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Colin Megill

Bio: Colin Megill is an academic researcher from Fred Hutchinson Cancer Research Center. The author has contributed to research in topics: Computer science & Codebase. The author has an hindex of 4, co-authored 4 publications receiving 1326 citations.

Papers
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Journal ArticleDOI
TL;DR: Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform that presents a real-time view into the evolution and spread of a range of viral pathogens of high public health importance.
Abstract: Summary Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike. Availability and implementation All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

2,305 citations

Posted ContentDOI
06 Apr 2021-bioRxiv
TL;DR: Cellxgene as mentioned in this paper is a web-based interface for exploring high-dimensional datasets along categorical, continuous and spatial dimensions, as well as feature annotation, with the ability to handle millions of observations.
Abstract: Quickly and flexibly exploring high-dimensional datasets, such as scRNAseq data, is underserved but critical for hypothesis generation, dataset annotation, publication, sharing, and community reuse cellxgene is a highly generalizable, web-based interface for exploring high dimensional datasets along categorical, continuous and spatial dimensions, as well as feature annotation cellxgene is differentiated by its ability to performantly handle millions of observations, and bridges a critical gap by enabling computational and experimental biologists to iteratively ask questions of private and public datasets In doing so, cellxgene increases the utility and reusability of datasets across the single-cell ecosystem The codebase can be accessed at https://githubcom/chanzuckerberg/cellxgene For questions and inquiries, please contact cellxgene@chanzuckerbergcom

51 citations

Posted ContentDOI
22 Nov 2017-bioRxiv
TL;DR: Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform that presents a real-time view into the evolution and spread of a range of viral pathogens of high public health importance.
Abstract: Summary : Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, publicly available for use by health professionals, epidemiologists, virologists and the public alike. Availability and implementation : All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

26 citations

Journal ArticleDOI
TL;DR: In this article , a generalized version of Twitter Birdwatch is proposed to produce maps of public opinion, which can be viewed as a first step towards a generalized deliberative system, using Twitter's misinformation problem as a proving ground.
Abstract: Systems for large scale deliberation have resolved polarized issues and shifted agenda setting into the public's hands. These systems integrate bridging-based ranking algorithms - including group informed consensus implemented in Polis and the continuous matrix factorization approach implemented by Twitter Birdwatch - making it possible to highlight statements which enjoy broad support from a diversity of opinion groups. Polis has been productively employed to foster more constructive political deliberation at nation scale in law making exercises. Twitter Birdwatch is implemented with the intention of addressing misinformation in the global public square. From one perspective, Twitter Birdwatch can be viewed as an anti-misinformation system which has deliberative aspects. But it can also be viewed as a first step towards a generalized deliberative system, using Twitter's misinformation problem as a proving ground. In this paper, we propose that Twitter could adapt Birdwatch to produce maps of public opinion. We describe a system in five parts for generalizing Birdwatch: activation of a deliberative system and topic selection, population sampling and the role of expert networks, deliberation, reporting interpretable results and finally distribution of the results to the public and those in power.

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Journal ArticleDOI
TL;DR: Some notable features of IQ-TREE version 2 are described and the key advantages over other software are highlighted.
Abstract: IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

4,337 citations

Journal ArticleDOI
Carly G. K. Ziegler, Samuel J. Allon, Sarah K. Nyquist, Ian M. Mbano1, Vincent N. Miao, Constantine N. Tzouanas, Yuming Cao2, Ashraf S. Yousif3, Julia Bals3, Blake M. Hauser3, Blake M. Hauser4, Jared Feldman3, Jared Feldman4, Christoph Muus5, Christoph Muus4, Marc H. Wadsworth, Samuel W. Kazer, Travis K. Hughes, Benjamin Doran, G. James Gatter6, G. James Gatter5, G. James Gatter3, Marko Vukovic, Faith Taliaferro5, Faith Taliaferro7, Benjamin E. Mead, Zhiru Guo2, Jennifer P. Wang2, Delphine Gras8, Magali Plaisant9, Meshal Ansari, Ilias Angelidis, Heiko Adler, Jennifer M.S. Sucre10, Chase J. Taylor10, Brian M. Lin4, Avinash Waghray4, Vanessa Mitsialis7, Vanessa Mitsialis11, Daniel F. Dwyer11, Kathleen M. Buchheit11, Joshua A. Boyce11, Nora A. Barrett11, Tanya M. Laidlaw11, Shaina L. Carroll12, Lucrezia Colonna13, Victor Tkachev4, Victor Tkachev7, Christopher W. Peterson13, Christopher W. Peterson14, Alison Yu15, Alison Yu7, Hengqi Betty Zheng13, Hengqi Betty Zheng15, Hannah P. Gideon16, Caylin G. Winchell16, Philana Ling Lin16, Philana Ling Lin7, Colin D. Bingle17, Scott B. Snapper11, Scott B. Snapper7, Jonathan A. Kropski10, Jonathan A. Kropski18, Fabian J. Theis, Herbert B. Schiller, Laure-Emmanuelle Zaragosi9, Pascal Barbry9, Alasdair Leslie1, Alasdair Leslie19, Hans-Peter Kiem13, Hans-Peter Kiem14, JoAnne L. Flynn16, Sarah M. Fortune5, Sarah M. Fortune4, Sarah M. Fortune3, Bonnie Berger6, Robert W. Finberg2, Leslie S. Kean7, Leslie S. Kean4, Manuel Garber2, Aaron G. Schmidt3, Aaron G. Schmidt4, Daniel Lingwood3, Alex K. Shalek, Jose Ordovas-Montanes, Nicholas E. Banovich, Alvis Brazma, Tushar J. Desai, Thu Elizabeth Duong, Oliver Eickelberg, Christine S. Falk, Michael Farzan20, Ian A. Glass, Muzlifah Haniffa, Peter Horvath, Deborah T. Hung, Naftali Kaminski, Mark A. Krasnow, Malte Kühnemund, Robert Lafyatis, Haeock Lee, Sylvie Leroy, Sten Linnarson, Joakim Lundeberg, Kerstin B. Meyer, Alexander V. Misharin, Martijn C. Nawijn, Marko Nikolic, Dana Pe'er, Joseph E. Powell, Stephen R. Quake, Jay Rajagopal, Purushothama Rao Tata, Emma L. Rawlins, Aviv Regev, Paul A. Reyfman, Mauricio Rojas, Orit Rosen, Kourosh Saeb-Parsy, Christos Samakovlis, Herbert B. Schiller, Joachim L. Schultze, Max A. Seibold, Douglas P. Shepherd, Jason R. Spence, Avrum Spira, Xin Sun, Sarah A. Teichmann, Fabian J. Theis, Alexander M. Tsankov, Maarten van den Berge, Michael von Papen, Jeffrey A. Whitsett, Ramnik J. Xavier, Yan Xu, Kun Zhang 
28 May 2020-Cell
TL;DR: The data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.

1,911 citations

Journal ArticleDOI
08 Jul 2021-Nature
TL;DR: In this paper, an infectious strain of the SARS-CoV-2 Delta variant was isolated from an individual with COVID-19 who had returned to France from India.
Abstract: The SARS-CoV-2 B.1.617 lineage was identified in October 2020 in India1–5. Since then, it has become dominant in some regions of India and in the UK, and has spread to many other countries6. The lineage includes three main subtypes (B1.617.1, B.1.617.2 and B.1.617.3), which contain diverse mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein that may increase the immune evasion potential of these variants. B.1.617.2—also termed the Delta variant—is believed to spread faster than other variants. Here we isolated an infectious strain of the Delta variant from an individual with COVID-19 who had returned to France from India. We examined the sensitivity of this strain to monoclonal antibodies and to antibodies present in sera from individuals who had recovered from COVID-19 (hereafter referred to as convalescent individuals) or who had received a COVID-19 vaccine, and then compared this strain with other strains of SARS-CoV-2. The Delta variant was resistant to neutralization by some anti-NTD and anti-RBD monoclonal antibodies, including bamlanivimab, and these antibodies showed impaired binding to the spike protein. Sera collected from convalescent individuals up to 12 months after the onset of symptoms were fourfold less potent against the Delta variant relative to the Alpha variant (B.1.1.7). Sera from individuals who had received one dose of the Pfizer or the AstraZeneca vaccine had a barely discernible inhibitory effect on the Delta variant. Administration of two doses of the vaccine generated a neutralizing response in 95% of individuals, with titres three- to fivefold lower against the Delta variant than against the Alpha variant. Thus, the spread of the Delta variant is associated with an escape from antibodies that target non-RBD and RBD epitopes of the spike protein. The SARS-CoV-2 Delta variant partially evades neutralization by several monoclonal antibodies and by sera from individuals who have had COVID-19, but two doses of anti-COVID-19 vaccines still generate a strong neutralizing response.

1,462 citations