Publications

Research Articles

Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells. Immanuel SRC, Ghanate AD, Parmar DS, Yadav R, Uthup R, Panchagnula V, Raghunathan A. npj Systems Biology and Applications 7:2 (2021). https://doi.org/10.1038/s41540-020-00161-7

Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum. Banerjee D, Raghunathan A. PLoS ONE 14(1): e0210008 (2019). https://doi.org/10.1371/journal.pone.0210008

Integrated constraints based analysis of an engineered violacein pathway in Escherichia coli. Immanuel SRC*, Banerjee D*, Rajankar MP*, Raghunathan A. Biosystems 171:10-19 (2018). https://doi.org/10.1016/j.biosystems.2018.06.002(*Equal contributors)

Knowledge, attitude and practice of antibiotic use and antimicrobial resistance: a study post the 'Red Line' initiative. Banerjee D, Raghunathan A. Current Science (00113891), 114(9) (2018). https://doi.org/10.18520/cs/v114/i09/1866-1877

Integrative analysis of rewired central metabolism in temozolomide resistant cells. Immanuel SRC, Ghanate AD, Parmar DS, Marriage F, Panchagnula V, Day PJ, Raghunathan A. Biochemical and Biophysical Research Communications 495(2):2010-2016 (2018). https://doi.org/10.1016/j.bbrc.2017.12.073

Absolute quantitation of poly(R)-3-hydroxybutyric acid using spectrofluorometry in recombinant Escherichia coli. Rajankar MP, Ravindranathan S, Rajamohanan PR, Raghunathan A. Biology Methods and Protocols 3(1):bpy007 (2018). https://doi.org/10.1093/biomethods/bpy007

A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance. Banerjee D, Parmar D, Bhattacharya N, Ghanate AD, Panchagnula V, Raghunathan A. BMC Systems Biology 11:51 (2017). https://doi.org/10.1186/s12918-017-0427-z

MEETING REPORT: Modelling natural and synthetic biological networks. Raghunathan A, Athale CA. Current Science 113(7):1221-1222 (2017).

Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. Jamshidi N, Raghunathan A. Frontiers in Microbiology 6:1032 (2015).https://doi.org/10.3389/fmicb.2015.01032

Identification of potential drug targets in Salmonella enterica sv. typhimurium using metabolic modelling and experimental validation. Hartman HB, Fell DA, Rossell S, Jensen PR, Woodward MJ, Thorndahl L, Jelsbak L, Olsen JE, Raghunathan A, Daefler S, Poolman MG. Microbiology 160(6):1252-1266 (2014). https://doi.org/10.1099/mic.0.076091-0

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2. Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RMT, Hsiung CA, De Keersmaecker SCJ, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BØ., Adkins JN, Bumann D. BMC Systems Biology 5(1):1-9 (2011). https://doi.org/10.1186/1752-0509-5-8

Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis. Raghunathan A, Shin S, Daefler S. BMC Systems Biology 4:118 (2010). https://doi.org/10.1186/1752-0509-4-118

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. Raghunathan A, Reed J, Shin S, Palsson B, Daefler S. BMC Systems Biology 3(1):1-16 (2009). https://doi.org/10.1186/1752-0509-3-38

Modeling and experimental studies on intermittent starch feeding and citrate addition in simultaneous saccharification and fermentation of starch to flavor compounds. Chavan AR, Raghunathan A, Venkatesh KV. Journal of Industrial Microbiology and Biotechnology 36(4):409-419 (2009).https://doi.org/10.1007/s10295-008-0520-9

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 → Asp Obtained Using Microfluidic Crystallization Devices. Anderson MJ, DeLaBarre B, Raghunathan A, Palsson BØ., Brunger AT, Quake SR. Biochemistry 46 (19), 5722-5731 (2007). https://doi.org/10.1021/bi700096p

Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, Boom Dvd, Cantor CR, Palsson BØ. Nature Genetics 38:1406–1412 (2006). https://doi.org/10.1038/ng1906

High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12. Honisch C, Raghunathan A, Cantor CR, Palsson BØ, Boom Dvd. Genome Research 14(12):2495-2502 (2004). http://www.genome.org/cgi/doi/10.1101/gr.2977704.

In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson Jr R, Tyler RE, Akerley BJ, Smith AL, Palsson BØ, Kolker E. OMICS: A Journal of Integrative Biology 8(1):25-41 (2004). https://doi.org/10.1089/153623104773547471

Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli. Raghunathan A, Palsson BØ. Biotechnology Letters 25(5):435-441 (2003). https://doi.org/10.1023/A:1022497310798

Simultaneous saccharification and fermentation of starch to lactic acid. Anuradha R, Suresh AK, Venkatesh KV. Process Biochemistry 35(3-4):367-375 (1999). https://doi.org/10.1016/S0032-9592(99)00080-1

Book Chapter(s)

Integrated host-pathogen metabolic reconstructions. Jamshidi N, Raghunathan A. Metabolic Network Reconstruction and Modeling, pp 197-217, Part of the Methods in Molecular Biology book series (MIMB, volume 1716). Humana Press, New York, NY (2017).Print ISBN 978-1-4939-7527-3. Online ISBN 978-1-4939-7528-0.https://doi.org/10.1007/978-1-4939-7528-0_9

Investigating host–pathogen behavior and their interaction using genome-scale metabolic network models. Sadhukhan PP, Raghunathan A. Immunoinformatics, pp 523-562, Part of the Methods in Molecular Biology book series (MIMB, volume 1184). Humana Press, New York, NY (2014). Print ISBN 978-1-4939-1114-1. Online ISBN 978-1-4939-1115-8. https://doi.org/10.1007/978-1-4939-1115-8_29

Microbial Strategies for the Depolymerization of Glucuronoxylan: Leads to the Biotechnological Applications of Endoxylanases in “Application of Enzymes to Lignocellulosics”. Preston JF, Hurlbert JC, Rice JD, Ragunathan A, St John FJ. ACS Symposium Series, Part of Applications of Enzymes to Lignocellulosics book (Volume 855). American Chemical Society (2003).ISBN13: 978-0-8412-3831-2. eISBN: 978-0-8412-1960-1.https://doi.org/10.1021/bk-2003-0855.ix002

Microbial Strategies for the Depolymerization of Glucuronoxylan: Leads to Biotechnological Applications of Endoxylanases. Preston JF, Hurlbert JC, Rice JD, Ragunathan A, St John FJ. ACS Symposium Series, Chapter 12, pp 191-210, Part of Applications of Enzymes to Lignocellulosics book (Volume 855). American Chemical Society (2003).ISBN13: 978-0-8412-3831-2. eISBN: 978-0-8412-1960-1.https://doi.org/10.1021/bk-2003-0855.ch012

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