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Archive for 'bioinformatics' Category

Bio-IT World Asia 2013

Mar 1st, 2013 by blog | 0

I am an invited speaker at the Bio-IT World Asia 2013 conference in the Bioinformatics and Cancer Genomics track, in Singapore May 28-31, 2013.

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HTML5 Bioinformatics Plots

Jun 20th, 2012 by blog | 0

I have been playing with HTML5 for my new tool for alignment comparisons. To visualize the graphs I’m using flotr2 by HumbleSoftware. Which produces an image like this — on the fly and without any actual graphic files: The first thing you need to include in your page is the library. You can do that [...]

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Software: NorahDesk

Jan 13th, 2012 by blog | 0

  NorahDesk non-coding RNA detection from deep sequencing data NorahDesk is a small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data, developed by my PhD student Chikako Ragan. NorahDesk utilizes the coverage-distribution of small RNA sequence data and thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. For more information [...]

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Software: Triplexator

Aug 3rd, 2011 by blog | 0

Triplexator is a bioinformatics tool (by Fabian Buske) harnessing the power of a so far underutilized mechanism for sequence-specific DNA binding that is  of great interest for biotechnological and gene-therapeutic applications. This potent homing mechanism is provided by nucleic acids triple helices, also called triplexes, which are oligonucleotide complexes made of three strands of either [...]

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PRIB 2008

Dec 5th, 2008 by blog | 0

This year’s Pattern Recognition in Bioinformatics (PRIB 2008) was organized by the Monash University and was therefore held in Melbourne. It was a very interesting conference with a great sessions and a good organization. On-top of that, our paper even won the best paper award. The slides from my talk are online on slideshare.

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Software: STREAM

Jul 12th, 2008 by blog | 0

I have developed a new bioinformatics tool called STREAM – Static Thermodynamic REgulAtory Model of transcription. STREAM is a application for researchers, who want to model the transcriptional regulation of a specific gene and predict its transcriptional output in different situations STREAM is available as java .jar file and java source code upon request. I [...]

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