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.
Research Areas
Environmental toxins & Neurological Disorders
Sequencing Artifacts
Microbiome and Behaviors
Metagenomics & Antibiotic Resistance
People
Principal Investigator
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 Students
AArohi Chopra (MS Computer Science)
Research interests: Studying and identifying sequencing artifacts with the application of machine learning and a Bioinformatic pipeline, Cyber Security and AI.
Education: 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.
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)
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
Nguyen Mai Anh (Emma) Do (MS Bioinformatics)
Research Interests: Artifacts in Low-Pass WGS
Education: MS Bioinformatics, SJSU
Favorite Phrase: "Life is not meant to be easy, but take courage, for it can be delightful."
Favorite Activities: cooking, dancing, and hiking
Aadit Kapoor (BS Computer Science)
Education: BS in Computer Science, San Jose State University (Recently graduated and currently volunteering in the Lee lab)
Rohit Mapakshi (MS Computer Science)
Research Interests: Artificial Intelligence, Natural Language Processing, Computer Vision
Education: MS Computer Science (Fall 22), Bachelor of Technology: Computer Science & Engineering 2019
Favorite Phrase: “In your actions, don’t procrastinate. In your conversations, don’t confuse. In your thoughts, don’t wander. In your soul, don’t be passive or aggressive. In your life, don’t be all about business.” – Marcus Aurelius
Favorite Activities: Painting, Horse Riding, watching Mixed Martial Arts
Felix Mbuga (MS Statistics)
Research interests: transcriptomics, genomics, all-omics
Education: MS Statistics
Favorite phrase: Make it count!
Favorite activities outside lab: hiking, Latin dance
Recently graduated and currently volunteering in the Lee Lab
Daniel Quintana (MS Computer Science)
Research interests: Somatic Variant Calling in Nanopore Sequencing
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
David Zhou (MS Bioinformatics)
Research interests: Characterizing and differentiating NGS sequencing artifacts using machine learning models
Education: B.S. Biochemistry and Molecular Biology, UCSB
Favorite phrase: "Get busy living, or get busy dying." - Andy Dufresne
Favorite activities outside the lab: Going to the gym, listening to music, watching films, reading
Publications
[Student mentored by Dr. Lee]
Niosi A, Võ NH, Sundaramurthy P*, Welch C, Penn A, Yuldasheva Y, Alfareh A, Rausch K, Amin-Rahbar T, Cavanaugh J, Yadav P, Peterson S, Brown R, Hu A, Ardon-Castro A, Nguyen D, Crawford R, Lee W, Morris M, Jensen H and Mulligan K. "Kismet/CHD7/CHD8 affects gut microbiota, mechanics, and gut-brain axis in Drosophila melanogaster." Biophysical Journal. 2024; doi:10.1016/j.bpj.2024.06.016.
Fishburn J, Larson H, Nguyen A*, Welch C, Moore T, Penn A, Newman J, Mangino A, Widman E, Ghobashy R, Witherspoon J, Lee W and Mulligan K. (2024). "Bisphenol F affects neurodevelopmental gene expression, mushroom body development and behavior in Drosophila melanogaster." Neurotoxicology and Teratology, 107331. ISSN 0892-0362. https://doi.org/10.1016/j.ntt.2024.107331.
Mbuga F*, Lam K* and Lee W. Machine Learning-Based Artifact Detection for Long-Read Sequencing Data. Accepted for 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).
Fishburn J, Larson H, Nguyen A*, Welch C, Moore T, Penn A, Newman J, Mangino A, Widman E, Ghobashy R, Witherspoon J, Lee W and Mulligan K. “Bisphenol F impairs neurodevelopment in Drosophila melanogaster.” Submitted to Neurotoxicology and Teratology (In review)
Welch C, Johnson E*, Tupikova A, Anderson J, Tinsley B, Newman J, Widman E, Alfareh A, Davis A, Rodriguez L, Visger C, Miller-Schulze JP, Lee W and Mulligan K: Bisphenol A affects neurodevelopmental gene expression, cognitive function, and neuromuscular synaptic morphology in Drosophila melanogaster. Neurotoxicology 2022, 89:67-78. https://doi.org/10.1016/j.neuro.2022.01.006.
Niosi A, Nguyên HV, Sundar P*, Welch C, Penn A, Yuldasheva Y, Alfareh A, Rausch K, Rukhsar T, Cavanaugh J, Yadav P, Peterson S, Brown R, Hu A, Ardon-Castro A, Nguyen D, Crawford R, Lee W, Jensen MH, Morris EJ and Mulligan K: Kismet/CHD7/CHD8 affects gut biomechanics, the gut microbiome, and gut-brain axis in Drosophila melanogaster. bioRxiv 2021.12.17.473216. https://doi.org/10.1101/2021.12.17.473216
Sundaramurthy P*, White B and Lee W. A Computational Approach to Identify Transcription Factor Binding Sites Containing Spacer Regions (2021) International Conference on Computational Science and Computational Intelligence (CSCI), Las Vegas, NV, USA, 2021, pp. 366-369, doi: 10.1109/CSCI54926.2021.00132.
Kool D*, Kao K and Lee W. Understanding How the Relative Abundance of Candida Species Impacts Transcriptional Regulation in Co-culture Biofilms (2021) International Conference on Computational Science and Computational Intelligence (CSCI), Las Vegas, NV, USA, 2021, pp. 376-378, doi: 10.1109/CSCI54926.2021.00134.
Gu C* and Lee, W. A Machine Learning Approach for Predicting Furin Cleavage Sites of Viral Envelope Proteins. Accepted for publication in Transactions on Computational Science & Computational Intelligence, Springer (2021), and presented at the 22nd International Conference on Bioinformatics & Computational Biology (BIOCOMP'21: July 26-29, 2021, Las Vegas, USA).
Tom Z* and Lee W. Bioinformatics Metadata Extraction for Machine Learning Analysis. Accepted for publication in Transactions on Computational Science & Computational Intelligence, Springer (2021), and presented at the 22nd International Conference on Bioinformatics & Computational Biology (BIOCOMP'21: July 26-29, 2021, Las Vegas, USA).
Chandak A*, Lee W, and M. Stamp, A comparison of Word2Vec, HMM2Vec, and PCA2Vec for malware classification, book chapter in Malware Analysis using Artificial Intelligence and Deep Learning, Springer (2020). https://doi.org/10.1007/978-3-030-62582-5_11
Khuri N, Lehmkhul-Dakhwe KV, Vanhoven M, Lee W, Khuri S. Interdisciplinary Minor in Bioinformatics: First Results and Outlook. Accepted for publication and presentation at the ACM SIGCSE; March 11-14, 2020; Portland, Oregon.
Khan SY, Ali M, Lee MW, Ma Z, Biswas P, Khan AA, Naeem MA, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA. Whole genome sequencing data of multiple individuals of Pakistani descent. Sci Data . 2020 Oct 13;7(1):350. doi: 10.1038/s41597-020-00664-2.
Khan SY, Ali M, Kabir F, Chen R, Chan HN, Lee MW, Pourmand N, Riazuddin SA,.Hackett SF. Identification of novel transcripts and peptides in developing murine lens. Sci Rep 8, 11162 (2018). https://doi.org/10.1038/s41598-018-28727-w
Fitzsimons M, Lee MW, Lee B & Subramanian L. Abstract 1518: Lung adenocarcinoma differential expression analysis using the Maverix RNA-Seq pipeline. Cancer Res July 15 2016 (76) (14 Supplement) 1518; DOI: 10.1158/1538-7445.AM2016-1518.
Franco M, Panas MW, Marino ND, Lee MW, Buchholz KR, Kelly FD, Bednarski JJ, Sleckman BP, Pourmand N & Boothroyd JC. A Novel Secreted Protein, MYR1, Is Central to Toxoplasma's Manipulation of Host Cells. mBio. 7, 2231 (2016).
Khan SY, Vasanth S, Kabir F, Gottsch JD, Khan AO, Chaerkady R, Lee MW, Leitch CC, Ma Z, Laux J, Villasmil R, Khan SN, Riazuddin S, Akram J, Cole RN, Talbot CC, Pourmand N, Zaghloul NA, Hejtmancik JF, Riazuddin SA. FOXE3 contributes to Peters anomaly through transcriptional regulation of an autophagy-associated protein termed DNAJB1. Nat. Commun. 7, 10953 (2016).
Khan SY, Hackett SF, Lee MW, Pourmand N, Talbot CC Jr & Riazuddin SA. Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing. Invest. Ophthalmol. Vis. Sci. 56, 4919-4926 (2015).
Lee MW, Lopez-Diaz FJ, Khan SY, Tariq MA, Dayn Y, Vaske C, Radenbaugh AJ, Kim HJ, Emerson BM & Pourmand N. Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):E4726-35. doi: 10.1073/pnas.1404656111.
Lee MW, Franco M, Vargas DM, Hudman DA, White SJ, Fowler RG & Sargentini NJ. (2014). A ΔdinB mutation that sensitizes Escherichia coli to the lethal effects of UV- and X-radiation. Mutat. Res. 763-764, 19-27 (2014).
Metagenomic profiling of antibiotic resistance genes and other resistome-related elements in wastewater (Supporting Information) 2013 https://doi.org/10.6084/M9.FIGSHARE.735922.V1
Lopez-Diaz F, Lee MW, Tariq M, Khan S, Dayn Y, Vaske C, Pourmand N & Emerson BM. Abstract PR05: Single-cell RNA sequencing reveals phenotypic plasticity of drug tolerant clonal populations of cancer cells. Cancer Res October 1, 2013 73(19 Supplement). DOI:10.1158/1538-7445.FBCR13-PR05
Dinis JM, Barton DE, Ghadiri J, Surendar D, Reddy K, Velasquez F, Chaffee CL, Lee MW, Gavrilova H, Ozuna H, Smits SA, Ouverney CC. In search of an uncultured human-associated TM7 bacterium in the environment. PLoS One. 6, e21280 (2011).
Good News
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.
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)
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).
Master's Projects
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
David Zhou (MSBI 2024)
Jihan Yehia (MSBI 2023)
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 @ Stanford University School of Medicine, Lecturer @ Master of Biotechnology Program at SJSU
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 I @ Graphite Bio
Christine Gu (MSBI 2020) - Clinical Data Analyst @ Notable
Zachary Tom (MSCS 2020) - Software Engineer @ Dell Technologies
Deepti Garg (MSCS 2019) - SDE @ Amazon