publications

publications by categories in reversed chronological order

Alternative sources for our publications:

preprint

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

2021

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

2020

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

2019

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

2018

  1. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia
    Pollyea, Daniel A, Stevens, Brett M, Jones, Courtney L, Winters, Amanda, Pei, Shanshan, Minhajuddin, Mohammad, D'Alessandro, Angelo, Culp-Hill, Rachel, Riemondy, Kent A, Gillen, Austin E, Hesselberth, Jay R, Abbott, Diana, Schatz, Derek, Gutman, Jonathan A, Purev, Enkhtsetseg, Smith, Clayton, and Jordan, Craig T
    Nat. Med. 2018
  2. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia
    Pollyea, Daniel A, Stevens, Brett M, Jones, Courtney L, Winters, Amanda, Pei, Shanshan, Minhajuddin, Mohammad, D'Alessandro, Angelo, Culp-Hill, Rachel, Riemondy, Kent A, Gillen, Austin E, Hesselberth, Jay R, Abbott, Diana, Schatz, Derek, Gutman, Jonathan A, Purev, Enkhtsetseg, Smith, Clayton, and Jordan, Craig T
    Nat. Med. 2018
  3. {O} Cdc7 kinase where art thou?
    Sclafani, Robert A, and Hesselberth, Jay R
    Curr. Genet. 2018
  4. {High-Resolution} Mapping of Modified {DNA} Nucleobases Using Excision Repair Enzymes
    Ransom, Monica, Bryan, D Suzi, and Hesselberth, Jay R
    Methods Mol. Biol. 2018
  5. {TCR} signal strength controls thymic differentiation of {iNKT} cell subsets
    Tuttle, Kathryn D, Krovi, S Harsha, Zhang, Jingjing, Bedel, Romain, Harmacek, Laura, Peterson, Lisa K, Dragone, Leonard L, Lefferts, Adam, Halluszczak, Catherine, Riemondy, Kent, Hesselberth, Jay R, Rao, Anjana, O'Connor, Brian P, Marrack, Philippa, Scott-Browne, James, and Gapin, Laurent
    Nat. Commun. 2018
  6. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia
    Pollyea, Daniel A, Stevens, Brett M, Jones, Courtney L, Winters, Amanda, Pei, Shanshan, Minhajuddin, Mohammad, D'Alessandro, Angelo, Culp-Hill, Rachel, Riemondy, Kent A, Gillen, Austin E, Hesselberth, Jay R, Abbott, Diana, Schatz, Derek, Gutman, Jonathan A, Purev, Enkhtsetseg, Smith, Clayton, and Jordan, Craig T
    Nat. Med. 2018
  7. Dynamic temperature-sensitive {A-to-I} {RNA} editing in the brain of a heterothermic mammal during hibernation
    Riemondy, Kent A, Gillen, Austin E, White, Emily A, Bogren, Lori K, Hesselberth, Jay R, and Martin, Sandra L
    RNA 2018
  8. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia
    Pollyea, Daniel A, Stevens, Brett M, Jones, Courtney L, Winters, Amanda, Pei, Shanshan, Minhajuddin, Mohammad, D'Alessandro, Angelo, Culp-Hill, Rachel, Riemondy, Kent A, Gillen, Austin E, Hesselberth, Jay R, Abbott, Diana, Schatz, Derek, Gutman, Jonathan A, Purev, Enkhtsetseg, Smith, Clayton, and Jordan, Craig T
    Nat. Med. 2018
  9. {TCR} signal strength controls thymic differentiation of {iNKT} cell subsets
    Tuttle, Kathryn D, Krovi, S Harsha, Zhang, Jingjing, Bedel, Romain, Harmacek, Laura, Peterson, Lisa K, Dragone, Leonard L, Lefferts, Adam, Halluszczak, Catherine, Riemondy, Kent, Hesselberth, Jay R, Rao, Anjana, O'Connor, Brian P, Marrack, Philippa, Scott-Browne, James, and Gapin, Laurent
    Nat. Commun. 2018
  10. Genetic bypass of essential {RNA} repair enzymes in budding yeast
    Cherry, Patrick D, White, Laura K, York, Kerri, and Hesselberth, Jay R
    RNA 2018

2017

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

2016

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

2015

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

2014

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

2013

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

2010

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

2009

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

2007

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

2006

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

2005

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

2004

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

2003

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

2002

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

2001

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

2000

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

1999