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Hui Jiang: Tools for the Surge of Sequencing Data


Title: Postdoc, Stanford University
Education: PhD, Stanford University, 2009
Recommended by: Wing Wong, Stanford University

The onslaught of next-gen sequencing data is still in the early days of its attack. One of Hui Jiang's research focuses is to develop software tools to aid researchers in their analysis of this data rush. "The next generation sequencing is very new — it has been a focus of bioinformatics for the past two or three years and a lot of people are using it. I have been one of the … batch of people to develop software tools for this, to analyze this type of data," Jiang says.

One of the first programs that Stanford's Jiang wrote was SeqMap, which can map a large amount of short reads to a genome quickly — the Bioinformatics paper introducing it notes that a typical mapping task takes a few hours on a desktop PC. Jiang then co-developed CisGenome, a tool for analyzing tiling array, ChIP-seq, genome and cis-regulatory element data, with Hongkai Ji at Johns Hopkins. "A lot of people — after I publish a paper on software — e-mail me with questions. These make me feel quite happy to help people out in their research because our users come from all different areas of biology," Jiang says. "Our community is using our software to analyze data, which makes me very happy." Currently, he is developing a tool called rSeq for analysis of RNA-seq data.

In the future

Next-generation sequencing is becoming ever more popular, Jiang says. "The next-generation sequencing type of biology will eventually take off and replace ... microarrays, and we'll be sequencing more and more different species and different individuals," he says, adding that sequencing will also influence health care.

Papers of note

In 2009, Jiang was a co-first author on a paper in Bioinformatics that discussed whether alternative splicing-derived isoforms could be identified using exon and splice junction arrays and RNA-seq data. He and his colleagues reported that about 97 percent of the approximately 2,200 alternatively spliced human genes in RefSeq "lead to identifiable gene models in RNA-seq." However, they also found that "in the Human Exon array only 26 percent of these genes lead to identifiable models, and even in the most comprehensive splice junction array only 69 percent lead to identifiable models." In addition, Jiang's paper on SeqMap was published in 2008 in Bioinformatics, and CisGenome was published in July in Nature Biotechnology.

And the Nobel goes to ...

If startled awake by a call from the Nobel committee, Jiang would like it to be for having made a contribution to the clinic.

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