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Photo Gallery, last updated 4/10/2021
I was the lead developer of SomaticSeq at Bina Technologies (acquired by Roche). SomaticSeq a machine learning algorithm to detect somatic mutations in cancer sequencing. SomaticSeq has placed Bina No. 1 in INDEL and No. 2 in SNV in the Stage 5 of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. Our paper describing the method was an Editor's pick in Genome Biology (2015).
At Roche, I led the project to establish the somatic mutation reference data and call sets for the pair of tumor-normal reference samples established by the FDA-led SEQC2 Consortium. This work was published in Nature Biotechnology (2021) / (SharedIt) along with the SEQC2 Collection on Nature Biotechnology by the Consortium. These resources can be used to train machine learning classifers (e.g., Sahraeian SME et al. bioRxiv 2019) or evaluate existing algorithms and pipelines (e.g., Xiao W et al. Nat Biotechnol 2021). There is also a commentary by FDA's acting commissioner Dr. Janet Woodcock.
A quick 8-minute video explaining SomaticSeq
Fang LT, et al. Genome Biol (2015)
Establishing reference samples and call sets for cancer mutation detection using whole-genome sequencing
1st place presentation award at the 2021 MCBIOS & MAQC Annual Meeting
Somatic Mutation Working Group of the SEQC2 Consortium
Fang LT, et al. Nat Biotechnol (2021) / SharedIt
This is my resume.
My Web Pages Elsewhere:
I maintain two identical mirrors in two different locations:
(1) My refurbished desktop with Duo Core AMD A4-5300B with 16GB RAM re-purposed as a low-end home server,
(2) the UCLA Chemistry Department's server that I have user access to.