PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences

Recent Developments on Therapeutic and Diagnostic Approaches for COVID-19

(2021) Joydeb Majumder et al.   AAPS Journal

COVID-19 Transmission, Current Treatment, and Future Therapeutic Strategies

(2021) Vrishali S. Salian et al.   MOLECULAR PHARMACEUTICS

Predicting Attributes of Nodes Using Network Structure

(2021) Sarwan Ali et al.   ACM Transactions on Intelligent Systems and Technology

Epidemiological Study of Betacoronaviruses in Captive Malayan Pangolins

(2021) Linmiao Li et al.   Frontiers in Microbiology

K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification

(2021) Davide Storato et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Robust Representation and Efficient Feature Selection Allows for Effective Clustering of SARS-CoV-2 Variants

(2021) Zahra Tayebi et al.   Algorithms

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

Clinical Characteristics of Coronavirus Disease 2019 in China

(2020) Wei-jie Guan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

(2020) Qihui Wang et al.   CELL

Combinatorial trace method for network immunization

(2020) Muhammad Ahmad et al.   INFORMATION SCIENCES

Pangolins Harbor SARS-CoV-2-Related Coronaviruses

(2020) Guan-Zhu Han   TRENDS IN MICROBIOLOGY

What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19?

(2020) Sergio Rosales-Mendoza et al.   Vaccines

Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19

(2020) Yuan Huang et al.   ACTA PHARMACOLOGICA SINICA

Machine learning methods accurately predict host specificity of coronaviruses based on spike sequences alone

(2020) Kiril Kuzmin et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

COVID-19 diagnosis —A review of current methods

(2020) Meral Yüce et al.   BIOSENSORS & BIOELECTRONICS

Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

(2020) Tingting Li et al.   Scientific Reports

COVID-19—Zoonosis or Emerging Infectious Disease?

(2020) Najmul Haider et al.   Frontiers in Public Health

MAFFT-DASH: integrated protein sequence and structural alignment

(2019) John Rozewicki et al.   NUCLEIC ACIDS RESEARCH

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

(2018) Giovanna Ambrosini et al.   BIOINFORMATICS

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes

(2018) Stephen Solis-Reyes et al.   PLoS One

Predicting protein–protein interactions from protein sequences by a stacked sparse autoencoder deep neural network

(2017) Yan-Bin Wang et al.   Molecular BioSystems

Structure, Function, and Evolution of Coronavirus Spike Proteins

(2016) Fang Li   Annual Review of Virology

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells

(2016) Valentina Boeva   Frontiers in Genetics

A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites

(2015) Jichen Yang et al.   BIOINFORMATICS

CoMeta: Classification of Metagenomes Using k-mers

(2015) Jolanta Kawulok et al.   PLoS One

L.U.St: a tool for approximated maximum likelihood supertree reconstruction

(2014) Wasiu A Akanni et al.   BMC BIOINFORMATICS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites

(2012) Soumyadeep Nandi et al.   BMC GENOMICS

An Improved Position Weight Matrix method based on an entropy measure for the recognition of prokaryotic promoters

(2011) Qinqin Wu et al.   International Journal of Data Mining and Bioinformatics

ViPR: an open bioinformatics database and analysis resource for virology research

(2011) Brett E. Pickett et al.   NUCLEIC ACIDS RESEARCH

Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles

(2011) Yingtao Bi et al.   PLoS One

Occupancy Classification of Position Weight Matrix-Inferred Transcription Factor Binding Sites

(2011) Hollis Wright et al.   PLoS One

On Position-Specific Scoring Matrix for Protein Function Prediction

(2010) Jong Cheol Jeong et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Pseudocounts for transcription factor binding sites

(2008) Keishin Nishida et al.   NUCLEIC ACIDS RESEARCH