Recent Publications 

[* Student mentored by Prof. 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.
• F. Mbuga*, K. Lam* and W. Lee, "Machine Learning-Based Artifact Detection for Long-Read Sequencing Data," 2023 International Conference on Computational Science and Computational Intelligence (CSCI), Las Vegas, NV, USA, 2023, pp. 582-584, doi: 10.1109/CSCI62032.2023.00103.
• 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, 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, 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 presentation 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 presentation 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

• 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 7, 350 (2020). https://doi.org/10.1038/s41597-020-00664-2
• N. Khuri, Lehmkhul-Dakhwe KV, Vanhoven M, Lee W, S. Khuri. Interdisciplinary Minor in Bioinformatics: First Results and Outlook. Accepted for publication and presentation at the ACM SIGCSE, Portland, Oregon, March 11 - March 14, 2020.
• 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 MC, 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 MC, 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 MC, 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).
• 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).

 

Referred Poster Presentations

• 2014 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
• 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.