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19 results on '"Subramaniam P"'

3. Gene expression signatures in blood from a West African sepsis cohort define host response phenotypes

Author

Chenoweth, Josh G., Colantuoni, Carlo, Striegel, Deborah A., Genzor, Pavol, Brandsma, Joost, Blair, Paul W., Krishnan, Subramaniam, Chiyka, Elizabeth, Fazli, Mehran, Mehta, Rittal, Considine, Michael, Cope, Leslie, Knight, Audrey C., Elayadi, Anissa, Fox, Anne, Hertzano, Ronna, Letizia, Andrew G., Owusu-Ofori, Alex, Boakye, Isaac, Aduboffour, Albert A., Ansong, Daniel, Biney, Eno, Oduro, George, Schully, Kevin L., and Clark, Danielle V.

Published
2024
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5. Author Correction: Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses

Author

Michael, Benedict D., Dunai, Cordelia, Needham, Edward J., Tharmaratnam, Kukatharmini, Williams, Robyn, Huang, Yun, Boardman, Sarah A., Clark, Jordan J., Sharma, Parul, Subramaniam, Krishanthi, Wood, Greta K., Collie, Ceryce, Digby, Richard, Ren, Alexander, Norton, Emma, Leibowitz, Maya, Ebrahimi, Soraya, Fower, Andrew, Fox, Hannah, Tato, Esteban, Ellul, Mark A., Sunderland, Geraint, Held, Marie, Hetherington, Claire, Egbe, Franklyn N., Palmos, Alish, Stirrups, Kathy, Grundmann, Alexander, Chiollaz, Anne-Cecile, Sanchez, Jean-Charles, Stewart, James P., Griffiths, Michael, Solomon, Tom, Breen, Gerome, Coles, Alasdair J., Kingston, Nathalie, Bradley, John R., Chinnery, Patrick F., Cavanagh, Jonathan, Irani, Sarosh R., Vincent, Angela, Baillie, J. Kenneth, Openshaw, Peter J., Semple, Malcolm G., Taams, Leonie S., and Menon, David K.

Published
2024
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7. Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses

Author

Michael, Benedict D., Dunai, Cordelia, Needham, Edward J., Tharmaratnam, Kukatharmini, Williams, Robyn, Huang, Yun, Boardman, Sarah A., Clark, Jordan J., Sharma, Parul, Subramaniam, Krishanthi, Wood, Greta K., Collie, Ceryce, Digby, Richard, Ren, Alexander, Norton, Emma, Leibowitz, Maya, Ebrahimi, Soraya, Fower, Andrew, Fox, Hannah, Tato, Esteban, Ellul, Mark A., Sunderland, Geraint, Held, Marie, Hetherington, Claire, Egbe, Franklyn N., Palmos, Alish, Stirrups, Kathy, Grundmann, Alexander, Chiollaz, Anne-Cecile, Sanchez, Jean-Charles, Stewart, James P., Griffiths, Michael, Solomon, Tom, Breen, Gerome, Coles, Alasdair J., Kingston, Nathalie, Bradley, John R., Chinnery, Patrick F., Cavanagh, Jonathan, Irani, Sarosh R., Vincent, Angela, Baillie, J. Kenneth, Openshaw, Peter J., Semple, Malcolm G., Taams, Leonie S., and Menon, David K.

Published
2023
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8. Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.

Author

Mandric, Igor, Schwarz, Tommer, Majumdar, Arunabha, Hou, Kangcheng, Briscoe, Leah, Perez, Richard, Subramaniam, Meena, Hafemeister, Christoph, Satija, Rahul, Ye, Chun Jimmie, Pasaniuc, Bogdan, and Halperin, Eran

Subjects
Humans, Gene Expression Profiling, Sequence Analysis, RNA, Computational Biology, Genomics, Gene Expression, Base Sequence, Quantitative Trait Loci, Single-Cell Analysis, Sequence Analysis, RNA
Abstract

Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and simultaneously measure cellular composition and state, which can otherwise only be estimated by applying deconvolution methods to bulk RNA-Seq estimates. However, it has not yet become a widely used tool in population-scale analyses, due to its prohibitively high cost. Here we show that given the same budget, the statistical power of cell-type-specific expression quantitative trait loci (eQTL) mapping can be increased through low-coverage per-cell sequencing of more samples rather than high-coverage sequencing of fewer samples. We use simulations starting from one of the largest available real single-cell RNA-Seq data from 120 individuals to also show that multiple experimental designs with different numbers of samples, cells per sample and reads per cell could have similar statistical power, and choosing an appropriate design can yield large cost savings especially when multiplexed workflows are considered. Finally, we provide a practical approach on selecting cost-effective designs for maximizing cell-type-specific eQTL power which is available in the form of a web tool.

Published
2020

9. Functional interpretation of single cell similarity maps.

Author

DeTomaso, David, Jones, Matthew G, Subramaniam, Meena, Ashuach, Tal, Ye, Chun J, and Yosef, Nir

Subjects
Humans, Reproducibility of Results, Gene Expression Profiling, Sequence Analysis, RNA, Computational Biology, Algorithms, Internet, Single-Cell Analysis, High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA
Abstract

We present Vision, a tool for annotating the sources of variation in single cell RNA-seq data in an automated and scalable manner. Vision operates directly on the manifold of cell-cell similarity and employs a flexible annotation approach that can operate either with or without preconceived stratification of the cells into groups or along a continuum. We demonstrate the utility of Vision in several case studies and show that it can derive important sources of cellular variation and link them to experimental meta-data even with relatively homogeneous sets of cells. Vision produces an interactive, low latency and feature rich web-based report that can be easily shared among researchers, thus facilitating data dissemination and collaboration.

Published
2019

10. Lineage dynamics of murine pancreatic development at single-cell resolution.

Author

Byrnes, Lauren E, Wong, Daniel M, Subramaniam, Meena, Meyer, Nathaniel P, Gilchrist, Caroline L, Knox, Sarah M, Tward, Aaron D, Ye, Chun J, and Sneddon, Julie B

Subjects
Pancreas, Epithelium, Cell Line, Mesoderm, Animals, Mice, Inbred C57BL, Mice, Transgenic, Humans, Microscopy, Fluorescence, In Situ Hybridization, Reverse Transcriptase Polymerase Chain Reaction, Cell Differentiation, Gene Expression Regulation, Developmental, Cell Lineage, Single-Cell Analysis, Human Embryonic Stem Cells
Abstract

Organogenesis requires the complex interactions of multiple cell lineages that coordinate their expansion, differentiation, and maturation over time. Here, we profile the cell types within the epithelial and mesenchymal compartments of the murine pancreas across developmental time using a combination of single-cell RNA sequencing, immunofluorescence, in situ hybridization, and genetic lineage tracing. We identify previously underappreciated cellular heterogeneity of the developing mesenchyme and reconstruct potential lineage relationships among the pancreatic mesothelium and mesenchymal cell types. Within the epithelium, we find a previously undescribed endocrine progenitor population, as well as an analogous population in both human fetal tissue and human embryonic stem cells differentiating toward a pancreatic beta cell fate. Further, we identify candidate transcriptional regulators along the differentiation trajectory of this population toward the alpha or beta cell lineages. This work establishes a roadmap of pancreatic development and demonstrates the broad utility of this approach for understanding lineage dynamics in developing organs.

Published
2018

12. SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization

Author

Mannar, Dhiraj, Saville, James W., Sun, Zehua, Zhu, Xing, Marti, Michelle M., Srivastava, Shanti S., Berezuk, Alison M., Zhou, Steven, Tuttle, Katharine S., Sobolewski, Michele D., Kim, Andrew, Treat, Benjamin R., Da Silva Castanha, Priscila Mayrelle, Jacobs, Jana L., Barratt-Boyes, Simon M., Mellors, John W., Dimitrov, Dimiter S., Li, Wei, and Subramaniam, Sriram

Published
2022
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14. Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function.

Author

Miao, Yifei, Ajami, Nassim E, Huang, Tse-Shun, Lin, Feng-Mao, Lou, Chih-Hong, Wang, Yun-Ting, Li, Shuai, Kang, Jian, Munkacsi, Hannah, Maurya, Mano R, Gupta, Shakti, Chien, Shu, Subramaniam, Shankar, and Chen, Zhen

Subjects
Cells, Cultured, Endothelial Cells, Animals, Mice, Inbred C57BL, Humans, RNA Polymerase II, Gene Expression Profiling, Transcription, Genetic, Gene Expression Regulation, Enzymologic, Male, Nitric Oxide Synthase Type III, Enhancer Elements, Genetic, Promoter Regions, Genetic, RNA, Long Noncoding, Cells, Cultured, Mice, Inbred C57BL, Transcription, Genetic, Gene Expression Regulation, Enzymologic, Enhancer Elements, Promoter Regions, RNA, Long Noncoding, Human Genome, Genetics, 1.1 Normal biological development and functioning, Cardiovascular, MD Multidisciplinary
Abstract

The optimal expression of endothelial nitric oxide synthase (eNOS), the hallmark of endothelial homeostasis, is vital to vascular function. Dynamically regulated by various stimuli, eNOS expression is modulated at transcriptional, post-transcriptional, and post-translational levels. However, epigenetic modulations of eNOS, particularly through long non-coding RNAs (lncRNAs) and chromatin remodeling, remain to be explored. Here we identify an enhancer-associated lncRNA that enhances eNOS expression (LEENE). Combining RNA-sequencing and chromatin conformation capture methods, we demonstrate that LEENE is co-regulated with eNOS and that its enhancer resides in proximity to eNOS promoter in endothelial cells (ECs). Gain- and Loss-of-function of LEENE differentially regulate eNOS expression and EC function. Mechanistically, LEENE facilitates the recruitment of RNA Pol II to the eNOS promoter to enhance eNOS nascent RNA transcription. Our findings unravel a new layer in eNOS regulation and provide novel insights into cardiovascular regulation involving endothelial function.

Published
2018

15. Cdk5 and GSK3β inhibit fast endophilin-mediated endocytosis

Author

Ferreira, Antonio P. A., Casamento, Alessandra, Carrillo Roas, Sara, Halff, Els F., Panambalana, James, Subramaniam, Shaan, Schützenhofer, Kira, Chan Wah Hak, Laura, McGourty, Kieran, Thalassinos, Konstantinos, Kittler, Josef T., Martinvalet, Denis, and Boucrot, Emmanuel

Published
2021
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