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Recent Publications

Publication Title Publication Date Author Publisher

Macrophage mediated recognition and clearance of Borrelia burgdorferinelicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation

April 2021

Sarah J. Benjamin, Kelly L. Hawley, Paola Vera-Licona, Carson J. La Vake, Jorge L. Cervantes, Rachel Burns, Oscar Luo, Yijun Ruan, Melissa J. Caimano, Justin D. Radolf, Juan C. Salazar

BMC Immunology

Quantitative Medicine and Reflection on Summer Research in Mathematical Biology Summer 2020 Sun M, Koshy-Chenthittayli S, D’Souza N Harvard Educational Review
Systems biology of ferroptosis: a modeling approach (source code) Feb 2020 Konstorum A Mendeley Data
Systems biology of ferroptosis: A modeling approach May 2020 Konstorum A, Tesfay L, Paul BT, Torti FM, Laubenbacher R, Torti SV Journal of Theoretical Biology
Control of Intracellular Molecular Networks using Algebraic Methods Sept 2019 Sordo Vieira L, Laubenbacher R, Murrugarra D Bull Math Biology
Connecting the molecular function of microRNAs to cell differentiation dynamics Sep 25, 2019 Posner R, Laubenbacher R Journal of the Royal Society Interface
A mathematical model of combined CD8 T cell costimulation by 4-1BB (CD137) and OX40 (CD134) receptors July 26, 2019 Konstorum A, Vella AT, Adler AJ, Laubenbacher R Scientific Reports
Steroyl-CoA Desaturase 1 (SCD1) protects ovarian cancer cells from ferroptotic cell death July 03, 2019 Tesfay L, Paul BT, Konstorum A, Deng Z, Cox AO, Lee J, Furdui CM, Hegde P, Torti FM, Torti SV Cancer Research
Neoantigens retention in patient derived xenograft models mediates autologous T cells activation in ovarian cancer March 30, 2019 Want MY, Konstorum A, Huang RY, Jain V, Matsueda S, Tsuji T, Lugade A, Odunsi K, Koya R, Battaglia S OncoImmunology
Dynamics of semilattice networks with strongly connected dependency graph January, 2019 Veliz-Cuba A,Laubenbacher R Automatica
An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study July 26, 2018 Parmar JH , Quintana J, Ramirez D, Laubenbacher R, Arguello J, Mendes P Molecular Microbiology
A systems biology approach to understanding the pathophysiology of high grade serous ovarian cancer: focus on iron and fatty acid metabolism July 01, 2018 Konstorum A, Lynch ML, Torti SV, Torti FM, Laubenbacher R OMICS: A Journal of Integrative Biology
Three-Dimensional Spatiotemporal Modeling of Colon Cancer Organoids Reveals that Multimodal Control of Stem Cell Self-Renewal is a Critical Determinant of Size and Shape in Early Stages of Tumor Growth May 01, 2018 Yan H, Konstorum A, Lowengrub JS Bull Math Biology
Contribution of three-dimensional architecture and tumor-associated fibroblasts to hepcidin regulation in breast cancer April 26, 2018 Blanchette-Farra N, Kita D, Konstorum A, Tesfay L, Lemler D, Hegde P, Claffey KP, Torti FM, Torti SV Oncogene
An Overview of Network-Based and Network-Free Approaches for Stochastic Simulation of Biochemical Systems January 31, 2018 Gupta A, Mendes P Computation
Diagonal equations over unramified extensions of Q_p April  20, 2018 Leep DB, Sordo Vieira L Bulletin of the London Mathematical Society
Activation of the HGF/c-Met axis in the tumor microenvironment: A multispecies model November 30, 2017 Konstorum A, Lowengrub JS Journal of Theoretical Biology
Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin October 31, 2017 Thibodeau A, Márquez E, Shin D, Vera-Licona P, Ucar D Scientific Reports
CD169+ macrophages orchestrate innate immune responses by regulating bacterial localization in the spleen October 06, 2017 Perez O, Yeung S, Vera-Licona P, Romagnoli P, Samji T, Ural B, Maher L, Tanaka M,  Khanna K Science Immunology
Applications of network analysis to routinely collected health care data: a systematic review February 01, 2018 Brunson J C, Laubenbacher R Journal of the American Medical Informatics Association
Addressing current challenges in cancer immunotherapy with mathematical and computational modeling June 28, 2017 Konstorum A, Vella AT, Adler AJ, Laubenbacher RC Journal of the Royal Society Interface
Effects of research complexity and competition on the incidence and growth of coauthorship in biomedicine March 22, 2017 Brunson J C, Wang X, Laubenbacher R PLoS One
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