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

Dr. 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. Dr. 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, Dr. 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

Laboratory Manager, Genomics & Microbiome Core Facility and Regional Innovative Public Health Laboratory

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.

Alyse Kittner, MPH

Senior Program Manager, Regional Innovative Public Health Laboratory

Alyse Kittner has experience in program management in health care settings, the public health department, and at advocacy organizations. Her focus is on the translation of scientific public health initiatives into public awareness and application. Kittner joined RIPHL in September 2021 after working most of the COVID-19 pandemic at the Chicago Department of Public Health. She graduated with her MPH from George Washington University in 2019.

Select presentations

1. 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.

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.

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

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.

Cecilia S. Chau

Laboratory Research Assistant 3, 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.

Kanakeshwari (Kim) Falzari, PhD

Research Bioengineer, Genomics & Microbiome Core Facility

Kim Falzari, PhD's research background includes microbiology and molecular biology studies with particular interest in microbial resistance and antibiotic development. Since joining the Genomic and Microbiome Core Facility in late April 2022, she is involved in developing in house single cell RNA library and performing sequence analysis on SARS-CoV-2 current variants. Falzari also focuses on retrospective SARS-CoV-2studies, which provides insights into the evolutionary and epidemiological viral dynamics during the past and current COVID-19 pandemic.

Selected publications

1. Falzari K, Zhu Z, Pan D, Liu H, and Franzblau SG. In vitro and in vivo activities of macrolide derivatives against Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2005 Apr; 49(4):1447-54.
2. Crew J, Falzari K, DiMario JX. Muscle Fiber Type Specific Induction of Slow Myosin Heavy Chain 2 Gene Expression by Electrical Stimulation. Exp Cell Res. 2010 Apr 1;316(6):1039-49. Epub 2010 Jan 11.
3. Roxas JL, Koutsouris A, Bellmeyer A, Tesfay S, Royan SV, Falzari K, Harris A, Cheng H, Rhee KJ, and Hecht GA. Enterohemorrhagic E. coli alters murine intestinal epithelial tight junction protein expression and barrier function in Shiga toxin independent manner. Lab Invest. 2010 Aug;90(8):1152-68. Epub 2010 May 17.
4. Punj V, Zaborina O, Dhiman N, Falzari K, Bagdasarian M, and Chakrabarty AM. Phagocytic cell killing mediated by secreted cytotoxic factors of Vibrio cholerae. Infect Immun. 2000 Sep; 68(9):4930-7.

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Trisha Jeon

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

With an academic background in Biochemistry and years of experience in molecular biology, Trisha specializes in Next-generation sequencing (NGS) for microbiome research. She joined RIPHL to participate in the Chicago wastewater poliovirus surveillance project.

Edith Perez

Research Associate 3, 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.

Lok Yiu Ashley Wu

Lab Research Assistant 3, Genomics & Microbiome Core Facility

Lok Yiu Ashley Wu (Ashley) graduated from UIC with a BS 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. At GMCF, Wu performs 16S microbiome amplicon next-generation sequencing for different internal and external investigators.