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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
Milner on science and language
“[Languages] should be treated as a part of a modelling theory. Up to now I don’t think we had sufficient incentive to make sure that our languages are close to scientific models. It’s only with the onset of computation as … Continue reading
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DREAM and RECOMB Satellite Conferences
I’m spending the week at the 3rd Annual Joint Conference on Systems Biology, Regulatory Genomics, and Reverse Engineering Challenges.
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Platform independent .bashrc file
The number of computers I have accounts on has recently exploded, and manually editing my .bashrc file on each of these computers started getting tedious. I decided to resolve this by writing a single .bashrc file that can be copied … Continue reading
Goodbye Yale. Hello NYU.
It’s official. I’m moving to NYU. This will be a great opportunity for me to push my agenda of bringing functional programming techniques to biology. I’m fortunate enough to be working there with Kris Gunsalus and Rich Bonneau. Many thanks … Continue reading
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Poincare on the necessity of hypothesis
“I consider a priori a law… Without this belief, … interpolation would be impossible; no law could be deduced from a finite number of observations; science would not exist.” — Poincare (1913, p. 170)
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Carnap on the challenge of interdisciplinary research
“If one is interested in the relations between fields which, according to customary academic divisions, belong to different departments, then he will not be welcomed as a builder of bridges, as he might have expected, but will rather be regarded … Continue reading
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Just registered for ICFP
Functional programmers unite at ICFP! I’ll also be at the ML Worskhop, Haskell Symposium, and CUFP.
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