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291 results on '"Dionne, Danielle"'

1. A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features

Author

Klughammer, Johanna, Abravanel, Daniel L., Segerstolpe, Åsa, Blosser, Timothy R., Goltsev, Yury, Cui, Yi, Goodwin, Daniel R., Sinha, Anubhav, Ashenberg, Orr, Slyper, Michal, Vigneau, Sébastien, Jané‐Valbuena, Judit, Alon, Shahar, Caraccio, Chiara, Chen, Judy, Cohen, Ofir, Cullen, Nicole, DelloStritto, Laura K., Dionne, Danielle, Files, Janet, Frangieh, Allison, Helvie, Karla, Hughes, Melissa E., Inga, Stephanie, Kanodia, Abhay, Lako, Ana, MacKichan, Colin, Mages, Simon, Moriel, Noa, Murray, Evan, Napolitano, Sara, Nguyen, Kyleen, Nitzan, Mor, Ortiz, Rebecca, Patel, Miraj, Pfaff, Kathleen L., Porter, Caroline B. M., Rotem, Asaf, Strauss, Sarah, Strasser, Robert, Thorner, Aaron R., Turner, Madison, Wakiro, Isaac, Waldman, Julia, Wu, Jingyi, Gómez Tejeda Zañudo, Jorge, Zhang, Diane, Lin, Nancy U., Tolaney, Sara M., Winer, Eric P., Boyden, Edward S., Chen, Fei, Nolan, Garry P., Rodig, Scott J., Zhuang, Xiaowei, Rozenblatt-Rosen, Orit, Johnson, Bruce E., Regev, Aviv, and Wagle, Nikhil

Published
2024
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2. Author Correction: Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types

Author

Ximerakis, Methodios, Holton, Kristina M., Giadone, Richard M., Ozek, Ceren, Saxena, Monika, Santiago, Samara, Adiconis, Xian, Dionne, Danielle, Nguyen, Lan, Shah, Kavya M., Goldstein, Jill M., Gasperini, Caterina, Gampierakis, Ioannis A., Lipnick, Scott L., Simmons, Sean K., Buchanan, Sean M., Wagers, Amy J., Regev, Aviv, Levin, Joshua Z., and Rubin, Lee L.

Published
2025
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3. Complexity vs. salience of alternatives in implicature: A cross-linguistic investigation

Author

Dionne, Danielle and Coppock, Elizabeth

Abstract

Scalar implicature depends on the activation of alternatives. For instance, in English, finger implicates 'not thumb', suggesting that thumb is an activated alternative. Is this because it is more specific (Quantity) and equally short (Manner)? Indeed, toe doesn't imply 'not big toe', perhaps because big toe is longer. As L. Horn points out, this Quantity/Manner explanation predicts that if English had the simplex Latin word pollex meaning 'thumb or big toe', then the asymmetry would disappear. But would it suffice for that word to exist in the language, or would the word also have to be sufficiently salient? We explore this question in four languages that are sometimes said to lack a single-word alternative for thumb: Spanish (which does have pulgar 'thumb or big toe' (< pollex), though it is a non-colloquial form), Russian, Persian, and Arabic. To gauge the salience of various ways of describing digits, we use a fill-in-the-blank production task. We then measure the availability of implicatures using a forced choice comprehension task. We find cross-linguistic differences in implicature, and moreover that implicature calculation tracks production probabilities more closely than structural complexity of the alternatives. A comparison between two Rational Speech Act models—one in which the speaker replicates our production data and a standard one in which the speaker chooses based on a standard cost/accuracy trade-off—shows that comprehension is more closely tied to production probability than to the complexity of alternatives.

Published
2022

4. Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus

Author

Perez, Richard K, Gordon, M Grace, Subramaniam, Meena, Kim, Min Cheol, Hartoularos, George C, Targ, Sasha, Sun, Yang, Ogorodnikov, Anton, Bueno, Raymund, Lu, Andrew, Thompson, Mike, Rappoport, Nadav, Dahl, Andrew, Lanata, Cristina M, Matloubian, Mehrdad, Maliskova, Lenka, Kwek, Serena S, Li, Tony, Slyper, Michal, Waldman, Julia, Dionne, Danielle, Rozenblatt-Rosen, Orit, Fong, Lawrence, Dall'Era, Maria, Balliu, Brunilda, Regev, Aviv, Yazdany, Jinoos, Criswell, Lindsey A, Zaitlen, Noah, and Ye, Chun Jimmie

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Immunology, Lupus, Human Genome, Autoimmune Disease, 2.1 Biological and endogenous factors, Inflammatory and immune system, Good Health and Well Being, CD8-Positive T-Lymphocytes, Case-Control Studies, Humans, Interferon Type I, Leukocytes, Mononuclear, Lupus Erythematosus, Systemic, RNA-Seq, Transcription, Genetic, General Science & Technology
Abstract

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). Cases exhibited elevated expression of type 1 interferon-stimulated genes (ISGs) in monocytes, reduction of naïve CD4+ T cells that correlated with monocyte ISG expression, and expansion of repertoire-restricted cytotoxic GZMH+ CD8+ T cells. Cell type-specific expression features predicted case-control status and stratified patients into two molecular subtypes. We integrated dense genotyping data to map cell type-specific cis-expression quantitative trait loci and to link SLE-associated variants to cell type-specific expression. These results demonstrate mux-seq as a systematic approach to characterize cellular composition, identify transcriptional signatures, and annotate genetic variants associated with SLE.

Published
2022

5. Protective role for kidney TREM2high macrophages in obesity- and diabetes-induced kidney injury

Author

Subramanian, Ayshwarya, Vernon, Katherine A., Zhou, Yiming, Marshall, Jamie L., Alimova, Maria, Arevalo, Carlos, Zhang, Fan, Slyper, Michal, Waldman, Julia, Montesinos, Monica S., Dionne, Danielle, Nguyen, Lan T., Cuoco, Michael S., Dubinsky, Dan, Purnell, Jason, Keller, Keith, Sturner, Samuel H., Grinkevich, Elizabeth, Ghoshal, Ayan, Kotek, Amanda, Trivioli, Giorgio, Richoz, Nathan, Humphrey, Mary B., Darby, Isabella G., Miller, Sarah J., Xu, Yingping, Weins, Astrid, Chloe-Villani, Alexandra, Chang, Steven L., Kretzler, Matthias, Rosenblatt-Rosen, Orit, Shaw, Jillian L., Zimmerman, Kurt A., Clatworthy, Menna R., Regev, Aviv, and Greka, Anna

Published
2024
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6. Spatially organized multicellular immune hubs in human colorectal cancer.

Author

Pelka, Karin, Hofree, Matan, Chen, Jonathan, Sarkizova, Siranush, Pirl, Joshua, Jorgji, Vjola, Bejnood, Alborz, Dionne, Danielle, Ge, William, Xu, Katherine, Chao, Sherry, Zollinger, Daniel, Lieb, David, Reeves, Jason, Fuhrman, Christopher, Hoang, Margaret, Delorey, Toni, Nguyen, Lan, Waldman, Julia, Klapholz, Max, Wakiro, Isaac, Cohen, Ofir, Albers, Julian, Smillie, Christopher, Cuoco, Michael, Wu, Jingyi, Su, Mei-Ju, Yeung, Jason, Vijaykumar, Brinda, Magnuson, Angela, Asinovski, Natasha, Moll, Tabea, Goder-Reiser, Max, Applebaum, Anise, Brais, Lauren, DelloStritto, Laura, Denning, Sarah, Phillips, Susannah, Hill, Emma, Meehan, Julia, Frederick, Dennie, Sharova, Tatyana, Kanodia, Abhay, Todres, Ellen, Jané-Valbuena, Judit, Biton, Moshe, Izar, Benjamin, Lambden, Conner, Clancy, Thomas, Bleday, Ronald, Melnitchouk, Nelya, Irani, Jennifer, Kunitake, Hiroko, Berger, David, Srivastava, Amitabh, Hornick, Jason, Ogino, Shuji, Rotem, Asaf, Vigneau, Sébastien, Johnson, Bruce, Corcoran, Ryan, Sharpe, Arlene, Kuchroo, Vijay, Ng, Kimmie, Giannakis, Marios, Nieman, Linda, Boland, Genevieve, Aguirre, Andrew, Anderson, Ana, Rozenblatt-Rosen, Orit, Regev, Aviv, and Hacohen, Nir

Subjects
MSI, MSS, anti-tumor immunity, cell-cell interactions, colorectal cancer, mismatch repair-deficient, mismatch repair-proficient, scRNA-seq, spatial, tumor atlas, Bone Morphogenetic Proteins, Cancer-Associated Fibroblasts, Cell Compartmentation, Cell Line, Tumor, Chemokines, Cohort Studies, Colorectal Neoplasms, DNA Mismatch Repair, Endothelial Cells, Gene Expression Regulation, Neoplastic, Humans, Immunity, Inflammation, Monocytes, Myeloid Cells, Neutrophils, Stromal Cells, T-Lymphocytes, Transcription, Genetic
Abstract

Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. To understand the rules governing these varied responses, we transcriptionally profiled 371,223 cells from colorectal tumors and adjacent normal tissues of 28 MMRp and 34 MMRd individuals. Analysis of 88 cell subsets and their 204 associated gene expression programs revealed extensive transcriptional and spatial remodeling across tumors. To discover hubs of interacting malignant and immune cells, we identified expression programs in different cell types that co-varied across tumors from affected individuals and used spatial profiling to localize coordinated programs. We discovered a myeloid cell-attracting hub at the tumor-luminal interface associated with tissue damage and an MMRd-enriched immune hub within the tumor, with activated T cells together with malignant and myeloid cells expressing T cell-attracting chemokines. By identifying interacting cellular programs, we reveal the logic underlying spatially organized immune-malignant cell networks.

Published
2021

7. Skin-resident innate lymphoid cells converge on a pathogenic effector state

Author

Bielecki, Piotr, Riesenfeld, Samantha J, Hütter, Jan-Christian, Torlai Triglia, Elena, Kowalczyk, Monika S, Ricardo-Gonzalez, Roberto R, Lian, Mi, Amezcua Vesely, Maria C, Kroehling, Lina, Xu, Hao, Slyper, Michal, Muus, Christoph, Ludwig, Leif S, Christian, Elena, Tao, Liming, Kedaigle, Amanda J, Steach, Holly R, York, Autumn G, Skadow, Mathias H, Yaghoubi, Parastou, Dionne, Danielle, Jarret, Abigail, McGee, Heather M, Porter, Caroline BM, Licona-Limón, Paula, Bailis, Will, Jackson, Ruaidhrí, Gagliani, Nicola, Gasteiger, Georg, Locksley, Richard M, Regev, Aviv, and Flavell, Richard A

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Immunology, Autoimmune Disease, Genetics, Psoriasis, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Inflammatory and immune system, Animals, Cell Differentiation, Cell Lineage, Chromatin, Disease Models, Animal, Female, Immunity, Innate, Inflammation, Interleukin-23, Latent Class Analysis, Lymphocytes, Male, Mice, RNA, Small Cytoplasmic, Reproducibility of Results, Skin, Time Factors, General Science & Technology
Abstract

Tissue-resident innate lymphoid cells (ILCs) help sustain barrier function and respond to local signals. ILCs are traditionally classified as ILC1, ILC2 or ILC3 on the basis of their expression of specific transcription factors and cytokines1. In the skin, disease-specific production of ILC3-associated cytokines interleukin (IL)-17 and IL-22 in response to IL-23 signalling contributes to dermal inflammation in psoriasis. However, it is not known whether this response is initiated by pre-committed ILCs or by cell-state transitions. Here we show that the induction of psoriasis in mice by IL-23 or imiquimod reconfigures a spectrum of skin ILCs, which converge on a pathogenic ILC3-like state. Tissue-resident ILCs were necessary and sufficient, in the absence of circulatory ILCs, to drive pathology. Single-cell RNA-sequencing (scRNA-seq) profiles of skin ILCs along a time course of psoriatic inflammation formed a dense transcriptional continuum-even at steady state-reflecting fluid ILC states, including a naive or quiescent-like state and an ILC2 effector state. Upon disease induction, the continuum shifted rapidly to span a mixed, ILC3-like subset also expressing cytokines characteristic of ILC2s, which we inferred as arising through multiple trajectories. We confirmed the transition potential of quiescent-like and ILC2 states using in vitro experiments, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and in vivo fate mapping. Our results highlight the range and flexibility of skin ILC responses, suggesting that immune activities primed in healthy tissues dynamically adapt to provocations and, left unchecked, drive pathological remodelling.

Published
2021

8. Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types

Author

Ximerakis, Methodios, Holton, Kristina M., Giadone, Richard M., Ozek, Ceren, Saxena, Monika, Santiago, Samara, Adiconis, Xian, Dionne, Danielle, Nguyen, Lan, Shah, Kavya M., Goldstein, Jill M., Gasperini, Caterina, Gampierakis, Ioannis A., Lipnick, Scott L., Simmons, Sean K., Buchanan, Sean M., Wagers, Amy J., Regev, Aviv, Levin, Joshua Z., and Rubin, Lee L.

Published
2023
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9. Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Author

Hwang, William L., Jagadeesh, Karthik A., Guo, Jimmy A., Hoffman, Hannah I., Yadollahpour, Payman, Reeves, Jason W., Mohan, Rahul, Drokhlyansky, Eugene, Van Wittenberghe, Nicholas, Ashenberg, Orr, Farhi, Samouil L., Schapiro, Denis, Divakar, Prajan, Miller, Eric, Zollinger, Daniel R., Eng, George, Schenkel, Jason M., Su, Jennifer, Shiau, Carina, Yu, Patrick, Freed-Pastor, William A., Abbondanza, Domenic, Mehta, Arnav, Gould, Joshua, Lambden, Conner, Porter, Caroline B. M., Tsankov, Alexander, Dionne, Danielle, Waldman, Julia, Cuoco, Michael S., Nguyen, Lan, Delorey, Toni, Phillips, Devan, Barth, Jaimie L., Kem, Marina, Rodrigues, Clifton, Ciprani, Debora, Roldan, Jorge, Zelga, Piotr, Jorgji, Vjola, Chen, Jonathan H., Ely, Zackery, Zhao, Daniel, Fuhrman, Kit, Fropf, Robin, Beechem, Joseph M., Loeffler, Jay S., Ryan, David P., Weekes, Colin D., Ferrone, Cristina R., Qadan, Motaz, Aryee, Martin J., Jain, Rakesh K., Neuberg, Donna S., Wo, Jennifer Y., Hong, Theodore S., Xavier, Ramnik, Aguirre, Andrew J., Rozenblatt-Rosen, Orit, Mino-Kenudson, Mari, Castillo, Carlos Fernandez-del, Liss, Andrew S., Ting, David T., Jacks, Tyler, and Regev, Aviv

Published
2022
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10. Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling

Author

Pawlak, Mathias, DeTomaso, David, Schnell, Alexandra, Meyer zu Horste, Gerd, Lee, Youjin, Nyman, Jackson, Dionne, Danielle, Regan, Brianna M.L., Singh, Vasundhara, Delorey, Toni, Schramm, Markus A., Wang, Chao, Wallrapp, Antonia, Burkett, Patrick R., Riesenfeld, Samantha J., Anderson, Ana C., Regev, Aviv, Xavier, Ramnik J., Yosef, Nir, and Kuchroo, Vijay K.

Published
2022
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11. Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy

Author

Luoma, Adrienne M., Suo, Shengbao, Wang, Yifan, Gunasti, Lauren, Porter, Caroline B.M., Nabilsi, Nancy, Tadros, Jenny, Ferretti, Andrew P., Liao, Sida, Gurer, Cagan, Chen, Yu-Hui, Criscitiello, Shana, Ricker, Cora A., Dionne, Danielle, Rozenblatt-Rosen, Orit, Uppaluri, Ravindra, Haddad, Robert I., Ashenberg, Orr, Regev, Aviv, Van Allen, Eliezer M., MacBeath, Gavin, Schoenfeld, Jonathan D., and Wucherpfennig, Kai W.

Published
2022
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12. Mobile language app learners' self-efficacy increases after using generative AI.

Author

Kittredge, Audrey K., Hopman, Elise W. M., Reuveni, Ben, Dionne, Danielle, Freeman, Cassie, and Jiang, Xiangying

Subjects
SELF-efficacy, GENERATIVE artificial intelligence, CONVERSATION, SECOND language acquisition, EDUCATIONAL outcomes, COMPUTER assisted language instruction
Abstract

Introduction: Although generative artificial intelligence (AI) is ubiquitous, there is little research on how it supports self-efficacy (learners' belief that they can perform at a particular level on a specific task). The purpose of these studies was to investigate self-efficacy development in a generative AI-based language learning experience. Methods: In two studies, learners (N = 385) of French/Spanish used AI-based features offering conversation practice and on-demand explanations in a mobile app (Duolingo) for 1 month. Before and after using the features, learners reported their self-efficacy and other perceptions. Results: In Study 1, learners who had already used the features felt significantly more prepared to use French/Spanish in real-life situations after 1 month, as did learners in Study 2 who used the features for the first time. Learners in Study 2 also felt significantly more prepared to share their opinions and navigate a city, and reported significantly higher self-efficacy for speaking and understanding grammar and mistakes. Across studies, the majority of learners agreed that the AI-based features effectively supported learning, and reported using their learning outside the app. Discussion: These results provide the first evidence of enhanced language learning self-efficacy after use of generative AI, building on findings from classroom interventions. [ABSTRACT FROM AUTHOR]

Published
2025
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13. Massively parallel phenotyping of coding variants in cancer with Perturb-seq

Author

Ursu, Oana, Neal, James T., Shea, Emily, Thakore, Pratiksha I., Jerby-Arnon, Livnat, Nguyen, Lan, Dionne, Danielle, Diaz, Celeste, Bauman, Julia, Mosaad, Mariam Mounir, Fagre, Christian, Lo, April, McSharry, Maria, Giacomelli, Andrew O., Ly, Seav Huong, Rozenblatt-Rosen, Orit, Hahn, William C., Aguirre, Andrew J., Berger, Alice H., Regev, Aviv, and Boehm, Jesse S.

Published
2022
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14. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

Author

Chen, Zuojia, Wu, Chuan, Ordovas-Montanes, Jose, Alvarez, David, Herbst, Rebecca, Biton, Moshe, Haber, Adam, Rogel, Noga, Burgin, Grace, Beyaz, Semir, Schnell, Alexandra, Ashenberg, Orr, Su, Chien-Wen, Smillie, Christopher, Zhang, Mei, Tirosh, Itay, Dionne, Danielle, Nguyen, Lan, Xifaras, Michael, Shalek, Alex, von Andrian, Ulrich, Graham, Daniel, Rozenblatt-Rosen, Orit, Shi, Hai, Kuchroo, Vijay, Yilmaz, Omer, Regev, Aviv, Xavier, Ramnik, and Shekhar, Karthik

Subjects
ISCs, MHC class II, MHCII, T helper, T regulatory, T(reg), Th, epithelial differentiation, gut biology, intestinal stem cells, mucosal immunity, scRNA-seq, single cell RNA-seq, stem cell renewal, tuft cells, Animals, Cell Differentiation, Cell Self Renewal, Cytokines, Epithelial Cells, Female, Histocompatibility Antigens Class II, Immune System, Interleukin-10, Intestines, Male, Mice, Mice, Inbred C57BL, Organoids, Receptors, G-Protein-Coupled, Salmonella enterica, Stem Cells, T-Lymphocytes, Helper-Inducer
Abstract

In the small intestine, a niche of accessory cell types supports the generation of mature epithelial cell types from intestinal stem cells (ISCs). It is unclear, however, if and how immune cells in the niche affect ISC fate or the balance between self-renewal and differentiation. Here, we use single-cell RNA sequencing (scRNA-seq) to identify MHC class II (MHCII) machinery enrichment in two subsets of Lgr5+ ISCs. We show that MHCII+ Lgr5+ ISCs are non-conventional antigen-presenting cells in co-cultures with CD4+ T helper (Th) cells. Stimulation of intestinal organoids with key Th cytokines affects Lgr5+ ISC renewal and differentiation in opposing ways: pro-inflammatory signals promote differentiation, while regulatory cells and cytokines reduce it. In vivo genetic perturbation of Th cells or MHCII expression on Lgr5+ ISCs impacts epithelial cell differentiation and IEC fate during infection. These interactions between Th cells and Lgr5+ ISCs, thus, orchestrate tissue-wide responses to external signals.

Published
2018

15. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation

Author

Biton, Moshe, Haber, Adam L, Rogel, Noga, Burgin, Grace, Beyaz, Semir, Schnell, Alexandra, Ashenberg, Orr, Su, Chien-Wen, Smillie, Christopher, Shekhar, Karthik, Chen, Zuojia, Wu, Chuan, Ordovas-Montanes, Jose, Alvarez, David, Herbst, Rebecca H, Zhang, Mei, Tirosh, Itay, Dionne, Danielle, Nguyen, Lan T, Xifaras, Michael E, Shalek, Alex K, von Andrian, Ulrich H, Graham, Daniel B, Rozenblatt-Rosen, Orit, Shi, Hai Ning, Kuchroo, Vijay, Yilmaz, Omer H, Regev, Aviv, and Xavier, Ramnik J

Subjects
Biodefense, Digestive Diseases, Regenerative Medicine, Stem Cell Research, Prevention, Vaccine Related, Stem Cell Research - Nonembryonic - Non-Human, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Animals, Cell Differentiation, Cell Self Renewal, Cytokines, Epithelial Cells, Female, Histocompatibility Antigens Class II, Immune System, Interleukin-10, Intestines, Male, Mice, Mice, Inbred C57BL, Organoids, Receptors, G-Protein-Coupled, Salmonella enterica, Stem Cells, T-Lymphocytes, Helper-Inducer, ISCs, MHC class II, MHCII, T helper, T regulatory, T(reg), Th, epithelial differentiation, gut biology, intestinal stem cells, mucosal immunity, scRNA-seq, single cell RNA-seq, stem cell renewal, tuft cells, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

In the small intestine, a niche of accessory cell types supports the generation of mature epithelial cell types from intestinal stem cells (ISCs). It is unclear, however, if and how immune cells in the niche affect ISC fate or the balance between self-renewal and differentiation. Here, we use single-cell RNA sequencing (scRNA-seq) to identify MHC class II (MHCII) machinery enrichment in two subsets of Lgr5+ ISCs. We show that MHCII+ Lgr5+ ISCs are non-conventional antigen-presenting cells in co-cultures with CD4+ T helper (Th) cells. Stimulation of intestinal organoids with key Th cytokines affects Lgr5+ ISC renewal and differentiation in opposing ways: pro-inflammatory signals promote differentiation, while regulatory cells and cytokines reduce it. In vivo genetic perturbation of Th cells or MHCII expression on Lgr5+ ISCs impacts epithelial cell differentiation and IEC fate during infection. These interactions between Th cells and Lgr5+ ISCs, thus, orchestrate tissue-wide responses to external signals.

Published
2018

16. Disruption of the IL-33-ST2-AKT signaling axis impairs neurodevelopment by inhibiting microglial metabolic adaptation and phagocytic function

Author

He, Danyang, Xu, Heping, Zhang, Huiyuan, Tang, Ruihan, Lan, Yangning, Xing, Ruxiao, Li, Shaomin, Christian, Elena, Hou, Yu, Lorello, Paul, Caldarone, Barbara, Ding, Jiarui, Nguyen, Lan, Dionne, Danielle, Thakore, Pratiksha, Schnell, Alexandra, Huh, Jun R., Rozenblatt-Rosen, Orit, Regev, Aviv, and Kuchroo, Vijay K.

Published
2022
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18. Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade

Author

Kaur, Gurman, Porter, Caroline B. M., Ashenberg, Orr, Lee, Jack, Riesenfeld, Samantha J., Hofree, Matan, Aggelakopoulou, Maria, Subramanian, Ayshwarya, Kuttikkatte, Subita Balaram, Attfield, Kathrine E., Desel, Christiane A. E., Davies, Jessica L., Evans, Hayley G., Avraham-Davidi, Inbal, Nguyen, Lan T., Dionne, Danielle A., Neumann, Anna E., Jensen, Lise Torp, Barber, Thomas R., Soilleux, Elizabeth, Carrington, Mary, McVean, Gil, Rozenblatt-Rosen, Orit, Regev, Aviv, and Fugger, Lars

Published
2022
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19. A single-cell survey of the small intestinal epithelium

Author

Haber, Adam L, Biton, Moshe, Rogel, Noga, Herbst, Rebecca H, Shekhar, Karthik, Smillie, Christopher, Burgin, Grace, Delorey, Toni M, Howitt, Michael R, Katz, Yarden, Tirosh, Itay, Beyaz, Semir, Dionne, Danielle, Zhang, Mei, Raychowdhury, Raktima, Garrett, Wendy S, Rozenblatt-Rosen, Orit, Shi, Hai Ning, Yilmaz, Omer, Xavier, Ramnik J, and Regev, Aviv

Subjects
Emerging Infectious Diseases, Digestive Diseases, Infectious Diseases, Vaccine Related, Aetiology, 2.1 Biological and endogenous factors, Animals, Cell Differentiation, Cytokines, Enterocytes, Epithelial Cells, Epithelium, Female, Gene Expression Profiling, Homeostasis, Intestine, Small, Leukocyte Common Antigens, Male, Mice, Organoids, Paneth Cells, Single-Cell Analysis, Transcription, Genetic, Thymic Stromal Lymphopoietin, General Science & Technology
Abstract

Intestinal epithelial cells absorb nutrients, respond to microbes, function as a barrier and help to coordinate immune responses. Here we report profiling of 53,193 individual epithelial cells from the small intestine and organoids of mice, which enabled the identification and characterization of previously unknown subtypes of intestinal epithelial cell and their gene signatures. We found unexpected diversity in hormone-secreting enteroendocrine cells and constructed the taxonomy of newly identified subtypes, and distinguished between two subtypes of tuft cell, one of which expresses the epithelial cytokine Tslp and the pan-immune marker CD45, which was not previously associated with non-haematopoietic cells. We also characterized the ways in which cell-intrinsic states and the proportions of different cell types respond to bacterial and helminth infections: Salmonella infection caused an increase in the abundance of Paneth cells and enterocytes, and broad activation of an antimicrobial program; Heligmosomoides polygyrus caused an increase in the abundance of goblet and tuft cells. Our survey highlights previously unidentified markers and programs, associates sensory molecules with cell types, and uncovers principles of gut homeostasis and response to pathogens.

Published
2017

20. Blood and immune development in human fetal bone marrow and Down syndrome

Author

Jardine, Laura, Webb, Simone, Goh, Issac, Quiroga Londoño, Mariana, Reynolds, Gary, Mather, Michael, Olabi, Bayanne, Stephenson, Emily, Botting, Rachel A., Horsfall, Dave, Engelbert, Justin, Maunder, Daniel, Mende, Nicole, Murnane, Caitlin, Dann, Emma, McGrath, Jim, King, Hamish, Kucinski, Iwo, Queen, Rachel, Carey, Christopher D., Shrubsole, Caroline, Poyner, Elizabeth, Acres, Meghan, Jones, Claire, Ness, Thomas, Coulthard, Rowen, Elliott, Natalina, O’Byrne, Sorcha, Haltalli, Myriam L. R., Lawrence, John E., Lisgo, Steven, Balogh, Petra, Meyer, Kerstin B., Prigmore, Elena, Ambridge, Kirsty, Jain, Mika Sarkin, Efremova, Mirjana, Pickard, Keir, Creasey, Thomas, Bacardit, Jaume, Henderson, Deborah, Coxhead, Jonathan, Filby, Andrew, Hussain, Rafiqul, Dixon, David, McDonald, David, Popescu, Dorin-Mirel, Kowalczyk, Monika S., Li, Bo, Ashenberg, Orr, Tabaka, Marcin, Dionne, Danielle, Tickle, Timothy L., Slyper, Michal, Rozenblatt-Rosen, Orit, Regev, Aviv, Behjati, Sam, Laurenti, Elisa, Wilson, Nicola K., Roy, Anindita, Göttgens, Berthold, Roberts, Irene, Teichmann, Sarah A., and Haniffa, Muzlifah

Published
2021
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21. A cellular and spatial map of the choroid plexus across brain ventricles and ages

Author

Dani, Neil, Herbst, Rebecca H., McCabe, Cristin, Green, Gilad S., Kaiser, Karol, Head, Joshua P., Cui, Jin, Shipley, Frederick B., Jang, Ahram, Dionne, Danielle, Nguyen, Lan, Rodman, Christopher, Riesenfeld, Samantha J., Prochazka, Jan, Prochazkova, Michaela, Sedlacek, Radislav, Zhang, Feng, Bryja, Vitezslav, Rozenblatt-Rosen, Orit, Habib, Naomi, Regev, Aviv, and Lehtinen, Maria K.

Published
2021
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23. The Human and Mouse Enteric Nervous System at Single-Cell Resolution

Author

Drokhlyansky, Eugene, Smillie, Christopher S., Van Wittenberghe, Nicholas, Ericsson, Maria, Griffin, Gabriel K., Eraslan, Gokcen, Dionne, Danielle, Cuoco, Michael S., Goder-Reiser, Max N., Sharova, Tatyana, Kuksenko, Olena, Aguirre, Andrew J., Boland, Genevieve M., Graham, Daniel, Rozenblatt-Rosen, Orit, Xavier, Ramnik J., and Regev, Aviv

Published
2020
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24. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes

Author

Lavaert, Marieke, Liang, Kai Ling, Vandamme, Niels, Park, Jong-Eun, Roels, Juliette, Kowalczyk, Monica S., Li, Bo, Ashenberg, Orr, Tabaka, Marcin, Dionne, Danielle, Tickle, Timothy L., Slyper, Michal, Rozenblatt-Rosen, Orit, Vandekerckhove, Bart, Leclercq, Georges, Regev, Aviv, Van Vlierberghe, Pieter, Guilliams, Martin, Teichmann, Sarah A., Saeys, Yvan, and Taghon, Tom

Published
2020
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26. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Author

Slyper, Michal, Porter, Caroline B. M., Ashenberg, Orr, Waldman, Julia, Drokhlyansky, Eugene, Wakiro, Isaac, Smillie, Christopher, Smith-Rosario, Gabriela, Wu, Jingyi, Dionne, Danielle, Vigneau, Sébastien, Jané-Valbuena, Judit, Tickle, Timothy L., Napolitano, Sara, Su, Mei-Ju, Patel, Anand G., Karlstrom, Asa, Gritsch, Simon, Nomura, Masashi, Waghray, Avinash, Gohil, Satyen H., Tsankov, Alexander M., Jerby-Arnon, Livnat, Cohen, Ofir, Klughammer, Johanna, Rosen, Yanay, Gould, Joshua, Nguyen, Lan, Hofree, Matan, Tramontozzi, Peter J., Li, Bo, Wu, Catherine J., Izar, Benjamin, Haq, Rizwan, Hodi, F. Stephen, Yoon, Charles H., Hata, Aaron N., Baker, Suzanne J., Suvà, Mario L., Bueno, Raphael, Stover, Elizabeth H., Clay, Michael R., Dyer, Michael A., Collins, Natalie B., Matulonis, Ursula A., Wagle, Nikhil, Johnson, Bruce E., Rotem, Asaf, Rozenblatt-Rosen, Orit, and Regev, Aviv

Published
2020
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27. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses

Author

Xu, Heping, Ding, Jiarui, Porter, Caroline B.M., Wallrapp, Antonia, Tabaka, Marcin, Ma, Sai, Fu, Shujie, Guo, Xuanxuan, Riesenfeld, Samantha J., Su, Chienwen, Dionne, Danielle, Nguyen, Lan T., Lefkovith, Ariel, Ashenberg, Orr, Burkett, Patrick R., Shi, Hai Ning, Rozenblatt-Rosen, Orit, Graham, Daniel B., Kuchroo, Vijay K., Regev, Aviv, and Xavier, Ramnik J.

Published
2019
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28. An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

Author

Neftel, Cyril, Laffy, Julie, Filbin, Mariella G., Hara, Toshiro, Shore, Marni E., Rahme, Gilbert J., Richman, Alyssa R., Silverbush, Dana, Shaw, McKenzie L., Hebert, Christine M., Dewitt, John, Gritsch, Simon, Perez, Elizabeth M., Gonzalez Castro, L. Nicolas, Lan, Xiaoyang, Druck, Nicholas, Rodman, Christopher, Dionne, Danielle, Kaplan, Alexander, Bertalan, Mia S., Small, Julia, Pelton, Kristine, Becker, Sarah, Bonal, Dennis, Nguyen, Quang-De, Servis, Rachel L., Fung, Jeremy M., Mylvaganam, Ravindra, Mayr, Lisa, Gojo, Johannes, Haberler, Christine, Geyeregger, Rene, Czech, Thomas, Slavc, Irene, Nahed, Brian V., Curry, William T., Carter, Bob S., Wakimoto, Hiroaki, Brastianos, Priscilla K., Batchelor, Tracy T., Stemmer-Rachamimov, Anat, Martinez-Lage, Maria, Frosch, Matthew P., Stamenkovic, Ivan, Riggi, Nicolo, Rheinbay, Esther, Monje, Michelle, Rozenblatt-Rosen, Orit, Cahill, Daniel P., Patel, Anoop P., Hunter, Tony, Verma, Inder M., Ligon, Keith L., Louis, David N., Regev, Aviv, Bernstein, Bradley E., Tirosh, Itay, and Suvà, Mario L.

Published
2019
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29. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Author

Smillie, Christopher S., Biton, Moshe, Ordovas-Montanes, Jose, Sullivan, Keri M., Burgin, Grace, Graham, Daniel B., Herbst, Rebecca H., Rogel, Noga, Slyper, Michal, Waldman, Julia, Sud, Malika, Andrews, Elizabeth, Velonias, Gabriella, Haber, Adam L., Jagadeesh, Karthik, Vickovic, Sanja, Yao, Junmei, Stevens, Christine, Dionne, Danielle, Nguyen, Lan T., Villani, Alexandra-Chloé, Hofree, Matan, Creasey, Elizabeth A., Huang, Hailiang, Rozenblatt-Rosen, Orit, Garber, John J., Khalili, Hamed, Desch, A. Nicole, Daly, Mark J., Ananthakrishnan, Ashwin N., Shalek, Alex K., Xavier, Ramnik J., and Regev, Aviv

Published
2019
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30. A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

Author

Baryawno, Ninib, Przybylski, Dariusz, Kowalczyk, Monika S., Kfoury, Youmna, Severe, Nicolas, Gustafsson, Karin, Kokkaliaris, Konstantinos D., Mercier, Francois, Tabaka, Marcin, Hofree, Matan, Dionne, Danielle, Papazian, Ani, Lee, Dongjun, Ashenberg, Orr, Subramanian, Ayshwarya, Vaishnav, Eeshit Dhaval, Rozenblatt-Rosen, Orit, Regev, Aviv, and Scadden, David T.

Published
2019
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31. Author Correction: Massively parallel phenotyping of coding variants in cancer with Perturb-seq

Author

Ursu, Oana, Neal, James T., Shea, Emily, Thakore, Pratiksha I., Jerby-Arnon, Livnat, Nguyen, Lan, Dionne, Danielle, Diaz, Celeste, Bauman, Julia, Mosaad, Mariam Mounir, Fagre, Christian, Lo, April, McSharry, Maria, Giacomelli, Andrew O., Ly, Seav Huong, Rozenblatt-Rosen, Orit, Hahn, William C., Aguirre, Andrew J., Berger, Alice H., Regev, Aviv, and Boehm, Jesse S.

Published
2022
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32. A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity

Author

Patel, Anand G., primary, Ashenberg, Orr, additional, Collins, Natalie B., additional, Segerstolpe, Åsa, additional, Jiang, Sizun, additional, Slyper, Michal, additional, Huang, Xin, additional, Caraccio, Chiara, additional, Jin, Hongjian, additional, Sheppard, Heather, additional, Xu, Ke, additional, Chang, Ti-Cheng, additional, Orr, Brent A., additional, Shirinifard, Abbas, additional, Chapple, Richard H., additional, Shen, Amber, additional, Clay, Michael R., additional, Tatevossian, Ruth G., additional, Reilly, Colleen, additional, Patel, Jaimin, additional, Lupo, Marybeth, additional, Cline, Cynthia, additional, Dionne, Danielle, additional, Porter, Caroline B.M., additional, Waldman, Julia, additional, Bai, Yunhao, additional, Zhu, Bokai, additional, Barrera, Irving, additional, Murray, Evan, additional, Vigneau, Sébastien, additional, Napolitano, Sara, additional, Wakiro, Isaac, additional, Wu, Jingyi, additional, Grimaldi, Grace, additional, Dellostritto, Laura, additional, Helvie, Karla, additional, Rotem, Asaf, additional, Lako, Ana, additional, Cullen, Nicole, additional, Pfaff, Kathleen L., additional, Karlström, Åsa, additional, Jané-Valbuena, Judit, additional, Todres, Ellen, additional, Thorner, Aaron, additional, Geeleher, Paul, additional, Rodig, Scott J., additional, Zhou, Xin, additional, Stewart, Elizabeth, additional, Johnson, Bruce E., additional, Wu, Gang, additional, Chen, Fei, additional, Yu, Jiyang, additional, Goltsev, Yury, additional, Nolan, Garry P., additional, Rozenblatt-Rosen, Orit, additional, Regev, Aviv, additional, and Dyer, Michael A., additional

Published
2024
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34. Decoding human fetal liver haematopoiesis

Author

Popescu, Dorin-Mirel, Botting, Rachel A., Stephenson, Emily, Green, Kile, Webb, Simone, Jardine, Laura, Calderbank, Emily F., Polanski, Krzysztof, Goh, Issac, Efremova, Mirjana, Acres, Meghan, Maunder, Daniel, Vegh, Peter, Gitton, Yorick, Park, Jong-Eun, Vento-Tormo, Roser, Miao, Zhichao, Dixon, David, Rowell, Rachel, McDonald, David, Fletcher, James, Poyner, Elizabeth, Reynolds, Gary, Mather, Michael, Moldovan, Corina, Mamanova, Lira, Greig, Frankie, Young, Matthew D., Meyer, Kerstin B., Lisgo, Steven, Bacardit, Jaume, Fuller, Andrew, Millar, Ben, Innes, Barbara, Lindsay, Susan, Stubbington, Michael J. T., Kowalczyk, Monika S., Li, Bo, Ashenberg, Orr, Tabaka, Marcin, Dionne, Danielle, Tickle, Timothy L., Slyper, Michal, Rozenblatt-Rosen, Orit, Filby, Andrew, Carey, Peter, Villani, Alexandra-Chloé, Roy, Anindita, Regev, Aviv, Chédotal, Alain, Roberts, Irene, Göttgens, Berthold, Behjati, Sam, Laurenti, Elisa, Teichmann, Sarah A., and Haniffa, Muzlifah

Published
2019
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35. Single-cell transcriptomic profiling of the aging mouse brain

Author

Ximerakis, Methodios, Lipnick, Scott L., Innes, Brendan T., Simmons, Sean K., Adiconis, Xian, Dionne, Danielle, Mayweather, Brittany A., Nguyen, Lan, Niziolek, Zachary, Ozek, Ceren, Butty, Vincent L., Isserlin, Ruth, Buchanan, Sean M., Levine, Stuart S., Regev, Aviv, Bader, Gary D., Levin, Joshua Z., and Rubin, Lee L.

Published
2019
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36. A deep lung cell atlas reveals cytokine-mediated lineage switching of a rare cell progenitor of the human airway epithelium

Author

Waghray, Avinash, primary, Monga, Isha, additional, Lin, Brian, additional, Shah, Viral, additional, Slyper, Michal, additional, Giotti, Bruno, additional, Xu, Jiajie, additional, Waldman, Julia, additional, Dionne, Danielle, additional, Nguyen, Lan T, additional, Lou, Wendy, additional, Cai, Peiwen, additional, Park, Eric, additional, Muus, Christoph, additional, Sun, Jiawei, additional, Surve, Manalee V, additional, Yang, Lujia Cha Cha, additional, Rozenblatt-Rosen, Orit, additional, Dolerey, Toni M, additional, Saladi, Srinivas Vinod, additional, Tsankov, Alexander M, additional, Regev, Aviv, additional, and Rajagopal, Jayaraj, additional

Published
2023
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37. Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease

Author

Olah, Marta, Menon, Vilas, Habib, Naomi, Taga, Mariko F., Ma, Yiyi, Yung, Christina J., Cimpean, Maria, Khairallah, Anthony, Coronas-Samano, Guillermo, Sankowski, Roman, Grün, Dominic, Kroshilina, Alexandra A., Dionne, Danielle, Sarkis, Rani A., Cosgrove, Garth R., Helgager, Jeffrey, Golden, Jeffrey A., Pennell, Page B., Prinz, Marco, Vonsattel, Jean Paul G., Teich, Andrew F., Schneider, Julie A., Bennett, David A., Regev, Aviv, Elyaman, Wassim, Bradshaw, Elizabeth M., and De Jager, Philip L.

Published
2020
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38. Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

Author

McFarland, James M., Paolella, Brenton R., Warren, Allison, Geiger-Schuller, Kathryn, Shibue, Tsukasa, Rothberg, Michael, Kuksenko, Olena, Colgan, William N., Jones, Andrew, Chambers, Emily, Dionne, Danielle, Bender, Samantha, Wolpin, Brian M., Ghandi, Mahmoud, Tirosh, Itay, Rozenblatt-Rosen, Orit, Roth, Jennifer A., Golub, Todd R., Regev, Aviv, Aguirre, Andrew J., Vazquez, Francisca, and Tsherniak, Aviad

Published
2020
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40. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

Author

Montoro, Daniel T., Haber, Adam L., Biton, Moshe, Vinarsky, Vladimir, Lin, Brian, Birket, Susan E., Yuan, Feng, Chen, Sijia, Leung, Hui Min, Villoria, Jorge, Rogel, Noga, Burgin, Grace, Tsankov, Alexander M., Waghray, Avinash, Slyper, Michal, Waldman, Julia, Nguyen, Lan, Dionne, Danielle, Rozenblatt-Rosen, Orit, Tata, Purushothama Rao, Mou, Hongmei, Shivaraju, Manjunatha, Bihler, Hermann, Mense, Martin, Tearney, Guillermo J., Rowe, Steven M., Engelhardt, John F., Regev, Aviv, and Rajagopal, Jayaraj

Published
2018
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43. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

Author

Venteicher, Andrew S., Tirosh, Itay, Hebert, Christine, Yizhak, Keren, Neftel, Cyril, Filbin, Mariella G., Hovestadt, Volker, Escalante, Leah E., Shaw, McKenzie L., Rodman, Christopher, Gillespie, Shawn M., Dionne, Danielle, Luo, Christina C., Ravichandran, Hiranmayi, Mylvaganam, Ravindra, Mount, Christopher, Onozato, Maristela L., Nahed, Brian V., Wakimoto, Hiroaki, Curry, William T., Iafrate, A. John, Rivera, Miguel N., Frosch, Matthew P., Golub, Todd R., Brastianos, Priscilla K., Getz, Gad, Patel, Anoop P., Monje, Michelle, Cahill, Daniel P., Rozenblatt-Rosen, Orit, Louis, David N., Bernstein, Bradley E., Regev, Aviv, and Suvà, Mario L.

Published
2017

46. Stem-like intestinal Th17 cells give rise to pathogenic effector T cells during autoimmunity

Author

Massachusetts Institute of Technology. Department of Biology, Schnell, Alexandra, Huang, Linglin, Singer, Meromit, Singaraju, Anvita, Barilla, Rocky M, Regan, Brianna ML, Bollhagen, Alina, Thakore, Pratiksha I, Dionne, Danielle, Delorey, Toni M, Pawlak, Mathias, Meyer zu Horste, Gerd, Rozenblatt-Rosen, Orit, Irizarry, Rafael A, Regev, Aviv, Kuchroo, Vijay K, Massachusetts Institute of Technology. Department of Biology, Schnell, Alexandra, Huang, Linglin, Singer, Meromit, Singaraju, Anvita, Barilla, Rocky M, Regan, Brianna ML, Bollhagen, Alina, Thakore, Pratiksha I, Dionne, Danielle, Delorey, Toni M, Pawlak, Mathias, Meyer zu Horste, Gerd, Rozenblatt-Rosen, Orit, Irizarry, Rafael A, Regev, Aviv, and Kuchroo, Vijay K

Published
2023

47. Stepwise-edited, human melanoma models reveal mutations’ effect on tumor and microenvironment

Author

Massachusetts Institute of Technology. Department of Biology, Hodis, Eran, Triglia, Elena Torlai, Kwon, John YH, Biancalani, Tommaso, Zakka, Labib R, Parkar, Saurabh, Hütter, Jan-Christian, Buffoni, Lorenzo, Delorey, Toni M, Phillips, Devan, Dionne, Danielle, Nguyen, Lan T, Schapiro, Denis, Maliga, Zoltan, Jacobson, Connor A, Hendel, Ayal, Rozenblatt-Rosen, Orit, Mihm, Martin C, Garraway, Levi A, Regev, Aviv, Massachusetts Institute of Technology. Department of Biology, Hodis, Eran, Triglia, Elena Torlai, Kwon, John YH, Biancalani, Tommaso, Zakka, Labib R, Parkar, Saurabh, Hütter, Jan-Christian, Buffoni, Lorenzo, Delorey, Toni M, Phillips, Devan, Dionne, Danielle, Nguyen, Lan T, Schapiro, Denis, Maliga, Zoltan, Jacobson, Connor A, Hendel, Ayal, Rozenblatt-Rosen, Orit, Mihm, Martin C, Garraway, Levi A, and Regev, Aviv

Abstract

Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly disrupted melanoma pathways, forming nine genetically distinct cellular models of melanoma. We connected mutant melanocyte genotypes to malignant cell expression programs in vitro and in vivo, replicative immortality, malignancy, rapid tumor growth, pigmentation, metastasis, and histopathology. Mutations in malignant cells also affected tumor microenvironment composition and cell states. Our melanoma models shared genotype-associated expression programs with patient melanomas, and a deep learning model showed that these models partially recapitulated genotype-associated histopathological features as well. Thus, a progressive series of genome-edited human cancer models can causally connect genotypes carrying multiple mutations to phenotype.

Published
2023

48. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

Author

Massachusetts Institute of Technology. Department of Biology, Eraslan, Gökcen, Drokhlyansky, Eugene, Anand, Shankara, Fiskin, Evgenij, Subramanian, Ayshwarya, Slyper, Michal, Wang, Jiali, Van Wittenberghe, Nicholas, Rouhana, John M, Waldman, Julia, Ashenberg, Orr, Lek, Monkol, Dionne, Danielle, Win, Thet Su, Cuoco, Michael S, Kuksenko, Olena, Tsankov, Alexander M, Branton, Philip A, Marshall, Jamie L, Greka, Anna, Getz, Gad, Segrè, Ayellet V, Aguet, François, Rozenblatt-Rosen, Orit, Ardlie, Kristin G, Regev, Aviv, Massachusetts Institute of Technology. Department of Biology, Eraslan, Gökcen, Drokhlyansky, Eugene, Anand, Shankara, Fiskin, Evgenij, Subramanian, Ayshwarya, Slyper, Michal, Wang, Jiali, Van Wittenberghe, Nicholas, Rouhana, John M, Waldman, Julia, Ashenberg, Orr, Lek, Monkol, Dionne, Danielle, Win, Thet Su, Cuoco, Michael S, Kuksenko, Olena, Tsankov, Alexander M, Branton, Philip A, Marshall, Jamie L, Greka, Anna, Getz, Gad, Segrè, Ayellet V, Aguet, François, Rozenblatt-Rosen, Orit, Ardlie, Kristin G, and Regev, Aviv

Abstract

Understanding gene function and regulation in homeostasis and disease requires knowledge of the cellular and tissue contexts in which genes are expressed. Here, we applied four single-nucleus RNA sequencing methods to eight diverse, archived, frozen tissue types from 16 donors and 25 samples, generating a cross-tissue atlas of 209,126 nuclei profiles, which we integrated across tissues, donors, and laboratory methods with a conditional variational autoencoder. Using the resulting cross-tissue atlas, we highlight shared and tissue-specific features of tissue-resident cell populations; identify cell types that might contribute to neuromuscular, metabolic, and immune components of monogenic diseases and the biological processes involved in their pathology; and determine cell types and gene modules that might underlie disease mechanisms for complex traits analyzed by genome-wide association studies.

Published
2023

49. Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Author

Slyper, Michal, Porter, Caroline B. M., Ashenberg, Orr, Waldman, Julia, Drokhlyansky, Eugene, Wakiro, Isaac, Smillie, Christopher, Smith-Rosario, Gabriela, Wu, Jingyi, Dionne, Danielle, Vigneau, Sébastien, Jané-Valbuena, Judit, Tickle, Timothy L., Napolitano, Sara, Su, Mei-Ju, Patel, Anand G., Karlstrom, Asa, Gritsch, Simon, Nomura, Masashi, Waghray, Avinash, Gohil, Satyen H., Tsankov, Alexander M., Jerby-Arnon, Livnat, Cohen, Ofir, Klughammer, Johanna, Rosen, Yanay, Gould, Joshua, Nguyen, Lan, Hofree, Matan, Tramontozzi, Peter J., Li, Bo, Wu, Catherine J., Izar, Benjamin, Haq, Rizwan, Hodi, F. Stephen, Yoon, Charles H., Hata, Aaron N., Baker, Suzanne J., Suvà, Mario L., Bueno, Raphael, Stover, Elizabeth H., Clay, Michael R., Dyer, Michael A., Collins, Natalie B., Matulonis, Ursula A., Wagle, Nikhil, Johnson, Bruce E., Rotem, Asaf, Rozenblatt-Rosen, Orit, and Regev, Aviv

Published
2020
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50. An experimental sociolinguistic study of Asian Americans in Boston (AAiB)

Author

Chang, Charles, Bombardo, Aspen, Dionne, Danielle, Fang, Jiangnan, Fraser, Katherine, and Rigor, Samantha

Subjects
Korean Americans, r-deletion, Boston English, speech production, Mandarin, Vietnamese Americans, phonetics, Tagalog, Korean, Vietnamese, dialects, Cebuano, l-vocalization, Filipino Americans, Asian Americans, ethnolects, low back raising, Chinese Americans, sociophonetics, l/r-conflation, Boston, sociolinguistics
Abstract

This repository contains data and materials from a project examining the speech production of Boston-based Asian Americans, the Asian Americans in Boston (AAiB) Project. Aspects of this project are reported in Fang and Chang (2020a,b), Bombardo and Chang (2020), Dionne and Chang (2021, 2022), Chang and Dionne (2022), Fraser and Chang (2023), and Rigor and Chang (2023); see wiki for full references and links.

Published
2022
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