Computational Systems Biology Lab

 Panera: A novel framework for surmounting uncertainty in microbial community modelling using Pan-genera metabolic models

Indumathi Palanikumar, Himanshu Sinha, Karthik Raman*,

iScience

 27:110358

 Designing function-specific minimal microbiomes from large microbial communities

Aswathy Raghu, Indumathi Palanikumar, Karthik Raman*,

npj Systems Biology and Applications

 10:46

 Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station

Pratyay Sengupta, Shobhan Karthick Muthamilselvi Sivabalan, Nitin Kumar Singh, Karthik Raman*, Kasthuri Venkateswaran*,

Microbiome

 12:62

 Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.

Georgios Miliotis, Pratyay Sengupta, Asif Hameed, Maria Chuvochina, Francesca McDonagh, Anna Simpson, Ceth Parker, Nitin Singh, Punchappady Rekha, Dearbháile Morris, Karthik Raman, Nikos Kyrpides, & more

mBio

 15:e00181-24

 Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes

Anna C. Simpson†, Pratyay Sengupta†, Flora Zhang, Asif Hameed, Ceth W. Parker, Nitin K. Singh, Georgios Miliotis, Punchappady D. Rekha, Karthik Raman, Christopher E. Mason*, Kasthuri Venkateswaran*,

Scientific Reports

 13:19207

 BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures

Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Issac Hecht, Aarthi Ravikrishnan, Rafael S. Gonçalves, & more

Nature Biotechnology

 42:709--804

 Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes

Dinesh Kumar Kuppa Baskaran, Shreyansh Umale, Zhichao Zhou, Karthik Raman*, Karthik Anantharaman*,

ISME Communications

 3:42

 Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

Pratyay Sengupta, Shobhan Karthick Muthamilselvi Sivabalan, Amrita Mahesh, Indumathi Palanikumar, Dinesh Kumar Kuppa Baskaran, Karthik Raman*,

Journal of the Indian Institute of Science

 103:891-907

 Metabolic modeling of the International Space Station microbiome reveals key microbial interactions

Rachita K Kumar, Nitin Singh, Sanjaay Balakrishnan, Ceth W. Parker, Karthik Raman*, Kasthuri Venkateswaran*,

Microbiome

 10:102

 Systems-Level Modelling of Microbial Communities: Theory and Practice

Aarthi Ravikrishnan, Karthik Raman,

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