Computational Biology

Full Article: AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK | PLOS Computational Biology Cite: Essegian, Derek, et al. “AI-assisted chemical probe discovery for the understudied calcium-calmodulin dependent kinase, PNCK.” bioRxiv (2022): 2022–06. Overview The study focuses on PNCK, an understudied kinase associated with cancer progression and survival…

Overview The development of KRAS G12C inhibitors in precision oncology has been a significant advancement, but response rates are often limited. To improve patient selection, researchers have created an integrated model called “K20” that predicts KRAS dependency. The model was built using molecular profiles of cell lines and features 19 genes…

Source: Weiser, Sydney C., et al. “Data-driven segmentation of cortical calcium dynamics.” PLOS Computational Biology 19.5 (2023): e1011085. Full Article: Data-driven segmentation of cortical calcium dynamics | PLOS Computational Biology Overview In this study, researchers demonstrate the use of independent component analysis to separate neural activity from artifacts in widefield recordings…

Introduction As part of my PhD studies in Bioinformatics and Computational Biology at GMU. I had to take at least three lab rotations to fulfill the program requirements. …

Guttà, Cristiano, Christoph Morhard, and Markus Rehm. “Applying a GAN-based classifier to improve transcriptome-based prognostication in breast cancer.” PLOS Computational Biology 19.4 (2023): e1011035. Full Article: Applying a GAN-based classifier to improve transcriptome-based prognostication in breast cancer | PLOS Computational Biology OVERVIEW Researchers proposed a classifier for breast cancer risk stratification…

Baptista, Delora, Pedro G. Ferreira, and Miguel Rocha. “A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer.” PLOS Computational Biology 19.3 (2023): e1010200. Full Article: A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer | PLOS Computational Biology Overview …

Kaggle Competition: CAFA 5 Protein Function Prediction | Kaggle 1. Proteins Proteins are vital biological molecules that perform various functions in cells, tissues, and organisms. They make up a significant portion of cell weight and are involved in activities such as catalysis, muscle contraction, structural support, defense against pathogens, signaling, regulation, protein…

Source: GenoVi, an open-source automated circular genome visualizer for bacteria and archaea Cumsille, Andrés, et al. “GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.” PLOS Computational Biology 19.4 (2023): e1010998. OVERVIEW The study introduces GenoVi, a Python command-line tool for creating custom circular genome representations and analyzing microbial…

Ihave been a data engineer in Roche, a pharmaceutical company, for about 2 years. I’m based in Malaysia, a middle-income country in South-East Asia. Before this position, I was in academic research in genomics, a branch of biology that studies the genome using computational methods. Sometimes, the broader term computational…