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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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• SciCrunch
• 2 years ago - submitted by Craig Praul

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• NIF
• 2 years 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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• RRID
• 2 years ago - submitted by Marco Cappellato

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• RRID
• 2 years ago - by Anonymous

Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group and single subject functional magnetic resonance imaging data.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Supplemental Data

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• RRID
• 2 years 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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• RRID
• 2 years 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
• 2 years 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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• SciCrunch
• 2 years 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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• RRID
• 2 years 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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• RRID
• 2 years ago - submitted by Melanie Weigert

• SciCrunch
• 2 years ago - by Anonymous

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• NIF
• 2 years ago - by Anonymous

Antibody for western blot or inmunoprecipitation.

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• RRID
• 2 years ago - submitted by Zhihui Ma

Antibody for western blot or inmunoprecipitation.

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• RRID
• 2 years ago - submitted by Zhihui Ma

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• NIF
• 2 years ago - by Anonymous

The Rat Leptin ELISA is used to measure & quantify Leptin levels in Metabolism & Endocrine research.

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• dkNET
• 2 years ago - submitted by Mahad Ahmed

GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms.

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• RRID
• 2 years ago - submitted by Agata Kilar

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• NIF
• 2 years ago - by Anonymous

Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values.

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• RRID
• 2 years ago - submitted by Nadine Tatto