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Enhancing Hematopoiesis from Murine Embryonic Stem Cells through MLL1-Induced Activation of a Rac/Rho/Integrin Signaling Axis.

Yang W, Trahan GD, Howell ED, Speck NA, Jones KL, Gillen AE, Riemondy K, Hesselberth J, Bryder D, Ernst P.

Stem Cell Reports. 2020 Jan 16. pii: S2213-6711(19)30448-5. doi: 10.1016/j.stemcr.2019.12.009. [Epub ahead of print]


Redistribution of EC-SOD resolves bleomycin-induced inflammation via increased apoptosis of recruited alveolar macrophages.

Allawzi A, McDermott I, Delaney C, Nguyen K, Banimostafa L, Trumpie A, Hernandez-Lagunas L, Riemondy K, Gillen A, Hesselberth J, El Kasmi K, Sucharov CC, Janssen WJ, Stenmark K, Bowler R, Nozik-Grayck E.

FASEB J. 2019 Dec;33(12):13465-13475. doi: 10.1096/fj.201901038RR. Epub 2019 Sep 27.


Addendum: Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA.

Koh KD, Balachander S, Hesselberth JR, Storici F.

Nat Methods. 2019 Aug;16(8):787-788. doi: 10.1038/s41592-019-0505-9. No abstract available.


Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver Lymphatic Endothelial Cells.

Tamburini BAJ, Finlon JM, Gillen AE, Kriss MS, Riemondy KA, Fu R, Schuyler RP, Hesselberth JR, Rosen HR, Burchill MA.

Front Immunol. 2019 May 15;10:1036. doi: 10.3389/fimmu.2019.01036. eCollection 2019.


Single cell RNA sequencing identifies TGFβ as a key regenerative cue following LPS-induced lung injury.

Riemondy KA, Jansing NL, Jiang P, Redente EF, Gillen AE, Fu R, Miller AJ, Spence JR, Gerber AN, Hesselberth JR, Zemans RL.

JCI Insight. 2019 Mar 26;5. pii: 123637. doi: 10.1172/jci.insight.123637.


Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response.

Cherry PD, Peach SE, Hesselberth JR.

Elife. 2019 Mar 15;8. pii: e42262. doi: 10.7554/eLife.42262.


Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries.

Riemondy KA, Ransom M, Alderman C, Gillen AE, Fu R, Finlay-Schultz J, Kirkpatrick GD, Di Paola J, Kabos P, Sartorius CA, Hesselberth JR.

Nucleic Acids Res. 2019 Feb 28;47(4):e20. doi: 10.1093/nar/gky1204.


Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia.

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.

Nat Med. 2018 Dec;24(12):1859-1866. doi: 10.1038/s41591-018-0233-1. Epub 2018 Nov 12.


Dynamic temperature-sensitive A-to-I RNA editing in the brain of a heterothermic mammal during hibernation.

Riemondy KA, Gillen AE, White EA, Bogren LK, Hesselberth JR, Martin SL.

RNA. 2018 Nov;24(11):1481-1495. doi: 10.1261/rna.066522.118. Epub 2018 Jul 31.


TCR signal strength controls thymic differentiation of iNKT cell subsets.

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.

Nat Commun. 2018 Jul 9;9(1):2650. doi: 10.1038/s41467-018-05026-6.


Genetic bypass of essential RNA repair enzymes in budding yeast.

Cherry PD, White LK, York K, Hesselberth JR.

RNA. 2018 Mar;24(3):313-323. doi: 10.1261/rna.061788.117. Epub 2017 Dec 6.


O Cdc7 kinase where art thou?

Sclafani RA, Hesselberth JR.

Curr Genet. 2018 Jun;64(3):677-680. doi: 10.1007/s00294-017-0782-8. Epub 2017 Nov 13.


High-Resolution Mapping of Modified DNA Nucleobases Using Excision Repair Enzymes.

Ransom M, Bryan DS, Hesselberth JR.

Methods Mol Biol. 2018;1672:63-76. doi: 10.1007/978-1-4939-7306-4_6.


Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae.

Rossbach D, Bryan DS, Hesselberth JR, Sclafani R.

G3 (Bethesda). 2017 Nov 6;7(11):3757-3774. doi: 10.1534/g3.117.300223.


Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes.

Gillen AE, Brechbuhl HM, Yamamoto TM, Kline E, Pillai MM, Hesselberth JR, Kabos P.

Mol Cancer Res. 2017 Dec;15(12):1741-1751. doi: 10.1158/1541-7786.MCR-17-0010. Epub 2017 Sep 14.


valr: Reproducible genome interval analysis in R.

Riemondy KA, Sheridan RM, Gillen A, Yu Y, Bennett CG, Hesselberth JR.

F1000Res. 2017 Jun 29;6:1025. doi: 10.12688/f1000research.11997.1. eCollection 2017.


Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells.

Hansen EC, Ransom M, Hesselberth JR, Hosmane NN, Capoferri AA, Bruner KM, Pollack RA, Zhang H, Drummond MB, Siliciano JM, Siliciano R, Stivers JT.

Elife. 2016 Sep 20;5. pii: e18447. doi: 10.7554/eLife.18447.


Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts.

Gillen AE, Yamamoto TM, Kline E, Hesselberth JR, Kabos P.

BMC Genomics. 2016 May 5;17:338. doi: 10.1186/s12864-016-2675-5.


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. doi: 10.1016/j.ydbio.2015.07.021. Epub 2015 Jul 21.


Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing.

Peach SE, York K, Hesselberth JR.

Nucleic Acids Res. 2015 Sep 30;43(17):e108. doi: 10.1093/nar/gkv536. Epub 2015 May 22.


Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator.

Grabek KR, Diniz Behn C, Barsh GS, Hesselberth JR, Martin SL.

Elife. 2015 Jan 27;4. doi: 10.7554/eLife.04517.


Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA.

Koh KD, Balachander S, Hesselberth JR, Storici F.

Nat Methods. 2015 Mar;12(3):251-7, 3 p following 257. doi: 10.1038/nmeth.3259. Epub 2015 Jan 26. Erratum in: Nat Methods. 2019 Aug;16(8):787-788.


Mitochondrial energy failure in HSD10 disease is due to defective mtDNA transcript processing.

Chatfield KC, Coughlin CR 2nd, Friederich MW, Gallagher RC, Hesselberth JR, Lovell MA, Ofman R, Swanson MA, Thomas JA, Wanders RJ, Wartchow EP, Van Hove JL.

Mitochondrion. 2015 Mar;21:1-10. doi: 10.1016/j.mito.2014.12.005. Epub 2015 Jan 6.


RNase L targets distinct sites in influenza A virus RNAs.

Cooper DA, Banerjee S, Chakrabarti A, García-Sastre A, Hesselberth JR, Silverman RH, Barton DJ.

J Virol. 2015 Mar;89(5):2764-76. doi: 10.1128/JVI.02953-14. Epub 2014 Dec 24.


The RtcB RNA ligase is an essential component of the metazoan unfolded protein response.

Kosmaczewski SG, Edwards TJ, Han SM, Eckwahl MJ, Meyer BI, Peach S, Hesselberth JR, Wolin SL, Hammarlund M.

EMBO Rep. 2014 Dec;15(12):1278-85. doi: 10.15252/embr.201439531. Epub 2014 Nov 3.


High resolution mapping of modified DNA nucleobases using excision repair enzymes.

Bryan DS, Ransom M, Adane B, York K, Hesselberth JR.

Genome Res. 2014 Sep;24(9):1534-42. doi: 10.1101/gr.174052.114. Epub 2014 Jul 11.


A homolog of lariat-debranching enzyme modulates turnover of branched RNA.

Garrey SM, Katolik A, Prekeris M, Li X, York K, Bernards S, Fields S, Zhao R, Damha MJ, Hesselberth JR.

RNA. 2014 Aug;20(8):1337-48. doi: 10.1261/rna.044602.114. Epub 2014 Jun 11.


HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer.

Pillai MM, Gillen AE, Yamamoto TM, Kline E, Brown J, Flory K, Hesselberth JR, Kabos P.

Breast Cancer Res Treat. 2014 Jul;146(1):85-97. doi: 10.1007/s10549-014-3004-9. Epub 2014 Jun 7.


Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs.

Cooper DA, Jha BK, Silverman RH, Hesselberth JR, Barton DJ.

Nucleic Acids Res. 2014 Apr;42(8):5202-16. doi: 10.1093/nar/gku118. Epub 2014 Feb 5.


Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells.

Balakrishnan I, Yang X, Brown J, Ramakrishnan A, Torok-Storb B, Kabos P, Hesselberth JR, Pillai MM.

Stem Cells. 2014 Mar;32(3):662-73. doi: 10.1002/stem.1531.


Lives that introns lead after splicing.

Hesselberth JR.

Wiley Interdiscip Rev RNA. 2013 Nov-Dec;4(6):677-91. doi: 10.1002/wrna.1187. Epub 2013 Jul 23. Review.


Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly.

Li X, Zhang W, Xu T, Ramsey J, Zhang L, Hill R, Hansen KC, Hesselberth JR, Zhao R.

Nucleic Acids Res. 2013 Apr 1;41(6):3805-18. doi: 10.1093/nar/gkt062. Epub 2013 Feb 7.


High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection.

Cooper SJ, Finney GL, Brown SL, Nelson SK, Hesselberth J, MacCoss MJ, Fields S.

Genome Res. 2010 Sep;20(9):1288-96. doi: 10.1101/gr.105825.110. Epub 2010 Jul 7.


A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.

Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS.

Bioinformatics. 2010 Jun 15;26(12):i334-42. doi: 10.1093/bioinformatics/btq175.


Nucleosome patterning evolution: steady aim despite moving targets.

Hittinger CT, Hesselberth JR.

Mol Syst Biol. 2010 May 11;6:376. doi: 10.1038/msb.2010.34. No abstract available.


Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates.

Schutz K, Hesselberth JR, Fields S.

RNA. 2010 Mar;16(3):621-31. doi: 10.1261/rna.1934910. Epub 2010 Jan 14.


Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.

Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA.

Nat Methods. 2009 Apr;6(4):283-9. doi: 10.1038/nmeth.1313. Epub 2009 Mar 22.


Genome-wide identification of spliced introns using a tiling microarray.

Zhang Z, Hesselberth JR, Fields S.

Genome Res. 2007 Apr;17(4):503-9. Epub 2007 Mar 9.


Computational selection of nucleic acid biosensors via a slip structure model.

Hall B, Hesselberth JR, Ellington AD.

Biosens Bioelectron. 2007 Apr 15;22(9-10):1939-47. Epub 2006 Sep 22.


Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins.

Hesselberth JR, Miller JP, Golob A, Stajich JE, Michaud GA, Fields S.

Genome Biol. 2006;7(4):R30. Epub 2006 Apr 10.


Binding specificity of Toll-like receptor cytoplasmic domains.

Brown V, Brown RA, Ozinsky A, Hesselberth JR, Fields S.

Eur J Immunol. 2006 Mar;36(3):742-53.


A protein interaction network of the malaria parasite Plasmodium falciparum.

LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, Schoenfeld LW, Ota I, Sahasrabudhe S, Kurschner C, Fields S, Hughes RE.

Nature. 2005 Nov 3;438(7064):103-7.


Aptamer database.

Lee JF, Hesselberth JR, Meyers LA, Ellington AD.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D95-100.


Simultaneous detection of diverse analytes with an aptazyme ligase array.

Hesselberth JR, Robertson MP, Knudsen SM, Ellington AD.

Anal Biochem. 2003 Jan 15;312(2):106-12.


A (ribo) switch in the paradigms of genetic regulation.

Hesselberth JR, Ellington AD.

Nat Struct Biol. 2002 Dec;9(12):891-3. No abstract available.


Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer.

Cox JC, Hayhurst A, Hesselberth J, Bayer TS, Georgiou G, Ellington AD.

Nucleic Acids Res. 2002 Oct 15;30(20):e108.


Switching nucleic acids for antibodies.

Hoffman D, Hesselberth J, Ellington AD.

Nat Biotechnol. 2001 Apr;19(4):313-4. No abstract available.


In vitro selection of nucleic acids for diagnostic applications.

Hesselberth J, Robertson MP, Jhaveri S, Ellington AD.

J Biotechnol. 2000 Mar;74(1):15-25. Review.


In vitro selection of RNA molecules that inhibit the activity of ricin A-chain.

Hesselberth JR, Miller D, Robertus J, Ellington AD.

J Biol Chem. 2000 Feb 18;275(7):4937-42.

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