Early cancer detection

• Led the Somatic Mutation Working Group of the FDA-led SEQC-II Consortium to define the somatic mutation reference call set (https://doi.org/10.1038/s41587-021-00993-6) for the cancer reference samples

• Led Bina's participation in the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, and placed #1 and #2 in Stage 5 of the INDEL and SNV challenges• Developed SomaticSeq, the somatic mutation detection algorithm based on machine learning (paper is editor's pick): Source code: https://github.com/bioinform/somaticseq/• Developed key SNV and CNV algorithms incorporated into Roche's AVENIO ctDNA RUO product• Designed the workflow for the 1000 TCGA Exome re-analysis project on Cancer Genomics Cloud• Managed sequencing data analysis collaboration projects with research groups at Roche Diagnostics and Pharma

• Developed somatic mutation detection pipeline• Provided customer engagement and technical support for strategic customers• Wrote technical blogs to reach a wider audience for Bina's blogs

We are a professional organization run by students and postdocs. Our mission is to engage our academic and industry communities to foster a conversation about the healthcare and life-sciences industry. • Organize bimonthly speaker events, discussion panels, and debates to foster productive relationship between academics and industry professionals• Write background articles for marketing purposes, build rapport with speakers• Recruit mentors for the GSK/Roche/McKinsey/QB3-sponsored $150K OneStart Business Plan Competition

• Implemented the very first NGS analysis pipeline for the UCSF Thoracic Oncology Lab• Developed internal data analysis software for Gene Expression and Next Generation Sequencing• Managed a 56-core computing cluster, group website, and co-authored 4 papers• Represented and spoke for the applied genomics research lab at Stanford Lung Cancer Symposium• Won $12,500 grant for BioNIKS as a team in the "Idea to IPO 2012" bioentrepreneurship course sponsored by Burrill & Co., by building a business plan and pitching it to the venture capitalists (two teams awarded)

SCIMALS is a non-profit student-led organization that provides objective third-party scientific and market due diligence for early stage life science investors and entrepreneurs.• Co-authored a Next Generation Sequencing & Genomic Medicine market analysis project for the venture arm of a hospital network, by leading a team of 5 scientists across different geographical locations• Prepared consulting proposals, progress reports, and attend conference calls with venture firms to adjust the direction of the project

Completed and formalized a mathematical theory regarding the secondary structure of RNA molecules during a 6-month research fellowship. The work has resulted in 2 first-authored publications in the Journal of Physical Chemistry B and the Journal of Chemical Physics.• Developed an intuitive RNA-folding model and implemented its computer simulation algorithm based on the work by Professor Ben-Shaul• Discovered a scaling law between RNA's 3D size and its linear length • Presented my theory of Randomly Self-Paired Polymers to the faculty of Fritz Haber Research Center for Molecular Dynamics

See Education for details.Led a total of 9 discussion and laboratory sections for upper division courses in • Statistical Mechanics • Physical Biochemistry • Biochemistry Methods• Chemical Thermodynamics • Quantum Mechanics.

Contributed both experimental and computational expertise in an effort to understand the DNA packaging process in bacterial viruses using Small Angle X-ray Scattering (SAXS). The results are published in Physical Review Letters.• Presented single-molecule experimental results on viruses at the National Institute of Child Health and Human Development• Trained my NIH collaborators to purify viruses, viral DNA, and proteins• Contributed calculation to the DNA packaging problem

Conducted a series of laboratory and on-the-field studies under the direction of Plant Mycotoxin Research division, related to the fungal problems affecting California's nuts industry.• Identified a number of yeast strains as biocontrol agents against aflatoxin-producing fungi, helping the US pistachio industry solve their pest problems without using chemical pesticides