ISCB COVID-19 Paper Collections

Here you will find links to collections dedicated to COVID-19 and Sars-Cov-2 from major publishers and scientific societies.

Publishers

Cambridge University Press
https://www.cambridge.org/de/academic/covid-19-resources-and-information

Elsevier
https://www.elsevier.com/connect/coronavirus-information-center

Frontiers
https://coronavirus.frontiersin.org/

Hindawi
https://www.hindawi.com/covid-19-collection/

JAMA
https://jamanetwork.com/journals/jama/pages/coronavirus-alert

Lancet
https://www.thelancet.com/coronavirus

New England Journal of Medicine
https://www.nejm.org/coronavirus

Oxford University Press
https://global.oup.com/about/covid19?cc=de

PNAS
https://www.pnas.org/page/coronavirus

Public Library of Science
https://plos.org/covid-19/

Science AAAS
https://www.sciencemag.org/tags/coronavirus

SpringerNature
https://www.springernature.com/gp/researchers/campaigns/coronavirus

Wiley
https://novel-coronavirus.onlinelibrary.wiley.com/

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Scientific Societies

American Chemical Society
https://www.acs.org/content/acs/en/covid-19.html

American Medical Association
https://jamanetwork.com/journals/jama/pages/coronavirus-alert

American Medical Informatics Association
https://www.amia.org/COVID19

American Society for the Advancement of Science
https://www.sciencemag.org/tags/coronavirus

American Society of Human Genetics
https://www.ashg.org/ashg-information-for-the-community-covid-19/

Royal Society, London
https://royalsociety.org/news/2020/03/coronavirus-covid-19/

World Health Organization
https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov

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ISCB COVID-19 Section

The COVID-19 pandemic is both severely affecting our lives and impacting our science. ISCB responds to the respective challenges by offering its expertise to the scientific community and empowering scientific networking. The ISCB COVID-19 Section offers four lines of this initiative:

ISCB COVID-19 Statements. Here you find statements on the ongoing pandemic that have been issued by ISCB.
ISCB COVID-19 Webinar collection. Here you find webinars specific to the topics of COVID-19 and Sars Cov-2 that are organized by ISCB.
ISCB COVID-19 Science collection. Here you find materials specific to the topics of COVID-19 and Sars Cov-2 that have been submitted by ISCB members. This collection has three subsections for (i) scientific articles, (ii) scientific data sets and, (iii) proposals of community science projects.
ISCB Tutorial collection. Here you find tutorials that present basic or advanced computational biology content for biologists and computational biologists in these times of increased digital education activity. The tutorials have been (i) presented at recent ISCB conferences and (ii) suggested by ISCB members.

Call for submissions

If you are a member of ISCB we encourage you to submit entries to the Science collection and Tutorial collection. Your submission entails a pointer to the science content, a short description of background or purpose (two lines) and lists your name as submitter. Submission will be subjected to a basic check of scope and purpose.

You find the relevant submission forms here.

ISCB COVID-19 Webinar Collection

The ISCB COVID-19 webinar collection points to webinars on ongoing research on COVID-19 and Sars-Cov2. The webianrs are split into two lists

A list of recent ISCBacademy COVID-19 webinars
A list of presentations given at ISMB 2020

ISCBacademy Covid-19 Webinars

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
By Nevan Krogan

May 19, 2020

Efforts to develop antiviral drugs versus COVID-19 or vaccines for its prevention have been hampered by limited knowledge of the molecular details of SARS-CoV-2 infection. This webinar will describe our efforts to address this challenge by expressing 26 of the 29 SARS-CoV-2 proteins in human cells and identifying the human proteins physically associated with each using affinity-purification mass spectrometry. Among 332 high-confidence SARS-CoV-2-human protein-protein interactions, we identified 66 druggable human proteins or host factors targeted by 69 compounds (29 FDA-approved drugs, 12 drugs in clinical trials, and 28 preclinical compounds). Within a subset of these, multiple viral assays identified two sets of pharmacological agents that displayed antiviral activity.

Click here to watch

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At Home with Covid-19
By Brian Shoichet

June 26, 2020

The urgency of the coronavirus pandemic has motivated investigators world wide to seek approved drugs or investigation new drugs as a way to rapidly advance therapeutics into clinical trials to treat the disease. I will describe a large collaboration, hosted by the UCSF Quantitative Biology Institute, to do that in a mechanistically focused way. Using AP-MS, a host-pathogen network of viral and human proteins was created, and drugs were sought targeting the human partner. From among 322 high confidence human proteins associated with 26 viral proteins emerged 63 that were druggable. Against those, 69 drugs were tested for efficacy, and from these 10 drugs in two broad classes emerged: those targeting protein biogenesis, and those acting against the Sigma1 and Sigma2 receptors. The activities of these drugs, and the chemoinformatics infrastructure that supported their selection, will be discussed. The mechanism-based repurposing strategy will be compared to a complementary effort that targets viral proteins and seeks novel chemical matter, using structure-based ultra-large library docking.

Click here to watch

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Global surveillance of COVID-19 by mining news media using a multi-source dynamic embedded topic model
By Yue Li and David Buckeridge

June 30, 2020

As the COVID-19 pandemic continues to unfold, understanding the global impact of non-pharmacological interventions (NPI) is important for formulating effective intervention strategies, particularly as many countries prepare for future waves. We used a machine learning approach to distill latent topics related to NPI from large-scale international news media. We hypothesize that these topics are informative about the timing and nature of implemented NPI, dependent on the source of the information (e.g., local news versus official government announcements) and the target countries. Given a set of latent topics associated with NPI (e.g., self-quarantine, social distancing, online education, etc), we assume that countries and media sources have different prior distributions over these topics, which are sampled to generate the news articles. To model the source-specific topic priors, we developed a semi-supervised, multi-source, dynamic, embedded topic model. Our model is able to simultaneously infer latent topics and learn a linear classifier to predict NPI labels using the topic mixtures as input for each news article. To learn these models, we developed an efficient end-to-end amortized variational inference algorithm. We applied our models to news data collected and labelled by the World Health Organization (WHO) and the Global Public Health Intelligence Network (GPHIN). Through comprehensive experiments, we observed superior topic quality and intervention prediction accuracy, compared to the baseline embedded topic models, which ignore information on media source and intervention labels. The inferred latent topics reveal distinct policies and media framing in different countries and media sources, and also characterize reaction COVID-19 and NPI in a semantically meaningful manner.

Click here to watch

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Evolutionary origins of SARS-CoV-2 and tracking its spread using phylodynamic data integration
By Philippe Lemey

October 2, 2020 at 11:00AM EDT!

There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination, and its time of divergence from animal viruses. I will describe a collaborative effort to reconstruct the origins of the virus. Our findings indicate that sarbecoviruses – the viral subgenus containing SARS-CoV and SARS-CoV-2 – undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. Contrary to other analyses, we find that SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses, not one acquired recently via recombination. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir indicates that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.

Following the emergence of the virus, unprecedented sequencing efforts have resulted in the accumulation of over 100,000 genome sequences sampled globally. Despite this rich source of information, evolutionary reconstructions are hindered by the slow accumulation of sequence divergence over its relatively short transmission history and the spatiotemporal bias in genome sequence sampling. I will describe a data phylodynamic data integration approach in a Bayesian framework to tries to address these issues in order to assist molecular epidemiological analyses.

Click here to register

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ISMB 2020 COVID-19 Related Presentations

Links within this section: COVID-19 Session | Other ISMB tracks

COVID-19 Session
Title	Presenter
Tools, Workflows and Infrastructure for Open and Reproducible Analysis of SARS-CoV-2 Data	Björn Grüning
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19	Brian Le
Viruses, Visualization, and Validation: Interactive mining of COVID-19 literature	Varun Mittal
CoV-AbDab: the Coronavirus Antibody Database	Matthew Raybould
Differentially conserved amino acid positions reflect differences in SARS-CoV-2 and SARS-CoV behaviour	Jake McGreig
Characterization of SARS-CoV-2 viral diversity within and across hosts	Palash Sashittal
Real-time tracking of SARS-CoV-2 spread and evolution	Richard Neher

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Other ISMB Tracks
Title - Track	Presenter
POCOVID-Net: Automatic Detection of COVID-19 From a New Lung Ultrasound Imaging Dataset (POCUS) - TransMed	Jannis Born
SST02-VIII: Gamers and experimentalists collaborate on COVID-19 - Special Sessions	Firas Khatib
SST02-IX: Crowdsourced design of stabilized COVID-19 mRNA vaccines with Eterna OpenVaccine - Special Sessions	Rhiju Das
SST01-XIII: Single-cell transcriptomic analysis of SARS-CoV-2 reactive CD4+ T cells - Special Sessions	Benjamin Meckiff

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ISCB COVID-19 Tutorial Collection

Below is a list of tutorials on general computational biology issues for use by computational biologists and bench scienists in this time of added digital education activities. The are two lists;

A list of tutorials presented at recent ISMB meetings
A list of tutorials submitted by ISCB members.

Tutorials and Special Sessions Presented at Recent ISMB Meetings

Session Title	Session Details
Recent Advances in Statistical Methods and Computational Algorithms for Single-Cell Omics Analysis	ISMB/ECCB 2019 Tutorial AM2
A Practical Introduction to Reproducible Computational Workflows	ISMB/ECCB 2019 Tutorial AM4
Biomarker discovery and machine learning in large pharmacogenomics datasets - Part 2	ISMB/ECCB 2019 Tutorial PM5
Single cell RNA-seq toolkit - Part 4	ISMB 2018 Tutorial AM1
Integrated network analysis: Cytoscape automation using R and Python	ISMB 2018 Tutorial AM3
Computational methods for comparative regulatory genomics	ISMB 2018 Tutorial AM4
Ontologies in computational biology - Part 4	ISMB 2018 Tutorial PM8
Text Mining for Biology and Healthcare	IMSB/ECCB 2019 Special Session 01
Omics Data Formats, Compression and Storage: Present and Future - Part 2D	ISMB/ECCB 2019 Special Session 05
3D Genomics: Computational approaches for analyzing the role of three-dimensional chromatin organization in gene regulation - Part 2	ISMB 2018 Special Session 01
Omics Data Compression and Storage: Present and Future - Part 4	ISMB 2018 Special Session 03
SCANGEN: Single-cell cancer genomics - Part 3	ISMB 2018 Special Session 05

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Tutorials Submitted by ISCB Members

To submit a tutorial to be added to the collection use the submission form.

Tutorial Title	Suggested By
Description and Reason for Suggesting
Bioinformatics for Benched Biologists	Lior Pachter
This workshop demonstrates an analysis of a single-cell RNA-seq dataset starting from the reads. It was designed for an online 1-2 hour Zoom workshop and uses a python notebook that runs in about 30 minutes on Google Colab.
Bioinformatics for Benched Biologists II (R Edition)	Lior Pachter
This workshop demonstrates an analysis of a single-cell RNA-seq dataset starting from the reads. It was designed for an online 1-2 hour Zoom workshop and uses an R notebook that runs on Google Colab.
GPU-Accelerated Single-Cell Analysis with RAPIDS	Avantika Lal
This tutorial demonstrates how to accelerate single-cell RNA-seq analysis using GPUs (Graphics Processing Units). RAPIDS, a free and open-source software suite for GPU-accelerated data science, is used to perform preprocessing, clustering, visualization and differential expression analysis of single cells, 5-100x faster than on CPUs. A demonstration is provided in the form of a Jupyter notebook. Single-cell RNA-seq is essential for Covid-19 research, e.g. identifying susceptible cells. Analysis requires speed and interactivity but tools are slow. This GPU pipeline performs scRNA-seq analysis 4-90 times faster than standard tools.
A Practical Introduction to Reproducible Computational Workflows	Peter W. Rose
This hands-on tutorial teaches participants the key requirements and practical skills to setup a reproducible and reusable computational research environment. The tutorial is intended for Python users and anyone interested in using Jupyter Notebooks. We also cover collaborative development practices. After working through this tutorial, participants should be able to set up their own projects by applying the principles and techniques learned and publish reproducible research protocols. Computational notebooks offer new opportunities to communicate computational analyses. This tutorial presents step-by-step instructions following our: "Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks" paper.

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ISCB COVID-19 Collection Submission Forms

ISCB COVID-19 Science Collection

To submit a scientific article to the ISCB COVID-19 science collection use this form.
To submit a scientific data set to the ISCB COVID-19 science collection use this form.
To propose a community science project to the ISCB COVID-19 science collection use this form or submit a proposal to This email address is being protected from spambots. You need JavaScript enabled to view it.

ISCB COVID-19 Tutorial Collection

To submit a tutorial to the ISCB COVID-19 tutorial collection use this form.

ISCB COVID-19 Statements

Notice of ISCB Official Statements

ISCB would like to stress that personal statements made and opinions held by its members on the COVID-19 pandemic origins, course, and consequences are not official statements of ISCB. Official ISCB statements may be found within the Society Announcements or Policies and Statements sections of the website - www.iscb.org. ISCB considers the pandemic a still growing serious global threat to human health that is currently poorly understood. The Society encourages abiding by the continued strong preventive measures and recommends that people follow the advice given by their country's public official directives. ISCB encourages tolerance and believes that it is not helpful to hold any population or individuals accountable for the appearance or progression of the epidemic and urges members to refrain from making any statements in this regard. The Society urges facilitating intensive research on the virus and its associated disease, targeted at prevention and cure, by openly sharing the relevant samples, data, and results globally.

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ISCB Press Release on COVID-19 impact on ISMB2020, March 18, 2020

ISCB leadership continues to closely monitor the spread of the coronavirus disease (COVID-19) and to assess the impact on our annual meeting ISMB 2020. Given the current situation we are assessing multiple possibilities including postponement or holding a virtual conference. We appreciate the patience of our community as we work to come to a decision. We will provide an update to the community on ISMB plans no later than April 9th.

We encourage participants to register. In the event we have to cancel the conference, we will refund all registration fees. If you are planning to book air travel, we recommend that you hold off on booking until a later date, book a refundable ticket, or book a ticket with insurance that covers the cancellation of the event. Most hotel reservations may be canceled up to 72 hours prior to arrival.

For those who have already been accepted or invited to present at ISMB 2020, ISCB is committed to providing you with a platform to present your research. For those considering to submit an abstract or poster, we encourage you to still submit. This will enable ISCB and our communities of special interest (COSI) track leaders to track interest and plan their programs.

ISCB knows how important it is to deliver timely information. Again, we ask for your patience to allow leadership the time to meet and discuss. We will provide an update to the community no later than April 9th.

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We can all do our part to prevent the spread of COVID-19.

Here are some simple yet highly effective tips for guarding against this virus and others like it, that you can apply at home, at work, and at the conference:

Wash your hands often with water and soap for at least 20 seconds (including between fingers, both palms, thumbs, and fingertips).
Cough or sneeze into a tissue or into your elbow. (Discard tissues in closed containers.)
Do not touch your face or ears.
Clean shared surfaces and items
If you are ill, stay home and limit contact with others.

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ISCB COVID-19 Science Collection

The ISCB COVID-19 science collection points to articles on ongoing research on COVID-19 and Sars-Cov2. The scientific papers in this list have been submitted by ISCB members to share with the community at large. Paper links are annotated with a short statement of background or purpose. Submissions have been subjected to basic scope-related filtering, no further assessment has been performed. This section has the following subsections;

Scientific Articles

Biomarkers/Host Genetics
Epidemiology
Evolution
Gene Expression
Immunology
Molecular Function
Molecular Structure

Scientific Data Sets
Proposals of Community Science Projects

Scientific Articles (41 articles)

Biomarkers/Host Genetics Subsection (5 articles) To submit a paper to be added to the collection use the submission form.
Article Title	Publication
Authors	Suggested By
Reason for suggesting
1. Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients	Cell - May, 2020
Pierre Bost, Amir Giladi, ...Ido Amit	Thomas Lengauer
Introduces the Viral-Track procedure that globally scans unmapped single-cell RNA sequencing data for the presence of viral RNA. Applying Viral-Track to bronchoalveloar-lavage samples from severe and mild COVID-19 patients reveals a dramatic impact of the virus on the immune system of severe patients compared to mild cases.
2. COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis	Nature Biotechnology - June, 2020
Robert Lorenz Chua, Soeren Lukassen, ...Roland Eils	Thomas Lengauer
Single-cell analysis of nasopharyngeal and bronchial samples from COVID-19 patients elucidating transcriptional and cellular signaling characteristics associated with severity of the disease and suggesting paths to therapy.
3. Genetic architecture of host proteins involved in SARS-CoV-2 infection	Nature Communications - December, 2020
Pietzner, M., E. Wheeler, ...C. Langenberg	COVID-19 Task Force
This is genetic discovery study of 179 host proteins using an aptamer-based technique. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links and evidence that putative viral interaction partners affect immune response.
4. Genetic mechanisms of critical illness in Covid-19	Nature - December, 2020
Pairo-Castineira, E., S. Clohisey, ...Baillie,J. K.	COVID-19 Task Force
This is a report of the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study (GWAS). The authors identify potential targets for repurposing of licensed medications.
5. Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements	Nucleic Acids Research - December, 2020
Manfredonia, I., C. Nithin, ...D. Incarnato	COVID-19 Task Force
The authors present single-base resolution secondary structure maps of the full SARS-CoV-2 coronavirus genome both in vitro and in living infected cells. Secondary structure-restrained 3D modeling of conserved segments further allows for the identification of putative druggable pockets. In addition, the authors identify conserved single-stranded segments suitable for the development of antisense oligonucleotide therapeutics.

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Epidemiology Subsection (11 articles) To submit a paper to be added to the collection use the submission form.
Article Title	Publication
Authors	Suggested By
Reason for suggesting
1. Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing	Science - May, 2020
Luca Ferretti, Chris Wymant, ...Christophe Fraser	COVID-19 Task Force
A paper from early May 2020 modeling epidemic spread in presence of noninventive protection measures based on contact tracing apps.
2. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period	Science - May, 2020
Stephen M. Kissler, Christine Tedijanto, ...Marc Lipsitch	COVID-19 Task Force
Widely noted early epidemiological model of the Sars-Cov-2/COVID-19 pandemic and effects of possible noninvasive interventions.
3. Inferring change points in the spread of COVID-19 reveals the effectiveness of interventions	Science - July, 2020
Jonas Dehning, Johannes Zierenberg, ...Viola Priesemann	COVID-19 Task Force
Epidemiological model by a German research group from Max Planck Society of the development of the pandemic and effects of noninvasive intervention measures.
4. An interactive web-based dashboard to track COVID-19 in real time	The Lancet - February, 2020
Ensheng Dong, Hongru Du, Lauren Gardner	COVID-19 Task Force
This short paper describes the Website by Johns-Hopkins University that is a major de-facto reference for epidemiological data on the pandemic.
5. Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China	Science - June, 2020
Juanjuan Zhang, Maria Litvinova, ...Hongjie Yu	COVID-19 Task Force
Study of the effectiveness of noninvasive interventions in Hunan province in China based on a transmission model.
6. Effective containment explains subexponential growth in recent confirmed COVID-19 cases in China	Science - May, 2020
Benjamin F. Maier, Dirk Brockmann	COVID-19 Task Force
Retrospective epidemiological study on the effect of noninvasive interventions in China in early 2020.
7. Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe	Nature - June, 2020
Seth Flaxman, Swapnil Mishra, ...Samir Bhatt	Thomas Lengauer
Epidemiological modeling study supporting a very substantial effect of early non-pharmaceutical interventions in several European countries. Based on death counts (collected more evenly between countries) rather than infection counts.
8. Forecasting the Spread of Covid-19 Under Control Scenarios Using LSTM and Dynamic Behavioral Models	Physics and Society - May, 2020
Seid Miad Zandavi, Taha Hossein Rashidi, Fatemeh Vafaee	Fatemeh Vafaee
An AI-based epidemiology model is developed to accurately forecast daily numbers of COVID-19 cases and deaths by simulating the impact of multiple control scenarios, from containment policies to intensive care services and hospitalization facilities.
9. Real-time prediction of COVID-19 spread and intervention assessment	Nature Research - April, 2020
Taha Hossein Rashidi, Siroos Shahriari, ...Fatemeh Vafaee	Fatemeh Vafaee
This study, for the first time, introduced a unified platform which integrates visualization capabilities with advanced time-series statistical methods for predicting the virus spread and effect of containment policies using real-time data.
10. Immunological characteristics govern the transition of COVID-19 to endemicity	Science - January, 2021
Jennie S. Lavine,Ottar N. Bjornstad, Rustom Antia	COVID-19 Task Force
The authors present an epidemiological and immunological model of SARS-Cov-2 that shows that infection-blocking immunity wanes rapidly, but disease-reducing immunity is long-lived. The model suggests that once the endemic phase is reached and primary exposure is in childhood, CoV-2 may be no more virulent than the common cold.
11. Mobility network models of COVID-19 explain inequities and inform reopening	Nature Research - November, 2020
Chang, S., E. Pierson, ...J. Leskovec	COVID-19 Task Force
The authors introduce an epidemiological model that integrates fine-grained, dynamic mobility networks derived from cell phone data to simulate the spread of SARS-CoV-2 in 10 of the largest US metropolitan statistical areas.

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Evolution Subsection (9 articles) To submit a paper to be added to the collection use the submission form.
Article Title	Publication
Authors	Suggested By
Reason for suggesting
1. The proximal origin of SARS-CoV-2	Nature Medicine
Kristian G. Andersen, Andrew Rambaut, ...Robert F. Garry	Thomas Lengauer
This paper analyzes the genome sequences of viruses related to SARS-Cov-2 and forms hypothesies of a (natural) origin of the virus.
2. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2	Infection, Genetics and Evolution - September, 2020
Lucyvan Dorp, Mislav Acman, ...François Balloux	COVID-19 Task Force
Study on the evolution of Sars-Cov-2 after the occurrence of the pandemic. Also provides a web-application for querying viral genome alignments.
3. A Genomic Perspective on the Origin and Emergence of SARS-CoV-2	Cell - April, 2020
Yong-Zhen Zhang, Edward C.Holmes	COVID-19 Task Force
Evolutionary study from China on the emergence of Sars-Cov-2.
4. Genetic Variant of SARS-CoV-2 Isolates in Indonesia: Spike Glycoprotein Gene	Journal of Pure and Applied Microbiology - May, 2020
Arif Nur Muhammad Ansori, Viol Dhea Kharisma, ...Arli Aditya Parikesit	Arli Parikesit
This article shed light about the molecular evolution repertoire of the COVID-19 S gene of Indonesian genetic variant. It was found that there were no significant changes in the genetic compositions, compared with the S gene of the Wuhan strain.
5. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic	Nature Microbiology - July, 2020
Maciej F. Boni, Philippe Lemey, ...David L. Robertson	Thomas Lengauer
The paper offers a refined phylogenetic analysis of corona virus genomes suggesting that the lineage of SARS-Cov-2 has been circulating in bats unnoticed for decades.
6. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2	Infection, Genetics and Evolution - September, 2020
van Dorp, L., M. Acman, ...F. Balloux	COVID-19 Task Force
The authors curated a dataset of 7666 public genome assemblies and analysed the emergence of genomic diversity over time. Our results point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host. The analysis identifies regions of the SARS-CoV-2 genome that have remained largely invariant to date, and others that have already accumulated diversity.
7. Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes	Bioinformatics - June, 2020
Cleemput, S., W. Dumon, ...T. de Oliveira	COVID-19 Task Force
The authors present a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes.
8. Stability of SARS-CoV-2 phylogenies	PLOS Genetics - November, 2020
Turakhia, Y., N. De Maio, ...R. Corbett-Detig	COVID-19 Task Force
The authors provide an approach to detect and remove nonrandom errors in genome sequences originating from idiosyncratic data generation or processing by identifying variants that appear to reoccur many times across a phylogeny and are associated with specific lab groups. They also provide methods for comparisons and visualization of extremely large phylogenies.
9. "Learning the language of viral evolution and escape	Science - January, 2021
Hie, B., E. D. Zhong, ...B. Bryson	COVID-19 Task Force
The authors model viral escape with machine learning algorithms originally developed for human natural language. They identify escape mutations as those that preserve viral infectivity but cause a virus to look different to the immune system, akin to word changes that preserve a sentence’s grammaticality but change its meaning.

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Gene Expression Subsection (3 articles) To submit a paper to be added to the collection use the submission form.
Article Title	Publication
Authors	Suggested By
Reason for suggesting
1. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes	Nature Medicine - April, 2020
Waradon Sungnak, Ni Huang, ...HCA Lung Biological Network	COVID-19 Task Force
An expression analysis of genes associated with viral cell entry using single-cell RNA-sequencing data from multiple tissues of healthy human donors. Coexpression with genes involved with innate immunity has been detected in nasal epithelial cells.
2. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues	Cell - May, 2020
Carly G.K. Ziegler, Samuel J. Allon, ...Kun Zhang	COVID-19 Task Force
Analysis of data from human, nonhuman primate and mouse cells across health and disease to uncover putative targets of Sars-Cov-2 amongst tissue-resident cell subsets. The study suggests that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2 to enhance infection.
3. SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage	Frontiers in Cell and Developmental Biology - August, 2020
Andres Mariano Alonso, Luis Diambra	Luis Diambra
The virus replication requires a lot tRNA resource for the most demanded codons. By integrating genomic, transcriptomic and proteomic data, we a select a list of 27 genes that are affected by this mechanism of epistasis.

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Immunology Subsection (2 articles) To submit a paper to be added to the collection use the submission form.
Article Title	Publication
Authors	Suggested By
Reason for suggesting
1. Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies	Viruses - February, 2020
Syed Faraz Ahmed, Ahmed A. Quadeer, Matthew R. McKay	Syed Ahmed
Provides potential immune targets for a COVID-19 vaccine. It screens the experimentally-determined SARS-derived B cell and T cell epitopes and identifies those which are highly conserved within the available SARS-CoV-2 sequences.
2. SARS-CoV-2-reactive T cells in patients and healthy donors	Nature Reviews Immunology - April, 2020
Luisanna Pia	Mark Borodovsky
It is of interest for computational biologists who attempt to model dynamics of propagation of the coronavirus infection. Particularly, an observation that 34% of SARS-CoV-2 healthy donors carry S-reactive CD4+ T cells reacted to the C-terminal epitopes of SARS-CoV-2 spike glycoprotein S. This observation shows that detailed models of infection transmission should be corrected to account for pre-existing immunity protecting to a certain degree a fraction of population.

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Molecular Function Subsection (6 articles) To submit a paper to be added to the collection use the submission form.
Article Title	Publication
Authors	Suggested By
Reason for suggesting
1. Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins	Viruses - March, 2020
Suhas Srinivasan, Hongzhu Cui, ...Dmitry Korkin	COVID-19 Task Force
Paper from late February 2020 presenting an early structural, functional and network analysis of virus-host interactions.
2. Master Regulator Analysis of the SARS-CoV-2/Human Interactome	Journal of Clinical Medicine - April, 2020
Pietro H. Guzzi, Daniele Mercatelli, ...Federico M. Giorgi	COVID-19 Task Force
Based on the host-virus interaction network by Korkin et al. and data on expression changes upon viral infection master regulator analysis was performed pointing to apoptotic and mitochondrial mechanisms most strongly affected and ACE2 expression being downregulated.
3. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing	Nature - April, 2020
David E. Gordon, Gwendolyn M. Jang, ...Nevan J. Krogan	COVID-19 Task Force
Large study on virus-host interactions and search for putatively effective of certified drugs. Was also the topic of the first COVID-19 seminar organized by ISCB.
4. Decoding SARS-CoV-2 Hijacking of Host Mitochondria in Pathogenesis of COVID-19	American Journal of Physiology: Cell Physiology - July, 2020
Keshav K. Singh, Gyaneshwer Chaubey, ...Prashanth Suravajhala	Jake Chen
Understanding the mechanisms underlying virus communication with host mitochondria can help understand COVID-19 pathologies. Our study suggests SARS-CoV-2 may manipulate mitochondrial function indirectly and directly to evade host cell immunity.
5. The short- and long-range RNA-RNA Interactome of SARS-CoV-2	Molecular Cell - November, 2020
Ziv, O., J. Price, ...E. A. Miska	COVID-19 Task Force
The authors experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs and thus uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides.
6. Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing	Nature Communications - July, 2020
Sadegh, S., J. Matschinske, ...J. Baumbach	COVID-19 Task Force
The authors present CoVex, an interactive online platform for SARS-CoV-2 host interactome exploration and drug (target) identification. CoVex integrates virus-human protein interactions, human protein-protein interactions, and drug-target interactions. It allows visual exploration of the virus-host interactome and implements systems medicine algorithms for network-based prediction of drug candidates.

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Molecular Structure Subsection (21 articles) To submit a paper to be added to the collection use the submission form.
Article Title	Publication
Authors	Suggested By
Reason for suggesting
1. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor	Cell - April, 2020
Markus Hoffmann, Hannah Kleine-Weber, ...Stefan Pöhlmann	COVID-19 Task Force
Structural study on the cell entry of the virus and its possible inhibition via the serine protease inhibitor camostat mesylate certified in Japan.
2. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop	Journal of Molecular Biology - May, 2020
Javier A Jaimes, Nicole M André, ...Gary R Whittaker	COVID-19 Task Force
Structural modeling of the spike glycoprotein of Sars-Cov-2 and related viruses pointing out structural differences possibly affecting virus stability and transmission.
3. Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2	Viruses - April, 2020
Jiahua He, Huanyu Tao, ...Yi Xiao	COVID-19 Task Force
Structural study of cell entry of the virus based on protein-protein docking and molecular dynamics, pointing to a possibly high temperature-sensitivity of the effectiveness of cell entry.
4. Structural basis of receptor recognition by SARS-CoV-2	Nature - March, 2020
Jian Shang, Gang Ye, ...Fang Li	COVID-19 Task Force
Crystal structure of the Sars-Cov-2 spike glycoprotein in complex with the ACE2 receptor.
5. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein	Cell - April, 2020
Alexandra C.Walls, Young-Jun Park, ...David Veesler	COVID-19 Task Force
Structural study of the Sars-Cov-2 spike glycoprotein based on cryo-EM data. Also includes experimental results on antigenicity.
6. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2	Cell - May, 2020
Qihui Wang, Yanfang Zhang, ...Jianxun Qi	COVID-19 Task Force
Interpretation of a crystal structure of part of the spike glycoprotein of Sars-Cov-2 complexed with the ACE2 receptor. Also reports on antigenicity experiments.
7. A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV	Science - May, 2020
Meng Yuan, Nicholas C. Wu, ...Ian A. Wilson	COVID-19 Task Force
An interesting study that illustrates how much we still need to learn about the link between antibody recognition, as revealed from structural studies, and its protective action. For more detailed comments see Wodak S: Faculty Opinions Recommendation of [Yuan M et al., Science 2020 368(6491):630-633]. In Faculty Opinions, 03 Jul 2020; 10.3410/f.737672195.793575954)
8. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors	Science - April, 2020
Linlin Zhang, Daizong Lin, ...Rolf Hilgenfeld	COVID-19 Task Force
Another structural study of the Sars-Cov-2 spike glycoprotein with implications for drug design.
9. Structure of the RNA-dependent RNA polymerase from COVID-19 virus	Sciecne - May, 2020
Yan Gao1, Liming Yan, ...Zihe Rao	COVID-19 Task Force
Cryo-EM structural study of the viral polymerase and its interaction with its co-factors.
10. Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence	Bioinformatics - May, 2020
Mayya Sedova, Lukasz Jaroszewski, ...Adam Godzik	Thomas Lengauer
Provides a website for visualization of viral protein structures as the Sars-Cov-2 acquires mutationswhile spreading through the human population.
11. Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease	Computational Chemistry - June, 2020
Son Tung Ngo, Ngoc Quynh Anh Pham, ...Van V. Vu	Thomas Lengauer
Structure-based computational search through a ligand database of about 4600 compounds for inhibitors of the main protease of SARS-Cov-2.
12. SARS-CoV-2 orthologs of pathogenesis-involved small viral RNAs of SARS-CoV	Genomics - July, 2020
Ali Ebrahimpour Boroojeny, Hamidreza Chitsaz	Hamidreza Chitsaz
In this paper, we report SARS-CoV-2 small viral RNAs (svRNA) that are drug target candidates. RNA therapeuritcs can be designed to target these svRNAs. Also, study of host targets of these svRNAs can lead to understanding pathogenesis mechanisms.
13. Structural insights into the binding modes of viral RNA - dependent RNA polymerases using a function - site interaction fingerprint method for RNA virus drug discovery	Chemistry - June, 2020
Zheng Zhao, Philip E. Bourne	Zheng Zhao
We obtained the structural insights into RNA dependent RNA polymerase, a common component of RNA virus like COVID-19, provided two well-defined binding sites to discover the target drug.
14. THE PREDICTED STRUCTURE FOR THE ANTI-SENSE SIRNA OF THE RNA POLYMERASE ENZYME (RDRP) GENE OF THE SARS-COV-2	Berita Biologi - April, 2020
Arli Aditya Parikesit, Rizky Nurdiansyah	Arli Parikesit
This article explains about the transcriptomics-based drug design for COVID-19. We utilized non(nc)RNA as a lead compound to deter SARS-CoV-2 virus. This contribution will serve to fill in the gap that currently exist in the rational drug design.
15. Drug Repurposing Option for COVID-19 with Structural Bioinformatics of Chemical Interactions Approach	Cermin Dunia Kedokteran - 2020
Arli Aditya Parikesit, Rizky Nurdiansyah	Arli Parikesit
This article deals with the drug repurposing efforts with bioinformatics tools. It utilizes standard structural bioinformatics tools to comprehend the QSAR, and most importantly, the protein-ligand interaction repertoire with Ligplus tools.
16. The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor	Viruses - April, 2020
Esther S. Brielle, Dina Schneidman-Duhovny, Michal Linial	Thomas Lengauer
This is a comparative study analyzing the molecular structure of the interactions of the viral spike protein with the human ACE2 receptor for different corona viruses.
17. Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource	Nature Genetics - September, 2020
Portelli, S., M. Olshansky, ...D. B. Ascher	COVID-19 Task Force
To enable easy exploration and spatial visualization of the potential implications of SARS-CoV-2 mutations in infection, host immunity and drug development, we have developed COVID-3D (http://biosig.unimelb.edu.au/covid3d/).
18. Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein	ACS Central Science - September, 2020
Casalino, L., Z. Gaieb, ...R. E. Amaro	COVID-19 Task Force
The authors present a full-length model of the glycosylated SARS-CoV-2 S protein, both in the open and closed states, augmenting the available structural and biological data.
19. Emerging COVID-19 coronavirus: glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26	Emerging Microbes & Infections - February, 2020
Vankadari, N. & Wilce, J. A.	Naveen Vankadari
Novel findings of SARS-CoV-2 glycosylation pattern & its interaction with human CD26 along with ACE2 has immediate importance to vast researchers in the fight against COVID-19. Received +350 citations, Top 10 articles of 2020 & F1000 recommendation.
20. Arbidol: A potential antiviral drug for the treatment of SARS-CoV-2 by blocking trimerization of the spike glycoprotein	International Journal of Antimicrobial Agents - August, 2020
Vankadari, N.	Naveen Vankadari
Potential drugs for COIVD-19 was a top priority in the world, & our finding of Arbidol that block function of the viral spike was internationally recognised. Successful clinical trials in several countries with viral clearance. Media, Grants, F1000.
21. Structure of the SARS-CoV-2 Nsp1/5′-Untranslated Region Complex and Implications for Potential Therapeutic Targets, a Vaccine, and Virulence	Journal of Physical Chemistry Letters - November, 2020
Vankadari, N., Jeyasankar, N. N., Lopes, W. J.	Jamshed Arslan
Novel structure & first study showing how SARS-2 viral Nsp1 regulate self and host translation by binding to its self RNA via the bipartite mechanism for hijacking host ribosomes. This leads to potential antivirals and vaccine strategy for COVID-19.

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Scientific Data Sets

To submit a data set to be added to the collection use the submission form.

Data Set Name	Suggested By
Description of Data Set and Reason for Suggesting
1. Gene Ontology Access Point	Judith Blake
Description In an effort to assist global research on the SARS-CoV-2 virus (the cause of the COVID-19 disease), the Gene Ontology Consortium has made a central point of access to the relevant information available in our knowledgebase. Currently, we have compiled the following information: functions of human proteins used by the virus to enter a human cell functions of human proteins possibly targeted by the virus after cell entry. Reason for Suggesting To provide access to existing data and information in the Gene Ontology resource to assist in global research on SARS-CoV2.
2. Mouse Models for Coronavirus Research	Judith Blake
Description MGI is a knowledgebase of mouse models of human disease. To aid the research community in addressing the COVID-19 pandemic, we have collected expertly curated information on publications, mouse models and both human and mouse genes relevant to coronavirus research. This special collection will be updated regularly. Reason for Suggesting To provide access to comparative research on coronoviruses.
3. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms	COVID-19 Task Force
A publication presenting a project creating a data repository on molecular processes underlying virus-host interaction processes as well as downstream immunological and repair processes in the host.
4. EMBL-EBI COVID-19 Data Portal	Catherine Brooksbank
Description The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research Reason for Suggesting To share data and findings in a coordinated way, EMBL-EBI and partners are bringing together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data.

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Proposals of Community Science Projects

To propose a community science project to be added to the collection use the submission form or send a proposal to This email address is being protected from spambots. You need JavaScript enabled to view it..

Proposal Title	Suggested By
Goals and Audience
1. COVID-19 EHR DREAM Challenge	Larry Hunter
The rapid rise of COVID-19 has challenged healthcare globally. Due to the importance and emergent need for better understanding of the condition and the development of patient specific clinical risk scores and early warning tools, we have developed a platform to support testing analytic and machine learning hypotheses on clinical data without data sharing as a platform to rapidly discover and implement approaches for care. This Challenges aims to identify risk factors that lead to a positive test utilizing electronic health recorded data mapped to the OMOP Common Data Model.
2. SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics	Halie Rando
We are writing a large-scale collaborative review of COVID-19 literature, including pre-prints. The goal is to track new science in this area as it emerges and to critically evaluate research that has not yet been peer-reviewed. We welcome scientists from all backgrounds and disciplines. The manuscript is written using Manubot on GitHub. There are opportunities to contribute by writing or editing text, by summarizing new research that comes out, by being a subject-matter expert willing to comment when there are questions related to your field/area, by developing continuous integration approaches to handling various issues that come up, and by helping support non-computational scientists as they learn GitHub. Intended for Scientists, researchers, grad students, and even undergraduates are welcome to participate! The broader our pool of contributors, the better we will be prepared to critically evaluate the emerging literature. The target audience of the manuscript is a general scientific audience.
3. COVID-19-Community	Peter Rose
This project is a community effort to build a Knowledge Graph (https://github.com/covid-19-net/covid-19-community) that integrates heterogeneous biomedical and environmental datasets to help researchers analyze the interplay between host, pathogen, and the environment. The avalanche of COVID-19-related data streams from agencies and public and private research teams, with little coordination and with little reliance on interoperability practices, creates enormous challenges for researchers who attempt to analyze the pandemic in its multi-disciplinary complexity. We are creating a comprehensive semantic integration platform to organize COVID-19 information into a transdisciplinary knowledge network. It enables data-driven analysis and development of policy interventions that take into account up-to-date health, social-economic, and demographic characteristics of populations in different areas; biomedical information such as virus strains and genetic profiles; and local policy decisions designed to combat the pandemic. We are looking for researchers, postdocs, and graduate students to: 1. Contribute new relevant data sources and integrate them into an open source reproducible workflow, 2. Develop analysis applications (Jupyter Notebooks, dashboards, etc.) using the data in the Knowledge Graph, or 3. Develop models based on data in the Knowledge Graph.

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A SARS-CoV-2 protein interaction map reveals targets for drug repurposingBy Nevan Krogan

At Home with Covid-19By Brian Shoichet

Global surveillance of COVID-19 by mining news media using a multi-source dynamic embedded topic modelBy Yue Li and David Buckeridge

Evolutionary origins of SARS-CoV-2 and tracking its spread using phylodynamic data integrationBy Philippe Lemey

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ISCB COVID-19 Science Collection

Scientific Articles (41 articles)

Biomarkers/Host Genetics Subsection (5 articles)To submit a paper to be added to the collection use the submission form.

Epidemiology Subsection (11 articles)To submit a paper to be added to the collection use the submission form.

Evolution Subsection (9 articles)To submit a paper to be added to the collection use the submission form.

Gene Expression Subsection (3 articles)To submit a paper to be added to the collection use the submission form.

Immunology Subsection (2 articles)To submit a paper to be added to the collection use the submission form.

Molecular Function Subsection (6 articles)To submit a paper to be added to the collection use the submission form.

Molecular Structure Subsection (21 articles)To submit a paper to be added to the collection use the submission form.

Scientific Data Sets

Proposals of Community Science Projects

Exclusively for members

Supporting ISCB

ISCB On the Web

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
By Nevan Krogan

At Home with Covid-19
By Brian Shoichet

Global surveillance of COVID-19 by mining news media using a multi-source dynamic embedded topic model
By Yue Li and David Buckeridge

Evolutionary origins of SARS-CoV-2 and tracking its spread using phylodynamic data integration
By Philippe Lemey

Biomarkers/Host Genetics Subsection (5 articles)
To submit a paper to be added to the collection use the submission form.

Epidemiology Subsection (11 articles)
To submit a paper to be added to the collection use the submission form.

Evolution Subsection (9 articles)
To submit a paper to be added to the collection use the submission form.

Gene Expression Subsection (3 articles)
To submit a paper to be added to the collection use the submission form.

Immunology Subsection (2 articles)
To submit a paper to be added to the collection use the submission form.

Molecular Function Subsection (6 articles)
To submit a paper to be added to the collection use the submission form.

Molecular Structure Subsection (21 articles)
To submit a paper to be added to the collection use the submission form.