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.
Paper list
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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, 31 July 2017 , 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, 28 August 2017 , 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, 2 September 2015 , 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, 14 November 2016 , 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, 12 June 2014 , 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, 1 June 2016 , 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, 9 November 2016 , 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, 1 April 2017 , 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, 22 December 2016 , doi: 10.1186/S12864-016-3317-7 , PubMed ID: 28155657 , PubMed Central ID: 5260093