Jonathan E. Bard PhD
Jonathan E. Bard
PhD
Research Assistant Professor; Associate Director of Bioinformatics Genomics and Bioinformatics Core
Jacobs School of Medicine & Biomedical Sciences
Specialty/Research Focus
Artificial Intelligence; Bioinformatics; Computational Biology; Genomics and proteomics; Transcriptomics
Professional Summary:
My research focuses on the development of computational methods for large-scale integration of next-generation sequencing data, with an emphasis on modeling the tumor microenvironment (TME) and its role in cancer progression and therapeutic response. Currently, I am investigating the role of alternative cleavage and polyadenylation (APA) in disrupting post-transcriptional regulation in oral squamous cell carcinoma (OSCC), using single-cell and spatial transcriptomics to map cell-type-specific APA events and their impact on microRNA-mediated control. This work aims to uncover novel mechanisms of oncogenesis and identify therapeutic targets.
Education and Training:
- PhD, Genetics, Genomics, and Bioinformatics, State University of New York at Buffalo (2023)
- MA, Biochemistry, State University of New York at Buffalo (2015)
- BS, Bioinformatics, Canisius College (2010)
Employment:
- Research Assistant Professor, Biochemistry, State University of New York at Buffalo (2023-present)
- Associate Director of Bioinformatics, Genomics and Bioinformatics Core, State University of New York at Buffalo (2020-present)
- Senior Programmer Analyst, Genomics and Bioinformatics Core, State University of New York at Buffalo (2017–2020)
- Bioinformatics Analyst, Genomics and Bioinformatics Core, State University of New York at Buffalo (2010–2017)
Awards and Honors:
- Genetics, Genomics, and Bioinformatics Program: GGB Research Day, Best Oral Presentation (2021)
- IBM Center for Advanced Studies Conference (CASCON): Best Demo Award (2009)
Research Centers:
- Center of Excellence in Bioinformatics and Life Sciences
Grants and Sponsored Research:
- July 2024–June 2029
Regulatory Mechanisms in Salivary Gland Development and Regeneration
NIDCR
Role: Co-Investigator
$3,743,537 - April 2025–March 2029
Impact of Sex on Mitochondrial and Epigenetic Mechanisms in Age-Related Macular Degeneration
National Institutes of Health
Role: Co-Investigator
$2,231,306 - August 2023–July 2028
Therapeutic targeting of master regulators in non-canonical AR driven advanced lethal prostate cancers.
NCI
Role: Co-Investigator
$3,823,553 - July 2025–June 2028
Cell Type Specific Activation of Endoplasmic Reticulum Sensor, ATF6, Drives Fibrotic Remodeling in Pericytes and SMC
American Heart Association
Role: Co-Investigator
$300,000
Journal Articles:
- Chak V, Ovalle EJ, Bard J, Wohlfert EA, Kay JG, Balu-Iyer S. (2025) Single-cell transcriptional analysis of murine mesenteric lymph nodes following oral lyso-phosphatidylserine nanoparticle administration reveals cellular heterogeneity in tolerance features. Journal of pharmaceutical sciences (Jul), 114(9): 103919.
- Kearly A, Saelee P, Bard J, Sinha S, Satterthwaite A, Garrett-Sinha LA. (2025) Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells. PloS one (Jan), 20(3): e0308896.
- Thiyagarajan R, Zhang L, Glover OD, Kwack KH, Ahmed S, Murray E, Yellapu NK, Bard J, Seldeen KL, Rosario SR, Troen BR, Kirkwood KL. (2024) Age-related increase of CD38 directs osteoclastogenic potential of monocytic myeloid-derived suppressor cells through mitochondrial dysfunction in male mice. Aging cell (Nov), 23(11): e14298.
- Bard JE, Tylec BL, Dubey AP, Lamb NA, Yergeau DA, Read LK. (2024) Life stage-specific poly(A) site selection regulated by Trypanosoma brucei DRBD18. Proceedings of the National Academy of Sciences of the United States of America (Jul), 121(29): e2403188121.
- Campbell CE, Webber K, Bard JE, Chaves LD, Osinski JM, Gronostajski RM. (2024) Nuclear Factor I A and Nuclear Factor I B Are Jointly Required for Mouse Postnatal Neural Stem Cell Self-Renewal. Stem cells and development (Apr), 33(7-8): 153-167.
- Zhang L, Kwack KH, Thiyagarajan R, Mullaney KK, Lamb NA, Bard JE, Sohn J, Seldeen KL, Arao Y, Blackshear PJ, Abrams SI, Troen BR, Kirkwood KL. (2024) Tristetraprolin regulates the skeletal phenotype and osteoclastogenic potential through monocytic myeloid-derived suppressor cells. FASEB journal : official publication of the Federation of American Societies for Experimental Biology (Jan), 38(1): e23338.
- Bard JE, Jiang N, Emerson J, Bartz M, Lamb NA, Marzullo BJ, Pohlman A, Boccolucci A, Nowak NJ, Yergeau DA, Crooks AT, Surtees JA. (2024) Genomic profiling and spatial SEIR modeling of COVID-19 transmission in Western New York. Frontiers in microbiology (Jan), 15: 1416580.
- Segelhurst E, Bard JE, Pillsbury AN, Alam MM, Lamb NA, Zhu C, Pohlman A, Boccolucci A, Emerson J, Marzullo BJ, Yergeau DA, Nowak NJ, Bradley IM, Surtees JA, Ye Y. (2023) Robust Performance of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method. ACS ES&T water (Apr), 3(4): 954-962.
- Ge Y, Chen X, Nan N, Bard J, Wu F, Yergeau D, Liu T, Wang J, Mu X. (2023) Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic acids research (Mar), 51(5): 2151-2176.
- Patel A, Pietromicca JG, Venkatesan M, Maity S, Bard JE, Madesh M, Alevriadou BR. (2023) Modulation of the mitochondrial Ca2+ uniporter complex subunit expression by different shear stress patterns in vascular endothelial cells. Physiological reports (Feb), 11(3): e15588.
- Lamb NA, Bard JE, Loll-Krippleber R, Brown GW, Surtees JA. (2022) Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes. Genetics (Jul), 221(4).
- Kwack KH, Zhang L, Kramer ED, Thiyagarajan R, Lamb NA, Arao Y, Bard JE, Seldeen KL, Troen BR, Blackshear PJ, Abrams SI, Kirkwood KL. (2022) Tristetraprolin limits age-related expansion of myeloid-derived suppressor cells. Frontiers in immunology (Jan), 13: 1002163.
- Bard JE, Nowak NJ, Buck MJ, Sinha S. (2022) Multimodal Dimension Reduction and Subtype Classification of Head and Neck Squamous Cell Tumors. Frontiers in oncology (Jan), 12: 892207.
- Glathar AR, Oyelakin A, Gluck C, Bard J, Sinha S. (2022) p63 Directs Subtype-Specific Gene Expression in HPV+ Head and Neck Squamous Cell Carcinoma. Frontiers in oncology (Jan), 12: 879054.
- Lamb NA, Bard JE, Buck MJ, Surtees JA. (2021) A selection-based next generation sequencing approach to develop robust, genotype-specific mutation profiles in Saccharomyces cerevisiae. G3 (Bethesda, Md.) (Jun), 11(6).
- Wu F, Bard JE, Kann J, Yergeau D, Sapkota D, Ge Y, Hu Z, Wang J, Liu T, Mu X. (2021) Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas. Nature communications (Mar), 12(1): 1465.
- Horeth E, Oyelakin A, Song EC, Che M, Bard J, Min S, Kiripolsky J, Kramer JM, Sinha S, Romano RA. (2021) Transcriptomic and Single-Cell Analysis Reveals Regulatory Networks and Cellular Heterogeneity in Mouse Primary Sjögren's Syndrome Salivary Glands. Frontiers in immunology (Jan), 12: 729040.
- Kwack KH, Lamb NA, Bard JE, Kramer ED, Zhang L, Abrams SI, Kirkwood KL. (2021) Discovering Myeloid Cell Heterogeneity in Mandibular Bone - Cell by Cell Analysis. Frontiers in physiology (Jan), 12: 731549.
- Ge Y, Wu F, Cheng M, Bard J, Mu X. (2020) Two new genetically modified mouse alleles labeling distinct phases of retinal ganglion cell development by fluorescent proteins. Developmental dynamics : an official publication of the American Association of Anatomists (Dec), 249(12): 1514-1528.
- Smith JT, Doleželová E, Tylec B, Bard JE, Chen R, Sun Y, Zíková A, Read LK. (2020) Developmental regulation of edited CYb and COIII mitochondrial mRNAs is achieved by distinct mechanisms in Trypanosoma brucei. Nucleic acids research (Sep), 48(15): 8704-8723.
- Min S, Oyelakin A, Gluck C, Bard JE, Song EC, Smalley K, Che M, Flores E, Sinha S, Romano RA. (2020) p63 and Its Target Follistatin Maintain Salivary Gland Stem/Progenitor Cell Function through TGF-ß/Activin Signaling. iScience (Sep), 23(9): 101524.
- Szigeti K, Ihnatovych I, Birkaya B, Chen Z, Ouf A, Indurthi DC, Bard JE, Kann J, Adams A, Chaves L, Sule N, Reisch JS, Pavlik V, Benedict RHB, Auerbach A, Wilding G. (2020) CHRFAM7A: A human specific fusion gene, accounts for the translational gap for cholinergic strategies in Alzheimer's disease. EBioMedicine (Sep), 59: 102892.
- Guerra JA, Zhang C, Bard JE, Yergeau D, Halasa N, Gómez-Duarte OG. (2020) Comparative genomic analysis of a Shiga toxin-producing Escherichia coli (STEC) O145:H25 associated with a severe pediatric case of hemolytic uremic syndrome in Davidson County, Tennessee, US. BMC genomics (Aug), 21(1): 564.
- Smith RJ, Nasiri B, Kann J, Yergeau D, Bard JE, Swartz DD, Andreadis ST. (2020) Endothelialization of arterial vascular grafts by circulating monocytes. Nature communications (Apr), 11(1): 1622.
- Tsompana M, Gluck C, Sethi I, Joshi I, Bard J, Nowak NJ, Sinha S, Buck MJ. (2020) Reactivation of super-enhancers by KLF4 in human Head and Neck Squamous Cell Carcinoma. Oncogene (Jan), 39(2): 262-277.
- Bloom ALM, Jin RM, Leipheimer J, Bard JE, Yergeau D, Wohlfert EA, Panepinto JC. (2019) Thermotolerance in the pathogen Cryptococcus neoformans is linked to antigen masking via mRNA decay-dependent reprogramming. Nature communications (Oct), 10(1): 4950.
- Li H, Jiang H, Yin X, Bard JE, Zhang B, Feng J. (2019) Attenuation of PRRX2 and HEY2 enables efficient conversion of adult human skin fibroblasts to neurons. Biochemical and biophysical research communications (Aug), 516(3): 765-769.
- Toffolo K, Osei J, Kelly W, Poulsen A, Donahue K, Wang J, Hunter M, Bard J, Wang J, Poulsen D. (2019) Circulating microRNAs as biomarkers in traumatic brain injury. Neuropharmacology (Feb), 145(Pt B): 199-208.
- Isackson PJ, Wang J, Zia M, Spurgeon P, Levesque A, Bard J, James S, Nowak N, Lee TK, Vladutiu GD. (2018) RYR1 and CACNA1S genetic variants identified with statin-associated muscle symptoms. Pharmacogenomics (Nov), 19(16): 1235-1249.
- Song EC, Min S, Oyelakin A, Smalley K, Bard JE, Liao L, Xu J, Romano RA. (2018) Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance. Scientific reports (Sep), 8(1): 14043.
- Osei J, Kelly W, Toffolo K, Donahue K, Levy B, Bard J, Wang J, Levy E, Nowak N, Poulsen D. (2018) Thymosin beta 4 induces significant changes in the plasma miRNA profile following severe traumatic brain injury in the rat lateral fluid percussion injury model. Expert opinion on biological therapy (Jul), 18(sup1): 159-164.
- Seldeen KL, Pang M, Leiker MM, Bard JE, Rodríguez-Gonzalez M, Hernandez M, Sheridan Z, Nowak N, Troen BR. (2018) Chronic vitamin D insufficiency impairs physical performance in C57BL/6J mice. Aging (Jun), 10(6): 1338-1355.
- Simpson RM, Bruno AE, Chen R, Lott K, Tylec BL, Bard JE, Sun Y, Buck MJ, Read LK. (2017) Trypanosome RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization. Nucleic acids research (Jul), 45(13): 7965-7983.
- Hefti E, Bard J, Blanco JG. (2017) Analysis of Heteroplasmic Variants in the Cardiac Mitochondrial Genome of Individuals with Down Syndrome. Human mutation (Jan), 38(1): 48-54.
- Simpson RM, Bruno AE, Bard JE, Buck MJ, Read LK. (2016) High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing. RNA (New York, N.Y.) (May), 22(5): 677-95.
- Yang S, Cai Q, Bard J, Jamison J, Wang J, Yang W, Hu BH. (2015) Variation analysis of transcriptome changes reveals cochlear genes and their associated functions in cochlear susceptibility to acoustic overstimulation. Hearing research (Dec), 330(Pt A): 78-89.
- Mechtler P, Singhal R, Kichina JV, Bard JE, Buck MJ, Kandel ES. (2015) MicroRNA analysis suggests an additional level of feedback regulation in the NF-?B signaling cascade. Oncotarget (Jul), 6(19): 17097-106.
- Tsompana M, Valiyaparambil S, Bard J, Marzullo B, Nowak N, Buck MJ. (2015) An automated method for efficient, accurate and reproducible construction of RNA-seq libraries. BMC research notes (Apr), 8: 124.
- Adelaiye R, Ciamporcero E, Miles KM, Sotomayor P, Bard J, Tsompana M, Conroy D, Shen L, Ramakrishnan S, Ku SY, Orillion A, Prey J, Fetterly G, Buck M, Chintala S, Bjarnason GA, Pili R. (2015) Sunitinib dose escalation overcomes transient resistance in clear cell renal cell carcinoma and is associated with epigenetic modifications. Molecular cancer therapeutics (Feb), 14(2): 513-22.
- Terranova C, Narla ST, Lee YW, Bard J, Parikh A, Stachowiak EK, Tzanakakis ES, Buck MJ, Birkaya B, Stachowiak MK. (2015) Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1). PloS one (Jan), 10(4): e0123380.
- Cai Q, Vethanayagam RR, Yang S, Bard J, Jamison J, Cartwright D, Dong Y, Hu BH. (2014) Molecular profile of cochlear immunity in the resident cells of the organ of Corti. Journal of neuroinflammation (Oct), 11: 173.
- Zhu L, Liu W, Alkhouri R, Baker RD, Bard JE, Quigley EM, Baker SS. (2014) Structural changes in the gut microbiome of constipated patients. Physiological genomics (Sep), 46(18): 679-86.
- Singhal R, Bard JE, Nowak NJ, Buck MJ, Kandel ES. (2013) FOXO1 regulates expression of a microRNA cluster on X chromosome. Aging (May), 5(5): 347-56.
- Hu BH, Cai Q, Hu Z, Patel M, Bard J, Jamison J, Coling D. (2012) Metalloproteinases and their associated genes contribute to the functional integrity and noise-induced damage in the cochlear sensory epithelium. The Journal of neuroscience : the official journal of the Society for Neuroscience (Oct), 32(43): 14927-41.
- Givens RM, Lai WK, Rizzo JM, Bard JE, Mieczkowski PA, Leatherwood J, Huberman JA, Buck MJ. (2012) Chromatin architectures at fission yeast transcriptional promoters and replication origins. Nucleic acids research (Aug), 40(15): 7176-89.
- Rizzo JM, Bard JE, Buck MJ. (2012) Standardized collection of MNase-seq experiments enables unbiased dataset comparisons. BMC molecular biology (May), 13: 15.
- Lai WK, Bard JE, Buck MJ. (2012) ArchTEx: accurate extraction and visualization of next-generation sequence data. Bioinformatics (Oxford, England) (Apr), 28(7): 1021-3.
- Nair D, Memmi G, Hernandez D, Bard J, Beaume M, Gill S, Francois P, Cheung AL. (2011) Whole-genome sequencing of Staphylococcus aureus strain RN4220, a key laboratory strain used in virulence research, identifies mutations that affect not only virulence factors but also the fitness of the strain. Journal of bacteriology (May), 193(9): 2332-5.