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SCGPM Seminar: Jun Ye and Dangna Li, Sentieon
Mon, August 22, 2016, 12:00 PM – 1:00 PM PDT
"Enabling Precision Data for Precision Medicine"
Jun Ye, CEO of Sentieon and Dangna Li, Stanford
August 22, 2016
12:00 - 1:00PM
Jun's Abstract: Sentieon (www.sentieon.com), incorporated in July 2014, develops and supplies a suite of bioinformatics secondary analysis tools that process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy, and 100% consistency. Currently released products include Sentieon DNAseq, a germline DNA pipeline, and Sentieon TNseq, for tumor-normal somatic variant detection. The Sentieon tools are easily scalable, easily deployable, easily upgradable, software-only solutions. The Sentieon tools achieve their efficiency and consistency through optimized computing algorithm design and enterprise-strength software implementation, and achieve high accuracy using the industry’s most validated mathematics models. Sentieon products have won multiple awards at precisionFDA challenges, and are currently at first place on ICGC-TCGA DREAM Mutation Calling challenge leaderboard. We strive to enable precision genomics data for precision medicine.
Dangna's Abstract: In this talk, we will describe some of the recent work on improving the stability of VQSR. We propose to use DSP (a density estimation algorithm via discrepancy based adaptive sequential partitioning), to stabilize the training process of VQSR. Experiments show the new algorithm is able to stabilize the results of VQSR completely, while achieving the same level of accuracy.
Jun's Bio: Jun Ye is co-founder, president, and CEO of Sentieon, a bioinformatics company established in July 2014. Prior to Sentieon, Ye was co-founder, president, and CEO of Founton Technologies, a company that specialized in datamining, which is now part of Alibaba Group. Prior to Founton, Ye was co-founder, president, and CTO of Brion Technologies, a company specializing in computational lithography for semiconductor manufacturing, now part of ASML. Prior to Brion, he was director of engineering at Onetta, an optical telecom company, working on communication system control. He also served as director of engineering at KLA-Tencor, where he worked on the software and algorithm for mask inspection. From 2001 to 2015, Ye also served as a consulting professor of electrical engineering at Stanford University, where he mentored and supervised graduate student research in microlithography and other areas. Ye earned BSEE from Fudan University in 1987, MS-Physics from Iowa State University in 1991, and Ph.D. EE from Stanford University in 1996. During his career, he has authored or co-authored more than 50 U.S. patents covering algorithm, software, hardware, and system architecture. In 2014 he received the ISU John V. Atanasoff Discovery Award for his work to advance scientific knowledge.
Dangna's Bio: Dangna Li is a third-year PhD student from the Institute of Computational and Mathematical Engineering at Stanford. She is also a member of the Wong lab. Before coming to Stanford, she received a BA in mathematics from Wuhan University in China. Her current research focuses on statistical machine learning algorithms and their applications in multi-sample single cell data analysis.
ABOUT THE SCGPM: The Stanford Center for Genomics and Personalized Medicine (SCGPM) seeks to advance genomic technology so that someday both genetic and molecular profiling will become powerful and routine tools for predicting disease risk and monitoring and treating a wide range of pathologies. Towards this mission, the SCGPM serves to centralize and develop collaborative intellectual and technological resources that promote genomic research and analysis, predict drug response, educate physicians, and examine the ethics of personalized medicine. This includes large basic science projects such as ENCODE that decipher the human genome as well as clinical research projects such as the sequencing of cancer genomes and individuals with inherited diseases. Through these efforts, the Center aims to bring genomics to the clinic.
For more information about the SCGPM, go to http://scgpm.stanford.edu.
The SCGPM supports the Genetics Bioinformatics Service Center, a SoM core facility for genomics research that provides a secure on-premise computing infrastructure, Google Cloud gateway, and bioinformatics consulting. The facilities are available to all faculty members at Stanford University.
More @ http://gbsc.stanford.edu. Send inquiries to email@example.com .