Search Results - "McFaline‐Figueroa, José L"

Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana by Jean-Baptiste, Ken, McFaline-Figueroa, José L, Alexandre, Cristina M, Dorrity, Michael W, Saunders, Lauren, Bubb, Kerry L, Trapnell, Cole, Fields, Stanley, Queitsch, Christine, Cuperus, Josh T

“…Single cell RNA sequencing can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of…”
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Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data by Pliner, Hannah A., Packer, Jonathan S., McFaline-Figueroa, José L., Cusanovich, Darren A., Daza, Riza M., Aghamirzaie, Delasa, Srivatsan, Sanjay, Qiu, Xiaojie, Jackson, Dana, Minkina, Anna, Adey, Andrew C., Steemers, Frank J., Shendure, Jay, Trapnell, Cole

“…Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an…”
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Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe by Qiu, Xiaojie, Rahimzamani, Arman, Wang, Li, Ren, Bingcheng, Mao, Qi, Durham, Timothy, McFaline-Figueroa, José L, Saunders, Lauren, Trapnell, Cole, Kannan, Sreeram

“…Here, we present Scribe (https://github.com/aristoteleo/Scribe-py), a toolkit for detecting and visualizing causal regulatory interactions between genes and…”
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The microtubule targeting agent ST-401 triggers cell death in interphase and prevents the formation of polyploid giant cancer cells by Vicente, Juan Jesus, Khan, Kainat, Tillinghast, Grant, McFaline-Figueroa, José L, Sancak, Yasemin, Stella, Nephi

“…Microtubule targeting agents (MTAs) are commonly prescribed to treat cancers and predominantly kill cancer cells in mitosis. Significantly, some MTA-treated…”
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Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma by O’Connor, Samantha A, Feldman, Heather M, Arora, Sonali, Hoellerbauer, Pia, Toledo, Chad M, Corrin, Philip, Carter, Lucas, Kufeld, Megan, Bolouri, Hamid, Basom, Ryan, Delrow, Jeffrey, McFaline‐Figueroa, José L, Trapnell, Cole, Pollard, Steven M, Patel, Anoop, Paddison, Patrick J, Plaisier, Christopher L

“…Single‐cell RNA sequencing has emerged as a powerful tool for resolving cellular states associated with normal and maligned developmental processes. Here, we…”
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High-capacity sample multiplexing for single cell chromatin accessibility profiling by Booth, Gregory T, Daza, Riza M, Srivatsan, Sanjay R, McFaline-Figueroa, José L, Gladden, Rula Green, Mullen, Andrew C, Furlan, Scott N, Shendure, Jay, Trapnell, Cole

“…Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling…”
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Nuclear oligo hashing improves differential analysis of single-cell RNA-seq by Kim, Hyeon-Jin, Booth, Greg, Saunders, Lauren, Srivatsan, Sanjay, McFaline-Figueroa, José L., Trapnell, Cole

“…Single-cell RNA sequencing (scRNA-seq) offers a high-resolution molecular view into complex tissues, but suffers from high levels of technical noise which…”
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Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma by Mikheev, Andrei M., Mikheeva, Svetlana A., Severs, Liza J., Funk, Cory C., Huang, Lei, McFaline‐Figueroa, José L., Schwensen, Jeanette, Trapnell, Cole, Price, Nathan D., Wong, Stephen, Rostomily, Robert C.

“…TWIST1 (TW) is a bHLH transcription factor (TF) and master regulator of the epithelial‐to‐mesenchymal transition (EMT). In vitro, TW promotes mesenchymal…”
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Massively multiplex chemical transcriptomics at single-cell resolution by Srivatsan, Sanjay R, McFaline-Figueroa, José L, Ramani, Vijay, Saunders, Lauren, Cao, Junyue, Packer, Jonathan, Pliner, Hannah A, Jackson, Dana L, Daza, Riza M, Christiansen, Lena, Zhang, Fan, Steemers, Frank, Shendure, Jay, Trapnell, Cole

“…High-throughput chemical screens typically use coarse assays such as cell survival, limiting what can be learned about mechanisms of action, off-target…”
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Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs by He, Siyu, Jin, Yinuo, Nazaret, Achille, Shi, Lingting, Chen, Xueer, Rampersaud, Sham, Dhillon, Bahawar S, Valdez, Izabella, Friend, Lauren E, Fan, Joy Linyue, Park, Cameron Y, Mintz, Rachel L, Lao, Yeh-Hsing, Carrera, David, Fang, Kaylee W, Mehdi, Kaleem, Rohde, Madeline, McFaline-Figueroa, José L, Blei, David, Leong, Kam W, Rudensky, Alexander Y, Plitas, George, Azizi, Elham

“…Spatially resolved gene expression profiling provides insight into tissue organization and cell-cell crosstalk; however, sequencing-based spatial…”
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On the design of CRISPR-based single-cell molecular screens by Hill, Andrew J, McFaline-Figueroa, José L, Starita, Lea M, Gasperini, Molly J, Matreyek, Kenneth A, Packer, Jonathan, Jackson, Dana, Shendure, Jay, Trapnell, Cole

“…CRISPR-based single-cell pooled screens that use linked barcodes suffer from lost sensitivity due to lentiviral template switching. The barcode-free CROP-seq…”
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Predicting cellular responses to complex perturbations in high‐throughput screens by Lotfollahi, Mohammad, Klimovskaia Susmelj, Anna, De Donno, Carlo, Hetzel, Leon, Ji, Yuge, Ibarra, Ignacio L, Srivatsan, Sanjay R, Naghipourfar, Mohsen, Daza, Riza M, Martin, Beth, Shendure, Jay, McFaline‐Figueroa, Jose L, Boyeau, Pierre, Wolf, F Alexander, Yakubova, Nafissa, Günnemann, Stephan, Trapnell, Cole, Lopez‐Paz, David, Theis, Fabian J

“…Recent advances in multiplexed single‐cell transcriptomics experiments facilitate the high‐throughput study of drug and genetic perturbations. However, an…”
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Minor Changes in Expression of the Mismatch Repair Protein MSH2 Exert a Major Impact on Glioblastoma Response to Temozolomide by McFaline-Figueroa, José L, Braun, Christian J, Stanciu, Monica, Nagel, Zachary D, Mazzucato, Patrizia, Sangaraju, Dewakar, Cerniauskas, Edvinas, Barford, Kelly, Vargas, Amanda, Chen, Yimin, Tretyakova, Natalia, Lees, Jacqueline A, Hemann, Michael T, White, Forest M, Samson, Leona D

“…Glioblastoma (GBM) is often treated with the cytotoxic drug temozolomide, but the disease inevitably recurs in a drug-resistant form after initial treatment…”
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A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition by McFaline-Figueroa, José L., Hill, Andrew J., Qiu, Xiaojie, Jackson, Dana, Shendure, Jay, Trapnell, Cole

“…Integrating single-cell trajectory analysis with pooled genetic screening could reveal the genetic architecture that guides cellular decisions in development…”
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A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens by Gasperini, Molly, Hill, Andrew J., McFaline-Figueroa, José L., Martin, Beth, Kim, Seungsoo, Zhang, Melissa D., Jackson, Dana, Leith, Anh, Schreiber, Jacob, Noble, William S., Trapnell, Cole, Ahituv, Nadav, Shendure, Jay

“…Over one million candidate regulatory elements have been identified across the human genome, but nearly all are unvalidated and their target genes uncertain…”
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Joint profiling of chromatin accessibility and gene expression in thousands of single cells by Cao, Junyue, Cusanovich, Darren A, Ramani, Vijay, Aghamirzaie, Delasa, Pliner, Hannah A, Hill, Andrew J, Daza, Riza M, McFaline-Figueroa, Jose L, Packer, Jonathan S, Christiansen, Lena, Steemers, Frank J, Adey, Andrew C, Trapnell, Cole, Shendure, Jay

“…Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays…”
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The promise of single-cell genomics in plants by McFaline-Figueroa, José L, Trapnell, Cole, Cuperus, Josh T

“…Single-cell genomic approaches have the potential to revolutionize the study of plant systems. Here, we highlight newly developed techniques to analyze…”
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A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens by Gasperini, Molly, Hill, Andrew J., McFaline-Figueroa, José L., Martin, Beth, Kim, Seungsoo, Zhang, Melissa D., Jackson, Dana, Leith, Anh, Schreiber, Jacob, Noble, William S., Trapnell, Cole, Ahituv, Nadav, Shendure, Jay

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Thyroid hormone regulates distinct paths to maturation in pigment cell lineages by Saunders, Lauren M, Mishra, Abhishek K, Aman, Andrew J, Lewis, Victor M, Toomey, Matthew B, Packer, Jonathan S, Qiu, Xiaojie, McFaline-Figueroa, Jose L, Corbo, Joseph C, Trapnell, Cole, Parichy, David M

“…Thyroid hormone (TH) regulates diverse developmental events and can drive disparate cellular outcomes. In zebrafish, TH has opposite effects on neural crest…”
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Modelling ciliopathy phenotypes in human tissues derived from pluripotent stem cells with genetically ablated cilia by Cruz, Nelly M., Reddy, Raghava, McFaline-Figueroa, José L., Tran, Christine, Fu, Hongxia, Freedman, Benjamin S.

“…The functions of cilia—antenna-like organelles associated with a spectrum of disease states—are poorly understood, particularly in human cells. Here we show…”
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