Bio

Computational systems biologist interested in high-dimensional data modeling and integration towards the characterization of cancer initiation, progression, and microenvironmental co-evolution.

Links

• ResearchGate
• ORCID: 0000-0002-1299-1628
• Lau Lab Website
• Lau Lab Software

Education

Vanderbilt University

Ph.D., Chemical & Physical Biology, 2023
Dissertation: “Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors”

University of Texas at Austin

B.S., Biomedical Engineering, 2016

Selected Publications

Kaur H, Heiser CN, McKinley ET, Ventura-Antunes L, Harris CR, Roland JT, Farrow MA, Selden HJ, Pingry EL, Moore JF, Ehrlich LIR, Shrubsole MJ, Spraggins JM, Coffey RJ, Lau KS, Vandekar SN. 2024. Consensus tissue domain detection in spatial multi-omics data using multiplex image labeling with regional morphology (MILWRM). Communications Biology. Springer Nature. doi: 10.1038/s42003-024-06281-8.
MILWRM package & documentation

Xiong J, Kaur H, Heiser CN, McKinley ET, Roland JT, Coffey RJ, Shrubsole MJ, Wrobel J, Ma S, Lau KS, Vandekar S. 2024. GammaGateR: semi-automated marker gating for single-cell multiplexed imaging. Bioinformatics. Oxford Academic. doi: 10.1093/bioinformatics/btae356.

Srinivasan J, Helm BR, Yang Y, Moore C, Moore JF, Calindi A, Selden HJ, Heiser CN, Liu Q, Lau KS, Ehrlich LIR. 2023. Single-cell transcriptomics reveals heterogenous thymic dendritic cell subsets with distinct functions and requirements for thymocyte-regulated crosstalk. Preprint doi: 10.1101/2023.12.18.572281.

Heiser CN, Simmons AJ, Revetta F, McKinley ET, Ramirez-Solano MA, Wang J, Kaur H, Shao J, Ayers GD, Wang Y, Glass SE, Tasneem N, Chen Z, Qin Y, Kim W, Rolong A, Chen B, Vega PN, Drewes JL, Markham NO, Saleh N, Nikolos F, Vandekar S, Jones AL, Washington MK, Roland JT, Chan KS, Schurpf T, Sears CL, Liu Q, Shrubsole MJ, Coffey RJ, Lau KS. 2023. Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors. Cell. Cell Press. doi: 10.1016/j.cell.2023.11.006.
spatial_CRC_atlas repository & spatial_CRC_atlas_imaging repository

Arceneaux D, Chen Z, Simmons AJ, Heiser CN, Southard-Smith AN, Brenan MJ, Yang Y, Chen B, Xu Y, Choi E, Campbell JD, Liu Q, Lau KS. 2023. A contamination focused approach for optimizing the single-cell RNA-seq experiment. iScience. Cell Press. doi: 10.1016/j.isci.2023.107242.

Lin J, Wang S, Coy S, Chen Y, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. 2023. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell. Cell Press. doi: 10.1016/j.cell.2022.12.028.

Drewes JL, Chen J, Markham NO, Knippel RJ, Domingue JC, Tam AJ, Chan JL, Kim L, McMann M, Stevens C, Dejea CM, Tomkovich S, Michel J, White JR, Mohammad F, Campodonico VL, Heiser CN, et al. 2022. Human colon cancer-derived Clostridioides difficile strains drive colonic tumorigenesis in mice. Cancer Discovery. American Association for Cancer Research. doi: 10.1158/2159-8290.CD-21-1273.

McKinley ET, Shao J, Ellis ST, Heiser CN, Roland JT, Macedonia MC, Vega PN, Shin S, Coffey RJ, Lau KS. 2022. MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images. Cytometry: Part A. Wiley. doi: 10.1002/cyto.a.24541.

Chen B, Scurrah CR, McKinley ET, Simmons AJ, Ramirez-Solano MA, Zhu X, Markham NO, Heiser CN, et al. 2021 Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell. Cell Press. doi: 10.1016/j.cell.2021.11.031.

Wylezinski LS, Harris CR, Heiser CN, Gray JD and Spurlock CF. 2021. Influence of social determinants of health and county vaccination rates on machine learning models to predict COVID-19 case growth in Tennessee. BMJ Health & Care Informatics. BMJ, 0:e100439. doi: 10.1136/bmjhci-2021-100439.

Chen B, Ramirez-Solano MA, Heiser CN, Liu Q, Lau KS. 2021. Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools. STAR Protocols. Cell Press. doi: 10.1016/j.xpro.2021.100450.
STAR_protocol repository

Heiser CN, Wang VM, Chen B, Hughey JJ, Lau KS. 2021. Automated quality control and cell identification of droplet-based single-cell data using dropkick. Genome Research. Cold Spring Harbor Press. doi: 10.1101/gr.271908.120.
dropkick package & documentation

Bao S, Chiron S, Tang Y, Heiser CN, et al. A cross-platform informatics system for the Gut Cell Atlas: integrating clinical, anatomical and histological data. Proc. SPIE 11601, Medical Imaging 2021: Imaging Informatics for Healthcare, Research, and Applications, 1160106. 15 Feb 2021. doi: 10.1117/12.2581074.

Yang X, Graff SM, Heiser CN, et al. 2020. Coregulator Sin3a promotes postnatal murine β-cell fitness by regulating genes in Ca 2+ homeostasis, cell survival, vesicle biosynthesis, glucose metabolism, and stress response. Diabetes. p. db190721. doi: 10.2337/db19-0721.

Heiser CN and Lau KS. 2020. A quantitative framework for evaluating single-cell data structure preservation by dimensionality reduction techniques. Cell Reports. Cell Press, 31(5), p. 107576. doi: 10.1016/j.celrep.2020.107576.
DR-structure repository & documentation

Additional Code

kitchen: automated manipulation and processing of scRNA-seq counts files from command line (documentation)

cnmf: packaged and streamlined version of cNMF, adapted from Kotliar, et al. 2019 (documentation)

Awards

• Graduate Student of the Year (Vanderbilt University Men’s Ice Hockey - 04/2023)
• Brighter Ventures Award (Vanderbilt University School of Medicine - 06/2022)
• Dean’s Award for Exceptional Achievement (Vanderbilt University School of Medicine - 07/2021)
• Lai Sulin Endowed Cancer Research Scholarship (Vanderbilt University - 04/2021)
• Russell G. Hamilton Graduate Leadership Institute Travel Grant Award (Vanderbilt University - 09/2019)