About

Liyan Xie is an Assistant Professor in the Department of Industrial & Systems Engineering at the University of Minnesota Twin Cities. Her research interests lie in the interface of statistics, optimization, and machine learning, inspired by important applications. Her work encompasses statistical inference topics such as time series analysis, sequential hypothesis testing, and change detection. In the areas of optimization and machine learning, she focuses on diffusion models, synthetic data generation, data-driven decision-making under uncertainty, distributionally robust methods, and adversarial robustness. Her application areas include healthcare, specifically wearable sensors and electronic health record data, as well as spatio-temporal data analysis, community detection, and manufacturing quality control.

Research topics

• Biology
• Computational biology
• Biochemistry
• Medicine
• Cancer research
• Internal medicine
• Cell biology
• Materials science
• Chemistry
• Genetics

Selected publications

• The Histone Demethylase HR Suppresses Breast Cancer Development through Enhanced CELF2 Tumor Suppressor Activity

  Cancers · 2022-09-24 · 3 citations

  articleOpen access

  The hairless (HR) gene encodes a transcription factor with histone demethylase activity that is essential for development and tissue homeostasis. Previous studies suggest that mutational inactivation of HR promotes tumorigenesis. To investigate HR mutations in breast cancer, we performed targeted next-generation sequencing using DNA isolated from primary breast cancer tissues. We identified HR somatic mutations in approximately 15% of the patient cohort (n = 85), compared with 23% for BRCA2, 13% for GATA3, 7% for BRCA1, and 3% for PTEN in the same patient cohort. We also found an average 23% HR copy number loss in breast cancers. In support of HR’s antitumor functions, HR reconstitution in HR-deficient human breast cancer cells significantly suppressed tumor growth in orthotopic xenograft mouse models. We further demonstrated that HR’s antitumor activity was at least partly mediated by transcriptional activation of CELF2, a tumor suppressor with RNA-binding activity. Consistent with HR’s histone demethylase activity, pharmacologic inhibition of histone methylation suppressed HR-deficient breast cancer cell proliferation, migration and tumor growth. Taken together, we identified HR as a novel tumor suppressor that is frequently mutated in breast cancer. We also showed that pharmacologic inhibition of histone methylation is effective in suppressing HR-deficient breast tumor growth and progression.

  PublisherOA PDFDOI

• A functional genomics screen identifying blood cell development genes in<i>Drosophila</i>by undergraduates participating in a course-based research experience

  G3 Genes Genomes Genetics · 2021 · 13 citations

  • Biology
  • Computational biology
  • Genetics

  Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 genes and identified 137 candidate genes for which loss of function leads to observable changes in the hematopoietic development. Targeting RNAi to maturing, progenitor, and regulatory cell types identified key subsets that either limit or promote blood cell maturation. Bioinformatic analysis reveals gene enrichment in several previously uncharacterized areas, including RNA processing and export and vesicular trafficking. Lastly, the participation of students in this course-based undergraduate research experience (CURE) correlated with increased learning gains across several areas, as well as increased STEM retention, indicating that authentic, student-driven research in the form of a CURE represents an impactful and enriching pedagogical approach.

  DOI

• 155 A biomarker function of HMGA2 in cutaneous squamous cell carcinoma development

  Journal of Investigative Dermatology · 2020-06-16

  article
  PublisherDOI

• 786 A master regulator function of hairless in skin homeostasis and immune regulation

  Journal of Investigative Dermatology · 2020-06-16

  article
  PublisherDOI

• Biomarker function of HMGA2 in ultraviolet‐induced skin cancer development

  Experimental Dermatology · 2020 · 12 citations

  • Cancer research
  • Chemistry
  • Medicine

  The high mobility group AT-hook 2 (HMGA2) gene encodes a transcription factor that is expressed during embryonic development but down-regulated in adult tissues. Its re-expression in adult tissues is often associated with tumorigenesis. In this study, we found that HMGA2 is highly expressed in human cutaneous squamous cell carcinoma (SCC) cell lines and primary SCC tumors, but not in adjacent normal skin. In non-ultraviolet (UV)-irradiated mouse skin, baseline Hmga2 expression was detected in the epidermis but not in hair follicles. Following chronic UV exposure, we found activation of Hmga2 in hair follicles. UV-induced mouse skin SCC tumors displayed a ubiquitous increase in Hmga2 expression compared to non-tumor-bearing adjacent skin. In human SCC cells, decreased HMGA2 expression was linked with reduced cell proliferation following depletion of FOXM1 and TRIP13, two UV master regulator genes. Taken together, these findings highlight an important biomarker function of HMGA2 expression in UV-induced skin tumorigenesis and cell proliferation.

  PublisherOA PDFDOI

Frequent coauthors

• Wootae Ha

  16 shared

• Liang Liu

  Meizhou City People's Hospital

  12 shared

• A. Hinde

  Hormel (United States)

  12 shared

• Lei Liu

  University of Florida

  10 shared

• Ravinder Kaur

  University of California, Los Angeles

  9 shared

• Vina Tran

  University of California, Los Angeles

  9 shared

• Lauren Johnson

  Howard Hughes Medical Institute

  9 shared

• Jaime S Tan

  University of California, Los Angeles

  9 shared

Awards & honors

• 2020 Selected to participate in EECS Rising Stars Workshop
• 2019 Runner up for INFORMS Computing Society Student Paper P…
• 2019 Finalist of INFORMS QSR Best Student Paper Award