User:Daniel Mietchen/Interesting publications/BDSTG hackathon 2017

About

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

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