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Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of…

Genomics · Quantitative Biology 2020-04-30 Rui Wang , Yuta Hozumi , Changchuan Yin , Guo-Wei Wei

The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The…

Genomics · Quantitative Biology 2020-06-02 Changchuan Yin

The increasing spread of COVID-19, caused by the virus SARS-CoV-2, raises concerns about the extent to which mutations have occurred across the viral genome. We present a partial replication of an earlier 2021 study by Wang, R. et al. that…

Genomics · Quantitative Biology 2021-12-28 William Svoboda , Brendan McManamon , Sara Schwartz

The emerging global infectious COVID-19 coronavirus disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December…

Genomics · Quantitative Biology 2020-03-25 Changchuan Yin

The transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of paramount importance to the controlling and combating of coronavirus disease 2019 (COVID-19) pandemic. Currently, near 15,000 SARS-CoV-2…

Genomics · Quantitative Biology 2020-08-21 Rui Wang , Yuta Hozumi , Yong-Hui Zheng , Changchuan Yin , Guo-Wei Wei

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current global COVID-19 pandemic, in which millions of lives have been lost. Understanding the zoonotic evolution of the coronavirus may provide…

Populations and Evolution · Quantitative Biology 2022-01-04 Changchuan Yin

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is a major concern in coronavirus disease 2019 (COVID-19) prevention and economic reopening. However, rigorous determination of SARS-COV-2 infectivity is essentially…

Biomolecules · Quantitative Biology 2020-06-01 Jiahui Chen , Rui Wang , Menglun Wang , Guo-Wei Wei

The importance of understanding SARS-CoV-2 evolution cannot be overemphasized. Recent studies confirm that natural selection is the dominating mechanism of SARS-CoV-2 evolution, which favors mutations that strengthen viral infectivity. We…

Populations and Evolution · Quantitative Biology 2021-10-12 Rui Wang , Jiahui Chen , Guo-Wei Wei

Replication of SARS-CoV2 virions is an error-prone process which may eventually generate a percentage of impaired protein copies with complete lack of functionality. For instance, after RNA mis-replication, a very premature stop codon (UAG,…

Genomics · Quantitative Biology 2021-06-08 Alessio D'Alessandro

SARS-CoV-2 is an upper respiratory system RNA virus that has caused over 3 million deaths and infecting over 150 million worldwide as of May 2021. With thousands of strains sequenced to date, SARS-CoV-2 mutations pose significant challenges…

Quantitative Methods · Quantitative Biology 2021-11-15 Yanyi Ding , Zhiyi Kuang , Yuxin Pei , Jeff Tan , Ziyu Zhang , Joseph Konan

The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail unlike any virus before it.…

Machine Learning · Computer Science 2021-10-20 Zahra Tayebi , Sarwan Ali , Murray Patterson

The outbreak of COVID-19 caused by SARS-CoV-2 has rapidly spread worldwide and has caused over 1,400,000 infections and 80,000 deaths. There are currently no drugs or vaccines with proven efficacy for its prevention and little knowledge was…

Genomics · Quantitative Biology 2020-04-13 Zhi Liu , Jianwei Wang , Yuyu Xu , Mengchen Guo , Kai Mi , Rui Xu , Yang Pei , Qiangkun Zhang , Xiaoting Luan , Zhibin Hu , Xingyin Liu#

SARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 59 million infections and 1.4 million deaths in 11 months. Understanding the origin…

Populations and Evolution · Quantitative Biology 2020-11-26 Erwan Sallard , José Halloy , Didier Casane , Etienne Decroly , Jacques van Helden

COVID-19 is an infection caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2), which has caused a global outbreak. Current research efforts are focused on the understanding of the molecular mechanisms involved in…

Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2500 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome…

Biomolecules · Quantitative Biology 2020-04-30 Andrea Vandelli , Michele Monti , Edoardo Milanetti , Riccardo Delli Ponti , Gian Gaetano Tartaglia

Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections. The last three waves of…

Populations and Evolution · Quantitative Biology 2022-10-19 Jiahui Chen , Rui Wang , Yuta Hozumi , Gengzhuo Liu , Yuchi Qiu , Xiaoqi Wei , Guo-Wei Wei

The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins:…

Biological Physics · Physics 2022-09-26 Siyu Li , Roya Zandi

Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute…

Genomics · Quantitative Biology 2020-05-06 Rui Wang , Yuta Hozumi , Changchuan Yin , Guo-Wei Wei

COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…

Biomolecules · Quantitative Biology 2020-04-10 Goksel Misirli

With the rapid spread of the novel coronavirus (COVID-19) across the globe and its continuous mutation, it is of pivotal importance to design a system to identify different known (and unknown) variants of SARS-CoV-2. Identifying particular…

Quantitative Methods · Quantitative Biology 2021-10-13 Sarwan Ali , Bikram Sahoo , Naimat Ullah , Alexander Zelikovskiy , Murray Patterson , Imdadullah Khan
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