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Jay R. Hesselberth

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BioChem&Molecular Genetics
Phone303/724-5384

    Collapse Research 
    Collapse research activities and funding
    R01AG071467     (HESSELBERTH, JAY R)Sep 11, 2020 - May 31, 2025
    NIH
    Biochemistry at single-cell resolution: a new approach to understand functional heterogeneity
    Role: Principal Investigator
    T32GM136444     (PREKERIS, RYTIS)Jul 1, 2020 - Jun 30, 2025
    NIH
    Predoctoral Training Program in Molecular and Cellular Biology
    Role: Co-Principal Investigator
    R35GM119550     (HESSELBERTH, JAY R)Aug 1, 2016 - May 31, 2026
    NIH
    Biology of RNA damage and repair
    Role: Principal Investigator
    F32HG003439     (HESSELBERTH, JAY R)Sep 1, 2004 - Aug 31, 2006
    NIH
    Peptide detection using the proximity ligation assay
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Kolakada D, Fu R, Biziaev N, Shuvalov A, Lore M, Campbell AE, Cort?zar MA, Sajek MP, Hesselberth JR, Mukherjee N, Alkalaeva E, Jagannathan S. Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay. bioRxiv. 2024 Mar 09. PMID: 38260612.
      View in: PubMed
    2. Lucas CJ, Sheridan RM, Reynoso GV, Davenport BJ, McCarthy MK, Martin A, Hesselberth JR, Hickman HD, Tamburini BA, Morrison TE. Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO. JCI Insight. 2024 Jan 09; 9(4). PMID: 38194268.
      View in: PubMed
    3. Lucas CJ, Sheridan RM, Reynoso GV, Davenport BJ, McCarthy MK, Martin A, Hesselberth JR, Hickman HD, Tamburini BAJ, Morrison TE. Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO. bioRxiv. 2023 Oct 13. PMID: 37873393.
      View in: PubMed
    4. Tamburini B, Doan T, Forward T, Lucas E, Fleming I, Uecker-Martin A, Hesselberth J, Morrison T. Vaccine-induced antigen archiving enhances local memory CD8+ T cell responses following an unrelated viral infection. Res Sq. 2023 Sep 25. PMID: 37841845.
      View in: PubMed
    5. Ivanova DL, Thompson SB, Klarquist J, Harbell MG, Kilgore AM, Lasda EL, Hesselberth JR, Hunter CA, Kedl RM. Vaccine adjuvant-elicited CD8+ T?cell immunity is co-dependent on T-bet and FOXO1. Cell Rep. 2023 08 29; 42(8):112911. PMID: 37516968.
      View in: PubMed
    6. White LK, Strugar SM, MacFadden A, Hesselberth JR. Nanopore sequencing of internal 2'-PO4 modifications installed by RNA repair. RNA. 2023 06; 29(6):847-861. PMID: 36854608.
      View in: PubMed
    7. White LK, Hesselberth JR. Modification mapping by nanopore sequencing. Front Genet. 2022; 13:1037134. PMID: 36386798.
      View in: PubMed
    8. Riemondy KA, Venkataraman S, Willard N, Nellan A, Sanford B, Griesinger AM, Amani V, Mitra S, Hankinson TC, Handler MH, Sill M, Ocasio J, Weir SJ, Malawsky DS, Gershon TR, Garancher A, Wechsler-Reya RJ, Hesselberth JR, Foreman NK, Donson AM, Vibhakar R. Neoplastic and immune single-cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma. Neuro Oncol. 2022 02 01; 24(2):273-286. PMID: 34077540.
      View in: PubMed
    9. Carvill GL, Matheny T, Hesselberth J, Demarest S. Haploinsufficiency, Dominant Negative, and Gain-of-Function Mechanisms in Epilepsy: Matching Therapeutic Approach to the Pathophysiology. Neurotherapeutics. 2021 07; 18(3):1500-1514. PMID: 34648141.
      View in: PubMed
    10. Carpentier KS, Sheridan RM, Lucas CJ, Davenport BJ, Li FS, Lucas ED, McCarthy MK, Reynoso GV, May NA, Tamburini BAJ, Hesselberth JR, Hickman HD, Morrison TE. MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination. EMBO J. 2021 11 15; 40(22):e108966. PMID: 34618370.
      View in: PubMed
    11. Puntambekar S, Hesselberth JR, Riemondy KA, Fu R. Cell-level metadata are indispensable for documenting single-cell sequencing datasets. PLoS Biol. 2021 05; 19(5):e3001077. PMID: 33945522.
      View in: PubMed
    12. Walsh SM, Sheridan RM, Lucas ED, Doan TA, Ware BC, Schafer J, Fu R, Burchill MA, Hesselberth JR, Tamburini BAJ. Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node. Elife. 2021 04 12; 10. PMID: 33843587.
      View in: PubMed
    13. Fu R, Gillen AE, Grabek KR, Riemondy KA, Epperson LE, Bustamante CD, Hesselberth JR, Martin SL. Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal. Front Physiol. 2020; 11:624677. PMID: 33536943.
      View in: PubMed
    14. Ancar R, Li Y, Kindler E, Cooper DA, Ransom M, Thiel V, Weiss SR, Hesselberth JR, Barton DJ. Physiologic RNA targets and refined sequence specificity of coronavirus EndoU. RNA. 2020 12; 26(12):1976-1999. PMID: 32989044.
      View in: PubMed
    15. Gillen AE, Riemondy KA, Amani V, Griesinger AM, Gilani A, Venkataraman S, Madhavan K, Prince E, Sanford B, Hankinson TC, Handler MH, Vibhakar R, Jones KL, Mitra S, Hesselberth JR, Foreman NK, Donson AM. Single-Cell RNA Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology. Cell Rep. 2020 08 11; 32(6):108023. PMID: 32783945.
      View in: PubMed
    16. Richer AL, Riemondy KA, Hardie L, Hesselberth JR. Simultaneous measurement of biochemical phenotypes and gene expression in single cells. Nucleic Acids Res. 2020 06 04; 48(10):e59. PMID: 32286626.
      View in: PubMed
    17. Fu R, Gillen AE, Sheridan RM, Tian C, Daya M, Hao Y, Hesselberth JR, Riemondy KA. clustifyr: an R package for automated single-cell RNA sequencing cluster classification. F1000Res. 2020; 9:223. PMID: 32765839.
      View in: PubMed
    18. Yang W, Trahan GD, Howell ED, Speck NA, Jones KL, Gillen AE, Riemondy K, Hesselberth J, Bryder D, Ernst P. Enhancing Hematopoiesis from Murine Embryonic Stem Cells through MLL1-Induced Activation of a Rac/Rho/Integrin Signaling Axis. Stem Cell Reports. 2020 02 11; 14(2):285-299. PMID: 31951812.
      View in: PubMed
    19. Allawzi A, McDermott I, Delaney C, Nguyen K, Banimostafa L, Trumpie A, Hernandez-Lagunas L, Riemondy K, Gillen A, Hesselberth J, Kasmi KE, Sucharov CC, Janssen WJ, Stenmark K, Bowler R, Nozik-Grayck E. Redistribution of EC-SOD resolves bleomycin-induced inflammation via increased apoptosis of recruited alveolar macrophages. FASEB J. 2019 12; 33(12):13465-13475. PMID: 31560857.
      View in: PubMed
    20. Koh KD, Balachander S, Hesselberth JR, Storici F. Addendum: Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat Methods. 2019 08; 16(8):787-788. PMID: 31324896.
      View in: PubMed
    21. Tamburini BAJ, Finlon JM, Gillen AE, Kriss MS, Riemondy KA, Fu R, Schuyler RP, Hesselberth JR, Rosen HR, Burchill MA. Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver Lymphatic Endothelial Cells. Front Immunol. 2019; 10:1036. PMID: 31156626.
      View in: PubMed
    22. Riemondy KA, Jansing NL, Jiang P, Redente EF, Gillen AE, Fu R, Miller AJ, Spence JR, Gerber AN, Hesselberth JR, Zemans RL. Single cell RNA sequencing identifies TGF? as a key regenerative cue following LPS-induced lung injury. JCI Insight. 2019 03 26; 5. PMID: 30913038.
      View in: PubMed
    23. Cherry PD, Peach SE, Hesselberth JR. Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response. Elife. 2019 03 15; 8. PMID: 30874502.
      View in: PubMed
    24. Riemondy KA, Ransom M, Alderman C, Gillen AE, Fu R, Finlay-Schultz J, Kirkpatrick GD, Di Paola J, Kabos P, Sartorius CA, Hesselberth JR. Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries. Nucleic Acids Res. 2019 02 28; 47(4):e20. PMID: 30496484.
      View in: PubMed
    25. Pollyea DA, Stevens BM, Jones CL, Winters A, Pei S, Minhajuddin M, D'Alessandro A, Culp-Hill R, Riemondy KA, Gillen AE, Hesselberth JR, Abbott D, Schatz D, Gutman JA, Purev E, Smith C, Jordan CT. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia. Nat Med. 2018 12; 24(12):1859-1866. PMID: 30420752.
      View in: PubMed
    26. Riemondy KA, Gillen AE, White EA, Bogren LK, Hesselberth JR, Martin SL. Dynamic temperature-sensitive A-to-I RNA editing in the brain of a heterothermic mammal during hibernation. RNA. 2018 11; 24(11):1481-1495. PMID: 30065024.
      View in: PubMed
    27. Tuttle KD, Krovi SH, Zhang J, Bedel R, Harmacek L, Peterson LK, Dragone LL, Lefferts A, Halluszczak C, Riemondy K, Hesselberth JR, Rao A, O'Connor BP, Marrack P, Scott-Browne J, Gapin L. TCR signal strength controls thymic differentiation of iNKT cell subsets. Nat Commun. 2018 07 09; 9(1):2650. PMID: 29985393.
      View in: PubMed
    28. Ransom M, Bryan DS, Hesselberth JR. High-Resolution Mapping of Modified DNA Nucleobases Using Excision Repair Enzymes. Methods Mol Biol. 2018; 1672:63-76. PMID: 29043617.
      View in: PubMed
    29. Cherry PD, White LK, York K, Hesselberth JR. Genetic bypass of essential RNA repair enzymes in budding yeast. RNA. 2018 03; 24(3):313-323. PMID: 29212664.
      View in: PubMed
    30. Sclafani RA, Hesselberth JR. O Cdc7 kinase where art thou? Curr Genet. 2018 Jun; 64(3):677-680. PMID: 29134273.
      View in: PubMed
    31. Rossbach D, Bryan DS, Hesselberth JR, Sclafani R. Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae. G3 (Bethesda). 2017 11 06; 7(11):3757-3774. PMID: 28924058.
      View in: PubMed
    32. Gillen AE, Brechbuhl HM, Yamamoto TM, Kline E, Pillai MM, Hesselberth JR, Kabos P. Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes. Mol Cancer Res. 2017 12; 15(12):1741-1751. PMID: 28912168.
      View in: PubMed
    33. Riemondy KA, Sheridan RM, Gillen A, Yu Y, Bennett CG, Hesselberth JR. valr: Reproducible genome interval analysis in R. F1000Res. 2017; 6:1025. PMID: 28751969.
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    34. Hansen EC, Ransom M, Hesselberth JR, Hosmane NN, Capoferri AA, Bruner KM, Pollack RA, Zhang H, Drummond MB, Siliciano JM, Siliciano R, Stivers JT. Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. Elife. 2016 09 20; 5. PMID: 27644592.
      View in: PubMed
    35. Gillen AE, Yamamoto TM, Kline E, Hesselberth JR, Kabos P. Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts. BMC Genomics. 2016 05 05; 17:338. PMID: 27150721.
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    36. Mosher J, Zhang W, Blumhagen RZ, D'Alessandro A, Nemkov T, Hansen KC, Hesselberth JR, Reis T. Coordination between Drosophila Arc1 and a specific population of brain neurons regulates organismal fat. Dev Biol. 2015 Sep 15; 405(2):280-90. PMID: 26209258.
      View in: PubMed
    37. Peach SE, York K, Hesselberth JR. Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing. Nucleic Acids Res. 2015 Sep 30; 43(17):e108. PMID: 26001965.
      View in: PubMed
    38. Grabek KR, Diniz Behn C, Barsh GS, Hesselberth JR, Martin SL. Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator. Elife. 2015 Jan 27; 4. PMID: 25626169.
      View in: PubMed
    39. Koh KD, Balachander S, Hesselberth JR, Storici F. Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat Methods. 2015 Mar; 12(3):251-7, 3 p following 257. PMID: 25622106.
      View in: PubMed
    40. Chatfield KC, Coughlin CR, Friederich MW, Gallagher RC, Hesselberth JR, Lovell MA, Ofman R, Swanson MA, Thomas JA, Wanders RJ, Wartchow EP, Van Hove JL. Mitochondrial energy failure in HSD10 disease is due to defective mtDNA transcript processing. Mitochondrion. 2015 Mar; 21:1-10. PMID: 25575635.
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    41. Cooper DA, Banerjee S, Chakrabarti A, Garc?a-Sastre A, Hesselberth JR, Silverman RH, Barton DJ. RNase L targets distinct sites in influenza A virus RNAs. J Virol. 2015 Mar; 89(5):2764-76. PMID: 25540362.
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    42. Kosmaczewski SG, Edwards TJ, Han SM, Eckwahl MJ, Meyer BI, Peach S, Hesselberth JR, Wolin SL, Hammarlund M. The RtcB RNA ligase is an essential component of the metazoan unfolded protein response. EMBO Rep. 2014 Dec; 15(12):1278-85. PMID: 25366321.
      View in: PubMed
    43. Bryan DS, Ransom M, Adane B, York K, Hesselberth JR. High resolution mapping of modified DNA nucleobases using excision repair enzymes. Genome Res. 2014 Sep; 24(9):1534-42. PMID: 25015380.
      View in: PubMed
    44. Garrey SM, Katolik A, Prekeris M, Li X, York K, Bernards S, Fields S, Zhao R, Damha MJ, Hesselberth JR. A homolog of lariat-debranching enzyme modulates turnover of branched RNA. RNA. 2014 Aug; 20(8):1337-48. PMID: 24919400.
      View in: PubMed
    45. Pillai MM, Gillen AE, Yamamoto TM, Kline E, Brown J, Flory K, Hesselberth JR, Kabos P. HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer. Breast Cancer Res Treat. 2014 Jul; 146(1):85-97. PMID: 24906430.
      View in: PubMed
    46. Balakrishnan I, Yang X, Brown J, Ramakrishnan A, Torok-Storb B, Kabos P, Hesselberth JR, Pillai MM. Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells. Stem Cells. 2014 Mar; 32(3):662-73. PMID: 24038734.
      View in: PubMed
    47. Cooper DA, Jha BK, Silverman RH, Hesselberth JR, Barton DJ. Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. Nucleic Acids Res. 2014 Apr; 42(8):5202-16. PMID: 24500209.
      View in: PubMed
    48. Hesselberth JR. Lives that introns lead after splicing. Wiley Interdiscip Rev RNA. 2013 Nov-Dec; 4(6):677-91. PMID: 23881603.
      View in: PubMed
    49. Li X, Zhang W, Xu T, Ramsey J, Zhang L, Hill R, Hansen KC, Hesselberth JR, Zhao R. Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly. Nucleic Acids Res. 2013 Apr 01; 41(6):3805-18. PMID: 23393194.
      View in: PubMed
    50. Cooper SJ, Finney GL, Brown SL, Nelson SK, Hesselberth J, MacCoss MJ, Fields S. High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. Genome Res. 2010 Sep; 20(9):1288-96. PMID: 20610602.
      View in: PubMed
    51. Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics. 2010 Jun 15; 26(12):i334-42. PMID: 20529925.
      View in: PubMed
    52. Hittinger CT, Hesselberth JR. Nucleosome patterning evolution: steady aim despite moving targets. Mol Syst Biol. 2010 May 11; 6:376. PMID: 20461077.
      View in: PubMed
    53. Schutz K, Hesselberth JR, Fields S. Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates. RNA. 2010 Mar; 16(3):621-31. PMID: 20075163.
      View in: PubMed
    54. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 2009 Apr; 6(4):283-9. PMID: 19305407.
      View in: PubMed
    55. Zhang Z, Hesselberth JR, Fields S. Genome-wide identification of spliced introns using a tiling microarray. Genome Res. 2007 Apr; 17(4):503-9. PMID: 17351133.
      View in: PubMed
    56. Hall B, Hesselberth JR, Ellington AD. Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron. 2007 Apr 15; 22(9-10):1939-47. PMID: 16996258.
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    57. Hesselberth JR, Miller JP, Golob A, Stajich JE, Michaud GA, Fields S. Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. Genome Biol. 2006; 7(4):R30. PMID: 16606443.
      View in: PubMed
    58. Brown V, Brown RA, Ozinsky A, Hesselberth JR, Fields S. Binding specificity of Toll-like receptor cytoplasmic domains. Eur J Immunol. 2006 Mar; 36(3):742-53. PMID: 16482509.
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    59. LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, Schoenfeld LW, Ota I, Sahasrabudhe S, Kurschner C, Fields S, Hughes RE. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature. 2005 Nov 03; 438(7064):103-7. PMID: 16267556.
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    60. Lee JF, Hesselberth JR, Meyers LA, Ellington AD. Aptamer database. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D95-100. PMID: 14681367.
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    61. Hesselberth JR, Robertson MP, Knudsen SM, Ellington AD. Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal Biochem. 2003 Jan 15; 312(2):106-12. PMID: 12531194.
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    62. Robertson MP, Hesselberth JR, Ellington AD. Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings. RNA. 2001 Apr; 7(4):513-23. PMID: 11345430.
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    63. Hoffman D, Hesselberth J, Ellington AD. Switching nucleic acids for antibodies. Nat Biotechnol. 2001 Apr; 19(4):313-4. PMID: 11283579.
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    64. Hesselberth J, Robertson MP, Jhaveri S, Ellington AD. In vitro selection of nucleic acids for diagnostic applications. J Biotechnol. 2000 Mar; 74(1):15-25. PMID: 10943569.
      View in: PubMed
    65. Hesselberth JR, Miller D, Robertus J, Ellington AD. In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. J Biol Chem. 2000 Feb 18; 275(7):4937-42. PMID: 10671531.
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    66. Singh PK, Jia HP, Wiles K, Hesselberth J, Liu L, Conway BA, Greenberg EP, Valore EV, Welsh MJ, Ganz T, Tack BF, McCray PB. Production of beta-defensins by human airway epithelia. Proc Natl Acad Sci U S A. 1998 Dec 08; 95(25):14961-6. PMID: 9843998.
      View in: PubMed
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