Publications

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Recent Publications

Publication Title Publication Date Author Publisher
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli February 10, 2017 Millard P,  Smallbone K, Mendes P PLoS Computational Biology
Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective February 6, 2017 Chifman J, Arat S, Deng Z, Lemler E, Pino J, Harris L, Kochen M, Lopez C, Akman S, Torti F, Torti S, Laubenbacher R PLoS Computational Biology
Optimization and control of agent-based models in biology: a perspective January 2017 An G, Fitzpatrick BG, Christley S, Federico P, Kanarek A, Neilan RM, Oremland M, Salinas R, Laubenbacher R, Lenhart S  Bull Math Biology
The Minimal Hitting Set Generation Problem: Algorithms and Computation October  2016 Vera-Licona P, Gainer-Dewar A SIAM Journal on Discrete Mathematics
Identification of control targets in molecular Boolean network models via computational algebra September 2016 Murrugarra D, Veliz-Cuba A,  Aguilar B, Laubenbacher R BMC Systems Biology
AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms August 2016 Hosny A, Vera-Licona P, Laubenbacher R, Favre T Bioinformatics
QuIN: Global interrogation and visualization of 3-D chromatin interaction networks June 2016 Thibodeau A, Marquez E, Luo O, Ruan Y, Menghi F, Shin D, Stitzel M, Vera-Licona P, Ucar D. PLoS Computational Biology
Feedback Regulation in a Cancer Stem Cell Model can Cause an Allee Effect April 2016 Konstorum A, Hillen T, Lowengrub J. Bull Math Biology
A computational model of invasive aspergillosis in the lung and the role of iron April 2016 Oremland M , Michels KR,  Bettina AM, Lawrence C, Mehrad B,  Laubenbacher R BMC Systems Biology
Costimulation Endows Immunotherapeutic CD8 T Cells with IL-36 Responsiveness during Aerobic Glycolysis January 2016 Tsurutani N, Mittal P, St Rose MC, Ngoi SM, Svedova J, Menoret A, Treadway FB, Laubenbacher R, Suárez-Ramírez JE, Cauley LS, Adler AJ, Vella AT The Journal of Immunology
Triadic analysis of affliation networks December 2015 Brunson J C Network Science
Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly November 2015 Mendes P, Oliver SG, Kell DB Trends in Pharmacological Sciences
ChEBI in 2016: Improved services and an expanding collection of metabolites October 2015 Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. Nucleic acids research
Impact of kinetic isotope effects in isotopic studies of metabolic systems September 2015 Millard P, Portais J-C, Mendes P BMC Systems Biology
Iron acquisition and oxidative stress response in aspergillus fumigatus April 2015 Brandon M, Howard B, Lawrence C, Laubenbacher R BMC Systems Biology
Stress tolerant transgenic plants over-expressing ascorbic acid and cell wall synthesis genes April 2015 Nessler C , Lorence A , Chevone B , Mendes P US Patents
Silence on the relevant literature and errors in implementation April 2015 Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN Nature Biotechnology
Optimal harvesting for a predator-prey agent-based model using difference equations March 2015 Oremland M, Laubenbacher R Bull Math Biology
A network biology approach to denitrification in Pseudomonas aeruginosa February 2015 Arat S, Bullerjahn GS, Laubenbacher R PLoS One
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology February 2015 Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR BMC Systems Biology
A Viewpoint of Security for Digital Health Care in the United States: What’s There? What Works? What’s Needed? May 2014 Demurjian S, Alberto De la Rosa Algarín, Bi J, Berhe S, Agresta T, Wang X, Blechner M The International Journal of Privacy and Health Information Mgmt
A systems biology approach to iron metabolism 2014 Chifman J, Laubenbacher R, Torti SV Advances in Experimental Medicine and Biology
A mathematical model of skeletal muscle disease and immune response in the mdx mouse 2014 Jarrah AS, Castiglione F, Evans NP, Grange RW, Laubenbacher R BioMed Research International
Steady state analysis of Boolean molecular network models via model reduction and computational algebra 2014 Veliz-Cuba A, Aguilar B, Hinkelmann F, Laubenbacher R BMC Bioinformatics
Using difference equations to find optimal tax structures on the SugarScape 2014 Oremland M, Laubenbacher R Economic Interaction and Coordination
Zinc depletion regulates the processing and secretion of IL-1β 2014 Summersgill H, England H, López-Castejón G, Lawrence CB, Luheshi NM, Pahle J, Mendes P, Brough D Cell Death and Disease
Bridging the gaps in systems biology 2014 Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M Molecular Genetics & Genomics
Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK 2014 Mendes P, Dada JO, Smallbone K Springer
An Algebra-Based Method for Inferring Gene Regulatory Networks 2014 Vera-Licona P, Jarrah AS, Garcia LD, Mcgee J, Laubenbacher R BMC Systems Biology