Category Archives: microarrays

Data request re paper “Prediction and characterization of noncoding RNAs in C.elegans by integrating conservation, seondary structure, and high-throughput sequencing and array data. Genome Research.2011”

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Q:
I have read your paper "Prediction and characterization of noncoding RNAs in
C.elegans by integrating conservation, seondary structure, and
high-throughput sequencing and array data. Genome Research.2011". I am
currently doing a project to analyze lncRNAs in C.elegans, therefore it will
be a great help to have the coordinates of the lncRNAs discovered in your
paper. I would be grateful if you can send me the lncRNA annotation
file (GFF,GTF or GFF3 file) by email.

A:
try
http://papers.gersteinlab.org/papers/incrna/
linking to
http://archive.gersteinlab.org/proj/incrna/

Tilescope source code request

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Q:
I’m reading your paper entitled "Tilescope: online analysis pipeline for high-density tiling microarray data", and trying to get the software from the links http://tilescope.gersteinlab.org & http://tilescope.gersteinlab.org/download.html, but these links did not work.

Could you please send me the java source code of Tilescope?

A:
Use the links on http://www.zdzlab.org/mosaic/resources/download.html instead. They work there.

Spectral biclustering

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Q:
I recently read
your 2003 paper titled "Spectral biclustering of microarray data: Coclustering
genes and conditions".

I would like to investigate implementing your approach on a GPU.
Is there any code (Matlab? Python?) you would be willing to share as a result of the paper?

A:
Sorry we’re just using simple SVD routines in matlab. No meaningful code available. -marK