Michael H. Farkas PhD
Michael H. Farkas
PhD
Associate Professor
Jacobs School of Medicine & Biomedical Sciences
Specialty/Research Focus
Bioinformatics; Eukaryotic Pathogenesis; Gene Expression; Gene Therapy; Genomics and proteomics; Molecular and Cellular Biology; Molecular Basis of Disease; Molecular genetics; RNA; Stem Cells; Vision science
Education and Training:
- Fellowship, Ophthalmology, Harvard Medical School (2014)
- Fellowship, Ophthalmology, University of Pennsylvania (2011)
- PhD, Biological Sciences, State University of New York at Buffalo (2009)
- MS, Biotechnology, Johns Hopkins University (2004)
- BS, Biology, University of Pittsburgh at Johnstown, Magna Cum Laude (2002)
Employment:
- Associate Professor, Ophthalmology, State University of New York at Buffalo (2023-present)
- Adjunct Assistant Professor, Biochemistry, State University of New York Jacobs School of Medicine & Biomedical Sciences (2017-present)
- Assistant Professor, Ophthalmology, State University of New York at Buffalo Jacobs School of Medicine & Biomedical Sciences (2016–2023)
- Instructor, Ophthalmology, Harvard Medical School (2014–2016)
- Investigator, Ophthalmology, Massachusetts Eye and Ear Infirmary (2014–2016)
Awards and Honors:
- Emerging Vision Scientist (2016)
- Ruth L. Kirschstein National Research Service Award (2010)
- Biological Sciences Fellow (2004)
- Presidential Fellow (2004)
Research Centers:
- Ira G. Ross Eye Institute Research Center
UB 2020 Strategic Strengths:
- Molecular Recognition in Biological Systems and Bioinformatics
Grants and Sponsored Research:
- October 2019–September 2023
Epigenetic-guided studies of AMD pathology and iPSC-RPE transplantation therapy
Department of Veterans Affairs
Role: Principal Investigator - July 2019–September 2021
Defining the functional role of RPE-expressed AMD risk-associated long non-coding RNAs
BrightFocus Foundation
Role: Principal Investigator - November 2020–August 2021
Equipment grant for a human donor iPSC repository
Carl Marshall Reeves & Mildred Almen Reeves Foundation
Role: Co-Principal Investigator - June 2015–May 2017
Functional characterization of a novel splice variant in PRPF31
Foundation Fighting Blindness
Role: Principal Investigator
$154,446 - April 2010–March 2013
The role of RNA splicing factors in retinal degeneration
National Eye Institute
Role: Principal Investigator
$151,086
Patents:
- Gene augmentation therapies for inherited retinal degeneration caused by mutations in the PRPF31 gene (2020)
Journal Articles:
- Shwani T, Zhang C, Owen LA, Shakoor A, Vitale AT, Lillvis JH, Barr JL, Cromwell P, Finley R, Husami N, Au E, Zavala RA, Graves EC, Zhang SX, Farkas MH, Ammar DA, Allison KM, Tawfik A, Sherva RM, Li M, Stambolian D, Kim IK, Farrer LA, DeAngelis MM. (2023) Patterns of Gene Expression, Splicing, and Allele-Specific Expression Vary among Macular Tissues and Clinical Stages of Age-Related Macular Degeneration. Cells (Nov), 12(23). doi:10.3390/cells12232668
- Kaczynski TJ, Husami NJ, Au ED, Farkas MH. (2023) Dysregulation of a lncRNA within the TNFRSF10A locus activates cell death pathways. Cell death discovery (Jul), 9(1): 242. doi:10.1038/s41420-023-01544-5
- Liang Q, Cheng X, Wang J, Owen L, Shakoor A, Lillvis JL, Zhang C, Farkas M, Kim IK, Li Y, DeAngelis M, Chen R. (2023) A multi-omics atlas of the human retina at single-cell resolution. Cell genomics (Jun), 3(6): 100298. doi:10.1016/j.xgen.2023.100298
- Orozco LD, Owen LA, Hofmann J, Stockwell AD, Tao J, Haller S, Mukundan VT, Clarke C, Lund J, Sridhar A, Mayba O, Barr JL, Zavala RA, Graves EC, Zhang C, Husami N, Finley R, Au E, Lillvis JH, Farkas MH, Shakoor A, Sherva R, Kim IK, Kaminker JS, Townsend MJ, Farrer LA, Yaspan BL, Chen HH, DeAngelis MM. (2023) A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration. Cell genomics (Jun), 3(6): 100302. doi:10.1016/j.xgen.2023.100302
- Barr JL, Feehan M, Tak C, Owen LA, Finley RC, Cromwell PA, Lillvis JH, Hicks PM, Au E, Farkas MH, Weiner A, Reynolds AL, Sieminski SF, Sherva RM, Munger MA, Brilliant MH, DeAngelis MM. (2023) Heritable Risk and Protective Genetic Components of Glaucoma Medication Non-Adherence. International journal of molecular sciences (Mar), 24(6). doi:10.3390/ijms24065636
- Hanineva A, Park KS, Wang JJ, DeAngelis MM, Farkas MH, Zhang SX. (2022) Emerging roles of circular RNAs in retinal diseases. Neural regeneration research (Sep), 17(9): 1875-1880. doi:10.4103/1673-5374.335691
- Kaczynski TJ, Au ED, Farkas MH. (2022) Exploring the lncRNA localization landscape within the retinal pigment epithelium under normal and stress conditions. BMC genomics (Jul), 23(1): 539. doi:10.1186/s12864-022-08777-1
- Farkas MH, Skelton LA, Ramachandra-Rao S, Au E, Fliesler SJ. (2022) Morphological, biochemical, and transcriptomic characterization of iPSC-derived human RPE cells from normal and Smith-Lemli-Opitz syndrome patients. Molecular vision (Jan), 28: 394-411.
- Kaczynski TJ, Au ED, Farkas MH. (2022) Oxidative stress alters transcript localization of disease-associated genes in the retinal pigment epithelium. Molecular vision (Jan), 28: 340-351.
- Hicks PM, Au E, Self W, Haaland B, Feehan M, Owen LA, Siedlecki A, Nuttall E, Harrison D, Reynolds AL, Lillvis JH, Sieminski S, Shulman JP, Barnoya M, Noguera Prera JJ, Gonzalez O, Murtaugh MA, Williams LB, Farkas MH, Crandall AS, DeAngelis MM. (2021) Pseudoexfoliation and Cataract Syndrome Associated with Genetic and Epidemiological Factors in a Mayan Cohort of Guatemala. International journal of environmental research and public health (Jul), 18(14). doi:10.3390/ijerph18147231
- Farkas MH, DeAngelis MM. (2021) Age-Related Macular Degeneration: From Epigenetics to Therapeutic Implications. Advances in experimental medicine and biology (Jan), 1256: 221-235.
- Sousa ME, Farkas MH. (2018) Micropeptide. PLoS genetics (Dec), 14(12): e1007764. doi:10.1371/journal.pgen.1007764
- Au ED, Fernandez-Godino R, Kaczynksi TJ, Sousa ME, Farkas MH. (2017) Characterization of lincRNA expression in the human retinal pigment epithelium and differentiated induced pluripotent stem cells. PloS one (Jan), 12(8): e0183939. doi:10.1371/journal.pone.0183939
- Pan J, Liu S, Farkas M, Consugar M, Zack D, Fernando Arevalo J, Pierce E, Qian J, Al Kahtani E. (2016) Identification of serum biomarker for proliferative diabetic retinopathy. Molecular Vision (Jan).
- Farkas MH, Au ED, Sousa ME, Pierce EA. (2015) RNA-Seq: Improving Our Understanding of Retinal Biology and Disease. Cold Spring Harb Perspect Med (Feb), 5(9): 017152-017152.
- Bujakowska KM, Consugar M, Place E, Harper S, Lena J, Taub DG, White J, Navarro-Gomez D, Weigel DiFranco C, Farkas MH, Gai X, Berson EL, Pierce EA. (2014) Targeted exon sequencing in Usher syndrome type I. Invest Ophthalmol Vis Sci (Dec), 55(12): 8488-8496.
- Farkas MH, Lew DS, Sousa ME, Bujakowska K, Chatagnon J, Bhattacharya SS, Pierce EA, Nandrot EF. (2014) Mutations in pre-mRNA processing factors 3, 8, and 31 cause dysfunction of the retinal pigment epithelium. Am J Pathol (Oct), 184(10): 2641-2652.
- Farkas MH, Grant GR, White JA, Sousa ME, Consugar MB, Pierce EA. (2013) Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. BMC Genomics (Jul), 14: 486-486.
- Farkas MH, Grant GR, Pierce EA. (2012) Transcriptome analyses to investigate the pathogenesis of RNA splicing factor retinitis pigmentosa. Adv Exp Med Biol (Jan), 723: 519-525.
- Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics (Sep), 27(18): 2518-2528.
- Graziotto JJ, Farkas MH, Bujakowska K, Deramaudt BM, Zhang Q, Nandrot EF, Inglehearn CF, Bhattacharya SS, Pierce EA. (2011) Three gene-targeted mouse models of RNA splicing factor RP show late-onset RPE and retinal degeneration. Invest Ophthalmol Vis Sci (Jan), 52(1): 190-198.
- Farkas MH, Mojica ER, Patel M, Aga DS, Berry JO. (2009) Development of a rapid biolistic assay to determine changes in relative levels of intracellular calcium in leaves following tetracycline uptake by pinto bean plants. Analyst (Aug), 134(8): 1594-1600.
- Farkas MH, Berry JO, Aga DS. (2007) Chlortetracycline detoxification in maize via induction of glutathione S-transferases after antibiotic exposure. Environ Sci Technol (Feb), 41(4): 1450-1456.
- Farkas MH, Berry JO, Aga DS. (2007) Determination of enzyme kinetics and glutathione conjugates of chlortetracycline and chloroacetanilides using liquid chromatography/mass spectrometry. Analyst (Jan), 132(7): 664-671.
- Perez S, Farkas MH, Barcelo D, Aga DS. (2007) Characterization of glutathione conjugates of chloroacetanilide pesticides using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry and liquid chromatography/ion trap mass spectrometry. Rapid Communications in Mass Spectrometry (Jan), 21(24): 4017-4022.
Books and Book Chapters:
- Farkas M. (2014) Retinal Disorders: Genetic Approaches to Diagnosis & Treatment. In: Interrogating the transcriptome to study inherited retinal degenerations. Cold Spring Harbor Perspectives
- Farkas M. (2009) In: Characterization of Chlortetracycline-induced Glutathione S-Transferase to Conjugate Chloroacetanilide and Chlorotriazine Herbicides. ACS Symposium Series
- Farkas M. (2008) In: Antibiotic transformation in plants via gluthathione conjugation. CRC Press
Professional Memberships:
- International Society for Eye Research (2023–present)
- American Society for Human Genetics (2013–present)
- Association for Research in Vision and Ophthalmology (2010–present)
- Society for Environmental Toxicology and Chemistry (2005–2009)
- American Chemical Society (2005–2009)
Presentations:
- "Building the case for lncRNA involvement in AMD pathophysiology" Duke Ophthalmology Seminar Series (2023)
- "Epigenetic memory in iPSC differentiation" International Society for Eye Research (2023)
- "An AMD-associated lncRNA: functional or just deadly?" Ohio State University Department of Ophthalmology (2022)
- "Envisioning a new pathophysiological mechanism for AMD onset" University of Pennsylvania, F.M. Kirby Center for Molecular Ophthalmology (2022)
- "Envisioning a new pathophysiological mechanism for AMD onset" University at Buffalo Program for Neuroscience Seminar Series (2022)
- "Exploring lncRNA dysregulation in AMD pathogenesis" Departmental Seminar Series, Flaum Eye Institute, University of Rochester (2021)
- "Identification and characterization of a novel lncRNA as a potential biomarker for AMD staging" Departmental Seminar Series, Department of Ophthalmology, SUNY Downstate (2020)
- "Inherited retinal dystrophies: bridging the mutation to therapy gap using iPS disease modeling" Seminar Series; Children‘s Hospital Los Angeles (2016)
- "RNA-Seq guided gene therapy for vision loss" Festival of Genomics (2016)
- "Targeted capture for RNA-Seq studies" Festival of Genomics (2016)
- "RNA splicing factor-associated RP: from genetics to gene therapy" Seminar Series; Massachusetts Eye and Ear Infirmary; Ocular Regenerative Medicine Institute (2016)
- "Insights into the pathogenesis of RNA splicing factor retinitis pigmentosa" Seminar Series; Cincinnati Children's Hospital; Visual Sciences Group (2015)
- "Insights into the pathogenesis of RNA splicing factor retinitis pigmentosa" Seminar Series; State University of New York at Buffalo; Department of Ophthalmology (2015)
- "Insights into the pathogenesis of RNA splicing factor retinitis pigmentosa" Seminar Series; Schepens Eye Research Institute; Genetic and Regenerative Medicine of Eye Disease Symposium (2015)
- "Genetics of and Gene Therapy for Inherited Retinal Degenerations" Program in Medical and Population Genetics; Broad Institute of MIT and Harvard (2014)
- "RNA-Seq" Illumina Users Group Meeting; Illumina (2013)
- "Preparation of High Quality RNA-Seq Libraries for Next-Generation sequencing" Webinar; Agilent; Agilent Users Group Meeting (2013)
- "The Role of Alternative Splicing in the Pathogenesis of RNA Splicing Factor Retinitis Pigmentosa" Seminar Series; State University of New York at Buffalo; Department of Biological Sciences (2013)
- "Insights into RNA Splicing Factor RP Through Functional Studies and Transcriptome Analyses" Retina Focus Group; Massachusetts Eye and Ear Infirmary; Department of Ophthalmology (2013)
- "Revealing the Retinal Transcriptome with Next-Generation Sequencing and its Implications for Disease" Illumina Technology Day; Illumina (2012)
- "Comprehensive Characterization of the Wild-type Mouse Neural Retina Transcriptome Using Next-Generation Sequencing" Seminar Series; University of Pennsylvania; Department of Genetics (2011)
- "Characterizing the Transcriptomes of RNA Splicing Factor mice" Seminar Series; University of Pennsylvania; F.M. Kirby Center for Molecular Ophthalmology (2010)
Service Activities:
- ZEY1 VSN(03); Ad Hoc Member (2023–present)
- ZRG1 MGG-V (50); Ad hoc Member (2023–present)
- BIVT study Section; Ad hoc member (2023–present)
- Translational Vision and Science Technology (2021–present)
- Moorfields Eye Hospital, Graduate Student Fellowship in Vision Research (2021–present)
- Buffalo Chapter of the Society for Neuroscience; President (2021–2022)
- (2021–present)
- Molecular Therapy (2021–present)
- UB Neuroscience Research Day (2021–present)
- NIH Study Section Special Emphasis Panel, NEI Vision Imaging, Bioengineering and Low Vision Technology Development, ZRG1-ETTN-P (81) S (2021–present)
- European Journal of Molecular Genetics (2021–present)
- Faculty and Graduate Professional Research Continuity Committee (2020)
- Exploration in Medicine (2019–present)
- Frontiers in Molecular Neuroscience (2019–present)
- Contingent Employment Committee, United University Professions, Statewide Member (2019–present)
- Officer for Contingent Employees, UUP; Officer (2019–present)
- Faculty Council (2019–2021)
- Online Education Advisory Committee, United University Professions, Statewide Member (2019–present)
- Data in Brief (2018–present)