Publications

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Primary

2015

  • Coordination between Drosophila Arc1 and a specific population of brain neurons regulates organismal fat. Mosher J, Zhang W, Blumhagen RZ, D'Alessandro A, Nemkov T, Hansen KC, Hesselberth JR, Reis T. Dev Biol. 2015 Sep 15;405(2):280-90.
  • Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing. Peach SE, York K, Hesselberth JR. Nucleic Acids Res. 2015 May 22. pii: gkv536
  • K. Grabek, C Diniz Behn, G. Barsh, J.R. Hesselberth, S. L. Martin. Enhanced stability and polyadenyl-ation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator. (2015) eLife.
  • KC Chatfield. C R Coughlin II MW Friederich RC Gallagher, J.R. Hesselberth, MA Lovell, M.D.; R Of-man, MA Swanson, JA Thomas, RJ Wanders, EP Wartchow, Mitochondrial energy failure in HSD10 disease is due to defective mtDNA transcript processing, (2015) Mitochondrion.
  • K.D. Koh, Balachander, S., Hesselberth, J.R., Storici F. Ribose-seq: global mapping of ribonucleo-tides embedded in DNA. (2015) Nature Methods.

2014

  • Daphne A. Cooper, Shuvojit Banerjee, Arindam Chakrabarti, Adolfo García-Sastre, Jay R. Hessel-berth, Robert H. Silverman, and David J. Barton. Ribonuclease L Targets Distinct Sites in Influenza A Virus RNAs. (2014) J. Virology.
  • Sara G. Kosmaczewski, Tyson J. Edwards, Sung Min Han, Matthew J. Eckwahl, Benjamin Meyer, Sally Peach, Jay R. Hesselberth, Sandra L. Wolin, Marc Hammarlund. The RtcB RNA ligase is an essential component of the metazoan unfolded protein response (2014). EMBO Reports.15:1278-85 PMCID: PMC4264930
  • Debra S. Bryan, Monica Ransom, Biniam Adane, Kerri York and Jay R. Hesselberth. High-resolution mapping of modified nucleobases in DNA with excision repair enzymes (2014) Genome Research.
  • Manoj M Pillai, Austin E. Gillen, Enos Kline, Joseph Brown, Kale Flory, Jay R. Hesselberth and Peter Kabos,, Genomewide analysis of miRNA-mRNA interactions in breast cancer. (2014) Breast Cancer Res Treat, In press.
  • Stephen M. Garrey, Adam Katolik, Mantas Prekeris, Xueni Li, Kerri York, Sarah Bernards, Stanley Fieldsh, Rui Zhao, Masad J. Damha, Jay R. Hesselberth, A homolog of lariat debranching en-zyme modulates turnover of branched RNA. (2014) RNA, In press.
  • Daphne Cooper, Babal Jha, Robert G. Silverman, Jay R. Hesselberth and David L. Barton. Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. (2014) NAR 42:5202-16 PMCID: PMC4005677

2013

  • Ilango Balakrishnan, Xiaodong Yang, Joseph Brown, Aravind Ramakrishnan, Beverly Torok-Storb, Pe-ter Kabos, Jay R Hesselberth and Manoj M Pillai, Genome-wide analysis of miR-mRNA interactions in the marrow microenvironment. (2013) Stem Cells 32:662-673
  • Li X, Zhang W, Xu T, Ramsey J, Zhang L, Hesselberth J.R., Zhao R., Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly. (2013) Nucleic Acids Res, 41:3805-18. PMCID: PMC3616732

Postdoc (2003 - 2009)

  • 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) Jul 28 PMCID: PMC2928507
  • Chen X, Hoffman MM, Bilmes JA, Hesselberth J.R., Noble WS, A dynamic Bayesian network for iden-tifying protein-binding footprints from single molecule-based sequencing data. (2010) Bioinformatics. 26:i334-42. PMCID: PMC2881360
  • Schutz, K., Hesselberth, J.R., Fields, S. Capture and sequence analysis of RNAs with terminal 2′,3′-cyclic phosphates. (2010) RNA, 16:621-31. PMCID: PMC2822926
  • Hesselberth, J.R., Zhang, Z.*, Chen, X.*, Sabo, P.J.*, Reynolds, A.P., Sandstrom, R., Weaver, M., Dorschner, M., Thurman, R.E., Noble, W.S., Fields, S., Stamatoyannopoulos, J.A. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. i) Nature Methods 6:283-289. PMCID: PMC2668528
  • Zhang, Z.*, Hesselberth, J.R., Fields, S. Genomewide identification of spliced introns using a tiling microarray. (2007) Genome Res. 17:503-9. PMCID: PMC1832097
  • Hesselberth, J.R., Miller, J.P., Golob, A, Stajich, J.E., Michaud, G.A., Fields, S., Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. (2006) Genome Biol. 7:R30. PMCID: PMC1557994
  • Brown, V, Brown, R.A., Ozinsky, A, Hesselberth, J.R., Fields, S. Binding specificity of Toll-like receptor cytoplasmic domains. (2006) Eur. J. Immunol. 36:742-753.
  • LaCount, D.J., Vignali, M, Chettier, R, Phansalkar, A, Bell, R, Hesselberth, J.R., Schoenfeld, LW, Ota, I, Sahasrabudhe, S, Kurschner, C, Fields, S, Hughes, R.E. A protein interaction network of the malaria parasite Plasmodium falciparum. (2005) Nature 438:103-7.

Graduate (1997 - 2003)

  • Hall, B.R, Hesselberth, J.R., Ellington, A.D. Computational selection of nucleic acid biosensors via a slip structure model. i) Biosens. and Bioelectron. 22:1939-1947.
  • Lee, J.F., Hesselberth, J.R., Meyers, L.A., Ellington, A.D. Aptamer Database. (2004) Nucleic Acids Res. 32:D95-100. PMCID: PMC2762736
  • Hesselberth, J.R., Knudsen, S., Robertson, M. P., and Ellington, 1. D. Simultaneous detection of di-verse analytes with an aptazyme ligase array. (2003) Anal. Biochem. 312:106-112.
  • Cox, J.C., Hayhurst, A., Hesselberth, J.R., Bayer, T.S., Georgiou, G., Ellington, A.D. Automated selec-tions of aptamers against protein targets translated in vitro: from gene to aptamer. (2002) Nucleic Acids Res. 30:e108. PMCID: PMC137152
  • Robertson, M.P., Hesselberth, J.R., Ellington, A.D.. Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings. (2001) RNA 7:513-523. PMCID: PMC1370105
  • Hesselberth, J. R., Miller, D., Robertus, J., and Ellington, A. D. In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. (2000) J. Biol. Chem. 275:4937-42.
  • Singh, P. K., Jia, H. P., Wiles, K., Hesselberth, J. R., Liu, L. Conway, B. A., Greenberg, E. P., Valore, E. V., Welsh, M. J., Ganz, T., Tack, B. F., McCray, P. B. Jr. Production of β-defensins by human airway epithelia. (1998) Proc. Natl. Acad. Sci. 95:14961-66. PMCID: PMC24558

Reviews

  • Hesselberth J. R., Lives that introns lead after splicing i) WIREs RNA Reviews 4:677-91
  • Hittinger CT, Hesselberth J.R., Nucleosome patterning evolution: steady aim despite moving targets. (2010) Mol Syst Biol. 6:376 PMCID: PMC2890328
  • Hesselberth, J.R. and Ellington, A.D. A (ribo) switch in the paradigms of genetic regulation. (2002) Nat Struct. Biol. 9:891-93.
  • Hoffman, D., Hesselberth, J.R. and Ellington, A.D. Switching nucleic acids for antibodies. (2001) Nat. Biotechnol. 19:313-14.
  • Hesselberth, J.R., Robertson, M.P., Jhaveri, S., and Ellington, A.D. In vitro selection of nucleic acids for diagnostic applications. (2000) Rev. in Mol. Biotech. 74:15-25.
  • Ellington, A.D., Hesselberth, J.R., Jhaveri, S., and Robertson, M.P. Combinatorial methods: Aptamers and aptazymes. (1999) Proc. SPIE-Int. Soc. Opt. Eng. 3858:126-34.

Patents

  • Regulatable, catalytically active nucleic acids (WO2001096559 A2)
  • Peptide identification and sequencing by single-molecule detection of peptides undergoing degradation (WO2013112745 A1)