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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
On my way to ICFP/CUFP/OUD and more in Copenhagen
I’m on my way to ICFP, CUFP, OUD, and more in Copenhagen. Especially interesting to me this year are the several biology related talks and events: ICFP: Sneaking Around concatMap — Efficient Combinators for Dynamic Programming, Christian Höner zu Siederdissen … Continue reading
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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
A Domain Specific Language Stack for Bio HPC
We have given several presentations on our DSL approach to the management and analysis of big-data in the field of Biology. Now, with Karl Ward, we have been extending this approach to the systems layer, enabling more robust management and … Continue reading
Shonan Meeting
I’ll be back in Tokyo, this time for the Shonan Meeting on Bridging the Theory of Staged Programming Languages and the Practice of High-Performance Computing. My talk will be on BINQ, a domain-specific-language for genomic computations.
A Comparison of Single-cell RNA-seq with Gene Expression Microarrays
Abstract Single-cell RNA-sequencing (SCRS) is a powerful technique to address biological variation by profiling expression in single cells and samples with low RNA input. Previous studies have shown that gene expression is highly correlated across array and standard RNA-sequencing technologies. … Continue reading
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