publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

Alternative sources for our publications:

2025

2025

  1. 2A-class-2.png
    Systematic identification and characterization of eukaryotic and viral 2A peptide-bond-skipping sequences
    Deviyani M Rao, Emma R Horton, Chloe L Barrington, and 10 more authors
    2025
  2. kolakada-nmd.png
    Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay
    Divya Kolakada, Rui Fu, Nikita Biziaev, and 10 more authors
    Cell Genom., 2025
  3. Activated polyreactive B cells are clonally expanded in autoantibody positive and patients with recent-onset type 1 diabetes
    Catherine A Nicholas, Fatima A Tensun, Spencer A Evans, and 7 more authors
    Cell Rep., 2025
  4. B cells shape naïve CD8 T cell programming
    Cameron Manes, Miguel Guerrero Moreno, Jennifer Cimons, and 14 more authors
    J. Clin. Invest., 2025
  5. GPR182 is a lipoprotein receptor for dietary fat absorption
    Zhiwei Sun, Robert J Torphy, Emily N Miller, and 16 more authors
    2025

2024

2024

  1. Co-regulator activity of Mediator of DNA Damage Checkpoint 1 (MDC1) is associated with DNA repair dysfunction and PARP inhibitor sensitivity in lobular carcinoma of the breast
    Joseph L Sottnik, Madeleine T Shackleford, Camryn S Nesiba, and 10 more authors
    2024
  2. white-aa-trna-seq.jpg
    Nanopore sequencing of intact aminoacylated tRNAs
    Laura K White, Aleksandar Radakovic, Marcin P Sajek, and 5 more authors
    bioRxiv, Nov 2024
  3. white-43-mods.jpg
    Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing
    Laura K White, Kezia Dobson, Samantha Pozo, and 10 more authors
    Jul 2024
  4. 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, and 5 more authors
    Apr 2024
  5. 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, and 8 more authors
    NPJ Vaccines, Mar 2024
  6. kolakada-nmd.png
    Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay
    Divya Kolakada, Rui Fu, Nikita Biziaev, and 9 more authors
    bioRxiv, Jan 2024
  7. Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
    Cormac J Lucas, Ryan M Sheridan, Glennys V Reynoso, and 7 more authors
    JCI Insight, Jan 2024

2023

2023

  1. Vaccine-induced antigen archiving enhances local memory CD8+ T cell responses following an unrelated viral infection
    Beth Tamburini, Thu Doan, Tadg Forward, and 5 more authors
    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, and 6 more authors
    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 1 more author
    RNA, Jun 2023

2022

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, and 3 more authors
    Aug 2022

2021

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 1 more author
    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, and 10 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 1 more author
    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, and 18 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, and 7 more authors
    Elife, Apr 2021

2020

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, and 7 more authors
    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, and 5 more authors
    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, and 5 more authors
    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 1 more author
    Nucleic Acids Res., Jun 2020
  5. Physiologic RNA targets and refined sequence specificity of coronavirus EndoU
    Rachel Ancar, Yize Li, Eveline Kindler, and 6 more authors
    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, and 14 more authors
    Cell Rep., Aug 2020
  7. chapman-xrrna.jpg
    Custom-designed, degradation-resistant messenger RNAs in yeast
    Ana L Franklin, Andrea Macfadden, Jeffrey S Kieft, and 2 more authors
    Jun 2020
  8. Single cell profiling identifies novel B cell populations that drive chronic rejection after lung transplantation
    N Smirnova, K Riemondy, S Collins, and 2 more authors
    J. Heart Lung Transplant., Apr 2020

2019

2019

  1. Addendum: Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA
    Kyung Duk Koh, Sathya Balachander, Jay R Hesselberth, and 1 more author
    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, and 14 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, and 7 more authors
    Front. Immunol., May 2019
  5. Single cell RNA sequencing identifies TGFβ as a key regenerative cue following LPS-induced lung injury
    Kent A Riemondy, Nicole L Jansing, Peng Jiang, and 8 more authors
    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, and 8 more authors
    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

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, and 13 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, and 14 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, and 3 more authors
    RNA, Nov 2018
  6. TCR signal strength controls thymic differentiation of iNKT cell subsets
    Kathryn D Tuttle, S Harsha Krovi, Jingjing Zhang, and 13 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 1 more author
    RNA, Mar 2018

2017

2017

  1. Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae
    Daniel Rossbach, D Suzi Bryan, Jay R Hesselberth, and 1 more author
    G3, Nov 2017
  2. Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes
    Austin E Gillen, Heather M Brechbuhl, Tomomi M Yamamoto, and 4 more authors
    Mol. Cancer Res., Dec 2017
  3. valr.png
    valr: Reproducible genome interval analysis in R
    Kent A Riemondy, Ryan M Sheridan, Austin Gillen, and 3 more authors
    F1000Res., Jun 2017

2016

2016

  1. Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts
    Austin E Gillen, Tomomi M Yamamoto, Enos Kline, and 2 more authors
    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, and 9 more authors
    Elife, Sep 2016

2015

2015

  1. Coordination between Drosophila Arc1 and a specific population of brain neurons regulates organismal fat
    Jeremy Mosher, Wei Zhang, Rachel Z Blumhagen, and 5 more authors
    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, and 2 more authors
    Elife, Jan 2015
  3. RNase L targets distinct sites in influenza A virus RNAs
    Daphne A Cooper, Shuvojit Banerjee, Arindam Chakrabarti, and 4 more authors
    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 1 more author
    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

2014

  1. A homolog of lariat-debranching enzyme modulates turnover of branched RNA
    Stephen M Garrey, Adam Katolik, Mantas Prekeris, and 7 more authors
    Sep 2014
  2. A homolog of lariat-debranching enzyme modulates turnover of branched RNA
    Stephen M Garrey, Adam Katolik, Mantas Prekeris, and 7 more authors
    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, and 6 more authors
    EMBO Rep., Aug 2014
  4. High resolution mapping of modified DNA nucleobases using excision repair enzymes
    D Suzi Bryan, Monica Ransom, Biniam Adane, and 2 more authors
    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, and 2 more authors
    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, and 6 more authors
    EMBO Rep., Dec 2014

2013

2013

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

2010

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, and 4 more authors
    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

2009

  1. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
    Jay R Hesselberth, Xiaoyu Chen, Zhihong Zhang, and 9 more authors
    Nat. Methods, Apr 2009

2007

2007

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

2006

2006

  1. Binding specificity of Toll-like receptor cytoplasmic domains
    Victoria Brown, Rachel A Brown, Adrian Ozinsky, and 2 more authors
    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, and 2 more authors
    Genome Biol., Apr 2006

2005

2005

  1. A protein interaction network of the malaria parasite Plasmodium falciparum
    Douglas J LaCount, Marissa Vignali, Rakesh Chettier, and 9 more authors
    Nature, Nov 2005
  2. A protein interaction network of the malaria parasite Plasmodium falciparum
    Douglas J LaCount, Marissa Vignali, Rakesh Chettier, and 9 more authors
    Nature, Nov 2005
  3. A protein interaction network of the malaria parasite Plasmodium falciparum
    Douglas J LaCount, Marissa Vignali, Rakesh Chettier, and 9 more authors
    Nature, Nov 2005

2004

2004

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

2003

2003

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

2002

2002

  1. Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer
    J Colin Cox, Andrew Hayhurst, Jay Hesselberth, and 3 more authors
    Nucleic Acids Res., Oct 2002

2001

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

2000

  1. In vitro selection of nucleic acids for diagnostic applications
    J Hesselberth, M P Robertson, S Jhaveri, and 1 more author
    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 1 more author
    J. Biol. Chem., Feb 2000

1999