Computational Systems Biology Lab

 Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Jonathan L. Golob*, Tomiko T. Oskotsky*, ..., The Preterm Birth DREAM Community, ..., James C. Costello, Marina Sirota*,

Cell Reports Medicine

 5:101350

 COWAVE: A Labelled COVID-19 Wave Dataset for Building Predictive Models

Melpakkam Pradeep, Karthik Raman*,

PLoS ONE

 18:e0284076

 Multi-omic data improve prediction of personalized tumor suppressors and oncogenes

Malvika Sudhakar, Raghunathan Rengaswamy*, Karthik Raman*,

Frontiers in Genetics

 13:854190

 Novel ratio-metric features enable the identification of new driver genes across cancer types

Malvika Sudhakar, Raghunathan Rengaswamy*, Karthik Raman*,

Scientific Reports

 12:5

 NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks

Vimaladhasan Senthamizhan, Balaraman Ravindran, Karthik Raman*,

Frontiers in Genetics

 12:722198

 Sequence Neighborhoods Enable Reliable Prediction of Pathogenic Mutations in Cancer Genomes

Shayantan Banerjee, Karthik Raman*, Balaraman Ravindran*,

Cancers

 13:2366

 Mycobacterium tuberculosis (Mtb) lipid–mediated lysosomal rewiring in infected macrophages modulates intracellular Mtb trafficking and survival

Kuldeep Sachdeva, Manisha Goel, Malvika Sudhakar, Mansi Mehta, Rajmani Raju, Karthik Raman, Amit Singh, Varadharajan Sundaramurthy*,

Journal of Biological Chemistry

 295:9192-9210

 Machine Learning Applications for Mass Spectrometry-Based Metabolomics

Ulf Liebal*, Thuy An Phan Nguyen, Malvika Sudhakar, Karthik Raman, Lars M. Blank,

Metabolites

 10:243

 Network-based features enable prediction of essential genes across diverse organisms

Karthik Azhagesan, Balaraman Ravindran*, Karthik Raman*,

PLoS ONE

 13:e0208722

 Predicting Novel Metabolic Pathways through Subgraph Mining

Aravind Sankar, Sayan Ranu*, Karthik Raman*,

Bioinformatics

 33:3955-3963