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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 (39 articles)

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

Article Title Suggested By
Reason for suggesting
1. Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients 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 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 Suggested By
Reason for suggesting
1. Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing 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 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 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 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 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 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 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 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 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 (4 articles)
To submit a paper to be added to the collection use the submission form.

Article Title Suggested By
Reason for suggesting
1. The proximal origin of SARS-CoV-2 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 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 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 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.

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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 Suggested By
Reason for suggesting
1.  SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes 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 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 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 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 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 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 Suggested By
Reason for suggesting
1.  Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins 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 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 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 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 (15 articles)
To submit a paper to be added to the collection use the submission form.

Article Title 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 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 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 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 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 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 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 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 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 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 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 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 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 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.
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 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.

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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
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
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
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.

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