User:Daniel Mietchen/Interesting publications/BDSTG hackathon 2017
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Harold Swerdlow, Christoph Hafemeister, Marlon Stoeckius, Brian Houck-Loomis, Rahul Satija, Peter Smibert, William Stephenson and Pratip K. Chattopadhyay, "Simultaneous epitope and transcriptome measurement in single cells", Nature Methods, vol. 14, 9, , doi: 10.1038/NMETH.4380, PubMed ID: 28759029 , PubMed Central ID: 5669064 Aviv Regev, Kristin Ardlie, Orit Rozenblatt-Rosen, Anindita Basu, Matan Hofree and Karthik Shekhar, "Massively parallel single-nucleus RNA-seq with DroNc-seq", Nature Methods, vol. 14, 10, , doi: 10.1038/NMETH.4407, PubMed ID: 28846088 , PubMed Central ID: 5623139 Aviv Regev, Rahul Satija, Roi Avraham, Alex K. Shalek, John J Trombetta, Ramnik J Xavier and Deborah T Hung, "Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses", Cell, vol. 162, 6, , doi: 10.1016/J.CELL.2015.08.027, PubMed ID: 26343579 , PubMed Central ID: 4578813 Jörg Vogel, Lei Li, Silke Appenzeller, Leon N Schulte and Sophie Helaine, "Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella", Nature Microbiology, vol. 2, , doi: 10.1038/NMICROBIOL.2016.206, PubMed ID: 27841856 Alex K. Shalek, Shawn M. Gillespie, Daniel P Cahill, Brian V. Nahed, Robert L Martuza, Aviv Regev, Orit Rozenblatt-Rosen, Itay Tirosh, John J Trombetta and Bradley Bernstein, "Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma", Science, vol. 344, 6190, , doi: 10.1126/SCIENCE.1254257, PubMed ID: 24925914 , PubMed Central ID: 4123637 Kun Zhang, Blue B. Lake, Yun C Yung, Song Chen and Jerold Chun, "Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain", Science, vol. 352, 6293, , doi: 10.1126/SCIENCE.AAF1204, PubMed ID: 27339989 , PubMed Central ID: 5038589 Daniel M DeLaughter, Jonathan G Seidman, Christine E. Seidman, Joshua M Gorham, Alexander G. Bick, Benoit G. Bruneau, Hiroko Wakimoto, Irfan S Kathiriya, John M Hinson and Jason Homsy, "Single-Cell Resolution of Temporal Gene Expression during Heart Development", Developmental Cell, vol. 39, 4, , doi: 10.1016/J.DEVCEL.2016.10.001, PubMed ID: 27840107 , PubMed Central ID: 5198784 Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, James Fletcher, Morgane Griesbeck, Andrew Butler, Shiwei Zheng, Suzan Lazo, David Dixon, Emily Stephenson, Emil Nilsson, Ida Grundberg, David McDonald, Muzlifah Haniffa, Aviv Regev, Nir Hacohen, Orit Rozenblatt-Rosen, Siranush Sarkizova, Laura Jardine, Philip L. De Jager and Karthik Shekhar, "Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors", Science, vol. 356, 6335, , doi: 10.1126/SCIENCE.AAH4573, PubMed ID: 28428369 , PubMed Central ID: 5775029 Shyam Prabhakar, "A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data", BMC Genomics, vol. 17, Suppl 13, , doi: 10.1186/S12864-016-3317-7, PubMed ID: 28155657 , PubMed Central ID: 5260093
About
[edit]This page is auxiliary to my participation in the BDSTG hackathon taking place at University of Virginia (Q213439) on November 7-8, 2017. BDSTG stands for the Biomedical Data Science Training Group.
The hackathon is centered around workflows for analysing single-cell RNA data, and it builds on the following publications, which I will focus on during the hackathon, e.g. in terms of annotating the associated datasets.