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)
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| 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. | |
Epidemiology Subsection (11 articles)
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| 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. | |
Evolution Subsection (9 articles)
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| 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. | |
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. | |
Immunology Subsection (2 articles)
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| 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. | |
Molecular Function Subsection (6 articles)
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| 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. | |
Molecular Structure Subsection (21 articles)
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| 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) |
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| 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. | |
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 |
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| 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. |
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| 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. |
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| 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 |
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| 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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| 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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