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Core provides services for maintaining Specific Pathogen Free status in macaque breeding colonies. Services include antibody detection in serum or plasma by Luminex-based assays and /or ELISA for SPF-agents like SIV, SRV, STLV, B virus, SFV. CMV, RRV, SVV, SV40, and LCV, and non-SPF infectious agents like measles, Burkholderia pseudomallei, Tripanosoma cruzi, Mycobacterium tuberculosis, and SARS-CoV-2. Offers services of cytokines quantification, and molecular assays for detection of SRV, CMV, SFV, and RRV.Performs nucleic acid purification from blood and tissue samples as well as qPRC for SIV viral load in plasma, cells, or tissue.

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• SciCrunch
• 7 months ago - submitted by Edyta Vieth

Immunology Assay Core provides several immunology services to core and affiliate investigators. Offers multicolor staining for flow cytometry, access to inventory of commonly used antibodies, reagent compounding, sample processing such as cell isolation, automated cell separation through RoboSep, and irradiation of biological samples.Offers multiplex assays using MESO QuickPlex SQ 120 Imager to investigators.

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• SciCrunch
• 7 months ago - submitted by Edyta Vieth

Anatomic Pathology Core is responsible for post-mortem examinations, tissue collection and distribution, fixation, processing, slide preparation, routine and special staining, and diagnostic gross and histologic pathology services. Processes and interprets biopsy specimens for both research and diagnostic purposes and provides tissue trimming, paraffin processing, sectioning, and routine and special staining for clinical and research staff and faculty. APC works closely with clinical veterinarians, and through diagnostic pathology on biopsies and necropsies, plays major role in monitoring and maintaining health of animals in breeding colonies.

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• 7 months ago - submitted by Edyta Vieth

Software toolkit to check reliability and to make some analysis of data from Live Mouse Tracker experiments. LMT stores data in SQLite files but LMT-toolkit makes it easy to compute and extract behavioral profiles for each animal tested.

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• 7 months ago - submitted by Kevin Chavez Lopez

With Stereo Investigator, you can perform unbiased quantification of cell populations, lengths of fibers or vessels, or area and volume of regions using design-based stereology, a set of methods for rigorous quantitative analysis of the size, shape, and number of objects. Stereo Investigator leverages unbiased statistical sampling, that helps enable researchers to count, measure, and precisely quantify visible features in microscope specimens without needing to examine the entire specimen to obtain statistically valid results.

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• 7 months ago - by Anonymous

Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data.

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• 7 months ago - submitted by Anita Bandrowski

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• 8 months ago - by Anonymous

Xenopus laevis defolliculated oocytes ready to use for mRNA or cDNA injections for expression studies.

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• 8 months ago - submitted by Ecocyte Bioscience

Our primary goal is to identify and quantify the small (

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• 8 months ago - submitted by Nigel Deighton

he Genomics Core Facility provides services using several different next-generation sequencing platforms. Applications supported include: Whole-genome and transcriptome sequencing of non-model organisms Amplicon sequencing for metagenomic studies Differential expression analysis of mRNA and miRNA Degradome sequencing ChIP and RIP sequencing In addition, the facility continues to offer a variety of traditional services, including: Sanger DNA sequencing Genotyping of SNPs and VNTRs Real-time qPCR

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• 8 months ago - submitted by Nigel Deighton

THIS TEST is a

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• 8 months ago - by Anonymous

Background Biomarker discovery exploiting feature importance of machine learning has risen recently in the microbiome landscape with its high predictive performance in several disease states. To have a concrete selection among a high number of features, Recursive Feature Elimination (RFE) has been widely used in the bioinformatics field. However, machine learning based RFE has factors that decrease the stability of feature selection. In this paper, we suggested methods to improve stability while sustaining performance. Results We exploited the abundance matrices of the gut microbiome (283 taxa at species level and 220 at genus level) to classify between patients with inflammatory bowel disease (IBD) and healthy control (1569 samples). We found that applying an already published data transformation before RFE improves feature stability significantly. Moreover, we performed an in-depth evaluation of different variants of the data transformation and identify those that demonstrate better improvement in stability while not sacrificing classification performance. To ensure a robust comparison, we evaluated stability using various similarity metrics, distances, the common number of features, and the ability to filter out noise features. We were able to confirm that the mapping by the Bray-Curtis similarity matrix before RFE consistently improves the stability while maintaining good performance. Multi-Layer Perceptron (MLP) algorithm exhibited the highest performance among eight different machine learning algorithms when a large number of features (a few hundred) were considered based on the best performance across 100 bootstrapped internal test sets. Conversely, when utilizing only a limited number of biomarkers as a tradeoff between optimal performance and method generalizability, the random forest algorithm demonstrated the best performance. Using the optimal pipeline we developed, we identified fourteen biomarkers for IBD at the species level and analyzed their roles using SHapley Additive exPlanations. Conclusion Taken together our work showed not only how to improve biomarker discovery in the metataxonomic field without sacrificing classification performance, but also provided useful insights for future comparative studies.

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• 8 months ago - submitted by Marco Cappellato

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• 8 months ago - by Anonymous

Supplemental Data

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• 9 months ago - submitted by Jing Wei

Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Atlas Network, and SCORCH. Supports processing of 10x 3' single-cell and single-nucleus gene expression (GEX) and chromatin accessibility (ATAC) data generated with the 10x Genomics Multiome assay.

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• 9 months ago - submitted by Kaylee Mathews

Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.

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• SciCrunch
• 9 months ago - submitted by Edyta Vieth

Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

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• 9 months ago - submitted by Edyta Vieth

Software tool for simulation of antigen experienced adaptive immune receptor repertoire datasets for benchmarking of machine learning methods.

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• 9 months ago - submitted by Chakravarthi Kanduri

A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files

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• 9 months ago - submitted by Melanie Weigert

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• 9 months ago - by Anonymous