CV

You can find my CV here: Tian Xia’s Curriculum Vitae.

Education

• Ph.D in Quantitative & Computational Biosciences, Baylor College of Medicine, 2024 (expected)
• B.S. in Pharmaceutical Sciences, Zhejiang University, 2019

Work experience

• 2024 - 2024: Intern/Co-op
  • Merck
  • Fine tuning self-supervised transformer-based deep learning image feature extraction method DINOv2 for classifying cells with different treatment
  • Classify RNA-seq data of patients’ for different locations with machine learning
  • Developed a machine learning pipeline for determining the suitable marker for Optical Pooled CRISPR Screening (OPS)
  • Established a CellProfiler and Cellpose (deep learning) pipeline to segment and quantify the cell images, which is integrated with Nextflow and deployed to High Performance Clustering (HPC).
  • Experience with processing scRNA-seq data from fastq file
  • Build and train GPT2 from scratch and generate Shakespeare-like dialogue
• 2019 - Current: Graduate Student
  • Baylor College of Medicine
  • Multiple projects involving develop imaging analysis procedure for investigation of dynamic phenomenon within mouse reproductive organs (Published at Optica, Biomedical Optics Express, in preparation for Nature)
  • Supervisor: Professor Irina Larina
• 2020 - 2023: Inter-institutional Student
  • Rice University
  • Constructed a machine learning pipeline to identify genomic signatures in age-related macular degeneration. Reduced the number of feature from >18000 to <100 using feature selection techniques.
  • Created a classification network (customized Resnet50 with Ensemble strategy) to distinguish finegrained food images.
  • Construct a generalized linear model to identify individuals with the high risk of stroke with more than 90% accuracy
• 2018 - 2019: Research Assistant
  • Massachusetts Institute of Technology
  • Help build a genetically defined syngeneic mouse model of ovarian cancer (Published at Cancer Discovery)
  • Supervisor: Professor Robert Weinberg
• 2018 - 2018: Research Assistant
  • Princeton University
  • Study the phenotype of mir200 knockout in the mouse model by immunohistochemistry (IHC) imaging
  • Supervisor: Professor Yibin Kang
• 2017 - 2018: Research Assistant
  • Zhejiang University
  • Study the IL-6, p-stat3, Fra-1, Nanog pathway in the progression and metastasis of colon cancer by immunofluorescence (IF) imaging (Published at Oncogene)
  • Supervisor: Professor Jimin Shao

Skills

• Programming: Python, R, MATLAB, C, Bash, SQL, Git, LaTex

• Data Science:
  • Data Structure: Pandas(Python), Anndata(Python), dplyr(R)
  • Visualization: Matplotlib (Python), Seaborn(Python), ggplot2 (R)
  • Machine Learning: scikit-learn, PyTorch

• Research: Data Science, Machine Learning, Deep Learning, Imaging Processing and Analysis, Computational Biology

• Soft skills: Creativity, Critical Thinking, Communication

Publications

The inflammatory cytokine IL-6 induces FRA1 deacetylation promoting colorectal cancer stem-like properties

Wang, T., Song, P., Zhong, T. et al. The inflammatory cytokine IL-6 induces FRA1 deacetylation promoting colorectal cancer stem-like properties. Oncogene 38, 4932–4947 (2019). https://doi.org/10.1038/s41388-019-0763-0

Tracking spermatozoa movement toward the egg with functional optical coherence tomography

Tian Xia, Kohei Umezu, Shang Wang, and Irina Larina "Tracking spermatozoa movement toward the egg with functional optical coherence tomography", Proc. SPIE 11959, Dynamics and Fluctuations in Biomedical Photonics XIX, 1195902 (2 March 2022); https://doi.org/10.1117/12.2608265

Dynamic volumetric imaging and cilia beat mapping in the mouse male reproductive tract with optical coherence tomography

Kohei Umezu, Tian Xia, and Irina V. Larina, "Dynamic volumetric imaging and cilia beat mapping in the mouse male reproductive tract with optical coherence tomography," Biomed. Opt. Express 13, 3672-3684 (2022)

In vivo volumetric depth-resolved imaging of cilia metachronal wave with dynamic optical coherence tomography

Tian Xia, Kohei Umezu, Deirdre M. Scully, Shang Wang, and Irina V. Larina, "In vivo volumetric depth-resolved imaging of cilia metachronal waves using dynamic optical coherence tomography," Optica 10, 1439-1451 (2023)

Achievements

• 2023 Travel Award for Invited Talk SPIE Photonic West 2023, San Francisco
• 2022 Second Place for Poster Presentation Texas Forum of Reproductive Sciences 2022, Houston
• 2018 First-Class Scholarship for Outstanding Students (Top 1%) Zhejiang University
• 2018 The President’s Scholarship Zhejiang University
• 2018 Championship of Men’s Singles Tennis Competition, Zhejiang University

Service and leadership

• 2023-present Invited Reviewer - JOSA A - Journal of the Optical Society of America A
• 2022-present Co-founder and Photographer - CATS OF HOUSTON - Stray Cat Adoption Platform