Search Results - "Samusik, Nikolay"

Three-dimensional intact-tissue sequencing of single-cell transcriptional states by Wang, Xiao, Allen, William E, Wright, Matthew A, Sylwestrak, Emily L, Samusik, Nikolay, Vesuna, Sam, Evans, Kathryn, Liu, Cindy, Ramakrishnan, Charu, Liu, Jia, Nolan, Garry P, Bava, Felice-Alessio, Deisseroth, Karl

“…Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult,…”
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CODEX multiplexed tissue imaging with DNA-conjugated antibodies by Black, Sarah, Phillips, Darci, Hickey, John W., Kennedy-Darling, Julia, Venkataraaman, Vishal G., Samusik, Nikolay, Goltsev, Yury, Schürch, Christian M., Nolan, Garry P.

“…Advances in multiplexed imaging technologies have drastically improved our ability to characterize healthy and diseased tissues at the single-cell level…”
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Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front by Schürch, Christian M., Bhate, Salil S., Barlow, Graham L., Phillips, Darci J., Noti, Luca, Zlobec, Inti, Chu, Pauline, Black, Sarah, Demeter, Janos, McIlwain, David R., Kinoshita, Shigemi, Samusik, Nikolay, Goltsev, Yury, Nolan, Garry P.

“…Antitumoral immunity requires organized, spatially nuanced interactions between components of the immune tumor microenvironment (iTME). Understanding this…”
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Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models by Ajami, Bahareh, Samusik, Nikolay, Wieghofer, Peter, Ho, Peggy P., Crotti, Andrea, Bjornson, Zach, Prinz, Marco, Fantl, Wendy J., Nolan, Garry P., Steinman, Lawrence

“…Neuroinflammation and neurodegeneration may represent two poles of brain pathology. Brain myeloid cells, particularly microglia, play key roles in these…”
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Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells by Good, Zinaida, Borges, Luciene, Vivanco Gonzalez, Nora, Sahaf, Bita, Samusik, Nikolay, Tibshirani, Robert, Nolan, Garry P., Bendall, Sean C.

“…Selective differentiation of naive T cells into multipotent T cells is of great interest clinically for the generation of cell-based cancer immunotherapies…”
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Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse by Good, Zinaida, Sarno, Jolanda, Jager, Astraea, Samusik, Nikolay, Aghaeepour, Nima, Simonds, Erin F, White, Leah, Lacayo, Norman J, Fantl, Wendy J, Fazio, Grazia, Gaipa, Giuseppe, Biondi, Andrea, Tibshirani, Robert, Bendall, Sean C, Nolan, Garry P, Davis, Kara L

“…Mass cytometry of diagnostic biopsies from children with B cell precursor acute lymphoblastic leukemia identifies a signaling state that predicts relapse…”
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High-resolution myogenic lineage mapping by single-cell mass cytometry by Porpiglia, Ermelinda, Samusik, Nikolay, Ho, Andrew Tri Van, Cosgrove, Benjamin D., Mai, Thach, Davis, Kara L., Jager, Astraea, Nolan, Garry P., Bendall, Sean C., Fantl, Wendy J., Blau, Helen M.

“…Muscle regeneration is a dynamic process during which cell state and identity change over time. A major roadblock has been a lack of tools to resolve a…”
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Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal by Fietz, Simone A., Lachmann, Robert, Brandl, Holger, Kircher, Martin, Samusik, Nikolay, Schröder, Roland, Lakshmanaperumal, Naharajan, Henry, Ian, Vogt, Johannes, Riehn, Axel, Distler, Wolfgang, Nitsch, Robert, Enard, Wolfgang, Pääbo, Svante, Huttner, Wieland B.

“…The expansion of the neocortex during mammalian brain evolution results primarily from an increase in neural progenitor cell divisions in its two principal…”
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Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry by Gonzalez, Veronica D., Samusik, Nikolay, Chen, Tiffany J., Savig, Erica S., Aghaeepour, Nima, Quigley, David A., Huang, Ying-Wen, Giangarrà, Valeria, Borowsky, Alexander D., Hubbard, Neil E., Chen, Shih-Yu, Han, Guojun, Ashworth, Alan, Kipps, Thomas J., Berek, Jonathan S., Nolan, Garry P., Fantl, Wendy J.

“…We have performed an in-depth single-cell phenotypic characterization of high-grade serous ovarian cancer (HGSOC) by multiparametric mass cytometry (CyTOF)…”
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PBOV1 is a human de novo gene with tumor-specific expression that is associated with a positive clinical outcome of cancer by Samusik, Nikolay, Krukovskaya, Larisa, Meln, Irina, Shilov, Evgeny, Kozlov, Andrey P

“…PBOV1 is a known human protein-coding gene with an uncharacterized function. We have previously found that PBOV1 lacks orthologs in non-primate genomes and is…”
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GateFinder: projection-based gating strategy optimization for flow and mass cytometry by Aghaeepour, Nima, Simonds, Erin F, Knapp, David J H F, Bruggner, Robert V, Sachs, Karen, Culos, Anthony, Gherardini, Pier Federico, Samusik, Nikolay, Fragiadakis, Gabriela K, Bendall, Sean C, Gaudilliere, Brice, Angst, Martin S, Eaves, Connie J, Weiss, William A, Fantl, Wendy J, Nolan, Garry P

“…Abstract Motivation High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using…”
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Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks by Li, Ye Henry, Li, Dangna, Samusik, Nikolay, Wang, Xiaowei, Guan, Leying, Nolan, Garry P, Wong, Wing Hung

“…Mass cytometry (CyTOF) has greatly expanded the capability of cytometry. It is now easy to generate multiple CyTOF samples in a single study, with each sample…”
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Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis by O’Huallachain, Maeve, Bava, Felice-Alessio, Shen, Mary, Dallett, Carolina, Paladugu, Sri, Samusik, Nikolay, Yu, Simon, Hussein, Razika, Hillman, Grantland R., Higgins, Samuel, Lou, Melanie, Trejo, Angelica, Qin, Laura, Tai, Yu Chuan, Kinoshita, Shigemi M., Jager, Astraea, Lashkari, Deval, Goltsev, Yury, Ozturk, Sedide, Nolan, Garry P.

“…Single-cell omics provide insight into cellular heterogeneity and function. Recent technological advances have accelerated single-cell analyses, but workflows…”
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Author Correction: Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis by O’Huallachain, Maeve, Bava, Felice-Alessio, Shen, Mary, Dallett, Carolina, Paladugu, Sri, Samusik, Nikolay, Yu, Simon, Hussein, Razika, Hillman, Grantland R., Higgins, Samuel, Lou, Melanie, Trejo, Angelica, Qin, Laura, Tai, Yu Chuan, Kinoshita, Shigemi M., Jager, Astraea, Lashkari, Deval, Goltsev, Yury, Ozturk, Sedide, Nolan, Garry P.

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
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Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging by Goltsev, Yury, Samusik, Nikolay, Kennedy-Darling, Julia, Bhate, Salil, Hale, Matthew, Vazquez, Gustavo, Black, Sarah, Nolan, Garry P.

“…A highly multiplexed cytometric imaging approach, termed co-detection by indexing (CODEX), is used here to create multiplexed datasets of normal and lupus…”
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Automated mapping of phenotype space with single-cell data by Samusik, Nikolay, Good, Zinaida, Spitzer, Matthew H, Davis, Kara L, Nolan, Garry P

“…X-shift software allows automated mapping of phenotypic space from large mass cytometry data sets. X-shift and the new representation algorithm Divisive Marker…”
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Abstract 5566: Streamlining tissue sample preparation: A comparative study on the efficiency and reproducibility of the Omni-Stainer™ dewaxing and HIER protocol by Samusik, Nikolay, Goltsev, Yury, Kedei, Noemi

“…Abstract The evolution of life sciences research has entailed a shift toward understanding cellular functions within tissue microenvironments, with an emphasis…”
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Abstract 3201: Single-cell trajectory analysis reveals a melanoma-driven distinct hematopoietic response in murine spleen by Kara, Nihan, Samusik, Nikolay, Shi, Xiaoshan, Lomas, Chip, Widmann, Stephanie, Tyznik, Aaron J.

“…Abstract Growing evidence suggests that tumor progression can interfere with normal hematopoiesis and skew the host system to undergo myeloid biased changes…”
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Single-cell trajectory analysis reveals a melanoma-driven distinct hematopoietic response in murine spleen by Kara, Nihan, Samusik, Nikolay, Shi, Xiaoshan, Lomas, Chip, Widmann, Stephanie, Tyznik, Aaron J

“…Abstract Hematopoietic stem and progenitor cells (HSPCs) are a rare population of precursor cells residing in bone marrow that replenish blood cells throughout…”
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Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction by Kennedy‐Darling, Julia, Bhate, Salil S., Hickey, John W., Black, Sarah, Barlow, Graham L., Vazquez, Gustavo, Venkataraaman, Vishal G., Samusik, Nikolay, Goltsev, Yury, Schürch, Christian M., Nolan, Garry P.

“…Multiparameter tissue imaging enables analysis of cell‐cell interactions in situ, the cellular basis for tissue structure, and novel cell types that are…”
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