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Science Collection

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;

  1. Scientific Articles
  2. Scientific Data Sets
  3. Proposals of Community Science Projects

Scientific Articles (41 articles)

Disease Biomarkers 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. 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.


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Epidemiology 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. 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.


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Evolution 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. 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.


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Gene Expression Subsection (3 articles)
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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 (4 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.


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Molecular Structure Subsection (16 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.


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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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