Research Areas: Quantitative Systems Biology, Computational Materials Design, Applied Machine Learning, & Applied Evolutionary Dynamics
Research Areas: Quantitative Systems Biology, Computational Materials Design, Applied Machine Learning, & Applied Evolutionary Dynamics
Chelius, C; Huso, W; Reese, S; Doan, A; Lincoln, S; Lawson, K; Tran, B; Purohit, R; Glaros, T; Srivastava, R; and others. Dynamic transcriptomic and phosphoproteomic analysis during cell wall stress in Aspergillus nidulans. Molecular & Cellular Proteomics (2020).
[BIO]
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]
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]
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]