Publications 

[* Student mentored by Dr. Wendy Lee]

    A. Niosi, N. H. Võ, P. Sundaramurthy*, C. Welch, A. Penn, Y. Yuldasheva, A. Alfareh, K. Rausch, T. Amin-Rahbar, J. Cavanaugh, P. Yadav, S. Peterson, R. Brown, A. Hu, A. Ardon-Castro, D. Nguyen, R. Crawford, W. Lee, E. J. Morris, M. H. Jensen, K. Mulligan, Kismet/CHD7/CHD8 affects gut microbiota, mechanics, and the gut-brain axis in Drosophila melanogaster. Biophys. J. 124, 933–941 (2025). https://doi.org/10.1016/j.bpj.2024.06.016 

    M. Moh, R. Khayrallah, W. Lee, T.-S. Moh, D. Taylor, C.-S. M. Wu, WIP: Diversifying the Computing Workforce-Rapid Development of Interdisciplinary Computing-Based Undergraduate Programs. 1–5 (2024). https://doi.org/10.1016/j.ntt.2024.107331  

    W. Lee, M. Moh, R. Khayrallah, N. Attar, K. Lam*, WIP: Python for Everyone as a Mathematics GE Course: Broaden Participation and Enhance Data Science Career Pipeline. 1–5 (2024). https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=10893527 

    V. A. Carr, J. Avena, M. Smith, W. Lee, D. Schuster, B. Wei, Board 63: Work in Progress: Community College Student Experiences with Interdisciplinary Computing Modules in Introductory Biology and Statistics Courses. (2024). https://peer.asee.org/47061.pdf 

    J. L. A. Fishburn, H. L. Larson, A. Nguyen*, C. J. Welch, T. Moore, A. Penn, J. Newman, A. Mangino, E. Widman, R. Ghobashy, J. Witherspoon, W. Lee, K. A. Mulligan, Bisphenol F affects neurodevelopmental gene expression, mushroom body development, and behavior in Drosophila melanogaster. Neurotoxicol. Teratol. 102, 107331 (2024).  

    F. Mbuga*, K. Lam*, W. Lee, Machine Learning-Based Artifact Detection for Long-Read Sequencing Data. 582–584 (2023). https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=10590143  

    V. A. Carr, J. Avena, D. Schuster, W. Lee, B. Wei, Board 61: Work in Progress: Applied Programming Experiences (APEX) for Community College Students. (2023). https://peer.asee.org/board-61-work-in-progress-applied-programming-experiences-apex-for-community-college-students.pdf  

    C. Welch, E. Johnson*, A. Tupikova, J. Anderson, B. Tinsley, J. Newman, E. Widman, A. Alfareh, A. Davis, L. Rodriguez, C. Visger, J. P. Miller-Schulze, W. Lee, K. Mulligan, Bisphenol a affects neurodevelopmental gene expression, cognitive function, and neuromuscular synaptic morphology in Drosophila melanogaster. Neurotoxicology 89, 67–78 (2022). https://doi.org/10.1016/j.neuro.2022.01.006  

    A. Niosi, N. H. Võ, P. Sundar*, C. Welch, A. Penn, Y. Yuldasheva, A. Alfareh, K. Rausch, T. Rukhsar, J. Cavanaugh, P. Yadav, S. Peterson, R. Brown, A. Hu, A. Ardon-Castro, D. Nguyen, R. Crawford, W. Lee, M. H. Jensen, E. J. Morris, K. Mulligan, Kismet/CHD7/CHD8 affects gut biomechanics, the gut microbiome, and gut-brain axis in Drosophila melanogaster, bioRxiv (2021)p. 2021.12. 17.473216. https://doi.org/10.1101/2021.12.17.473216 

    D. Kool*, K. Kao, W. Lee, Understanding How the Relative Abundance of Candida Species Impacts Transcriptional Regulation in Co-culture Biofilms. 376–378 (2021). https://ieeexplore.ieee.org/iel7/9798893/9798894/09798950.pdf 

    P. Sundaramurthy*, B. White, W. Lee, A Computational Approach to Identify Transcription Factor Binding Sites Containing Spacer Regions. 366–369 (2021). https://ieeexplore.ieee.org/iel7/9798893/9798894/09799212.pdf 

    A. Chandak*, W. Lee, M. Stamp, A Comparison of Word2Vec, HMM2Vec, and PCA2Vec for Malware Classification, arXiv [cs.CR] (2021)pp. 287–320. https://doi.org/10.1007/978-3-030-62582-5_11 

    Gu, C.*, W. Lee. A machine learning approach for predicting furin cleavage sites of viral envelope proteins. Trans. Comput. Sci. Comput. Intell. (Springer, in press, 2021); presented at the 22nd Int. Conf. Bioinformatics & Computational Biology (BIOCOMP’21), Las Vegas, NV, 26–29 July 2021.

    Tom, Z.*, W. Lee. Bioinformatics metadata extraction for machine learning analysis. Trans. Comput. Sci. Comput. Intell. (Springer, in press, 2021); presented at the 22nd Int. Conf. Bioinformatics & Computational Biology (BIOCOMP’21), Las Vegas, NV, 26–29 July 2021.

    Khan, S.Y., M. Ali, M.W. Lee, Z. Ma, P. Biswas, A.A. Khan, M.A. Naeem, S. Riazuddin, R. Ayyagari, J.F. Hejtmancik, S.A. Riazuddin. Whole genome sequencing data of multiple individuals of Pakistani descent. Sci. Data 7, 350 (2020). https://doi.org/10.1038/s41597-020-00664-2

    N. Khuri, W. Lee, K. V. Lehmkuhl-Dakhwe, M. VanHoven, S. Khuri, “Interdisciplinary minor in bioinformatics: First results and outlook” in Proceedings of the 51st ACM Technical Symposium on Computer Science Education (ACM, New York, NY, USA, 2020; https://dl.acm.org/doi/pdf/10.1145/3328778.3366804), pp. 407–412.     

    Khan, S.Y., M. Ali, F. Kabir, R. Chen, H.N. Chan, M.W. Lee, N. Pourmand, S.A. Riazuddin, S.F. Hackett. Identification of novel transcripts and peptides in developing murine lens. Sci. Rep. 8, 11162 (2018). https://doi.org/10.1038/s41598-018-28727-w 

    M. Fitzsimons, M. W. Lee, B.-I. Lee, L. Subramanian, Abstract 1518: Lung adenocarcinoma differential expression analysis using the Maverix RNA-Seq pipeline. Cancer Research 76, 1518–1518 (2016). https://doi.org/10.1158/1538-7445.AM2016-1518 

    M. Franco, M. W. Panas, N. D. Marino, M.-C. W. Lee, K. R. Buchholz, F. D. Kelly, J. J. Bednarski, B. P. Sleckman, N. Pourmand, J. C. Boothroyd, A novel secreted protein, MYR1, is central to toxoplasma’s manipulation of host cells. MBio 7, e02231-15 (2016). https://doi.org/10.1128/mBio.02231-15 

    F. Lopez-Diaz, M. W. Lee, M. Tariq, S. Y. Khan, Y. Dayn, C. J. Vaske, N. Pourmand, B. Emerson, Abstract A09: Single-cell RNA sequencing reveals phenotypic plasticity of drug tolerant, clonal populations of cancer cells. Clinical Cancer Research 21, A09–A09 (2015). https://doi.org/10.1158/1557-3265.PMS14-A09 

    M.-C. W. Lee, F. J. Lopez-Diaz, S. Y. Khan, M. A. Tariq, Y. Dayn, C. J. Vaske, A. J. Radenbaugh, H. J. Kim, B. M. Emerson, N. Pourmand, Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. Proc. Natl. Acad. Sci. U. S. A. 111, E4726-35 (2014). https://doi.org/10.1073/pnas.1404656111 

    Khan, S.Y., A.O. Khan, M.C.W. Lee, Z. Ma, S. Riazuddin, R.N. Cole, N. Pourmand, et al. Transcriptional characterization of the nonsense allele of FOXE3 responsible for Peters anomaly. Invest. Ophthalmol. Vis. Sci. 55, 6414 (2014). https://iovs.arvojournals.org/article.aspx?articleid=2272117 

    MCW Lee (2014) Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. PhD dissertation. University of California, Santa Cruz. https://escholarship.org/uc/item/22f219xb 

    MCW Lee, M Franco, DM Vargas, DA Hudman, SJ White, RG Fowler (2014) A ΔdinB mutation that sensitizes Escherichia coli to the lethal effects of UV and X-radiation. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 763: 19–27. https://doi.org/10.1016/j.mrfmmm.2014.03.003 

    F. Lopez-Diaz, M. W. Lee, M. Tariq, Y. Dayn, S. Y. Khan, C. J. Vaske, N. Pourmand, B. Emerson, Abstract PR05: Single-cell RNA sequencing reveals phenotypic plasticity of drug tolerant clonal populations of cancer cells. Cancer Research 73, PR05–PR05 (2013). https://doi.org/10.1158/1538-7445.FBCR13-PR0  

    J. M. Dinis, D. E. Barton, J. Ghadiri, D. Surendar, K. Reddy, F. Velasquez, C. L. Chaffee, M.-C. W. Lee, H. Gavrilova, H. Ozuna, S. A. Smits, C. C. Ouverney, In search of an uncultured human-associated TM7 bacterium in the environment. PLoS One 6, e21280 (2011). https://doi.org/10.1371/journal.pone.0021280 

    MC Lee, M Franco, DM Vargas, DA Hudman, RG Fowler, NJ Sargentini (2011) A role for DinB in protecting Escherichia coli from the lethal effects of UV and ionizing radiation. Environmental and Molecular Mutagenesis 52: S43–S43. 

    Dinis, J., D. Barton, J. Ghadiri, D. Surendar, K. Reddy, F. Velasquez, C. Chaffee, W. Lee, H. Gavrilova, H. Ozuna, S. Smits, C. Ouverney. An uncultured human-associated bacterium model. Nature Precedings, 1 (2011). https://www.nature.com/articles/npre.2011.5757.1 

    M.-C. W. Lee, "The role of dinB in UV survival and UV-induced mutagenesis in Escherichia coli" (2009). Master's Theses. 3686. DOI: https://doi.org/10.31979/etd.us32-w67v    

 

Referred Poster Presentations

• Khan SY, Khan AO, Lee MC, Ma Z, Riazuddin S, Cole R, Pourmand N, Hejtmancik J, Gottach J & Riazuddin A. (2014). Transcriptional characterization of the nonsense allele of FOXE3 responsible for Peters anomaly. Scheduled to be presented at The Association for Research in Vision and Ophthalmology (ARVO) Annual Meeting, Orlando, Florida, United States, on 8 May 2014.
• Lee MC, Lopez-Diaz FJ, Khan SY, Tariq MA, Dayn Y, Vaske C, Radenbaugh AJ, Kim HJ,
  Austin RH, Emerson BM & Pourmand N. (2013). Single cell analyses of the role of mitochondria in paclitaxel-tolerance. Presented at The NCI Princeton Physical Sciences-Oncology Centers (PS-OC) Site Visit, La Jolla, CA, United States
• Lee MC, Lopez-Diaz FJ, Khan SY, Tariq MA, Dayn Y, Vaske C, Radenbaugh AJ, Kim HJ, Emerson BM, Pourmand N & Austin RH. Single-cell sequencing reveals genetic heterogeneity in cell population. Presented at The NCI Physical Sciences – Oncology Centers (PS-OCs) Network Investigators’ Meeting, Scottsdale, AZ, United States
• Lee MC, Lopez-Diaz F, Castro P, Vaske C, Kim HJ, Emerson B & Pourmand N. (2012). Single-cell sequencing reveals genetic heterogeneity in cell population. Presented at the Cancer Genome Summit, Boston, MA, United States
• Vaske CJ, Lee W, Benz S, Sanborn JZ, Lopez-Diaz F, Emerson B & Pourmand N. (2012). Single-cell RNA sequencing of a paclitaxel-treated breast cancer cell line to find individual cell response. Presented at The CTRC-AACR San Antonio Breast Cancer Symposium, San Antonio, TX, United States
• Lee MC, Franco M, Vargas DM, Hudman DA, Fowler RG, Sargentini NJ. (2011). A role for DinB in protecting Escherichia coli from the lethal effects of UV and ionizing radiation. Presented at Environmental Mutagen Society Annual Conference, Montréal, Quebec, Canada https://cdn.ymaws.com/emgs-us.org/resource/resmgr/custompages/past_annual_meetings/2011_abstracts.pdf 
• 2010 Zerbino DR, Lee W, Wilks C, Diekhans M, Paten BJ, Sanborn ZJ, Schulz HM, Haussler D. (2010). Columbus: Hybrid de novo and mapped assembly of short read transcriptomic or genomic data. Presented at Cold Spring Harbor's Genome Informatics Conference, Cold Spring Harbor, NY, United States
• Lee W, Fong N, Franco M, Fowler R & Khuri S. (2008). Inferring Phylogenetic Relationships between Organisms for Y-Family Polymerases Using HMMER 2.0 and the Neighbor-Joining Method. Presented at CSB, the 7th Annual International Conference on Computational Systems Bioinformatics, Stanford CA, United States
• Lee W, Fong N, Franco M, Fowler R & Khuri S. (2008). Detection of Remote Protein Homology by Comparing Profile Hidden Markov Models for the Y-Family Polymerase Family. Presented at CSB, the 7th Annual International Conference on Computational Systems Bioinformatics, Stanford CA, United States

 

Invited talks

• The Silicon Valley Women in Engineering (WiE) Conference. San Jose State University. March 25, 2017. Invited talk on: How next-generation sequencing is changing health care.
• SLAC Summer Panel. SLAC National Accelerator Laboratory. Invited talk on: The experience of being an under-represented minority in science and engineering. July 21, 2015.

 

Webinars
Best practices for data analysis when using UMI adapters to improve variant
detection. Integrated DNA Technologies.