Computer science Integrative Approaches for Mining High-Throughput Genomic Data UNIVERSITY OF CALIFORNIAIRVINE Pierre Baldi DailyKennethThe study of transcriptional regulation encompasses many fields in molecular, cell, evolutionary, and computational biology. For any given genome, only a small fraction of ...
Principal component analysis (PCA) has gained popularity as a method for the analysis of high-dimensional genomic data. However, it is often difficult to interpret the results because the principal components are linear combinations of all variables, and the coefficients (loadings) are typically non...
A Perspective on the open-source and open-development software project Bioconductor provides an overview for prospective users and developers dealing with high-throughput data in genomics and molecular biology. Bioconductor is an open-source, open-develo
Single-cell sequencing: 10x Genomics platform, for high-throughput single-cell sequencing for transcriptomics and epigenetics analysis. NanoString: nCounter and GeoMx platforms, for high-throughput gene expression analysis and spatial biology.Standard Genomics Services Sample preparation: DNA/RNA extraction...
This thesis deals with integrative analysis of two (different) multi-dimensional data types in the context of genomic cancer research. Firstly, simultaneous clustering of two high-throughput data sets optimizing the output of iCluster program. Secondly, developing a novel the Gene Set Score (GSS) ...
Given recent advances in the generation of high-throughput data such as whole-genome genetic variation and transcriptome expression, it is critical to come up with novel methods to integrate these heterogeneous datasets and to assess the significance of identified phenotype-genotype relationships. Recent...
Gene expression, transcription factor, and methylation analysis of Next-Generation Sequencing (NGS) data, including RNA-Seq and ChIP-SeqHigh-throughput sequencing methods generate large amounts of sequence data and require robust computational tools for further analysis. Bioinformatics Toolbox™ provides...
GRiD-MG for high throughput, multiplex estimations of growth rate. a Pipeline for GRiD-MG. Sample reads from a dataset are mapped to a GRiD-MG database. The database can be updated using metagenomic bins or newly sequenced genomes. Two output files are generated for every sample; a text ...
bíogo/hts provides a Go native implementation of theSAM specificationfor SAM and BAM alignment formats commonly used for representation of high throughput genomic data, the BAI, CSI and tabix indexing formats, and the BGZF blocked compression format. The bíogo/hts packages perform parallelized read...
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhichao Zhou, Patricia Q. Tran, Adam M. Breister, Yang Liu, Kristopher Kieft, Elise S. Cowley, Ulas Karaoz & Karthik Anantharaman Microbio...