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!

kyle-dyson commented 4 years ago
jifenli commented 4 years ago

Your name: Jifen Li Your job other than this review: Molecular biologist at James Eberwine lab, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania. What you hope to get out of participating: Learn most recent development on diagnosis and therapeutic aspects for COVID-19. How you feel best prepared to contribute: Hope to get deeper understanding on the mechanism of virus infection and provide insight into targeting therapy by using my expertise. What you have the most trepidation about: Lots of literature are generated and published in a very short time, I am worried about the quality of data. Some may need to repeat and verified.

trking10 commented 4 years ago

- Your Name: Tiffany King

- Your job other than this review: I am a Postdoctoral Researcher at the University of Pennsylvania Perelman School of Medicine.

- What you hope to get out of participating: I hope stay current on the latest data around the biology, spread, and countermeasures of SARS-CoV-2. I want to learn as much as I can, while becoming an active participant in the dissemination of data-driven information to the public and research community.

- How you feel best prepared to contribute: I am most interested in distinct immune responses to COVID-19 (what has driven recovery, and methods to quell such robust responses if needed, as in the case of cytokine release syndrome observed in some patients). My experience in the field of cellular immunotherapy will be beneficial in understanding the literature around COVID-19 immune response.

- What you have the most trepidation about: This will be my first experience writing a review with such a massive group of collaborators, and I am unsure of how I can make a significant impact. With all of the literature coming out daily, staying on top of the data and trends also seems daunting.

rnguin commented 4 years ago

Hello everyone! Your Name: Rohini Guin Your job other than this review: I am currently an undergraduate studying Biology and Chemistry at Emory University. What you hope to get out of participating: I hope to understand the multiple strategies used to address the SARS-CoV-2 outbreak. I am also excited to contribute in a meaningful way within my own capacity and collaborate with so manyI want to learn as much as I can, while becoming an active participant in the dissemination of data-driven information to the public and research community. How you feel best prepared to contribute: My current research focuses on cancer immunotherapy and vaccine design to generate immunogenic responses in preclinical models. I hope to apply this knowledge to assess some of the literature surrounding ACE2/spike protein interactions. I also have worked on a drug repurposing literature review project for identifying potent, safe, and affordable treatments for other diseases lacking robust options. Given the rapid spread of COVID-19, I hope to evaluate the efficacy of repurposed drug candidates to better identify promising new therapies. I am also interested in the public health and policy implementation aspects that can help to mitigate pandemics from a top-down approach and evaluating those measures. What you have the most trepidation about: I worry most about keeping up with the rapid changes and growing body of literature. I also worry if I will be able to contribute in a meaningful way to this review given my lack of experience and age. I am new to GitHub and have a steep learning curve there as well.

grevetjd commented 4 years ago

Your name: Jeremy Grevet Your job other than this review: MD/PhD student graduating in May, starting as a resident in Internal Medicine at MGH this summer. What you hope to get out of participating: I hope to learn about progress on diagnostics and therapeutics, stay current with the literature, and be an active participant in this review. How you feel best prepared to contribute: able to evaluate science and medical literature, interested in learning more about ongoing strategies for antivirals and progress on vaccine development. What you have the most trepidation about: this is a little outside the fields I've trained but really interested in learning more about virology and immunology, being able to stay on top of literature.

ldbruce-2018 commented 4 years ago

Your name: Liana Bruce, PhD, MSPH Your job other than this review: Senior Insights Analyst at Blue Cross and Blue Shield of NC, Visiting Professor of Health Sciences at Campbell University Lundy-Fetterman School of Business, Editor In Chief of Patient Related Outcome Measures (Dove Medical Press, part of Taylor & Francis Group) What you hope to get out of participating: I hope to contribute epidemiology analytic & research synthesis to the project. How you feel best prepared to contribute: Able to help evaluate the quality of research published, and suggest reporting standards What you have the most trepidation about: New to Github

SiminaB commented 4 years ago

Folks - Please join us on https://gitter.im/covid19-review/community if you're not on already! It's an easy way to chat with folks involved in the project, ask for help on pull requests etc. About half of the folks here are on there.

esell17 commented 4 years ago

Your name: Elizabeth (Ellie) Sell

Your job other than this review: MD student at the University of Pennsylvania

What you hope to get out of participating: I hope to gain a better understanding of SARS-CoV-2, especially with regard to its affect on the olfactory epithelium resulting in anosmia.

How you feel best prepared to contribute: I have some background in the study of olfaction and chemoreception sciences -- I studied chemistry for 4 years at Princeton and have been involved with the Smell and Taste Center in the department of Otorhinolaryngology at Penn since starting medical school. I also have some experience contributing to literature reviews, and would be excited to contribute to a section of this that covers the unusual effects of this virus on smell and taste.

What you have the most trepidation about: I don't have much experience in immunology or virology, but I think I can make a focused contribution to a specific aspect of the SARS-CoV-2 literature that should not be overlooked. I've also never written a collaborative-style review like this, but I'm excited to learn!

dziakj1 commented 4 years ago

Your name: John J. Dziak

Your job other than this review: Research Associate Professor, Penn State

What you hope to get out of participating: I hope to help out with this very worthy project. I don't know if it would involve adding to the text or just helping in some other way.

How you feel best prepared to contribute: I can help read and take notes about articles.

What you have the most trepidation about: I am limited in time available and in expertise because I am not really trained in biology or medicine.

b-akshay commented 4 years ago

Your name: Akshay Balsubramani

Your job other than this review: Postdoctoral researcher at Stanford (Kundaje lab).

What you hope to get out of participating: Learn about the larger therapeutic picture behind COVID, and augment my knowledge of the biology as the project evolves.

How you feel best prepared to contribute: I can help screen/distill the inflow of genomics papers attempting to understand how the virus disrupts regulation. I can also help drafting portions of the manuscript.

What you have the most trepidation about: Very limited bandwidth for this (only ~weekly), and my first time on a self-organized project of this kind!

jinhui2 commented 4 years ago

Your name: Jinhui Wang Your job other than this review: Research Specialist in Eberwine lab, University of Penn What you hope to get out of participating: I want to learn the various diagnosis and therapeutic methods for COVID-19. How you feel best prepared to contribute: I have particular interest in the therapeutic effect of hydroxychloroquine and other drugs, and hope to contribute on this aspect. What you have the most trepidation about: time is limited

likhithakolla commented 4 years ago

Your name: Likhitha Kolla

Your job other than this review: MD/PhD Student at the University of Pennsylvania. I am currently in the Genomics and Computational Biology program.

What you hope to get out of participating: I am looking forward to working with an interdisciplinary team to learn about the quickly evolving biomedical, biosocial, and bioethical efforts to assuage this pandemic. In doing so, I will hone my writing skills as well as my ability to report on results of similar studies with potentially differing results. How you feel best prepared to contribute: My background is in computational biology and medicine. I can contribute to data analyses, literature summaries of computational biology papers, including those on disease modeling and viral genomics, and the process of writing/editing the review.

What you have the most trepidation about: Although I have formal educational training in the fundamentals of Immunology and Virology, I am not yet fluent in these subjects.

yemarshall commented 4 years ago

Your name: Yael Evelyn Marshall Your job other than this review: recently completed PhD, researcher (currently just continuing a bit of the projects from my Princeton doctoral research), & also long-time-intermittent-part-time-proofreading-and-formatting-for-educational-books-and-research-articles-and-dissertations; PhD on computational models of malaria control and drug resistance in populations, also participated and assisted in group Ebola epidemic data analysis project, science background MIT B.Sc. Chemistry, B.Sc. Physics, Princeton PhD Biology. What you hope to get out of participating: contribute some writing (or at least reading material or suggestions) to a review which can be used by researchers and scientists developing tools against this disease & epidemic. How you feel best prepared to contribute: since I have a varied science (& computational) background, then I will contribute writing or suggestions for whatever types of research & technical materials I have the preparation to understand and communicate. What you have the most trepidation about: I will just see what I can contribute based on my scientific (& computational) background & if I have small questions along the way then I will ask.

adebali commented 4 years ago

Your name: Ogun Adebali

Your job other than this review: I am a PI mentoring undergrad and graduate students in my computational genomics group at Sabanci University. I work on the molecular evolution of eukaryotic signal transduction, genome-wide DNA damage and repair analysis.

What you hope to get out of participating: I am interested in analyzing the evolution of this virus. Since I have been learning, it would be nice to document them, contribute to the understanding of the virus and computational techniques and serve to the public.

How you feel best prepared to contribute: I believe I can summarize the recent NGS-based literature as well as my understanding of how to analyze genomic datasets associated with the virus and patients.

What you have the most trepidation about: I am nervous about prioritizing the massive amount of papers related to the subject.

qiyanjun commented 4 years ago

Your name: Yanjun Qi Your job other than this review: Associate Prof @ UVA, Computer Science, Machine Learning, Bioinformatics 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 data analysis and text mining of COVID-19. What you have the most trepidation about: Thanks for leading and I am interested to see how this goes.

davemai commented 4 years ago

Your name: David Mai Your job other than this review: Bioengineering PhD student What you hope to get out of participating: I think the manubot platform is pretty cool, so hoping to explore it a bit and contribute and review some text. How you feel best prepared to contribute: Reading papers and synthesizing, and offer on technological developments, particularly diagnostics. What you have the most trepidation about: Mostly excited to see how this goes!

ypar commented 4 years ago

Your name: YoSon Park Your job other than this review: Postdoc, Greenelab, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania. My current research primarily focuses on large-scale -omics analyses for disease mechanism studies and in silico drug target discoveries using public data. What you hope to get out of participating: I am thrilled to learn about how this massively multi-author online review paper will evolve. How you feel best prepared to contribute: I have studied microbiology and immunology and got a doctorate in statistical and computational genetics. I am no expert but can contribute to evaluating some relevant aspects in this review. What you have the most trepidation about: This is my first crowd-sourced, online review. I am excited and nervous.

shiktadas commented 4 years ago

Your name: Shikta Das Your job other than this review: Honorary lecturer, data scientist What you hope to get out of participating: I have expertise in epidemiology and systematic review and would like to contribute to a noble cause. Also, learn in the meanwhile. How you feel best prepared to contribute: I have an MSc in Epidemiology (covering infectious disease) and a Phd in Epidemiology with several years of post-doc experience. What you have the most trepidation about: That I can be useful!!!

michaelmhoffman commented 4 years ago
bethanyd1 commented 4 years ago

Your name- Bethany Dus Your job other than this review- MD student at the University of Pennsylvania What you hope to get out of participating- I’m hoping to gain a deeper understanding of SARS-CoV-2, as well as understanding treatment options. How you feel best prepared to contribute- I worked on a literature review as part of my MSc Public Health. What you have the most trepidation about- I’ve never worked on a collaborative review on a platform like this, but I’m excited to contribute!

byrdjb commented 4 years ago

Your name- J. Brian Byrd Your job other than this review- hypertension researcher, with an interest in extracellular vesicles What you hope to get out of participating- annotate some of the weaker claims about putative effects of antihypertensive drugs in COVID-19 How you feel best prepared to contribute- I feel best prepared to summarize the strengths and weaknesses of some of the treatment papers What you have the most trepidation about- Trepidation isn't a word that comes to mind. Glad to be here.

tuncadogan commented 4 years ago

Your name: Tunca Dogan

Your job other than this review: Scientist, faculty member at the Institute of Informatics / Dept. of CS at Hacettepe University, Turkey. I work on biological data science and development of predictive models in bioinformatics and cheminformatics.

What you hope to get out of participating: I am interested in computational approaches to identify potential long-term molecular solutions to COVID-19, other than the fast-track drug repurposing. I believe one of the best ways to learn on a subject is participating in a collaborative effort like this one.

How you feel best prepared to contribute: I can summarise computational studies for predictive approaches on SARS-CoV-2 mechanisms and on potential novel treatments.

What you have the most trepidation about: The great void...

fmughal commented 4 years ago
vsharma1 commented 4 years ago

Thanks Casey for the great initiative!

• Vishakha Sharma • I am a Principal Data Scientist in Diagnostics Division at Roche. • Excited to be part of this timely COVID review. • I am Computer Scientist by training with focus on Machine Learning, NLP and Computer Vision. I serve in numerous Program Committees and can summarize findings and methods from literature to include in this review. • Staying on top of research.

davidmanheim commented 4 years ago

Your name: David Manheim

Your job other than this review: I have a PhD in public policy and decision theory, with a large part of my dissertation involving infectious disease modeling and biosurveillance. I now work with Oxford's Future of Humanity Institute on policy and mitigation of large scale risks, mostly considering pandemic events. I'm also currently involved in a number of projects on COVID-19, including several that are trying to better understand testing and how it can scale. I'm also doing a part-time postdoc at University of Haifa in their Health and Risk Communication Research Center.

How you feel best prepared to contribute: I'm primarily working on the section on testing methods. (I'm also happy to help with anything related to public policy or bio-surveillance that comes up.)

What you have the most trepidation about: My limited (i.e. nonexistent) academic preparation related to molecular virology / never actually having worked in a lab. (I've been working on understanding microbiology better as a side project for the past 3 years, but I'm nowhere near as competent as most of this group.)

bansalvi commented 4 years ago

Your name: Vikas Bansal Your job other than this review: I recently (2019) accepted a group leader offer for Biomedical Data Science & Machine Learning research group at the German Center for Neurodegenerative Diseases, Tuebingen, Germany. What you hope to get out of participating: I would like to learn more about COVID-19. Also, would learn online collab and Manubot. How you feel best prepared to contribute: We have a paper under review related to COVID-19 https://www.biorxiv.org/content/10.1101/2020.05.08.084806v2 While preparing the manuscript, I reviewed many papers related to COVID-19. What you have the most trepidation about: I may criticise some papers/journals. Seems like some studies were published in rush and may have compromised quality of research.

mzamanian commented 4 years ago

Your name: Mostafa Zamanian

Your job other than this review: Assistant Professor, University of Wisconsin-Madison. My research lab is mainly focused on neglected infectious diseases caused by parasites.

What you hope to get out of participating: To help clarify the state of new and historical literature on antiparasitics repurposed as antivirals, and to support this mode of community review writing.

How you feel best prepared to contribute: My research program is largely focused on antiparasitics. Many antiparasitics, including anthelmintics, have been forwarded as potential COVID-19 treatments. I'd be happy to contribute by evaluating the strength of recent claims about the antiviral properties of these drugs and squaring these claims with pharmacological considerations.

What you have the most trepidation about: Learning Manubot - though I'm hopeful the learning curve isn't very steep.

scapone01 commented 4 years ago

Your name: Stephen Capone Your job other than this review: Third Year Medical Student in Brooklyn, NY What you hope to get out of participating: To help provide clinical context from the epicenter of the COVID pandemic and to help facilitate the quick and accurate sharing of information. How you feel best prepared to contribute: Have a current COVID paper under review, can provide clinical context and have time to help edit and revise the paper. What you have the most trepidation about: Brand new to Github, so navigating the software is all new to me.

Sergey-Knyazev commented 4 years ago

Your name: Sergey Knyazev Your job other than this review: Computer Science PhD candidate at Georgia State University. Next year I am joining Dr. Mangul lab at USC. I am working on NGS data analysis for viral studies. What you hope to get out of participating: I want to highlight the benefits of SARS-CoV-2 genome data analysis for public health, summarize the successful practices of SARS-CoV-2 outbreak investigations, and discuss the challenges and limitations that one can meet during the genome analysis. How you feel best prepared to contribute: Have papers published about viral genome analysis, benchmarks, and outbreak investigations using genome data. I will read and summarize articles about the usage of genome data for the SARS-CoV-2 outbreak response. What you have the most trepidation about: It will be hard to summarize the whole scope of information about using SARS-CoV-2 genomes because of the big number of recently published researches of different quality.

jharenza commented 3 years ago
LSH2126 commented 3 years ago

Your name: Lamonica Shinholster

Your job other than this review: Biology student at Mercer University; research assistant.

What you hope to get out of participating: additional experience with scientific collaboration.

How you feel best prepared to contribute: literary review, writing/editing.

What you have the most trepidation about: Consolidating a vast amount of information about COVID-19 from multiple sources.

tlukan commented 3 years ago

Your name: Temitayo Lukan

Your job other than this review: Psychology/pre-med student at the University of Pennsylvania

What you hope to get out of participating: more experience with literature, academic writing, and collaborating research

How you feel best prepared to contribute: writing portions of literature review and health disparities

What you have the most trepidation about: being able to produce solid work on the literature review; consolidating information about covid-19

smangul1 commented 3 years ago

Your name: Serghei Mangul Your job other than this review: Assistant Professor of Clinical Pharmacy and Biological Sciences, Titus Department of Clinical Pharmacy, USC School of Pharmacy, The Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California What you hope to get out of participating: Together with Sergey Knyazev, we would like to highlight the benefits of SARS-CoV-2 genome data analysis for public health, summarize the successful practices of SARS-CoV-2 outbreak investigations, and discuss the challenges and limitations that one can meet during the genome analysis. How you feel best prepared to contribute: Both I and Sergey Knyazev have papers published about viral genome analysis, benchmarks, and outbreak investigations using genome data. I will read and summarize articles about the usage of genome data for the SARS-CoV-2 outbreak response. What you have the most trepidation about: It will be hard to summarize the whole scope of information about using SARS-CoV-2 genomes because of the big number of recently published researches of different quality.

SystemsResearch commented 3 years ago
athril commented 3 years ago
ipsitak commented 3 years ago

Your name: Ipsita Krishnan Your job other than this review: I work in Public Health Practice at NYU’s School of Global Public Health What you hope to get out of participating: Happy to help on this timely and important work How you feel best prepared to contribute: I have an MPH in applied global epidemiology and feel confident in looking into the public health relevant sections What you have the most trepidation about: I have limited knowledge on the pathophysiology and pharmacology aspects of the project

lubianat commented 3 years ago

Your name: Tiago Lubiana Your job other than this review: PhD candidate in Bioinformatics at the University of São Paulo What you hope to get out of participating: I'm quite interested in the process of collaborative scholarly manuscripts. I am mostly interested in understanding better how to do an open collaborative review. How you feel best prepared to contribute: I've been busy with Wikiproject COVID-19 earlier this year, and I`m a biomedical scientist by training. I feel confident in looking at molecular mechanisms and fact-checking claims. What you have the most trepidation about: I'm late to help as much as I would like. I hope I can still contribute somehow.

rando2 commented 3 years ago

Welcome @lubianat! We are wrapping up our first checkpoint over the next week, but we are planning to keep making new versions until the crisis reaches some sort of stable point (so we'll probably be going for a while, sadly). We'd be delighted to have you onboard and you're actually joining at the perfect time! I'm also really glad to know about the Wikiproject!

SabrinaSawhney commented 3 years ago

Hello everyone! My name is Sabrina Sawhney I’m a research assistant at the survivorship institute at Georgetown Lombardi Comprehensive Cancer Center. I hope to learn more about the far-reaching consequences of COVID. I feel best prepared to contribute with writing and summarizing literature since I have experience in that with other research and classes. I have the most trepidation about using GitHub and coding since this is my first time doing something like this.

NAIKA86 commented 3 years ago

Your name: Amruta Naik Your job other than this review: When I'm not doing this, I work on the circadian biology of lung repair and regeneration by developing 3d lung organoids. What you hope to get out of participating: Our research group has found that outcomes of influenza infection are dependant on the time of day infection and this can be applied to many other types of infections including bacteria. It would be cool to know if it holds true for COVID from an infection and vaccination perspective. How you feel best prepared to contribute: I have contributed to a published article in JBR that summarizes the role of the circadian clock in infections and how to tackle COVID, so would be interested in contributing on vaccine development and circadian biology. What you have the most trepidation about: I am late to the party but excited to learn and contribute as much as I could.

aimundo commented 2 years ago

Your name: Ariel Mundo Your job other than this review: PhD candidate in Biomedical Engineering at the University of Arkansas What you hope to get out of participating: collaborative manuscripts are something new to me, and I know I am joining the party a little (very) late, but I would like to get on-hands experience with large-scale projects like this on GitHub. How you feel best prepared to contribute: I feel confident about doing literature searches about relevant topics and collaborating on checking information. What you have the most trepidation about: Large-scale projects in GitHub are something new to me, but I am also looking forward to learn more about the biology and pathogenesis of COVID-19 as it keeps changing.

rando2 commented 2 years ago

Welcome @aimundo! We are able to submit updates to the papers that are already published (they are living reviews) so please feel free to hop in wherever you are interested! Also, let me know if you need any help or guidance -- the gitter chat is a particularly good way to chat informally with other contributors!

jessegmeyerlab commented 2 years ago

Your name: Jesse Meyer Your job other than this review: Assistant Professor at Medical College of Wisconsin in Milwaukee What you hope to get out of participating: learn the strengths and weaknesses of the manubot platform for collaborative publishing, contribute useful information to this summary of knowledge How you feel best prepared to contribute: looks like the diagnostics section is missing a couple sections I can add What you have the most trepidation about: many unknowns about this process, but excited to learn and contribute