Tyler M., additional, Johnson, L. Syd M, additional, Jones, Robert C., additional, Kymlicka, Will, additional, Meynell, Letitia, additional, Nobis, Nathan, additional, Peña-Guzmán, David, additional, and Sebo, Jeff, additional

Published
2018
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35. The community membership conception

Author

Andrews, Kristin, primary, Comstock, Gary, additional, Crozier, G.K.D., additional, Donaldson, Sue, additional, Fenton, Andrew, additional, John, Tyler M., additional, Johnson, L. Syd M, additional, Jones, Robert C., additional, Kymlicka, Will, additional, Meynell, Letitia, additional, Nobis, Nathan, additional, Peña-Guzmán, David, additional, and Sebo, Jeff, additional

Published
2018
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36. Chimpanzee Rights

Author

Andrews, Kristin, primary, Comstock, Gary, additional, Crozier, G.K.D., additional, Donaldson, Sue, additional, Fenton, Andrew, additional, John, Tyler M., additional, Johnson, L. Syd M, additional, Jones, Robert C., additional, Kymlicka, Will, additional, Meynell, Letitia, additional, Nobis, Nathan, additional, Peña-Guzmán, David, additional, and Sebo, Jeff, additional

Published
2018
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37. The species membership conception

Author

Andrews, Kristin, primary, Comstock, Gary, additional, Crozier, G.K.D., additional, Donaldson, Sue, additional, Fenton, Andrew, additional, John, Tyler M., additional, Johnson, L. Syd M, additional, Jones, Robert C., additional, Kymlicka, Will, additional, Meynell, Letitia, additional, Nobis, Nathan, additional, Peña-Guzmán, David, additional, and Sebo, Jeff, additional

Published
2018
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38. Conclusions

Author

Andrews, Kristin, primary, Comstock, Gary, additional, Crozier, G.K.D., additional, Donaldson, Sue, additional, Fenton, Andrew, additional, John, Tyler M., additional, Johnson, L. Syd M, additional, Jones, Robert C., additional, Kymlicka, Will, additional, Meynell, Letitia, additional, Nobis, Nathan, additional, Peña-Guzmán, David, additional, and Sebo, Jeff, additional

Published
2018
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39. Introduction: Chimpanzees, rights, and conceptions of personhood

Author

Andrews, Kristin, primary, Comstock, Gary, additional, Crozier, G.K.D., additional, Donaldson, Sue, additional, Fenton, Andrew, additional, John, Tyler M., additional, Johnson, L. Syd M, additional, Jones, Robert C., additional, Kymlicka, Will, additional, Meynell, Letitia, additional, Nobis, Nathan, additional, Peña-Guzmán, David, additional, and Sebo, Jeff, additional

Published
2018
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40. The social contract conception

Author

Andrews, Kristin, primary, Comstock, Gary, additional, Crozier, G.K.D., additional, Donaldson, Sue, additional, Fenton, Andrew, additional, John, Tyler M., additional, Johnson, L. Syd M, additional, Jones, Robert C., additional, Kymlicka, Will, additional, Meynell, Letitia, additional, Nobis, Nathan, additional, Peña-Guzmán, David, additional, and Sebo, Jeff, additional

Published
2018
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41. Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution

Author

Lu, Tzu-Chiao, primary, Brbić, Maria, additional, Park, Ye-Jin, additional, Jackson, Tyler, additional, Chen, Jiaye, additional, Kolluru, Sai Saroja, additional, Qi, Yanyan, additional, Katheder, Nadja Sandra, additional, Cai, Xiaoyu Tracy, additional, Lee, Seungjae, additional, Chen, Yen-Chung, additional, Auld, Niccole, additional, Welsch, Doug, additional, D’Souza, Samuel, additional, Pisco, Angela Oliveira, additional, Jones, Robert C., additional, Leskovec, Jure, additional, Lai, Eric C., additional, Bellen, Hugo J., additional, Luo, Liqun, additional, Jasper, Heinrich, additional, Quake, Stephen R., additional, and Li, Hongjie, additional

Published
2022
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44. Global principles for restorative aquaculture to foster aquaculture practices that benefit the environment.

Author

Alleway, Heidi K., Waters, Tiffany J., Brummett, Randall, Cai, Junning, Cao, Ling, Cayten, Megan Reilly, Costa‐Pierce, Barry Antonio, Dong, Yun‐Wei, Brandstrup Hansen, Steffen Cole, Liu, Shurong, Liu, Qing, Shelley, Colin, Theuerkauf, Seth J., Tucker, Lisa, Wang, Yue, and Jones, Robert C.

Subjects
AQUACULTURE, ECOSYSTEM health, INFORMATION needs, FOOD production, DECISION making
Abstract

The magnitude of negative environmental impacts generated by food production means it is now imperative we develop food systems in a way that can actively support the recovery of degraded ecosystems, while also meeting increasing demands for food and livelihoods. Aquaculture, when it utilizes the right practices and species and occurs in the right places, can strike this balance, enabling food production that supports the health of aquatic ecosystems. To ensure the efficacy of this approach, however, a clear, common understanding of the ways in which this industry can achieve this outcome is needed. This paper highlights a definition of "restorative aquaculture", identifies global principles for the use and development of restorative practices, and identifies needs for information, data, and tools that, if addressed, would greatly expand our understanding of the ways in which aquaculture and restorative activities can have positive environmental outcomes. This guidance was developed by a working group of representatives from global aquaculture, environment, economic and academic organizations. It can assist industry and government in making decisions about sustainability as well as restoration and rehabilitation strategies that intersect with aquaculture. [ABSTRACT FROM AUTHOR]

Published
2023
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47. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Author

Tabula Sapiens Consortium, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, and Vo, Kim Chi

Subjects
B-Lymphocytes, General Science & Technology, Cells, T-Lymphocytes, RNA Splicing, Human Genome, Tabula Sapiens Consortium, Atlases as Topic, Organ Specificity, Genetics, Humans, Generic health relevance, Single-Cell Analysis, Transcriptome, Biotechnology
Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

48. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.

Author

Tabula Sapiens Consortium*, Tabula Sapiens Consortium*, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Tabula Sapiens Consortium*, Tabula Sapiens Consortium*, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, and Vo, Kim Chi

Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

49. Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly

Author

National Institutes of Health (US), Stanford University, Howard Hughes Medical Institute, KU Leuven, Flemish Department of Economy, Science and Innovation (Belgium), Li, Hongjie, Janssens, Jasper, Waegeneer, Maxime De, Saroja Kolluru, Sai, Davie, Kristofer, Gardeux, Vincent, Saelens, Wouter, David, Fabrice, Brbić, Maria, Spanier, Katina, Leskovec, Jure, McLaughlin, Colleen N., Xie, Qijing, Jones, Robert C., Brueckner, Katja, Shim, Jiwon, Gopal Tattikota, Sudhir, Schnorrer, Frank, Rust, Katja, Nystul, Todd G., Carvalho-Santos, Zita, Ribeiro, Carlos, Pal, Soumitra, Mahadevaraju, Sharvani, Przytycka, Teresa M., Allen, Aaron M., Goodwin, Stephen F., Berry, Cameron W., Fuller, Margaret T., White-Cooper, Helen, Matunis, Erika L., DiNardo, Stephen, Galenza, Anthony, O'Brien, Lucy Erin, Dow, Julian A. T., FCA Consortium, Jasper, Heinrich, Oliver, Brian, Perrimon, Norbert, Deplancke, Bart, Quake, Stephen R., Luo, Liqun, Aerts, Stein, National Institutes of Health (US), Stanford University, Howard Hughes Medical Institute, KU Leuven, Flemish Department of Economy, Science and Innovation (Belgium), Li, Hongjie, Janssens, Jasper, Waegeneer, Maxime De, Saroja Kolluru, Sai, Davie, Kristofer, Gardeux, Vincent, Saelens, Wouter, David, Fabrice, Brbić, Maria, Spanier, Katina, Leskovec, Jure, McLaughlin, Colleen N., Xie, Qijing, Jones, Robert C., Brueckner, Katja, Shim, Jiwon, Gopal Tattikota, Sudhir, Schnorrer, Frank, Rust, Katja, Nystul, Todd G., Carvalho-Santos, Zita, Ribeiro, Carlos, Pal, Soumitra, Mahadevaraju, Sharvani, Przytycka, Teresa M., Allen, Aaron M., Goodwin, Stephen F., Berry, Cameron W., Fuller, Margaret T., White-Cooper, Helen, Matunis, Erika L., DiNardo, Stephen, Galenza, Anthony, O'Brien, Lucy Erin, Dow, Julian A. T., FCA Consortium, Jasper, Heinrich, Oliver, Brian, Perrimon, Norbert, Deplancke, Bart, Quake, Stephen R., Luo, Liqun, and Aerts, Stein

Abstract

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type–related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

Published
2022

50. Finance and capital in the 21st century

Author

Jones, Robert C.

Subjects
Capital in the Twenty-First Century (Nonfiction work) -- Criticism and interpretation, Rate of return -- Analysis, Finance -- Analysis, Economists -- Criticism and interpretation -- Works, Return on investment, Political science
Abstract

In Thomas Piketty's controversial, ambitious, but ultimately flawed book, Capital in the Twenty-First Century, he claims that: (1) the return on capital (r) has exceeded the growth rate of the [...]

Published
2015

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