Workflow Analysis Driven Recommendations for Integration of Electronically-Enhanced Sexually Transmitted Infection Screening Tools in Pediatric Emergency Departments. - Howe, Jessica L.; Reed, Jennifer L.; Adams, Katharine T.; Elsholz, Cara; Augustine, Erin M.; Cruz, Andrea T.; Mollen, Cynthia; Pickett, Michelle L.; Schmidt, Sara; Stukus, Kristin; Ratwani, Raj M.; Goyal, Monika K. (J. Medical Syst., 2020)

Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4. - Ong, Wai Kit; Courtney, Dylan K.; Pan, Shu; Andrade, Ramon Bonela; Kiley, Patricia J.; Pfleger, Brian F.; Reed, Jennifer L. (PLoS Comput. Biol., 2020)

Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis. - Tian, Mingyuan; Reed, Jennifer L. (Bioinform., 2018)

Improving flux predictions by integrating data from multiple strains. - Long, Matthew R.; Reed, Jennifer L. (Bioinform., 2017)

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community. - Hamilton, Joshua J.; Contreras, Montserrat Calixto; Reed, Jennifer L. (PLoS Comput. Biol., 2015)

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. - Ong, Wai; Vu, Trang T.; Lovendahl, Klaus N.; Llull, Jenna M.; Serres, Margrethe H.; Romine, Margaret F.; Reed, Jennifer L. (BMC Syst. Biol., 2014)

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models. - Cotten, Cameron; Reed, Jennifer L. (BMC Bioinform., 2013)

Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. - Baumler, David J.; Ma, Bing; Reed, Jennifer L.; Perna, Nicole T. (BMC Syst. Biol., 2013)

Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. - Schellenberger, Jan; Zielinski, Daniel C.; Choi, Wing; Madireddi, Sunthosh; Portnoy, Vasiliy; Scott, David A.; Reed, Jennifer L.; Osterman, Andrei; Palsson, Bernhard Ø. (BMC Syst. Biol., 2012)

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142. - Vu, Trang T.; Stolyar, Sergey M.; Pinchuk, Grigoriy E.; Hill, Eric A.; Kucek, Leo A.; Brown, Roslyn N.; Lipton, Mary S.; Osterman, Andrei; Fredrickson, Jim K.; Konopka, Allan E.; Beliaev, Alexander S.; Reed, Jennifer L. (PLoS Comput. Biol., 2012)

Shrinking the Metabolic Solution Space Using Experimental Datasets. - Reed, Jennifer L. (PLoS Comput. Biol., 2012)

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. - Thiele, Ines; Hyduke, Daniel R.; Steeb, Benjamin; Fankam, Guy; Allen, Douglas K.; Bazzani, Susanna; Charusanti, Pep; Chen, Feng-Chi; Fleming, Ronan M. T.; Hsiung, Chao A.; Keersmaecker, Sigrid C. J. De; Liao, Yu-Chieh; et al. (BMC Syst. Biol., 2011)

iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. - Imam, Saheed; Yilmaz, Safak; Sohmen, Ugur; Gorzalski, Alexander S.; Reed, Jennifer L.; Noguera, Daniel R.; Donohue, Timothy J. (BMC Syst. Biol., 2011)

The evolution of metabolic networks of E. coli. - Baumler, David J.; Peplinski, Roman G.; Reed, Jennifer L.; Glasner, Jeremy D.; Perna, Nicole T. (BMC Syst. Biol., 2011)

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. - Kim, Joonhoon; Reed, Jennifer L. (BMC Syst. Biol., 2010)

Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation. - Pinchuk, Grigoriy E.; Hill, Eric A.; Geydebrekht, Oleg V.; Ingeniis, Jessica De; Zhang, Xiaolin; Osterman, Andrei; Scott, James H.; Reed, Samantha B.; Romine, Margaret F.; Konopka, Allan E.; Beliaev, Alexander S.; Fredrickson, Jim K.; et al. (PLoS Comput. Biol., 2010)

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models. - Barua, Dipak; Kim, Joonhoon; Reed, Jennifer L. (PLoS Comput. Biol., 2010)

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. - Raghunathan, Anu; Reed, Jennifer L.; Shin, Sook-Il; Palsson, Bernhard Ø.; Daefler, Simon (BMC Syst. Biol., 2009)

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli. - Resendis-Antonio, Osbaldo; Reed, Jennifer L.; Encarnación, Sergio; Collado-Vides, Julio; Palsson, Bernhard Ø. (PLoS Comput. Biol., 2007)