The advances in high-throughput technologies have given rise to a wealth of biological data at the system level, including genome, epigenome, transcriptome, proteome, metabolome, and metagenome. Our research focuses on developing and applying computational methods to analyze and integrate large scale 'omics' datasets, which help us understand how genes work together to comprise functioning cells and organisms, and how diseases arise due to genetic mutations.
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Research Areas
Research Areas
Environmental toxins & Neurological Disorders
Sequencing Artifacts
Microbiome and Behaviors
Metagenomics & Antibiotic Resistance
People
People
Principal Investigator
Principal Investigator
Wendy Lee, PhD
Wendy Lee, PhD
Research interests: Antibiotic resistance in complex microbial communities; Systematic sequencing/assembly errors in challenging genomic regions including segmental duplications, homopolymers, and tandem repeats; Transcriptional regulation in evolution, development, and disease.
Education: BMath Computer Science, University of Waterloo; MS Molecular Biology & Microbiology, SJSU; PhD Bioinformatics, UC Santa Cruz.
Favorite phrase: "Hope lies in dreams, in imagination and in the courage of those who dare to make dreams into reality." - Jonas Salk
Favorite activities outside the lab: Cooking, Playing piano, Spending time with family
Current Graduate Students
Current Graduate Students
Hannah Debaets (MS Bioinformatics)
Hannah Debaets (MS Bioinformatics)
Research interests: BPA
Education: BS Biochemistry Tufts University 2016
Favorite phrase: Don’t be concerned about whether people are watching you or criticizing you. The chances are that they aren’t paying any attention to you. - Eleanor Roosevelt
Favorite activities outside the lab: Dancing, Pickleball
Radha Dhayal (MS Bioinformatics)
Radha Dhayal (MS Bioinformatics)
Research Interest: Effect of BPA/BPF on neurodevelopmental gene expression in humans.
Education: Bachelor's degree in Biotechnology from Cal Poly Pomona
Favorite Phrase: Absolutely, don't grant others the authority to dictate what you can or cannot do. No one knows your strengths and capabilities better than you do.
Favorite Activities: Hiking, Reading, Spending time with family
Lawrence Fung (MS Bioinformatics)
Lawrence Fung (MS Bioinformatics)
Research interests: PFAS, Pharmacogenomics
Education: UC Davis, BS in Biological Sciences
Favorite phrase: “In a world myriad as ours, the gaze is a singular act: to look at something is to fill your whole life with it, if only briefly.” ― Ocean Vuong
Favorite activities outside the lab: swimming, hiking, biking, reading, spending time with my cats
Ananya Gupta (MS Bioinformatics)
Ananya Gupta (MS Bioinformatics)
Research interests: Exploring single cell and other small-scale systems to understand large-scale patterns through automation, visualization, and machine learning.
Education: BS Life Sciences, University of Delhi
Favourite phrase: The main thing that sets you apart from an expert in the field is time spent trying.
Favorite activities outside the lab: Going to concerts, trying out new food places and sharing cat videos
Rajshri Iyer (MS Bioinformatics)
Rajshri Iyer (MS Bioinformatics)
Research interests: Building a DL model for NGS artifact detection; Using ML/AI to build robust bioinformatics pipelines for DNA-seq/RNA-seq etc.
Education: B.Tech Industrial Biotechnology from A.C. Tech, Anna University, Chennai, India
Favorite phrase: "When things change inside you, things change around you!"
Favorite activities outside the lab: Gardening, Baking, Singing, Reading non-fiction, Watching crime / courtroom drama TV shows
Allen Kalampukattussery (MS Bioinformatics)
Allen Kalampukattussery (MS Bioinformatics)
Research interests: Intersection of Sequencing and Microbiome Analysis
Education: BS Human Biology - University of California, Merced
Favorite phrase: "The world now is too dangerous and too beautiful for anything but love"
Favorite activities outside the lab: Running, Biking, Baking
Daniel Quintana (MS Computer Science)
Daniel Quintana (MS Computer Science)
Research interests: Emergent Deck Discovery via Trading Card Game Agents
Education: Bachelor of Science degrees in Mathematics, Applied Physics, and Computer Science from CSU Channel Islands
Favorite phrase: "Sounds good!"
Favorite activities outside the lab: Playing the piano, video games, and rock climbing
Shwethal Trikannad (MS Bioinformatics)
Shwethal Trikannad (MS Bioinformatics)
Research interests: Anything Human Health and AI related
Education: Bachelor of Dental Surgery, RGUHS, India
Favorite phrase: "TATAKAE !"- Eren Yeagar
Favorite activities outside the lab: Anime, Reading , Collecting funky socks, Napping and Swimming
Justin Wong (MS Bioinformatics)
Justin Wong (MS Bioinformatics)
Research interests: Computational analysis of single-cell RNA-seq data, and integrative approaches for understanding cellular heterogeneity and gene regulation.
Education: B.S. in Biotechnology - University of California, Davis
Favorite phrase: “I'm always right... 33% of the time.”
Favorite activities outside the lab: Exercising, Gaming, Baking
Current Research Assistants
Current Research Assistants
AArohi Chopra
AArohi Chopra
Research interests: Studying and identifying sequencing artifacts with the application of machine learning and a Bioinformatic pipeline, Cyber Security and AI.
Education: MS in Computer Science & BS in Computer Science, San Jose State University
Favorite phrase: I know it is hard and you are scared but one day you are gonna look back and think that it was worth it.
Favorite activities outside the lab: Singing, Playing the guitar, and Eating.
Aadit Kapoor
Aadit Kapoor
Research Interest: Large Language Models for Genomics
Education: MS Artificial Intelligence & BS in Computer Science, San Jose State University
Research Publications
Research Publications
[Student mentored by Dr. Lee]
A. Kapoor* and W. Lee, "In-Context Learning in Genomic Language Models as an Evaluation Task," 2025 International Conference on Computational Science and Computational Intelligence (CSCI'25) (Accepted)
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
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). DOI: 10.1109/CSCI62032.2023.00103
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). DOI: 10.1109/CSCI54926.2021.00134
P. Sundaramurthy*, B. White, W. Lee, A Computational Approach to Identify Transcription Factor Binding Sites Containing Spacer Regions. 366–369 (2021). DOI: 10.1109/CSCI54926.2021.00132
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
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
Good News
Good News
Aadit Kapoor's poster paper abstract, titled "In-Context Learning in Genomic Language Models as an Evaluation Task,” has been accepted for both publication in the IEEE CPS proceedings and presentation at The 2025 International Conference on Computational Science and Computational Intelligence (CSCI'25: December 3-5, 2025; Las Vegas, USA)
Congrats to Aadit Kapoor on receiving the SJSU 2024-2025 Research and Innovation Student RSCA Fellowship to support his research on applying large language models (LLMs) to sequencing artifact data.
An Nguyen's research on the effects of Bisphenol F on neurodevelopment, a collaboration with Dr. Mulligan at Sacramento State, has been published in Neurotoxicology and Teratology https://doi.org/10.1016/j.ntt.2024.107331.
Hannah’s poster abstract, titled “Exploring Gene Expression Changes in Drosophila melanogaster treated with 50µM and 1µM Bisphenol A,” has been accepted for presentation at the 36th Annual CSU Biotechnology Symposium (January 11-13, 2024 in Santa Clara, CA).
David’s poster abstract, titled “Characterizing Sequencing Artifacts in Next-Generation Sequencing Platforms,” has been accepted for presentation at the 36th Annual CSU Biotechnology Symposium (January 11-13, 2024 in Santa Clara, CA).
Felix and Kathy’s poster paper abstract, titled "Machine Learning-Based Artifact Detection for Long-Read Sequencing Data,” has been accepted for both publication in the IEEE CPS proceedings and presentation at the 2023 International Conference on Computational Science and Computational Intelligence (CSCI'23: December 13-15, 2023; Las Vegas, USA)
Master's Projects
Master's Projects
Aarohi Chopra (MSCS 2025) - Uncovering Xenoestrogenic Effects of BPA and 15 BPA Alternatives Through Transcriptomics
Nguyen Mai Anh Do (MSBI 2024) - Artifacts in Low-Pass Whole Genome Sequencing
David Zhou (MSBI 2024) - Characterizing Nanopore Sequencing Artifacts with Deep Learning
Jihan Yehia (MSBI 2023) - Evaluation of the Effect of Walnut Extract on Sp1-Related Pathways
Kathy Lam (MSBI 2023).- Characterizing Sequencing Artifacts
Tyler Stewart (MSBI 2023) - The Search for Metabolic Variants in Response to Climate Change in the American Pika
Hannelle Padre (MSBI 2023) - Modeling Sequencing Artifacts in Artificial Low Frequency Cancer Data
Uyen Hoang (MSBI 2023) - Identification of Oral Microbiome with full-length 16S Sequencing Using Nanopore Technology
Sara Bell (MSBI 2022) - An Investigation of Segmental Duplications Across Topologically Associating Domains
Alex Rios (MSBI 2022) - A LIMS-less System for Genotyping Data in Marker-Assisted Selection
An Nguyen (MSBI 2022) - The Impact of Bisphenol A and Its Analogues on Neurodevelopment Transcriptomes in Drosophila melanogaster
Rashi Raghulan (MSBI 2022) - mRNA-Sequencing Pipeline and Pathway Analysis for the Effects of Bisphenol A on FMR1 Drosophila Melanogaster
Punit Sundar (MSBI 2022) - Conservation and Prevalence of Sequence Paired Sites in Humans
Alexis Torres (MSBI 2022) - miRNA-seq Analysis Pipeline and R Shiny App
Yvonna Leung (MSBI 2022) - Modeling Sequencing Artifacts for Next Generation Sequencing
Diksha Kool (MSBI 2022) - Understanding How The Relative Abundance Of Candida Species Impacts Transcriptional Regulation In Coculture Biofilms
Crystal Han (MSBI 2021) - mRNA-Sequencing Pipeline for Differential Gene Expression Analysis
My Chung (MSBI 2021) - Effective Cancer Detection Using Higher-Order Genome Architecture and Chromatin Interactions
Eden Johnson (MSBI 2021) - Transcriptional Profiling of Neurological Development of Drosophila Following Bisphenol A Exposure
Alan Le (MSBI 2021) - Detection of Antibiotic Resistance Genes in the Wastewater Microbial Metagenome
Christine Gu (MSBI 2020) - FindFur: A Tool for Predicting Furin Cleavage Sites of Viral Envelope Substrates
Zachary Tom (MSCS 2020) - Bioinformatics Metadata Extraction for Machine Learning Analysis
Deepti Garg (MSCS 2019) - Information Extraction from Biomedical Text Using Machine Learning
Lab Alumni
Lab Alumni
Nguyen Mai Anh (MSBI 2024) - Captial One
David Zhou (MSBI 2024)
Jihan Yehia (MSBI 2023) - NASA Genelab
Kathy Lam (MSBI 2023) - Bioinformatics Scientist @ AQTUAL
Tyler Stewart (MSBI 2023) - Abbvie
Hannelle Padre (MSBI 2023) - 10x Genomics
Uyen Hoang (MSBI 2023) - Amgen
Manasa Gadepalli (BSCS 2023) - Dell
Luc Tang (BSCS 2023) - Northrop
Rashi Raghulan (MSBI 2022) - Revolution Medicines
An Nguyen (MSBI 2022) - Twist Bioscience
Alex Rios (MSBI 2022) - Sakata Seed America
Sara Bell (MSBI 2022) - Orca Bio
Aadit Kapoor (BS Computer Science 2022) - @ NIH
Punit Sundar (MSBI 2022) - Bioinformatician @ UCSF
Alexis Torres (MSBI 2022) - NASA GeneLab
Yvonna Leung (MSBI 2022)
Brian Huynh (BSCS 2022) - Consultant @ TCS IT Consulting
Diksha Kool (MSBI 2022) - Bioinformatics Engineer II @ Curio Bioscience
Crystal Han (MSBI 2021) - Life Science Research Professional @ Stanford University
My Chung (MSBI 2021) - Bioinformatics Research Associate @ Seqmatic
Eden Johnson (MSBI 2021) - Bioinformatics Developer @ Bio-Rad Laboratories
Alan Le (MSBI 2021) - Scientist II @ Maro Bio
Christine Gu (MSBI 2020) - Clinical Data Analyst @ Notable
Zachary Tom (MSCS 2020) - Software Engineer @ Dell Technologies
Deepti Garg (MSCS 2019) - SDE @ Amazon
Department of Computer Science San José State University One Washington Square San José, CA 95192-0249
Last updated: 11/04/2025
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