greenelab / covid19-review

A collaborative review of the emerging COVID-19 literature. Join the chat here:
https://gitter.im/covid19-review/community
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Introduce yourself here first! #17

Open cgreene opened 4 years ago

cgreene commented 4 years ago

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!

cgreene commented 4 years ago
averyposey commented 4 years ago
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.
mprobson commented 4 years ago
KhiabanianLab commented 4 years ago

– 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.

LucyMcGowan commented 4 years ago

This is great, just saw your post in NPIS.

luispedro commented 4 years ago

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

SiminaB commented 4 years ago

Thank you for starting this Casey!

abreddy8 commented 4 years ago
cbrueffer commented 4 years ago
nilswellhausen commented 4 years ago

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.

agitter commented 4 years ago
juliettemarie0405 commented 4 years ago

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!

rays1987 commented 4 years ago

• 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.

rmrussell commented 4 years ago

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.

gregszetoAI commented 4 years ago
Huiyanangelchow commented 4 years ago

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

rando2 commented 4 years ago

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

orpanag commented 4 years ago
shrutir commented 4 years ago
soumitagh commented 4 years ago

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.

eberwine commented 4 years ago

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.

rdvelazquez commented 4 years ago

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.

aadattoli commented 4 years ago

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.

rhagenson commented 4 years ago
mikemitchellupenn commented 4 years ago

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

rbharath commented 4 years ago

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.

aadattoli commented 4 years ago

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

ivlachos commented 4 years ago

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

RLordan commented 4 years ago

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).

a-r-j commented 4 years ago

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.

adamlmaclean commented 4 years ago
marouenbg commented 4 years ago

Hi everyone!

dziakj1 commented 4 years ago

Hello!

Your name: John J. Dziak Your job other than this review: Research associate professor, The Methodology Center, Penn State What you hope to get out of participating: Contribute my talent in a small way at this critical time How you feel best prepared to contribute: Searching for information on the Internet What you have the most trepidation about: My lack of medical knowledge; difficulty analyzing data due to strict data protection policies at my institution Here are some links I found that might be helpful: https://bestpractice.bmj.com/topics/en-gb/3000165/ https://www.cochranelibrary.com/collections/doi/SC000040/full https://www.ipcrg.org/news/covid-19-open-source-sources-of-information https://www.dropbox.com/s/1jvsqd2quphukqt/RuDASA%20COVID-19%20in%20a%20Rural%20Setting-1.pdf?dl=0 https://www.ncbi.nlm.nih.gov/research/coronavirus/ https://openwho.org/courses/COVID-19-IPC-EN https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance

Sachin Shah, a scientist from UCSF, has put together this large collection of academic articles on COVID-19: https://ucsf.app.box.com/s/2laxq0v00zg2ope9jppsqtnv1mtxd52z/folder/107867635118

kexinhuang12345 commented 4 years ago

Your name: Kexin Huang Your job other than this review: MS student in Health Data Science at Harvard, working with Prof. Marinka Zitnik at DMBI and Prof. Jimeng Sun at UIUC. What you hope to get out of participating: I want to learn more about how ML could help tackle COVID-19 and potentially engage in one project. How you feel best prepared to contribute: my background is in CS&math, so I could contribute to the more method side review on ML for drug repurposing, including network-based, literature-based, chemical-based and etc.
What you have the most trepidation about: I don't have a formal domain training, would love to learn more from fellow domain experts

hufengling commented 4 years ago

Your name: Fengling Hu Your job other than this review: I am an MD-PhD student in Biostatistics at Perelman School of Medicine. What you hope to get out of participating: I want to contribute to important work and read literature in broad fields. How you feel best prepared to contribute: My background is in statistics, RCTs, machine learning and the like. I'd love to contribute/write on these topics. What you have the most trepidation about: I have strong background in these fields above, but acknowledge I am an early-phase student. I'd love to be a part of conversations with domain experts where I can learn from them while still offering insights about statistics/data. I would be worried if my contributions were not reviewed for accuracy.

rishirajgoel commented 4 years ago

Hi all,

Your name: Rishi Goel

Your job other than this review: MD student at Penn

What you hope to get out of participating: learn more about COVID-19 and help consolidate information to inform the public and scientific community

How you feel best prepared to contribute: my academic/research background is in immunology (feel quite comfortable reading/writing in this area). I worked on vaccine development for 4 years as an undergraduate at Michigan. I also completed a master's degree in immunology where I investigated immune responses to chronic hepatitis C virus infection. Most recently, I worked at the NIH where I studied the pathogenesis of autoimmune diseases like lupus and RA. I am especially interested in discussing experimental therapies for COVID that have a crossover with rheum e.g. HCQ and tocilizumab

What you have the most trepidation about: never done a crowd-sourced review but excited to see how different ideas may develop

allucas commented 4 years ago

Your name: Alfredo Lucas

Your job other than this review: I am an MD-PhD student in Bioengineering at the University of Pennsylvania

What you hope to get out of participating: I hope to become more informed about current developments in COVID related research, and be able to succinctly, but clearly, explain new developments to those not heavily involved in scientific research

How you feel best prepared to contribute: I have both a Bachelor's and Master's degree in Bioengineering, with a focus in the application of machine learning for the development of predictive models in cardiovascular and neurological diseases. I have also experience in medical imaging (both optics and radiology), which becomes relevant in the development of quantitative assays for in vitro diagnostic approaches. I also have past experience in medical device and microfluidic design, and rapid prototyping, which can become relevant in assessing potential engineering solutions to the rapid changing environment of the COVID pandemic

What you have the most trepidation about: I have never worked in this type of collaborative environment before, but I am very eager to try it out

dianerafi commented 4 years ago

Your name: Diane Rafizadeh

Your job other than this review: I am an MD-PhD student in Chemistry at the University of Pennsylvania.

What you hope to get out of participating: I'm hoping to become informed about where the scientific community stands with respect to COVID-19 and the diffuse research that's out there. I'm excited to help curate a centralized resource of information on the subject as it evolves, which I feel is necessary for all scientists and physicians as well as the lay public. It will be especially helpful to have a measure of how strong the evidence is for a given claim that floats around on social media and in the news.

How you feel best prepared to contribute: I am interested in therapeutics and drug design as part of my future career, and am excited to use that interest here. I have strong scientific and non-scientific writing skills.

What you have the most trepidation about: I don't have very much prior experience with viruses and infectious diseases; I have more experience with cancer biology.

Jeff-Field commented 4 years ago

Your name: Jeffrey Field

Your job other than this review: Professor Pharmacology, UPenn

What you hope to get out of participating: Assist in evaluating literature, learn about Covid

How you feel best prepared to contribute: I have taught pharmacology for many years and can help evaluate evidence underlying treatment strategies, especially targeted treatments. In areas I cannot evaluate myself, I can also use my network to direct questions to those who are better equipped.

What you have the most trepidation about: My background is primarily cancer research, though I my thesis on adenovirus, it was a long time a go in a research galaxy far far away...

nolankav commented 4 years ago

Your name: Nolan M. Kavanagh

Your job other than this review: MD student at the University of Pennsylvania and adjunct clinical lecturer at the University of Michigan.

What you hope to get out of participating: Understanding how scientific and clinical information can be efficiently synthesized and distributed for COVID. I'm also intrigued about how the structure of a collaboration like this could coordinate experts on other issues.

How you feel best prepared to contribute: I am most useful for statistical analysis, writing, and working through policy/political implications. My background is in public health and health policy; I did my M.P.H. at Michigan. I continue to research policy/politics, e.g. on the relationship between health and voting. I also teach a biostatistics course at the University of Michigan.

What you have the most trepidation about: Whether or not my skill set will add value or just get in the way... But there might be a health policy angle in here somewhere.

ressy commented 4 years ago
nafisajadavji commented 4 years ago

Your name: Nafisa Jadavji Your job other than this review: Assistant Professor at Midwestern University, where I teach, and run a research lab. Most recently, I have also taken on the job of being a home school teacher to a 6th grader. What you hope to get out of participating: Learn more about the virus and potential therapies from primary sources and not the news. How you feel best prepared to contribute: I love to read scientific literature. What you have the most trepidation about: My days are packed with added responsibilities, but I am interested in contributing.

raghuyennamalli commented 4 years ago

Your name: Ragothaman M Yennamalli

Your job other than this review: Assistant Professor at SASTRA University, I teach computational biology to UG and PG students.

What you hope to get out of participating: We are currently working on antivirals for SARS-CoV-2 and this would orient me in the right direction as there is an avalanche of information.

How you feel best prepared to contribute: I have knowledge of Virology as I worked with another RNA enveloped virus, Dengue virus. I am also fairly good at reading literature and hope to do my bit towards helping the society.

What you have the most trepidation about: We are under nationwide lockdown until April 14th and there is only so much news I can watch. I have time in hand, but not utilized properly. I need to take my mind off news and concentrate on something that is productive. Like this review paper.

anskelly commented 4 years ago

Your name: Ashwin Skelly

Your job other than this review: MD-PhD student in the Department of Immunology at the University of Pennsylvania

What you hope to get out of participating: I hope to gain a better understanding of the evolution and biology of SARS-CoV-2. I'm especially looking forward to learning more about the host immune response to the virus and how we can leverage this to develop effective therapeutics and vaccines.

How you feel best prepared to contribute: I have a strong background in immunology, particularly relating to host-microbe interactions -- I studied the microbiome for 4 years at Harvard and 2 years at Keio University in Japan. I also have experience writing literature reviews, and would be excited to contribute to the synthesis, drafting, and editing of this manuscript.

What you have the most trepidation about: I don't have much experience in virology, so I'm a little anxious about the learning curve when it comes to reading and succinctly summarizing articles in this area. I've also never written a collaborative-style review like this, but I'm excited to learn a lot and contribute in any way I can! :)

johnbarton commented 4 years ago

Your name: John Barton

Your job other than this review: I'm an Assistant Professor of Physics at the University of Californa, Riverside. My group is computational, and we focus on the development of statistical inference methods and mathematical modeling. Our biological focus is on virus evolution and immunity.

What you hope to get out of participating: I'd like to help consolidate knowledge about SARS-CoV-2 and COVID-19 as it becomes available.

How you feel best prepared to contribute: I experience with Bayesian inference methods and mathematical modeling, as well as some background knowledge in virology and immunology. I might be a good fit for evaluating and summarizing papers that have a computational/inference focus.

What you have the most trepidation about: My knowledge of immunology and virology is mostly in the context of HIV. I'm also juggling childcare with other research and teaching responsibilities, so quick turnaround times may be a challenge.

bphilipson commented 4 years ago

Your name: Ben Philipson Your job other than this review: MD-PhD Student at University of Pennsylvania What you hope to get out of participating: Help disseminate clear and actionable information on COVID-19 How you feel best prepared to contribute: Having recently completed a PhD in Cell and Molecular Biology focusing on CAR T cell biology, I am familiar with writing reviews and interpreting data. I hope that I can combine that experience with my clinical education to contribute actionable recommendations to providers and policy makers. What you have the most trepidation about: Being useless. I am not exactly sure how to contribute effectively using this interface with so many people.

catherinedawn commented 4 years ago

Hi everyone!

Your name: Catherine LeBlanc

Your job other than this review: biochemistry undergrad at Northeastern University; research assistant for the Lewis Lab/Antimicrobial Discovery Center

What you hope to get out of participating: to learn more about COVID-19 and virology overall

How you feel best prepared to contribute: I have had a lot of experience reading scientific literature

What you have the most trepidation about: being one of the youngest (i.e. least experienced) of the group here, I might not be adding much value to the project

rdilley commented 4 years ago

Your name: Robert Dilley Your job other than this review: MD-PhD student at Penn What you hope to get out of participating: Learn more about COVID-19 and provide useful knowledge to the medical and scientific communities. How you feel best prepared to contribute: I recently finished my PhD in cell/molecular biology. I have a particular interest in the treatment of COVID-19 in patients with active comorbid conditions. What you have the most trepidation about: I've never participated in a review like this.

boxiangliu commented 4 years ago

Your name: Boxiang Liu Your job other than this review: I am a senior research scientist at Baidu Research Institute. Prior to that, I completed my PhD training in bioinformatics from Stanford University. What you hope to get out of participating: I would like to learn more about COVID-19 from peers and provide useful knowledge to the community. How you feel best prepared to contribute: As part of my job, I am optimizing RNA vaccines for COVID-19, as well as studying the evolution of COVID-19 using genetic data. I would be keen to review papers on vaccines and genetics of COVID-19. What you have the most trepidation about: I am writing two other papers at the time, so I might be crunched for time.

ajlee21 commented 4 years ago

Your name Alexandra Lee Your job other than this review I am a third year Genomics and Computational Biology PhD student in Casey Greene's lab What you hope to get out of participating To learn more about CoV family and to improve my critical reading skills How you feel best prepared to contribute I have studied viruses (though not specifically CoV) at my previous job. I also had previous coursework studying epidemiological models. I think I could help to peer review basic biology about the virus and contribute sections about the background of the virus. What you have the most trepidation about I have never participated in a review like this before, specifically of this scale so trying to contribute feels a bit daunting.