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Babur O.,Sloan Kettering Cancer Center | Aksoy B.A.,Sloan Kettering Cancer Center | Aksoy B.A.,Tri Institutional Training Program | Rodchenkov I.,University of Toronto | And 3 more authors.
Bioinformatics | Year: 2014

Motivation: BioPAX is a standard language for representing complex cellular processes, including metabolic networks, signal transduction and gene regulation. Owing to the inherent complexity of a BioPAX model, searching for a specific type of subnetwork can be non-trivial and difficult.Results: We developed an open source and extensible framework for defining and searching graph patterns in BioPAX models. We demonstrate its use with a sample pattern that captures directed signaling relations between proteins. We provide search results for the pattern obtained from the Pathway Commons database and compare these results with the current data in signaling databases SPIKE and SignaLink. Results show that a pattern search in public pathway data can identify a substantial amount of signaling relations that do not exist in signaling databases.Availability: BioPAX-pattern software was developed in Java. Source code and documentation is freely available at pattern under Lesser GNU Public License.Contact: Supplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author .

Demir E.,Sloan Kettering Cancer Center | Babur O.,Sloan Kettering Cancer Center | Rodchenkov I.,University of Toronto | Aksoy B.A.,Sloan Kettering Cancer Center | And 6 more authors.
PLoS Computational Biology | Year: 2013

A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from © 2013 Demir et al.

Roble G.S.,Tri institutional Training Program | Roble G.S.,Sloan Kettering Cancer Center | Boteler W.,XpressBio | Riedel E.,Sloan Kettering Cancer Center | And 2 more authors.
Journal of the American Association for Laboratory Animal Science | Year: 2012

Mites of 3 genera - Myobia, Myocoptes, and Radfordia - continue to plague laboratory mouse facilities, even with use of stringent biosecurity measures. Mites often spread before diagnosis, predominantly because of detection difficulty. Current detection methods have suboptimal sensitivity, are time-consuming, and are costly. A sensitive serodiagnostic technique would facilitate detection and ease workload. We evaluated whether total IgE increases could serve as a serodiagnostic marker to identify mite infestations. Variables affecting total IgE levels including infestation duration, sex, age, mite species, soiled-bedding exposure, and ivermectin treatment were investigated in Swiss Webster mice. Strain- and pinworm-associated effects were examined by using C57BL/6 mice and Swiss Webster mice dually infested with Syphacia obvelata and Aspiculuris tetraptera, respectively. Mite infestations led to significant increases in IgE levels within 2 to 4 wk. Total IgE threshold levels and corresponding sensitivity and specificity values were determined along the continuum of a receiver-operating characteristic curve. A threshold of 81 ng/mL was chosen for Swiss Webster mice; values above this point should trigger screening by a secondary, more specific method. Sex-associated differences were not significant. Age, strain, and infecting parasite caused variability in IgE responses. Mice exposed to soiled bedding showed a delayed yet significant increase in total IgE. Treatment with ivermectin reduced total IgE levels within 2 wk. Our data suggest that increases in total IgE in Swiss Webster and C57BL/6 mice warrant investigation, especially because mite infestations can rapidly elevate total IgE levels. We propose that using total IgE levels routinely in serologic panels will enhance biosecurity. Copyright 2012 by the American Association for Laboratory Animal Science.

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