Recent Publications

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High temporal resolution of glucosyltransferase dependent and independent effects of Clostridium difficile toxins across multiple cell types.

Related Articles High temporal resolution of glucosyltransferase dependent and independent effects of Clostridium difficile toxins across multiple cell types. BMC Microbiol. 2015 Feb 4;15(1):7 Authors: D Auria KM, Bloom MJ, Reyes Y, Gray MC, van Opstal EJ, Papin JA, Hewlett EL Abstract Background Clostridium difficile toxins A and B (TcdA and TcdB), considered to be essential for C. difficile infection, affect the morphology of several cell types with di...

Miniaturized plate readers for low-cost, high-throughput phenotypic screening.

Related Articles Miniaturized plate readers for low-cost, high-throughput phenotypic screening. J Lab Autom. 2015 Feb;20(1):51-5 Authors: Jensen PA, Dougherty BV, Moutinho TJ, Papin JA Abstract We present a miniaturized plate reader for measuring optical density in 96-well plates. Our standalone reader fits in most incubators, environmental chambers, or biological containment suites, allowing users to leverage their existing laboratory infrastructure. The dev...

A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest.

Related Articles A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest. PLoS One. 2014;9(9):e105631 Authors: Newhook TE, Blais EM, Lindberg JM, Adair SJ, Xin W, Lee JK, Papin JA, Parsons JT, Bauer TW Abstract BACKGROUND: Currently, prognostication for pancreatic ductal adenocarcinoma (PDAC) is based upon a coarse clinical staging system. Thus, more accurate prognostic tests are need...

MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.

Related Articles MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. Bioinformatics. 2014 May 1;30(9):1327-8 Authors: Jensen PA, Papin JA Abstract MOTIVATION: Metabolic reaction maps allow visualization of genome-scale models and high-throughput data in a format familiar to many biologists. However, creating a map of a large metabolic model is a difficult and time-consuming process. MetDraw fully automates the ...

Clinical, molecular and genetic validation of a murine orthotopic xenograft model of pancreatic adenocarcinoma using fresh human specimens.

Related Articles Clinical, molecular and genetic validation of a murine orthotopic xenograft model of pancreatic adenocarcinoma using fresh human specimens. PLoS One. 2013;8(10):e77065 Authors: Walters DM, Stokes JB, Adair SJ, Stelow EB, Borgman CA, Lowrey BT, Xin W, Blais EM, Lee JK, Papin JA, Parsons JT, Bauer TW Abstract BACKGROUND: Relevant preclinical models that recapitulate the key features of human pancreatic ductal adenocarcinoma (PDAC) are need...

Comparative metabolic systems analysis of pathogenic Burkholderia.

Related Articles Comparative metabolic systems analysis of pathogenic Burkholderia. J Bacteriol. 2014 Jan;196(2):210-26 Authors: Bartell JA, Yen P, Varga JJ, Goldberg JB, Papin JA Abstract Burkholderia cenocepacia and Burkholderia multivorans are opportunistic drug-resistant pathogens that account for the majority of Burkholderia cepacia complex infections in cystic fibrosis patients and also infect other immunocompromised individuals. While they share ...

Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation.

Related Articles Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation. PLoS One. 2013;8(10):e78011 Authors: Biggs MB, Papin JA Abstract Multiscale modeling is used to represent biological systems with increasing frequency and success. Multiscale models are often hybrids of different modeling frameworks and programming languages. We present the MATLAB-NetLogo extension (MatNet) as a novel tool for multiscale modeling. We demo...

MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab.

Related Articles MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab. J Transl Med. 2013;11:218 Authors: Wagenseller AG, Shada A, D'Auria KM, Murphy C, Sun D, Molhoek KR, Papin JA, Dutta A, Slingluff CL Abstract BACKGROUND: Targeted therapies directed at commonly overexpressed pathways in melanoma have clinical activity in numerous trials. Little is known about how these therapies influence microRNA (mi...

In vivo physiological and transcriptional profiling reveals host responses to Clostridium difficile toxin A and toxin B.

Related Articles In vivo physiological and transcriptional profiling reveals host responses to Clostridium difficile toxin A and toxin B. Infect Immun. 2013 Oct;81(10):3814-24 Authors: D'Auria KM, Kolling GL, Donato GM, Warren CA, Gray MC, Hewlett EL, Papin JA Abstract Toxin A (TcdA) and toxin B (TcdB) of Clostridium difficile cause gross pathological changes (e.g., inflammation, secretion, and diarrhea) in the infected host, yet the molecular and cellu...

Multiscale computational models of complex biological systems.

Related Articles Multiscale computational models of complex biological systems. Annu Rev Biomed Eng. 2013;15:137-54 Authors: Walpole J, Papin JA, Peirce SM Abstract Integration of data across spatial, temporal, and functional scales is a primary focus of biomedical engineering efforts. The advent of powerful computing platforms, coupled with quantitative data from high-throughput experimental methodologies, has allowed multiscale modeling to expand as a...

A community-driven global reconstruction of human metabolism.

Related Articles A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25 Authors: Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Pric...

Linking genome-scale metabolic modeling and genome annotation.

Related Articles Linking genome-scale metabolic modeling and genome annotation. Methods Mol Biol. 2013;985:61-83 Authors: Blais EM, Chavali AK, Papin JA Abstract Genome-scale metabolic network reconstructions, assembled from annotated genomes, serve as a platform for integrating data from heterogeneous sources and generating hypotheses for further experimental validation. Implementing constraint-based modeling techniques such as flux balance analysis (FB...

Mechanistic systems modeling to guide drug discovery and development.

Related Articles Mechanistic systems modeling to guide drug discovery and development. Drug Discov Today. 2013 Feb;18(3-4):116-27 Authors: Schmidt BJ, Papin JA, Musante CJ Abstract A crucial question that must be addressed in the drug development process is whether the proposed therapeutic target will yield the desired effect in the clinical population. Pharmaceutical and biotechnology companies place a large investment on research and development, long...

Integration of expression data in genome-scale metabolic network reconstructions.

Related Articles Integration of expression data in genome-scale metabolic network reconstructions. Front Physiol. 2012;3:299 Authors: Blazier AS, Papin JA Abstract With the advent of high-throughput technologies, the field of systems biology has amassed an abundance of "omics" data, quantifying thousands of cellular components across a variety of scales, ranging from mRNA transcript levels to metabolite quantities. Methods are needed to not only integrat...