Research Areas: Quantitative Systems Biology, Computational Material Design, Applied Machine Learning, Applied Evolutionary Dynamics,
Research Areas: Quantitative Systems Biology, Computational Material Design, Applied Machine Learning, Applied Evolutionary Dynamics,
Pardakhti, M; Nanda, P; Srivastava, R. Impact of chemical features on methane adsorption by porous materials at varying pressures. The Journal Of Physical Chemistry C 124:4534-4544 (2020).
[COMP MAT]
Gao, T; Wang, Y; Zhang, C; Pittman, ZA; Oliveira, AM; Fu, K; Zhao, J; Srivastava, R; Willis, BG. Classification of Tea Aromas Using Multi-Nanoparticle Based Chemiresistor Arrays. Sensors 19:2547 (2019).
[COMP MAT]
Chelius, CL; Ribeiro, LF; Huso, W; Kumar, J; Lincoln, S; Tran, B; Goo, YA; Srivastava, R; Harris, SD; Marten, MR. Phosphoproteomic and transcriptomic analyses reveal multiple functions for Aspergillus nidulans MpkA independent of cell wall stress. Fungal Genetics and Biology 125:1--12 (2019).
[BIO]
Ribeiro, LF; Chelius, C; Boppidi, KR; Naik, NS; Hossain, S; Ramsey, JJ; Kumar, J; Ribeiro, LF; Ostermeier, M; Tran, B; and others. Comprehensive analysis of Aspergillus nidulans PKA phosphorylome identifies a novel mode of CreA regulation. mBio 10:e02825--18 (2019).
[BIO]
Moharreri, E; Pardakhti, M; Srivastava, R; Suib, SL. Energy--Geometry Dependency of Molecular Structures: A Multistep Machine Learning Approach. ACS combinatorial science 21:614--621 (2019).
[COMP MAT]
Pardakhti, M; Jafari, T; Tobin, Z; Dutta, B; Moharreri, E; Saveh Shemshaki, N; Suib, SL; Srivastava, R. Trends in Solid Adsorbent Materials Development for CO2 Capture. ACS applied materials & interfaces 11:4533-34559 (2019).
[MAT]
Rogers, I; Srivastava, R. Using ensemble modeling to determine causes of multifactorial disorders. Proceedings of the Genetic and Evolutionary Computation Conference Companion 302--302 (2018).
[BIO COMP]
Boppidi, KR; Ribeiro, LF; Iambamrung, S; Nelson, SM; Wang, Y; Momany, M; Richardson, EA; Lincoln, S; Srivastava, R; Harris, SD; and others. Altered secretion patterns and cell wall organization caused by loss of PodB function in the filamentous fungus Aspergillus nidulans. Scientific reports 8:11433 (2018).
[BIO]
Benjamino, J; Lincoln, S; Srivastava, R; Graf, J. Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration. Microbiome 6:86 (2018).
[BIO COMP]
White, JR; Srivastava, R. Integration of Reaction Kinetics Theory and Gene Expression Programming to Infer Reaction Mechanism. European Conference on the Applications of Evolutionary Computation 53--66 (2017).
[BIO COMP]
Pardakhti, M; Moharreri, E; Wanik, D; Suib, SL; Srivastava, R. Machine learning using combined structural and chemical descriptors for prediction of methane adsorption performance of metal organic frameworks (MOFs). ACS combinatorial science 19:640--645 (2017).
[COMP MAT]
Lincoln, S; Benjamino, J; Graf, J; Srivastava, R. Metabolite Overproduction through Engineering and Optimization of Microbiome Composition Dynamics. Proceedings of the 2016 on Genetic and Evolutionary Computation Conference Companion 9--10 (2016).
[BIO COMP]
Peterson, D; Srivastava, R; Lalla, R. Oral mucosal injury in oncology patients: perspectives on maturation of a field. Oral diseases 21:133--141 (2015).
[BIO]
Kanjilal, B; Noshadi, I; Bautista, EJ; Srivastava, R; Parnas, RS. Batch, design optimization, and DNA sequencing study for continuous 1, 3-propanediol production from waste glycerol by a soil-based inoculum. Applied microbiology and biotechnology 99:2105--2117 (2015).
[BIO MAT]
Lincoln, S; Rogers, I; Srivastava, R. Metabolic Design And Engineering Through Ant Colony Optimization. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation 225--232 (2015).
[BIO COMP]
Bautista, EJ; Srivastava, R. Enhancing genetic algorithm-based genome-scale metabolic network curation efficiency. Proceedings of the 2014 Annual Conference on Genetic and Evolutionary Computation 257--264 (2014).
[BIO COMP]
Bautista, EJ; Srivastava, R. Leveraging ensemble information of evolving populations in genetic algorithms to identify incomplete metabolic pathways. Proceedings of the 15th annual conference companion on Genetic and evolutionary computation 39--40 (2013).
[BIO COMP]
Bautista, EJ; Zinski, J; Szczepanek, SM; Johnson, EL; Tulman, ER; Ching, W; Geary, SJ; Srivastava, R. Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum. PLoS computational biology 9:e1003208 (2013).
[BIO COMP]
Johnson, E; Srivastava, R. Volatility in mRNA secondary structure as a design principle for antisense. Nucleic acids research 41:e43--e43 (2012).
[BIO COMP]
Li, S; Srivastava, R; Parnas, RS. Study of in situ 1-butanol pervaporation from A-B-E fermentation using a PDMS composite membrane: Validity of solution-diffusion model for pervaporative A-B-E fermentation. Biotechnology progress 27:111--120 (2011).
[BIO MAT]
Srivastava, R; White, J; Lalla, R; Loew, L; Peterson, D. Optimizing personalized treatment of oral mucositis secondary to cancer therapy through systems biology.. Journal of Clinical Oncology 29:e19690--e19690 (2011).
[BIO COMP]
Li, S; Srivastava, R; Suib, SL; Li, Y; Parnas, RS. Performance of batch, fed-batch, and continuous A--B--E fermentation with pH-control. Bioresource technology 102:4241--4250 (2011).
[BIO]
Li, S; Srivastava, R; Parnas, RS. Separation of 1-butanol by pervaporation using a novel tri-layer PDMS composite membrane. Journal of Membrane Science 363:287--294 (2010).
[BIO MAT]
Jain, R; Srivastava, R. Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli. BMC systems biology 3:121 (2009).
[BIO COMP]
Peterson, DE; Srivastava, R; White, JR; Lalla, RV; Loew, LM. Systems biology of mucosal injury in cancer patients. Journal of Clinical Oncology 26:9634--9634 (2008).
[BIO COMP]
Srivastava, R; Varner, J. Emerging technologies: systems biology. Biotechnology progress 23:24--27 (2007).
[BIO]
Yilmaz, O; Achenie, LE; Srivastava, R. Systematic tuning of parameters in support vector clustering. Mathematical biosciences 205:252--270 (2007).
[BIO COMP]
Peterson, D; Lalla, R; Srivastava, R; Loew, L. Mucositis in cancer patients: Prototypic semi-mechanistic kinetic model. Journal of Clinical Oncology 25:19617--19617 (2007).
[BIO COMP]
Jain, R; Knorr, AL; Bernacki, J; Srivastava, R. Investigation of bacteriophage MS2 viral dynamics using model discrimination analysis and the implications for phage therapy. Biotechnology progress 22:1650--1658 (2006).
[BIO COMP]
Knorr, AL; Jain, R; Srivastava, R. Bayesian-based selection of metabolic objective functions. Bioinformatics 23:351--357 (2006).
[BIO COMP]
Knorr, AL; Srivastava, R. Evaluation of HIV-1 kinetic models using quantitative discrimination analysis. Bioinformatics 21:1668--1677 (2004).
[BIO COMP]
Srivastava, R; Peterson, M; Bentley, W. Stochastic kinetic analysis of the Escherichia coli stress circuit using $\sigma$32-targeted antisense. Biotechnology and Bioengineering 75:120--129 (2001).
[BIO COMP]
Srivastava, R; Peterson, M; Bentley, W. Stochastic kinetic analysis of the Escherichia coli stress circuit using $\sigma$32-targeted antisense. Biotechnology and Bioengineering 75:120--129 (2001).
[BIO COMP]
Srivastava, R; Cha, HJ; Peterson, MS; Bentley, WE. Antisense Downregulation of $\varsigma$32 as a Transient Metabolic Controller in Escherichia coli: Effects on Yield of Active Organophosphorus Hydrolase. Appl. Environ. Microbiol. 66:4366--4371 (2000).
[BIO]
Cha, HJ; Srivastava, R; Vakharia, VN; Rao, G; Bentley, WE. Green fluorescent protein as a noninvasive stress probe in resting Escherichia coli cells. Appl. Environ. Microbiol. 65:409--414 (1999).
[BIO]