PubMed comprises more than 25 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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 |