Yin, Jialing Li, Chengcheng Ye, Chunhong Ruan, Zhihui Liang, Yicong Li, Yongkui Wu, Jianguo Luo, Zhen
Published in
Computational and Structural Biotechnology Journal
Since Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was identified in late 2019, the coronavirus disease 2019 (COVID-19) pandemic has challenged public health around the world. Currently, there is an urgent need to explore antiviral therapeutic targets and effective clinical drugs. In this study, we systematically summarized two main...
Gupta, Suchetana Mallick, Ditipriya Banerjee, Kumarjeet Mukherjee, Shrimon Sarkar, Soumyadev Lee, Sonny TM Basuchowdhuri, Partha Jana, Siddhartha S
Published in
Computational and Structural Biotechnology Journal
The clinical manifestation of the recent pandemic COVID-19, caused by the novel SARS-CoV-2 virus, varies from mild to severe respiratory illness. Although environmental, demographic and co-morbidity factors have an impact on the severity of the disease, contribution of the mutations in each of the viral genes towards the degree of severity needs a ...
Luedemann, Max Stadler, Daniela Cheng, Cho-Chin Protzer, Ulrike Knolle, Percy A. Donakonda, Sainitin
Published in
Computational and Structural Biotechnology Journal
Drug-repurposing has been instrumental to identify drugs preventing SARS-CoV-2 replication or attenuating the disease course of COVID-19. Here, we identify through structure-based drug-repurposing a dual-purpose inhibitor of SARS-CoV-2 infection and of IL-6 production by immune cells. We created a computational structure model of the receptor bindi...
Donzelli, Sara Spinella, Francesca di Domenico, Enea Gino Pontone, Martina Cavallo, Ilaria Orlandi, Giulia Iannazzo, Stefania Ricciuto, Giulio Maria ISG Virology Covid Team, Pellini, Raul
...
Published in
Computational and Structural Biotechnology Journal
Objectives Despite extensive efforts to monitor the diffusion of COVID-19, the actual wave of infection is worldwide characterized by the presence of emerging SARS-CoV-2 variants. The present study aims to describe the presence of yet undiscovered SARS-CoV-2 variants in Italy. Methods Next Generation Sequencing was performed on 16 respiratory sampl...
Thielemann, Nadja Herz, Michaela Kurzai, Oliver Martin, Ronny
Published in
Computational and Structural Biotechnology Journal
The human body is a dynamic ecosystem consisting of millions of microbes which are often comprised under the term microbiome. Compared to bacteria, which count for the overwhelming majority of the microbiome, the number of human-associated fungi is small and often underestimated. Nonetheless, they can be found in different host niches such as the g...
Cao, Yipeng Yang, Rui Wang, Wei Jiang, Shengpeng Yang, Chengwen Liu, Ningbo Dai, Hongji Lee, Imshik Meng, Xiangfei Yuan, Zhiyong
...
Published in
Computational and Structural Biotechnology Journal
The M protein of the novel coronavirus 2019 (SARS-CoV-2) is the major structural component of the viral envelope and is also the minimum requirement for virus particle budding. M proteins generally exist as dimers. In virus assembly, they are the main driving force for envelope formation through lateral interactions and interactions with other vira...
Kleine Bardenhorst, Sven Vital, Marius Karch, André Rübsamen, Nicole
Published in
Computational and Structural Biotechnology Journal
The quantification of richness within a sample—either measured as the number of observed species or approximated by estimation—is a common first step in microbiome studies and is known to be highly dependent on sequencing depth, which itself is highly variable between samples. Rarefaction curves serve as a tool to investigate this dependency and it...
Zeng, Zihang Gao, Yanping Li, Jiali Zhang, Gong Sun, Shaoxing Wu, Qiuji Gong, Yan Xie, Conghua
Published in
Computational and Structural Biotechnology Journal
Background Cox proportional hazard regression (CPH) model relies on the proportional hazard (PH) assumption: the hazard of variables is independent of time. CPH has been widely used to identify prognostic markers of the transcriptome. However, the comprehensive investigation on PH assumption in transcriptomic data has lacked. Results The whole tran...
Pezoulas, Vasileios C. Goules, Andreas Kalatzis, Fanis Chatzis, Luke Kourou, Konstantina D. Venetsanopoulou, Aliki Exarchos, Themis P. Gandolfo, Saviana Votis, Konstantinos Zampeli, Evi
...
Published in
Computational and Structural Biotechnology Journal
For many decades, the clinical unmet needs of primary Sjögren’s Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity of the underlying pathogenic mechanisms, including the pSS-associated lymphomagenesis process. Here, we present the HarmonicSS cloud-computing exemplar which offers beyond the state-of-the-ar...
Bohannan, Zachary S. Coffman, Frederick Mitrofanova, Antonina
Published in
Computational and Structural Biotechnology Journal
High-risk pediatric B-ALL patients experience 5-year negative event rates up to 25%. Although some biomarkers of relapse are utilized in the clinic, their ability to predict outcomes in high-risk patients is limited. Here, we propose a random survival forest (RSF) machine learning model utilizing interpretable genomic inputs to predict relapse/deat...
