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Tag Archives: Bioinformatics
Challenges in Genomics Data Visualization
Genomics, like many fields, is generating data at an ever increasing rate with the promise to enable personalized medicine, improve agriculture, and advance fundamental research. Data visualization is a key component of the scientific process and often the bottleneck in … Continue reading
A Validated Regulatory Network for Th17 Cell Specification
Abstract Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining … Continue reading
Functional Big-Data Genomics
Abstract High-throughput genomic sequencing is characterized by large diverse datasets and numerous analysis methods. It is normal for an individual bioinformatician to work with thousands of data files and employ hundreds of distinct computations during the course of a single … Continue reading
Biocaml: The OCaml Bioinformatics Library
Abstract Biology is an increasingly computational discipline due to rapid advances in experimental techniques, especially DNA sequencing, that are generating data at unprecedented rates. The computational techniques needed range from the complex (.e.g algorithms, distributed computing) to the simple (e.g. … Continue reading
Managing and Analyzing Big-Data in Genomics
Abstract Biology is an increasingly computational discipline. Rapid advances in experimental techniques, especially DNA sequencing, are generating data at exponentially increasing rates. Aside from the algorithmic challenges this poses, researchers must manage large volumes and innumerable varieties of data, run … Continue reading
The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics
Abstract Biological data is often tabular but finding statistically valid connections between entities in a sequence of tables can be problematic – for example, connecting particular entities in a drug property table to gene properties in a second table, using … Continue reading
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
Abstract We present an integrative machine learning method, incRNA, for whole-genome identification of noncoding RNAs (ncRNAs). It combines a large amount of expression data, RNA secondary-structure stability, and evolutionary conservation at the protein and nucleic-acid level. Using the incRNA model … Continue reading
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Abstract We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin … Continue reading
RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries
Abstract Summary: The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle. Moreover, sequence reads from a specific individual can contain sufficient information … Continue reading
