publications

publications by categories in reversed chronological order

Alternative sources for our publications:

preprint

  1. chapman-xrrna.jpg
    Custom-designed, degradation-resistant messenger {RNAs} in yeast
    Ana L Franklin, Andrea Macfadden, Jeffrey S Kieft, Jay R Hesselberth, and Erich G Chapman
    Jun preprint

2024

  1. Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing
    Laura K White, Kezia Dobson, Samantha Pozo, Jill M Bilodeaux, Shelby E Andersen, Amber Baldwin, Chloe Barrington, Nadine Koertel, Federico Martinez-Seidel, Saylor M Strugar, and 3 more authors
    Jul 2024
  2. sheridan-portable-program.jpg
    A specific and portable gene expression program underlies antigen archiving by lymphatic endothelial cells
    Ryan M Sheridan, Thu A Doan, Cormac Lucas, Tadg S Forward, Aspen Uecker-Martin, Thomas E Morrison, Jay R Hesselberth, and Beth A Jiron Tamburini
    Apr 2024
  3. Immunization-induced antigen archiving enhances local memory CD8+ T cell responses following an unrelated viral infection
    Thu A Doan, Tadg S Forward, Johnathon B Schafer, Erin D Lucas, Ira Fleming, Aspen Uecker-Martin, Edgardo Ayala, Jenna J Guthmiller, Jay R Hesselberth, Thomas E Morrison, and 1 more author
    NPJ Vaccines, Mar 2024
  4. kolakada-nmd.png
    Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay
    Divya Kolakada, Rui Fu, Nikita Biziaev, Alexey Shuvalov, Mlana Lore, Amy E Campbell, Michael A Cortazar, Marcin P Sajek, Jay R Hesselberth, Neelanjan Mukherjee, and 2 more authors
    bioRxiv, Jan 2024
  5. Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
    Cormac J Lucas, Ryan M Sheridan, Glennys V Reynoso, Bennett J Davenport, Mary K McCarthy, Aspen Martin, Jay R Hesselberth, Heather D Hickman, Beth Aj Tamburini, and Thomas E Morrison
    JCI Insight, Jan 2024

2023

  1. Vaccine-induced antigen archiving enhances local memory CD8+ T cell responses following an unrelated viral infection
    Beth Tamburini, Thu Doan, Tadg Forward, Erin Lucas, Ira Fleming, Aspen Uecker-Martin, Jay Hesselberth, and Thomas Morrison
    Res Sq, Sep 2023
  2. Vaccine adjuvant-elicited CD8+ T cell immunity is co-dependent on T-bet and FOXO1
    Daria L Ivanova, Scott B Thompson, Jared Klarquist, Michael G Harbell, Augustus M Kilgore, Erika L Lasda, Jay R Hesselberth, Christopher A Hunter, and Ross M Kedl
    Cell Rep., Jul 2023
  3. rna-repair.jpg
    Nanopore sequencing of internal 2'-PO4 modifications installed by RNA repair
    Laura K White, Saylor M Strugar, Andrea MacFadden, and Jay R Hesselberth
    RNA, Jun 2023

2022

  1. white-review-nanopore.jpg
    Modification mapping by nanopore sequencing
    Laura K White, and Jay R Hesselberth
    Front. Genet., Oct 2022
  2. scraps-logo.png
    scraps: an end-to-end pipeline for measuring alternative polyadenylation at high resolution using single-cell {RNA-seq}
    Rui Fu, Kent A Riemondy, Ryan M Sheridan, Jay R Hesselberth, Craig T Jordan, and Austin E Gillen
    Aug 2022

2021

  1. Haploinsufficiency, Dominant Negative, and {Gain-of-Function} Mechanisms in Epilepsy: Matching Therapeutic Approach to the Pathophysiology
    Gemma L Carvill, Tyler Matheny, Jay Hesselberth, and Scott Demarest
    Neurotherapeutics, Jul 2021
  2. {MARCO+} lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination
    Kathryn S Carpentier, Ryan M Sheridan, Cormac J Lucas, Bennett J Davenport, Frances S Li, Erin D Lucas, Mary K McCarthy, Glennys V Reynoso, Nicholas A May, Beth A J Tamburini, and 3 more authors
    EMBO J., Oct 2021
  3. Cell-level metadata are indispensable for documenting single-cell sequencing datasets
    Sidhant Puntambekar, Jay R Hesselberth, Kent A Riemondy, and Rui Fu
    PLoS Biol., May 2021
  4. Neoplastic and immune single cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma
    Kent A Riemondy, Sujatha Venkataraman, Nicholas Willard, Anandani Nellan, Bridget Sanford, Andrea M Griesinger, Vladimir Amani, Siddhartha Mitra, Todd C Hankinson, Michael H Handler, and 11 more authors
    Neuro. Oncol., Jun 2021
  5. sheridan-umap.png
    Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node
    Shannon M Walsh, Ryan M Sheridan, Erin D Lucas, Thu A Doan, Brian C Ware, Johnathon Schafer, Rui Fu, Matthew A Burchill, Jay R Hesselberth, and Beth Ann Jiron Tamburini
    Elife, Apr 2021

2020

  1. Enhancing Hematopoiesis from Murine Embryonic Stem Cells through {MLL1-Induced} Activation of a {Rac/Rho/Integrin} Signaling Axis
    Weiwei Yang, G Devon Trahan, Elizabeth D Howell, Nancy A Speck, Kenneth L Jones, Austin E Gillen, Kent Riemondy, Jay Hesselberth, David Bryder, and Patricia Ernst
    Stem Cell Reports, Feb 2020
  2. Dynamic {RNA} Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal
    Rui Fu, Austin E Gillen, Katharine R Grabek, Kent A Riemondy, L Elaine Epperson, Carlos D Bustamante, Jay R Hesselberth, and Sandra L Martin
    Front. Physiol., Feb 2020
  3. clustifyr.png
    clustifyr: an R package for automated single-cell RNA sequencing cluster classification
    Rui Fu, Austin E Gillen, Ryan M Sheridan, Chengzhe Tian, Michelle Daya, Yue Hao, Jay R Hesselberth, and Kent A Riemondy
    F1000Res., Apr 2020
  4. richer-umap.jpg
    Simultaneous measurement of biochemical phenotypes and gene expression in single cells
    Amanda L Richer, Kent A Riemondy, Lakotah Hardie, and Jay R Hesselberth
    Nucleic Acids Res., Jun 2020
  5. Physiologic {RNA} targets and refined sequence specificity of coronavirus {EndoU}
    Rachel Ancar, Yize Li, Eveline Kindler, Daphne A Cooper, Monica Ransom, Volker Thiel, Susan R Weiss, Jay R Hesselberth, and David J Barton
    RNA, Dec 2020
  6. {Single-Cell} {RNA} Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology
    Austin E Gillen, Kent A Riemondy, Vladimir Amani, Andrea M Griesinger, Ahmed Gilani, Sujatha Venkataraman, Krishna Madhavan, Eric Prince, Bridget Sanford, Todd C Hankinson, and 7 more authors
    Cell Rep., Aug 2020
  7. Single cell profiling identifies novel {B} cell populations that drive chronic rejection after lung transplantation
    N Smirnova, K Riemondy, S Collins, J Hesselberth, and O Eickelberg
    J. Heart Lung Transplant., Apr 2020

2019

  1. Addendum: Ribose-seq: global mapping of ribonucleotides embedded in genomic {DNA}
    Kyung Duk Koh, Sathya Balachander, Jay R Hesselberth, and Francesca Storici
    Nat. Methods, Aug 2019
  2. {METHODS} {TO} {MEASURE} {FUNCTIONAL} {HETEROGENEITY} {AMONG} {SINGLE} {CELLS}
    A L Richer, and J R Hesselberth
    Aug 2019
  3. Single-cell {RNAseq} of childhood ependymoma reveals distinct neoplastic cell subpopulations that impact etiology, molecular classification and outcome
    Austin Gillen, Kent Riemondy, Vladimir Amani, Andrea Griesinger, Ahmed Gilani, Sujatha Venkataraman, Krishna Madhavan, Eric Prince, Bridget Sandford, Todd Hankinson, and 7 more authors
    SSRN Electron. J., Aug 2019
  4. Chronic liver disease in humans causes expansion and differentiation of liver lymphatic endothelial cells
    Beth A Jiron Tamburini, Jeffrey M Finlon, Austin E Gillen, Michael S Kriss, Kent A Riemondy, Rui Fu, Ronald P Schuyler, Jay R Hesselberth, Hugo R Rosen, and Matthew A Burchill
    Front. Immunol., May 2019
  5. Single cell {RNA} sequencing identifies {TGF$\beta$} as a key regenerative cue following {LPS-induced} lung injury
    Kent A Riemondy, Nicole L Jansing, Peng Jiang, Elizabeth F Redente, Austin E Gillen, Rui Fu, Alyssa J Miller, Jason R Spence, Anthony N Gerber, Jay R Hesselberth, and 1 more author
    JCI Insight, Mar 2019
  6. Recovery and analysis of transcriptome subsets from pooled single-cell {RNA-seq} libraries
    Kent A Riemondy, Monica Ransom, Christopher Alderman, Austin E Gillen, Rui Fu, Jessica Finlay-Schultz, Gregory D Kirkpatrick, Jorge Di Paola, Peter Kabos, Carol A Sartorius, and 1 more author
    Nucleic Acids Res., Feb 2019
  7. upr.jpg
    Multiple decay events target {HAC1} {mRNA} during splicing to regulate the unfolded protein response
    Patrick D Cherry, Sally E Peach, and Jay R Hesselberth
    Elife, Mar 2019

2018

  1. {O} Cdc7 kinase where art thou?
    Robert A Sclafani, and Jay R Hesselberth
    Curr. Genet., Jun 2018
  2. {High-Resolution} Mapping of Modified {DNA} Nucleobases Using Excision Repair Enzymes
    Monica Ransom, D Suzi Bryan, and Jay R Hesselberth
    Methods Mol. Biol., Jun 2018
  3. {TCR} signal strength controls thymic differentiation of {iNKT} cell subsets
    Kathryn D Tuttle, S Harsha Krovi, Jingjing Zhang, Romain Bedel, Laura Harmacek, Lisa K Peterson, Leonard L Dragone, Adam Lefferts, Catherine Halluszczak, Kent Riemondy, and 6 more authors
    Nat. Commun., Jul 2018
  4. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia
    Daniel A Pollyea, Brett M Stevens, Courtney L Jones, Amanda Winters, Shanshan Pei, Mohammad Minhajuddin, Angelo D'Alessandro, Rachel Culp-Hill, Kent A Riemondy, Austin E Gillen, and 7 more authors
    Nat. Med., Dec 2018
  5. Dynamic temperature-sensitive {A-to-I} {RNA} editing in the brain of a heterothermic mammal during hibernation
    Kent A Riemondy, Austin E Gillen, Emily A White, Lori K Bogren, Jay R Hesselberth, and Sandra L Martin
    RNA, Nov 2018
  6. {TCR} signal strength controls thymic differentiation of {iNKT} cell subsets
    Kathryn D Tuttle, S Harsha Krovi, Jingjing Zhang, Romain Bedel, Laura Harmacek, Lisa K Peterson, Leonard L Dragone, Adam Lefferts, Catherine Halluszczak, Kent Riemondy, and 6 more authors
    Nat. Commun., Jul 2018
  7. trna-block.png
    Genetic bypass of essential {RNA} repair enzymes in budding yeast
    Patrick D Cherry, Laura K White, Kerri York, and Jay R Hesselberth
    RNA, Mar 2018

2017

  1. Localization of Cdc7 Protein Kinase During {DNA} Replication in Saccharomyces cerevisiae
    Daniel Rossbach, D Suzi Bryan, Jay R Hesselberth, and Robert Sclafani
    G3, Nov 2017
  2. Alternative Polyadenylation of {PRELID1} Regulates Mitochondrial {ROS} Signaling and Cancer Outcomes
    Austin E Gillen, Heather M Brechbuhl, Tomomi M Yamamoto, Enos Kline, Manoj M Pillai, Jay R Hesselberth, and Peter Kabos
    Mol. Cancer Res., Dec 2017
  3. valr.png
    valr: Reproducible genome interval analysis in R
    Kent A Riemondy, Ryan M Sheridan, Austin Gillen, Yinni Yu, Christopher G Bennett, and Jay R Hesselberth
    F1000Res., Jun 2017

2016

  1. Improvements to the {HITS-CLIP} protocol eliminate widespread mispriming artifacts
    Austin E Gillen, Tomomi M Yamamoto, Enos Kline, Jay R Hesselberth, and Peter Kabos
    BMC Genomics, May 2016
  2. Diverse fates of uracilated {HIV-1} {DNA} during infection of myeloid lineage cells
    Erik C Hansen, Monica Ransom, Jay R Hesselberth, Nina N Hosmane, Adam A Capoferri, Katherine M Bruner, Ross A Pollack, Hao Zhang, Michael Bradley Drummond, Janet M Siliciano, and 2 more authors
    Elife, Sep 2016

2015

  1. Coordination between Drosophila Arc1 and a specific population of brain neurons regulates organismal fat
    Jeremy Mosher, Wei Zhang, Rachel Z Blumhagen, Angelo D'Alessandro, Travis Nemkov, Kirk C Hansen, Jay R Hesselberth, and T{\^a}nia Reis
    Dev. Biol., Sep 2015
  2. Enhanced stability and polyadenylation of select {mRNAs} support rapid thermogenesis in the brown fat of a hibernator
    Katharine R Grabek, Cecilia Diniz Behn, Gregory S Barsh, Jay R Hesselberth, and Sandra L Martin
    Elife, Jan 2015
  3. {RNase} {L} targets distinct sites in influenza A virus {RNAs}
    Daphne A Cooper, Shuvojit Banerjee, Arindam Chakrabarti, Adolfo Garc{\'\i}a-Sastre, Jay R Hesselberth, Robert H Silverman, and David J Barton
    J. Virol., Mar 2015
  4. Global analysis of {RNA} cleavage by 5'-hydroxyl {RNA} sequencing
    Sally E Peach, Kerri York, and Jay R Hesselberth
    Nucleic Acids Res., Sep 2015
  5. Ribose-seq: global mapping of ribonucleotides embedded in genomic {DNA}
    Kyung Duk Koh, Sathya Balachander, Jay R Hesselberth, and Francesca Storici
    Nat. Methods, Mar 2015
  6. Global analysis of {RNA} cleavage by 5'-hydroxyl {RNA} sequencing
    Sally E Peach, Kerri York, and Jay R Hesselberth
    Nucleic Acids Res., Sep 2015

2014

  1. A homolog of lariat-debranching enzyme modulates turnover of branched {RNA}
    Stephen M Garrey, Adam Katolik, Mantas Prekeris, Xueni Li, Kerri York, Sarah Bernards, Stanley Fields, Rui Zhao, Masad J Damha, and Jay R Hesselberth
    Sep 2014
  2. A homolog of lariat-debranching enzyme modulates turnover of branched {RNA}
    Stephen M Garrey, Adam Katolik, Mantas Prekeris, Xueni Li, Kerri York, Sarah Bernards, Stanley Fields, Rui Zhao, Masad J Damha, and Jay R Hesselberth
    RNA, Aug 2014
  3. The {RtcB} {RNA} ligase is an essential component of the metazoan unfolded protein response
    Sara Guckian Kosmaczewski, Tyson James Edwards, Sung Min Han, Matthew J Eckwahl, Benjamin Isaiah Meyer, Sally Peach, Jay R Hesselberth, Sandra L Wolin, and Marc Hammarlund
    EMBO Rep., Aug 2014
  4. High resolution mapping of modified {DNA} nucleobases using excision repair enzymes
    D Suzi Bryan, Monica Ransom, Biniam Adane, Kerri York, and Jay R Hesselberth
    Genome Res., Sep 2014
  5. Ribonuclease {L} and metal-ion-independent endoribonuclease cleavage sites in host and viral {RNAs}
    Daphne A Cooper, Babal K Jha, Robert H Silverman, Jay R Hesselberth, and David J Barton
    Nucleic Acids Res., Apr 2014
  6. The {RtcB} {RNA} ligase is an essential component of the metazoan unfolded protein response
    Sara Guckian Kosmaczewski, Tyson James Edwards, Sung Min Han, Matthew J Eckwahl, Benjamin Isaiah Meyer, Sally Peach, Jay R Hesselberth, Sandra L Wolin, and Marc Hammarlund
    EMBO Rep., Dec 2014

2013

  1. Lives that introns lead after splicing
    Jay R Hesselberth
    Wiley Interdiscip. Rev. RNA, Nov 2013

2010

  1. Capture and sequence analysis of {RNAs} with terminal 2',3'-cyclic phosphates
    Kevin Schutz, Jay R Hesselberth, and Stanley Fields
    RNA, Mar 2010
  2. High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection
    S J Cooper, G L Finney, S L Brown, S K Nelson, J Hesselberth, M J MacCoss, and S Fields
    Mar 2010
  3. Capture and sequence analysis of {RNAs} with terminal 2',3'-cyclic phosphates
    Kevin Schutz, Jay R Hesselberth, and Stanley Fields
    RNA, Mar 2010

2009

  1. Global mapping of {protein-DNA} interactions in vivo by digital genomic footprinting
    Jay R Hesselberth, Xiaoyu Chen, Zhihong Zhang, Peter J Sabo, Richard Sandstrom, Alex P Reynolds, Robert E Thurman, Shane Neph, Michael S Kuehn, William S Noble, and 2 more authors
    Nat. Methods, Apr 2009

2007

  1. Genome-wide identification of spliced introns using a tiling microarray
    Z Zhang, J R Hesselberth, and S Fields
    Apr 2007

2006

  1. Binding specificity of Toll-like receptor cytoplasmic domains
    Victoria Brown, Rachel A Brown, Adrian Ozinsky, Jay R Hesselberth, and Stanley Fields
    Eur. J. Immunol., Apr 2006
  2. Comparative analysis of Saccharomyces cerevisiae {WW} domains and their interacting proteins
    J R Hesselberth, J P Miller, A Golob, J E Stajich, and  {others}
    Genome Biol., Apr 2006

2005

  1. A protein interaction network of the malaria parasite Plasmodium falciparum
    Douglas J LaCount, Marissa Vignali, Rakesh Chettier, Amit Phansalkar, Russell Bell, Jay R Hesselberth, Lori W Schoenfeld, Irene Ota, Sudhir Sahasrabudhe, Cornelia Kurschner, and 2 more authors
    Nature, Nov 2005
  2. A protein interaction network of the malaria parasite Plasmodium falciparum
    Douglas J LaCount, Marissa Vignali, Rakesh Chettier, Amit Phansalkar, Russell Bell, Jay R Hesselberth, Lori W Schoenfeld, Irene Ota, Sudhir Sahasrabudhe, Cornelia Kurschner, and 2 more authors
    Nature, Nov 2005
  3. A protein interaction network of the malaria parasite Plasmodium falciparum
    Douglas J LaCount, Marissa Vignali, Rakesh Chettier, Amit Phansalkar, Russell Bell, Jay R Hesselberth, Lori W Schoenfeld, Irene Ota, Sudhir Sahasrabudhe, Cornelia Kurschner, and 2 more authors
    Nature, Nov 2005

2004

  1. Aptamer database
    Jennifer F Lee, Jay R Hesselberth, Lauren Ancel Meyers, and Andrew D Ellington
    Nucleic Acids Res., Jan 2004

2003

  1. Simultaneous detection of diverse analytes with an aptazyme ligase array
    Jay R Hesselberth, Michael P Robertson, Scott M Knudsen, and Andrew D Ellington
    Anal. Biochem., Jan 2003

2002

  1. Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer
    J Colin Cox, Andrew Hayhurst, Jay Hesselberth, Travis S Bayer, George Georgiou, and Andrew D Ellington
    Nucleic Acids Res., Oct 2002

2001

  1. Optimization and optimality of a short ribozyme ligase that joins {non-Watson--Crick} base pairings
    Michael P Robertson, Jay R Hesselberth, and Andrew D Ellington
    Oct 2001
  2. Optimization and optimality of a short ribozyme ligase that joins {non-Watson-Crick} base pairings
    M P Robertson, J R Hesselberth, and A D Ellington
    RNA, Apr 2001

2000

  1. In vitro selection of nucleic acids for diagnostic applications
    J Hesselberth, M P Robertson, S Jhaveri, and A D Ellington
    J. Biotechnol., Mar 2000
  2. In vitro selection of {RNA} molecules that inhibit the activity of ricin A-chain
    J R Hesselberth, D Miller, J Robertus, and A D Ellington
    J. Biol. Chem., Feb 2000

1999