Our Staff

Meet the GMCF team members:

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Stefan J. Green, PhD

Faculty Advisor, Genomics and Microbiome Core Facility
Director of Core Laboratory Services
Associate Professor, Department of Internal Medicine

Green’s research is focused on the interaction of complex microbial communities with hosts across a range of experimental and diseases systems. He has a B.A. in Earth and Environmental Sciences (Wesleyan University), an M.S. in Environmental Engineering (Northwestern University), and a PhD in Microbiology (Hebrew University of Jerusalem). He has a broad background in microbial ecology and molecular biology, with an emphasis on the acquisition and analysis of next-generation sequence data from biological systems. As Co-Principal Investigator of RIPHL, a public-academic partnership between RUSH University and the Chicago Department of Public Health, his laboratory performs surveillance and outbreak sequencing of SARS-CoV-2 genomes from viral transport medium as well as other pathogens of public health relevance. Green is funded on research projects studying the mammalian gut microbiome under spaceflight conditions, gut microbiome in traumatic brain injury, gut microbiome in Alzheimer’s Disease, vaginal microbiome and bacterial vaginosis, and more. Previously, Green was director of the Genome Research Core at the University of Illinois at Chicago (UIC).

Selected publications

1. Garrett-Bakelman, F.E., Darshi, M., Green, S.J., Gur, R.C., Lin, L., Macias, B.R., McKenna, M.J., Meydan, C., Mishra, T., Nasrini, J. and Piening, B.D., 2019. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science, 364(6436), p.eaau8650.
2. Keshavarzian, A., Green, S.J., Engen, P.A., Voigt, R.M., Naqib, A., Forsyth, C.B., Mutlu, E. and Shannon, K.M., 2015. Colonic bacterial composition in Parkinson's disease. Movement Disorders, 30(10), pp.1351-1360.
3. Naqib, A., Poggi, S. and Green, S.J., 2019. Deconstructing the Polymerase Chain Reaction II: an improved workflow and effects on artifact formation and primer degeneracy. PeerJ, 7, p.e7121.
4. Ofek-Lalzar, M., Sela, N., Goldman-Voronov, M., Green, S.J., Hadar, Y. and Minz, D., 2014. Niche and host-associated functional signatures of the root surface microbiome. Nature communications, 5(1), pp.1-9.

Complete list of publications on Google Scholar (https://scholar.google.com/citations?user=n7puvo8AAAAJ&hl).

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Kevin J. Kunstman

Director of Genomics and Microbiome Core Facility and Regional Public Health Lab (RIPHL)

Kevin Kunstman has 30+ years of experience as a molecular biologist and molecular virologist, with laboratory experience at the BSL3 level. His specialties include Next Generation library prep, sequence data acquisition and analysis, real time PCR, and sequence capture for sequencing. He is responsible for NGS DNA sequencing services, including consultations, study design, DNA library prep, sequencing, and data analyses. Kunstman came to Rush in January of 2021 to establish the Genomics and Microbiome Core Facility. Previously he was the Assistant Director at the UIC Genome Research Core.

Selected publications

1. Doyle K, Teran RA, Reefhuis J, Kerins JL, Qiu X, Green SJ, Choi H, Madni SA, Kamal N, Landon E, Albert RC, Pacilli M, Furtado LE, Hayden MK, Kunstman KJ, Bethel C, Megger L, Fricchione MJ, Ghinai I. Multiple Variants of SARS-CoV-2 in a University Outbreak After Spring Break - Chicago, Illinois, March-May 2021. MMWR Morb Mortal Wkly Rep. 2021 Sep 3;70(35):1195-1200. doi: 10.15585/mmwr.mm7035a3. PubMed PMID: 34473687; PubMed Central PMCID: PMC8422867.
2. Braesel J, Crnkovic CM, Kunstman KJ, Green SJ, Maienschein-Cline M, Orjala J, Murphy BT, Eustáquio AS. Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete. J Nat Prod. 2018 Sep 28;81(9):2057-2068. doi: 10.1021/acs.jnatprod.8b00394. Epub 2018 Aug 15. PubMed PMID: 30110167; PubMed Central PMCID: PMC6174880.
3. Worobey M, Gemmel M, Teuwen DE, Haselkorn T, Kunstman K, Bunce M, Muyembe JJ, Kabongo JM, Kalengayi RM, Van Marck E, Gilbert MT, Wolinsky SM.Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature. 2008 Oct 2;455(7213):661-4. doi: 10.1038/nature07390. PubMed PMID: 18833279; PubMed Central PMCID: PMC3682493.
4. Kunstman KJ, Puffer B, Korber BT, Kuiken C, Smith UR, Kunstman J, Stanton J, Agy M, Shibata R, Yoder AD, Pillai S, Doms RW, Marx P, Wolinsky SM.Structure and function of CC-chemokine receptor 5 homologues derived from representative primate species and subspecies of the taxonomic suborders Prosimii and Anthropoidea. J Virol. 2003 Nov;77(22):12310-8. doi: 10.1128/jvi.77.22.12310-12318.2003. PubMed PMID: 14581567; PubMed Central PMCID: PMC254294.

Complete list of publications on MyBibliography.

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Félix Araújo-Pérez, MS

Research Bioengineer

Félix Araújo-Pérez is a graduate from University of Puerto Rico receiving a master’s degree in biology focused on the molecular evolution of Heliconius butterflies. He has 20+ years of experience as a molecular biologist and has performed research covering topics in ecology, evolution, microbiology, and immunology. Before joining Rush University Medical Center, Araújo-Pérez worked at the Stanley-Manne Children’s Research Institute in Chicago doing research on the human microbiome development and its interaction with the immune system. He is currently involved in all aspects of Next-generation sequencing library preps and Illumina sequencing runs at GMCF and RIPHL.

Selected publications

1. Young RR, Jenkins K, Araujo-Perez F, Seed PC, Kelly MS. Long-term stability of microbiome diversity and composition in fecal samples stored in eNAT medium. Microbiologyopen. 2020 Jul;9(7):e1046. doi: 10.1002/mbo3.1046. Epub 2020 May 10. PMID: 32390344; PMCID: PMC7349174.
2. Younge N, McCann JR, Ballard J, Plunkett C, Akhtar S, Araújo-Pérez F, Murtha A, Brandon D, Seed PC. Fetal exposure to the maternal microbiota in humans and mice. JCI Insight. 2019 Oct 3;4(19):e127806. doi: 10.1172/jci.insight.127806. PMID: 31479427; PMCID: PMC6795398.
3. Younge NE, Araújo-Pérez F, Brandon D, Seed PC. Early-life skin microbiota in hospitalized preterm and full-term infants. Microbiome. 2018 May 31;6(1):98. doi: 10.1186/s40168-018-0486-4. PMID: 29855335; PMCID: PMC5984431.
4. Araújo-Pérez F, McCoy AN, Okechukwu C, Carroll IM, Smith KM, Jeremiah K, Sandler RS, Asher GN, Keku TO. Differences in microbial signatures between rectal mucosal biopsies and rectal swabs. Gut Microbes. 2012 Nov-Dec;3(6):530-5. doi: 10.4161/gmic.22157. Epub 2012 Oct 11. PMID: 23060016; PMCID: PMC3495790.

Complete list of publications on PubMed.

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Giancarlo S. Balangue, MSc

Lab Research Assistant 3, Genomics & Microbiome Core Facility

Giancarlo S. Balangue (Gian) grew up in the Philippines and graduated from Ateneo de Manila University’s B.S. in Life Sciences program with a specialization in Molecular Biology and Biotechnology, studying agricultural waste fermentation and biofuel production. He moved to Chicago to earn his master’s degree in Biotechnology at Northwestern University and explored the therapeutic potential of bispecific spherical nucleic acid nanoparticles. Since joining Rush in February 2022, Balangue has specialized in nucleic acid extraction and next-generation sequencing. He regularly assists in extracting viral RNA from SARS-CoV-2 samples as part of the RIPHL initiative.

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Hannah Barbian, PhD

Genomic Epidemiologist, Regional Innovative Public Health Laboratory

Hannah Barbian, PhD’s scientific training and interest are in molecular virology and viral genomics. She has expertise in HIV/SIV molecular biology and next-generation sequencing, with past research focused on the genomic fate of viruses upon transmission, immune pressure, and chronic infection. Since joining RIPHL as a genomic epidemiologist in October 2021, she performs SARS-CoV-2 genomic analyses as part of pandemic genomic surveillance, including outbreak investigation and identifying variants and mutations of interest. Barbian has expertise on the topics of viral next-generation sequencing, genotyping, and phylogenetic, mutational, evolutionary, and bioinformatic analyses.

Selected publications

1. Barbian HJ, Jackson-Jewett R, Brown CS, Bibollet-Ruche F, Learn GH, Decker T, Kreider EF, Li Y, Denny TN, Sharp PM, Shaw GM, Lifson J, Acosta EP, Saag MS, Bar KJ, Hahn BH. Effective treatment of SIVcpz-induced immunodeficiency in a captive western chimpanzee. Retrovirology. 2017 Jun 2;14(1):35.
2. Barbian HJ, Li Y, Ramirez M, Klase Z, Lipende I, Mjungu D, Moeller AH, Wilson ML, Pusey AE, Lonsdorf EV, Bushman FD, Hahn BH. Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees. American Journal of Primatology. 2018 Jan;80(1).
3. Barbian HJ, Connell AJ, Avitto AN, Russell RM, Smith AG, Gundlapally MS, Shazad AL, Li Y, Bibollet-Ruche F, Wroblewski EE, Mjungu D, Lonsdorf EV, Stewart FA, Piel AK, Pusey AE, Sharp PM, Hahn BH. CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecology and Evolution. 2018 Jul 16;8(16):7946-7963.
4. Spencer H, Teran RA, Barbian HJ, Love S, Berg, R, Black SR, Ghinai I, Kerins JL. 2022. Multistate Outbreak of Infection with SARS-CoV-2 Omicron Variant after Event in Chicago, Illinois, USA, 2021. Emerging Infectious Diseases. 2022 Jun.

Complete list of publications on MyBibliography.

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Sofiya Bobrovska, MPH

Data Analyst, Regional Innovative Public Health Laboratory (RIPHL)

Sofiya Bobrovska’s areas of interest include infectious diseases and environmental health. She earned an MPH in Epidemiology from University of Illinois Chicago and a BS in Integrative Biology from University of Illinois Urbana Champaign. Bobrovska joined RIPHL as a data analyst in August 2021. She organizes SARS-CoV-2 specimen intake, guides partnerships, and works with Dr. Hannah Barbian and the Chicago Department of Public Health to perform analysis on genomic data.

Select presentations

1. Bobrovska, S., Fiorillo, M., Ganesh, A., English, K., Green, S., Ghinai, I. Hospitalization risk by SARS-CoV-2 lineages in Chicago, Illinois. Pathogen Genomics Symposium: Genes, Genomes, and Infection. Chicago. 2022 May 4.
2. Kittner, A., Barbian, H., Bobrovska, S., English, K., Green, S., Hayden, M., & Ghinai, I. Early detection and population surveillance of SARS-CoV-2 variants through variant PCR and genomic sequencing. Pathogen Genomics Symposium: Genes, Genomes, and Infection. Chicago. 2022 May 4.
3. Bobrovska, S., Barbian, H., English, K., Fiorillo, M., Green, S., Hayden, M., & Teran, R. Integrated molecular surveillance of SARS-CoV-2 at the Regional Innovative Public Health Laboratory in Chicago, IL. Pathogen Genomics Symposium. Chicago. 2023 April 24.

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Latifah Boyd, MPH

Senior Program Manager, Regional Innovative Public Health Laboratory (RIPHL)

Latifah Boyd graduated with her MPH from Benedictine University in 2013. She has 10+ years of experience in managed care and healthcare policies. Latifah has embarked on an exciting career transition from managed care to the realm of genomics. She joined RIPHL as the Senior Program Manager in March 2023, where she oversees a wide range of projects, ensuring their successful planning, execution and completion.

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Cecilia S. Chau

Research Scientist, Genomics & Microbiome Core Facility

Cecilia Chau has 20+ years of experience in molecular biology. Her professional skill and experience can assist in the overall management of experiment protocol, sample preparation, and data analysis in the research. Chau was a Research Technologist Manager in Genome Research Core at University of Illinois at Chicago (UIC) in Sanger Sequencing and other molecular biology projects. Since joining Genomics & Microbiome Core Facility in November 2021, she performs SARS-Cov-2 sequencing project such as Real time PCR runs, NGS 16S amplicon projects and digital PCR projects.

Selected publications

1. Lei Bao, Cecilia S. Chau, Zhengdeng Le, Hong Hu, Angelina G. Chan, Kyle T. Amber, Mark Maienschein‑Cline, Maria M. Tsoukas. 2020. Dysregulated microRNA expression in IL-4 transgenic mice, an animal model of atopic dermatitis
2. Lei Bao, Cecilia Chau, Jeremy Bao, Maria M. Tsoukas, Lawrence S. Chan, 2018. IL-4 dysregulates microRNAs involved in inflammation, angiogenesis and apoptosis in epidermal keratinocytes

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Marisol Dominguez

Lab Research Assistant 3, Genomics & Microbiome Core Facility (GMCF)

Marisol Dominguez graduated from Loyola University Chicago with a B.S. in Biology and Forensic Science and a minor in Chemistry. Having worked in forensic, clinical, and pharmaceutical labs, her experience includes working with a variety of sample types and different instrumentation. She joined the team in April 2023 and primarily works on SARS-CoV-2 samples as part of the RIPHL initiative.

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Trisha Jeon

Lab Research Assistant 3, Genomics & Microbiome Core Facility (GMCF), Regional Public Health Lab (RIPHL)

Trisha has an academic background in Biochemistry and years of experience in genome research laboratories. With her experience and knowledge in molecular biology, Trisha specializes in Next-generation sequencing (NGS) and Oxford Nanopore sequencing technologies for whole-genome, shot-gun, and amplicon sequencing for microbiome and metagenomic research. She joined RIPHL in 2023 to participate in the Chicago wastewater poliovirus surveillance project. In 2024, she began a new academic journey to pursue a master's degree in bioinformatics.  

Selected publications 

1. Kahsen J, Sherwani SK, Naqib A, Jeon T, Wu LYA, Green SJ. 2024. Quantitating primer-template interactions using deconstructed PCR. PeerJ 12:e17787
2. Kittner, A., Korban, C., Jeon, T., Kunstman, K. J., Foulkes, D., Anderson, K. W., Barbian, H. J., Bobrovska, S., Poretsky, R., Green, S. J., Pacilli, M. (2024). Leveraging existing wastewater surveillance infrastructure for short-term Poliovirus surveillance. Association of Public Health Laboratories 2024 Annual Conference. Chicago.  
3. Naqib, A., Jeon, T., Kunstman, K., Wang, W., Shen, Y., Sweeney, D., Hyde, M., & Green, S. J. (2019). PCR effects of melting temperature adjustment of individual primers in degenerate primer pools. PeerJ, 7, e6570.

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Ping Li, MSc

Laboratory Manager, Genomics & Microbiome Core Facility (GMCF) 

Holding a master's degree in microbiology and molecular genetics, Ping has built a diverse range of research experiences. She spent nine years each at the University of Notre Dame and the IU Medical School, focusing on research projects. She also has four years of experience in the pharmaceutical industry with Immunogen Inc., and recently, she served for two years as an operations manager at the Genomics Core of the University of Arkansas for Medical Sciences. 

Her expertise extends to a variety of research models and sample types, from microorganisms to mammalian tissues and cell cultures. Her technical skills are primarily in molecular genetics techniques, including cloning and real-time PCR. She is also proficient in next-generation library preparation methods, which include DNA and DNA Methylation Libraries, RNA-seq libraries, and single-cell sequencing libraries. In September 2023, Ping joined RMCF, where she is responsible for overseeing NGS single-cell RNA sequencing and NGS DNA/RNA sequencing services. 

Selected publications 

1. Mysore K, Sun L, Li P, Roethele JB, Misenti JK, Kosmach J, Igiede J, Duman-Scheel M. A Conserved Female-Specific Requirement for the GGT Gene in Mosquito Larvae Facilitates RNAi-Mediated Sex Separation in Multiple Species of Disease Vector Mosquitoes. Pathogens. 2022 Jan 27;11(2). doi: 10.3390/pathogens11020169. PubMed PMID: 35215113; PubMed Central PMCID: PMC8879970. 
2. Mysore K, Li P, Wang CW, Hapairai LK, Scheel ND, Realey JS, Sun L, Roethele JB, Severson DW, Wei N, Duman-Scheel M. Characterization of a yeast interfering RNA larvicide with a target site conserved in the synaptotagmin gene of multiple disease vector mosquitoes. PLoS Negl Trop Dis. 2019 May;13(5):e0007422. doi: 10.1371/journal.pntd.0007422. eCollection 2019 May. PubMed PMID: 31107878; PubMed Central PMCID: PMC6544322. 
3. Li P, Chaurasia SS, Gao Y, Carr AL, Iuvone PM, Li L. CLOCK is required for maintaining the circadian rhythms of Opsin mRNA expression in photoreceptor cells. J Biol Chem. 2008 Nov 14;283(46):31673-8. doi: 10.1074/jbc.M803875200. Epub 2008 Aug 7. PubMed PMID: 18687681; PubMed Central PMCID: PMC2581545. 
4. Li P, Temple S, Gao Y, Haimberger TJ, Hawryshyn CW, Li L. Circadian rhythms of behavioral cone sensitivity and long wavelength opsin mRNA expression: a correlation study in zebrafish. J Exp Biol. 2005 Feb;208(Pt 3):497-504. doi: 10.1242/jeb.01424. PubMed PMID: 15671338. 

Complete list of publications on https://www.ncbi.nlm.nih.gov/myncbi/ping.li.16/bibliography/public/.

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Erin P. Newcomer, PhD

Genomic Epidemiologist, Regional Innovative Public Health Laboratory (RIPHL) 

Erin P. Newcomer, PhD's training background is in biomedical engineering, and she has largely focused her research on using next generation sequencing data and genomics analyses to characterize and track pathogens of high clinical importance. Her thesis work focused on characterizing the transmission and residence of antibiotic resistant bacteria in a hospital setting. Since joining RIPHL, she performs genomic analyses for public health surveillance of pathogens from patient specimens such as SARS-CoV-2, Candida auris, and Mpox virus for the Chicago area. She is developing computational methods to correlate air sampling collection of SARS-CoV-2 with clinical data for environmental variant surveillance. Newcomer is also developing methods for metagenomic sequencing-based tracking of C. auris and carbapenem resistance genes from wastewater sampling.  

Selected publications

1. Sukhum KV, Newcomer EP, Cass C, Wallace MA, Johnson C, Fine J, Sax S, Barlet MH, Burnham CD, Dantas G, Kwon JH. Antibiotic-resistant organisms establish reservoirs in new hospital built environments and are related to patient blood infection isolates. Commun Med (Lond). 2022;2:62. doi: 10.1038/s43856-022-00124-5. eCollection 2022. PubMed PMID: 35664456; PubMed Central PMCID: PMC9160058.
2. Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Burnham C-AD, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. mBio. 2024 Mar 13;15(3):e0330023. doi: 10.1128/mbio.03300-23. Epub 2024 Feb 8. PubMed PMID: 38329369; PubMed Central PMCID: PMC10936198. 

Complete list of publications on My Bibliography. 

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Edith Perez, MSc

Research Scientist, Genomics & Microbiome Core Facility

Edith Perez graduated from Loyola University Chicago with a BS in both Biology and Forensic Science, with minors in Chemistry and Anthropology. She went on to earn an MS in Forensic Science from UIC. After working in both academic and industry labs, Perez joined the GMCF/RIPHL lab in the Summer of 2021 where her experience working with a variety of sample types translated to development of more efficient nucleic acid extraction methods. Perez primarily works on RNAseq and NGS projects for the lab handling projects from nucleic acid extractions through to library prep and sequencing.

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Lok Yiu Ashley Wu

Lab Research Assistant 3, Genomics & Microbiome Core Facility

Lok Yiu Ashley Wu (Ashley) graduated from UIC with a B.S. in Biological Sciences in 2019. She has experience with a range of molecular biology techniques and platforms, as well as clinical molecular diagnostics as a research and medical technologist. Since joining GMCF in April 2022, Ashley now manages all 16S rRNA gene amplicon next-generation sequencing projects for internal and external investigators. Ashley is currently pursuing a master’s degree in bioinformatics. 

Selected publications

1. Kahsen J, Sherwani SK, Naqib A, Jeon T, Wu LYA, Green SJ. 2024. Quantitating primer-template interactions using deconstructed PCR. PeerJ 12:e17787