covid19-review
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greenelab
Introduce yourself here first!
Hello interested contributors! Welcome to the covid19-review project. Our goal here is to provide an up-to-date perspective on the current peer reviewed and preprinted literature around diagnostics and therapeutics relevant to COVID-19. There's more in our README, which you may have already seen: https://github.com/greenelab/covid19-review#sars-cov-2-and-covid-19-an-evolving-review-of-diagnostics-and-therapeutics
As a first step, let's get to know each other. Please answer these questions!
- Your name
- Your job other than this review
- What you hope to get out of participating
- How you feel best prepared to contribute
- What you have the most trepidation about
- Your name: Casey Greene
- Your job other than this review: When I'm not doing this, I mentor folks in a computational biology lab at UPenn and help Alex's Lemonade Stand Foundation with their Childhood Cancer Data Lab
- What you hope to get out of participating: It has become increasingly clear that diagnostics and therapeutics will have key roles to play in addressing COVID-19. I'm interested in learning more about what's being evaluated and what stage it's at. I'm excited about the rapid sharing, especially on twitter and social media, but I'm concerned that a lot of nuance is being lost.
- How you feel best prepared to contribute: This will be my second massively open online review paper that I've worked on. I'm happy to review text, read some papers, and contribute in whatever way I can.
- What you have the most trepidation about: I was a PhD student in a Molecular and Cellular Biology program a while ago and have some experience reading such papers from journal club, but it's been a while. I'm excited and nervous about getting back into that literature.
Your name: Avery Posey
Your job other than this review: Assistant Prof @ UPenn, CAR-T cell engineering for cancer as well as pro-inflammatory diseases
What you hope to get out of participating: I want to contribute to distilling the large body of work in this rapidly evolving area.
How you feel best prepared to contribute: I want to read papers that have assessed immune-related components of COVID-19.
What you have the most trepidation about: This is my first massive open online review and I am interested to see how this goes.
- Your Name: Michael Robson
- Your job other than this review: Assistant Professor of Computer Science at Villanova University
- What you hope to get out of participating: Make a meaningful contribution to a high-impact project that will help in the ongoing crisis (by making it easier for scientists and others to contribute)
- How you feel best prepared to contribute: Software, git tutorials, GitHub maintenance, general non-biology but technical expertise
- What you have the most trepidation about: I know very little helpful biology
– Your name: Hossein Khiabanian – Your job other than this review: Assistant Professor at Rutgers (computational biology, cancer genomics) – What you hope to get out of participating: Small contribution to a large review (my first) of literature as we learn more about this coronavirus and the pandemic it has caused. – How you feel best prepared to contribute: I have previously worked on molecular epidemiology of influenza and ebola using simple statistical models. – What you have the most trepidation about: I am very interested in modes of transmission and their relationship with the viral load given the wide spectrum of symptoms and severity during the infection.
This is great, just saw your post in NPIS.
- Lucy D’Agostino McGowan
- Assistant Professor in Statistics, Wake Forest University
- I’ve been trying to synthesize the medical literature for my friends / family - Would be great to have lots of minds on this (and be able to contribute as well!)
- My PhD & postdoc were in biostatistics & I have a lot of GitHub experience - happy to contribute both to the stats & organization
- I’m currently committed to a lot of projects, but this is important - biggest trepidation is just finding time for everything
Your name: Luis Pedro Coelho
Your job other than this review: Junior Principal Investigator in computational biology, Fudan University
What you hope to get out of participating: I hope to learn more myself most of all
How you feel best prepared to contribute: I am switching some of my time to Covid-19 related work starting this week, so I will be reading a lot in the very near future
What you have the most trepidation about: this is a bit far from my main area of expertise, although I put some of that on hold given the state of emergency
Thank you for starting this Casey!
- Simina Boca
- Faculty at the Innovation Center for Biomedical Informatics and Oncology & Biostatistics at Georgetown
- Help with a relevant and timely project! Also, I had a ton of fun with the collaborative deep review, and some fun is sorely needed right now
- Statistical and study design issues, systematizing results. My background is in biostats and I've taught evidence-based data analysis to med and grad students
- Finding the time to keep on top of everything, especially since I know many preprints are coming out daily
- Your name: Akhilesh Reddy
- Your job other than this review: When I'm not doing this, I lead a research group at Penn focused on the molecular biology of circadian (24 hour) clocks and sleep.
- What you hope to get out of participating: Some proper fact-based insights into the emerging literature in this field.
- How you feel best prepared to contribute: I am a clinician-scientist (MD-PhD) with a broad interest, and my lab has previously investigated the interactions between virus and host in the context of the circadian cycle. I should be able to provide a discerning eye for the clinical aspects, as well as the basic science. I'm happy to review text, read some papers, and contribute in whatever way I can.
- What you have the most trepidation about: Juggling lots of new COVID projects working virtually.
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Your name: Christian Brueffer
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Your job other than this review: Bioinformatician at SAGA Diagnostics working on cancer molecular diagnostics, and PhD student in cancer genomics at Lund University.
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What you hope to get out of participating: Learning more about virology, particularly in the SARS-CoV-19 context, and getting experience in writing reviews.
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How you feel best prepared to contribute Experience with (non-virology) scientific literature, programming, data analysis/visualization, GitHub, and reviewing/writing/editing text.
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What you have the most trepidation about: Keeping on top of literature outside my area of expertise while my normal obligations continue.
Your name: Nils Wellhausen
Your job other than this review: Being a Pharmacology Graduate student. Learning computational biology, keeping up with the literature in general and playing guitar.
What you hope to get out of participating: Learning more about the current approaches to tackle this global issue but also being able to expand my knowledge and help writing a comprehensive review informing the community.
How you feel best prepared to contribute: We started a COVID 19 journal club in the wherry lab so I have been relatively up to date with the literature. I also worked with the high throughput screening core around David Schultz that is currently screening drugs for COVID-19.
What you have the most trepidation about: Being able to critically evaluate all the preprints coming out and of course keeping up with all commitments.
- Your name: Anthony Gitter
- Your job other than this review: I lead a computational biology research group at the University of Wisconsin-Madison and the Morgridge Institute for Research
- What you hope to get out of participating: This is a perfect use case for Manubot, and I want the review to thrive; I also want to better educate myself about COVID-19
- How you feel best prepared to contribute: I have experience with Manubot and collaborative reviews so I'd like to help domain experts become comfortable with this nontraditional writing process
- What you have the most trepidation about: This a fast-moving, high-stakes area; it will be difficult but imperative to summarize the literature accurately and review contributions thoroughly
Your name: Juliette Rando
Your job other than this review: I'm a research specialist in a virology lab (studying HIV/SIV) at the Perelman School of Medicine at UPenn and an MPH candidate.
What you hope to get out of participating: I want to help in this time of crisis in any way possible.
How you feel best prepared to contribute: I'm ready and willing to put time into sifting through the literature. I have experience conducting a systematic review in the past.
What you have the most trepidation about: My virology knowledge is HIV-focused, and I do not have an advanced degree in biology. So I will definitely be deferring to the experts in this project!
• Your name: Sandipan Ray (Ph.D., MRSB) • Your job other than this review: I am a senior post-doctoral fellow at the Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania • What you hope to get out of participating: Getting more information regarding this new SARS-CoV-2 infection. Bringing the essential information regarding this novel infection from the published and pre-print literature • How you feel best prepared to contribute: I have considerable expertise in cutting-edge proteomics (and systems biology) for studying infectious diseases (including dengue fever, malaria and leptospirosis). I have experience of writing systematic reviews in the past. Systems level approaches (including transcriptomics, proteomics and metabolomics) can provide extremely useful information regarding coronavirus 2 infection and may help in identifying effective early diagnostic and therapeutic (for both drugs and vaccines) targets. In this vein, the full-length genome sequences of nCoV-2019 and the phylogenetic analysis of the complete viral genome are published very recently (Wu et al., Nature 2020, PMID: 32015508; Lu et al., Lancet. 2020, PMID: 32007145, and Zhou et al., 2020, PMID: 32015507), while the proteome level studies are on their way (https://www.researchsquare.com/article/rs-17218/v1). I would like to contribute in a section on how systems approaches are proving new mechanistic insights into the pathogenesis of nCoV-2019 and host responses towards this infection. Additionally, I will be happy to review the other sections of manuscript. • What you have the most trepidation about: Trying to be familiar with the current trends of this novel pathogenic SARS-coronavirus 2 while working virtually.
Your name: Ronnie Russell
Your job other than this review: PhD student at the University of Pennsylvania studying HIV and SIV
What you hope to get out of participating: I hope to gain a more comprehensive understanding of coronaviruses (SARS-CoV-2 + the many others waiting to emerge!) and utilize my current knowledge of viruses in a useful way
How you feel best prepared to contribute: Part of my thesis work is studying cross-species transmission of primate lentiviruses (HIV and SIV), specifically barriers to these events (ie host receptor diversity) and viral adaptations following successful zoonoses. As SARS-CoV-2 is a zoonotic virus, a lot of basic biology lessons we have learned over the years for SIV/HIV should be directly translatable.
What you have the most trepidation about: My background on coronavirus biology is limited and papers are being published so quickly that trying to distill the accurate, peer-reviewed information from the deluge of preprints is like (as they say) trying to drink from a firehose.
- Your name: Greg Szeto
- Your job other than this review: about to be former TT assistant professor at UMBC. Just started my role as PI/Assistant Investigator at the Allen Institute for Immunology. I lead trainees and teams to do a lot of immunology (systems and molecular) and immunoengineering across healthy organisms and in diverse diseases, most recently cancer immunology and immunotherapy, lupus, and traumatic brain injury.
- What you hope to get out of participating: Contributing to a critical assessment of the literature, with hopefully some idea generation about host factors that may be contributing to the many differences in SARS-CoV2 vs. recent emergent coronaviruses. This also seems like a great time to refresh my domain knowledge in virology. How you feel best prepared to contribute: I TA'd Hopkins SPH Virology for multiple years and did my PhD in HIV latency, so I feel confident in interpreting critical readings of the literature on viral pathogenesis and drug development. I also have a solid footing in bioinformatics to help contribute to sections on -omics studies.
- What you have the most trepidation about: I have never done a fully crowd-sourced review. The rate of publications and data release has my head spinning. I am also concerned about the broader impacts of ongoing and upcoming control measures on society.
Your name: Huiyanangel(Angel) Chow
Your job other than this review: I am a research specialist in Dr. Carl June lab at the Perelman School of Medicine at the University of Pennsylvania.
What you hope to get out of participating: 1) trace the animal origin of COVID-19, 2) invalidate some rumors and disinformation about COVID-19, 3) know more about testing, metastasis, a model of this global epidemic, role of the environment in this crisis
How you feel best prepared to contribute: while I compare this outbreak with SARS in hongkong, I will look at factors that make this outbreak deviated from the SARS crisis.
What you have the most trepidation about: not being able to sleep well and think clearly
Your name: Halie Rando Your job other than this review: I'm a new post-doc at UPenn working with Casey Green (@cgreene). I'm a computational biologist and typically work on animal models of complex diseases, but right now I am here almost full-time to answer questions, provide technical support, and open discussions for different topics related to this review. What you hope to get out of participating: I'm excited to be part of a multi-disciplinary effort that will allow us to use our collective interest in this topic and varied skill sets to make a real difference during a stressful time How you feel best prepared to contribute: I am helping run the technical side of things, recruiting subject area experts, and trying to make this project as user friendly as possible. I also love to write and edit! What you have the most trepidation about: I don't have much virology background -- if you want a three-minute distraction, these experimentally bred foxes were the subject of my genomics-focused PhD
- Name: Orestis Panagiotou
- Job other than this review: Epidemiologist and Health Services Researcher; Assistant Professor, Brown University SPH
- What I hope to get out of participating: I am just glad to join this effort
- How you feel best prepared to contribute: I have expertise in evidence synthesis, meta-analysis, bias assessments, clinical epidemiology, and evidence-based medicine. Among other things, I conduct systematic reviews for AHRQ
- What you have the most trepidation about: There are many components in this project, ranging from basic science (e.g. viral genome sequencing) to treatment (e.g. comparing drugs) to decision analysis (e.g. decisions need to be made based on limited evidence but we don't have the luxury of waiting for RCTs).
- Your name: Shruti Rao
- Your job other than this review: Research Instructor at the Innovation Center for Biomedical Informatics and Dept of Oncology at Georgetown University
- What you hope to get out of participating: I am excited to be part of this crowdsourcing effort to write a such a timely review paper.
- How you feel best prepared to contribute: I have a background in molecular biology and primarily work as a biocurator on research projects, which involves extracting, organizing and standardizing information from scientific literature and presenting them in databases. Happy to critically evaluate literature on COVID-19 and summarize information for the manuscript.
- What you have the most trepidation about: Finding the time to keep up with emerging literature on this topic while simultaneously refreshing my virology and immunology knowledge.
Your name: Soumita Ghosh Your job other than this review: Research Associate in Dr. Garret Fitgzerald lab, University of Pennsylvania. What you hope to get out of participating: It is timely to focus on a problem that affected the world with my current expertise. It is important to combine knowledge as well as misconception that is presently going on. T How you feel best prepared to contribute: I am working in a lab where NSAIDs and prostaglandins are important topic for research. Previously I worked in malaria hence I read about chloroquine. I would like to focus on different drugs that has been suggested to soIve the crisis. What you have the most trepidation about: I donot have much of virology background.
Your name: Jim Eberwine Your job other than this review: Professor of Systems Pharmacology and Translational Therapeutics What you hope to get out of participating: Better understanding of COVID-19 biology How you feel best prepared to contribute: I am a genomicist, neuroscientist, molecular biologist and hope the this expertise will be useful in understanding aspects of the viruses biology What you have the most trepidation about: I hope that the literature is filled with good quality data but I worry that the data may not be as good as we want and need.
Your name: Ryan Velazquez Your job other than this review: Data Scientist at Azimuth1 What you hope to get out of participating: Learn more about COVID-19 and help in any way needed How you feel best prepared to contribute: Help people with domain knowledge who aren't familiar with GitHub or Manubot.
Your name: Anna Ada Dattoli Your job other than this review: Postdoc in the Eberwine lab (system pharmacology and translational therapeutics) at UPenn What you hope to get out of participating:make a substancial contribution to help the ongoing crisis How you feel best prepared to contribute: molecular biology and data analysis expert. What you have the most trepidation about: critical analysis of the data.
- Your name: Ryan A. Hagenson
- Your job other than this review: Bioinformatics Scientist (and HPC SysAdmin) at Omaha's Henry Doorly Zoo and Aquarium
- What you hope to get out of participating: Enable the growth and legitimization of large-scale open collaborations
- How you feel best prepared to contribute: Most of my training and career thus far has been enabling non-computational biologists to learn and utilize computational resources effectively. Beyond that I focus on taking "slow" analysis and making it "fast" via ample use of concurrency, HPC, and reproducible elements.
- What you have the most trepidation about: Literature in this collab being misinterpreted by the most willing or most available rather than the most fit to review and understand it.
Your name: Mike Mitchell Your job other than this review: Assistant Professor of Bioengineering @ UPenn; Drug delivery, nucleic acid therapeutics What you hope to get out of participating: Better understanding of COVID-19 treatments How you feel best prepared to contribute: My collaborator Drew Weissman (UPenn) and I have significant interests in the design and implementation of mRNA vaccines, and are following COVID-19 mRNA vaccine research closely. Would be happy to review this literature if needed. What you have the most trepidation about: Never done a crowd-sourced review
Thanks for starting this effort!
Your name: Bharath Ramsundar Your job other than this review: Entrepreneur. Lead developer of the DeepChem project. What you hope to get out of participating: Help build understanding of Covid19 among the scientific community How you feel best prepared to contribute: I've been maintaining a running list of summaries/commentaries on interesting preprints/papers at https://forum.deepchem.io/t/interesting-preprints-papers-on-coronavirus/99. I'd be glad to add some of these references to the manuscript What you have the most trepidation about: I'm not an expert at virology/immunology and want to be careful not to misrepresent something.
Dear Casey,
Here I upload a document with several points of discussion, including the most recent literature on the most hopeful experimental drugs (I have found 4 of them), as well as diagnostic tests, based on antibody detection, recently developed. I also added some thoughts concerning the Italian Covid-19 situation.
Please let me know your feedback.
Best,
Ada 20200326_Corona virus review.pdf
Awesome Initiative! Your name: Ioannis Vlachos Your job other than this review: PI at HMS/BIDMC/Broad, and also run the non-coding RNA bioinformatics Unit at the HIRM non-coding RNA Core. What you hope to get out of participating: Become part of a community effort to create a useful resource for tackling COVID-19 How you feel best prepared to contribute: We are switching part of our research resources to COVID-19 and I'm following the relevant literature closely. What you have the most trepidation about: Juggling one more fast-paced project
Great idea folks! Your name: Ronan Lordan Your job other than this review: Postdoctoral Researcher, Garret A. FitzGerald’s Lab at the University of Pennsylvania What you hope to get out of participating: Contribute whatever I can to consolidate and critique the current influx of papers appearing relating to therapeutics for coronavirus. How you feel best prepared to contribute: My previous background was on researching anti-inflammatory therapeutics and nutraceuticals. I want to critique the novel therapeutics being proposed in the literature. In particular, I am interested in a recent mini-review discussing potential nutraceuticals targeting RNA viruses as there is little clinical evidence in this research field. (https://www.sciencedirect.com/science/article/pii/S0033062020300372?via%3Dihub). What you have the most trepidation about: Making an impactful contribution with my limited virology knowledge and using github (a learning curve for me).
Your Name: Arian Jamasb You job other than this review: PhD student, Co-supervised by Tom Blundell & Pietro Lio at the University of Cambridge What you hope to get out of participating: I'd like to keep on top of the papers relating to structural biology & drug repurposing for COVID-19 How you feel best prepared to contribute: I am happy to write about structural biology and virtual screening campaigns relating to COVID-19 What you have the most trepidation about: I'm not a virologist & I've never written a review in this manner.
