Spike2vec: An efficient and scalable embedding approach for covid-19 spike sequences

S Ali, M Patterson - 2021 IEEE international conference on big …, 2021 - ieeexplore.ieee.org
With the rapid global spread of COVID-19, more and more data related to this virus is
becoming available, including genomic sequence data. The total number of genomic …

[HTML][HTML] PWM2Vec: An efficient embedding approach for viral host specification from coronavirus spike sequences

S Ali, B Bello, P Chourasia, RT Punathil, Y Zhou… - Biology, 2022 - mdpi.com
Simple Summary The family of coronaviruses comprises a diverse set of strains and variants
which cause diseases from the common cold to COVID-19. Moreover, they infect a wide …

Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks

F Mohebbi, A Zelikovsky, S Mangul, G Chowell… - Nature …, 2024 - nature.com
The emergence of viral variants with altered phenotypes is a public health challenge
underscoring the need for advanced evolutionary forecasting methods. Given extensive …

Efficient analysis of COVID-19 clinical data using machine learning models

S Ali, Y Zhou, M Patterson - Medical & Biological Engineering & Computing, 2022 - Springer
Because of the rapid spread of COVID-19 to almost every part of the globe, huge volumes of
data and case studies have been made available, providing researchers with a unique …

Efficient approximate kernel based spike sequence classification

S Ali, B Sahoo, MA Khan, A Zelikovsky… - IEEE/ACM …, 2022 - ieeexplore.ieee.org
Machine learning (ML) models, such as SVM, for tasks like classification and clustering of
sequences, require a definition of distance/similarity between pairs of sequences. Several …

Robust representation and efficient feature selection allows for effective clustering of sars-cov-2 variants

Z Tayebi, S Ali, M Patterson - Algorithms, 2021 - mdpi.com
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 …

Reads2vec: Efficient embedding of raw high-throughput sequencing reads data

P Chourasia, S Ali, S Ciccolella… - Journal of …, 2023 - liebertpub.com
The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the
COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a …

Clustering sars-cov-2 variants from raw high-throughput sequencing reads data

P Chourasia, S Ali, S Ciccolella… - … Advances in Bio and …, 2021 - Springer
The massive amount of genomic data appearing over the past two years for SARS-CoV-2
has challenged traditional methods for studying the dynamics of the COVID-19 pandemic …

Community structure and temporal dynamics of SARS-CoV-2 epistatic network allows for early detection of emerging variants with altered phenotypes

F Mohebbi, A Zelikovsky, S Mangul, G Chowell… - bioRxiv, 2023 - biorxiv.org
The rise of viral variants with altered phenotypes presents a significant public health
challenge. In particular, the successive waves of COVID-19 have been driven by emerging …

Enhancing t-sne performance for biological sequencing data through kernel selection

P Chourasia, T Murad, S Ali, M Patterson - International symposium on …, 2023 - Springer
The genetic code for many different proteins can be found in biological sequencing data,
which offers vital insight into the genetic evolution of viruses. While machine learning …