Publications

Publications (chronological order)

  1. Le Texier, V., J.J.M. Riethoven, V. Kumanduri, C. Gopalakhrishnan, F. Lopez, D. Gautheret, and T.A. Thanaraj (2006). AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics 7:169.
  2. Stamm, S., J.J.M. Riethoven, V. Le Texier, C. Gopalakhrishnan, V. Kumanduri, Y. Tang, N.L. Barbosa-Morais, and T.A. Thanaraj (2006). ASD: A Bioinformatics Resource on Alternative Splicing. Nucleic Acids Research 34: D46-D55.
  3. LaRosa, P.C., J.J.M. Riethoven, H. Chen, Y. Xia, Y. Zhou, M. Chen, J. Miner, M.E. Fromm (2007) Trans-10, Cis-12 Conjugated Linoleic Acid Activates the Integrated Stress Response Pathway in Adipocytes, Physiological Genomics, 31 (544), 553.
  4. Koscielny, G.,  V. Le Texier, C. Gopalakrishnan, V. Kumanduri, J.J.M. Riethoven, F. Nardone, E. Whitfield, C. Fallsehr, O. Hofmann, M. Knull, E. Harrington, S. Boue, E. Eyras, M. Plass, F. Lopez, W. Ritchie, V. Moucadel, T. Ara, H. Pospisil, A. Herrmann, J.G. Reich, R. Guigo, P. Bork, M. von Knebel Doeberitz, J. Vilo, W. Hide, R. Apweiler, T.A. Thanaraj, D. Gautheret (2008) ASTD: the Alternative Splicing and Transcript Diversity Database, Genomics 93 (3), 213-20.
  5. Galeota, J.A., Napier J.E., Armstrong D.L., Riethoven J.J., Rogers, D.G. (2009) Herpesvirus infections in rock hyraxes (Procavia capensis). Journal of Veterinary Diagnostic Investigation 21 (4) : 531-5.
  6. Ding, Y., Lapko, H., Ndamukong, I., Xia, Y., Al-Abdallat, A., Lalithambika, S., Sadder, M., Saleh, A., Fromm, M. Riethoven, J.J.,  Lu, G., Avramova, Z. (2009) The Arabidopsis Chromatin Modifier ATX1, the Myotubularin-like AtMTM, and the Response to Drought; a view from the other end of the pathway. Plant Signaling & Behavior, 4 (11) : 1049-58.
  7. Jiang, S., Wang, Z., Riethoven, J.J., Xia. Y., Miner, J., Fromm, M. (Oct 2009) Conjugated Linoleic Acid Activates AMP-Activated Protein Kinase and Reduces Adiposity More Effectively When Used with Metformin in Mice. Journal of Nutrition 139 (12) : 2244-51.
  8. Li, C., Riethoven, J.J.M., Ma, L. (2010) Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes. BMC Evolutionary Biology 10:90.
  9. Belch, Y., Yang, J., Liu, Y., Malkaram, S.A., Liu, R., Riethoven, J.J.M., Ladunga, I. (2010) The Transcriptional Competence of Chromatin and Weakly Positioned Nucleosomes. PLoS ONE 5(9): e12984. doi:10.1371/journal.pone.0012984
  10. van Dijk, K., Ding, Y., Malkaram, S., Riethoven, J.J.M., Liu, R., Yang, J., Laczko, P., Chen, H., Xia, Y., Ladunga, I., Avramova, Z., Fromm, M. (2010) Dynamic changes in genome-wide Histone H3 Lysine 4 methylaton patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biology 2010, 10:238.
  11. Jiang, S., Chen, H., Wang, Z., Riethoven, J.J.M., Xia, Y., Miner, J., Fromm, M. (2010) Activated AMPK and prostaglandins are involved in the response to conjugated linoleic acid and are sufficient to cause lipid reductions in adipocytes. J Nutritional Biochemistry [E-pub ahead of print]. PMID 20965713
  12. Riethoven, J.J.M. Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators, In: I. Ladunga (Eds) Computational Biology of Transcription Factor Binding. In the series: Methods in Molecular Biology, Vol. 674. USA, Humana Press, NJ. ISBN 978-1-60761-853-9. PMID 20827584
  13. Plautz, S.A., Boanca, G., Riethoven, J.J.M., Pannier, A.K. (2010) Intracellular Signaling Pathways in Nonviral Gene Delivery: Microarray Analysis of Gene Expression Profiles in Transfected Cells. Molecular Therapy 2011 Dec;19(12):2144-51 [Epub 2011 Aug 9] PMID 21829178
  14. Ding Y, Ndamukong I, Zhao Y, Xia Y, Riethoven J.J.M, Jones D, Divecha N, Avramova Z. (2012) Divergent Functions of the Myotubularin (MTM) Homologs AtMTM1 and AtMTM2 in Arabidopsis thaliana: Evolution of the plant MTM family. The Plant Journal 2012 Jun;70(5):866-878. Online: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2012.04936.x/abstract
  15. Ding Y, Virlouvet L, Riethoven JJM, Fromm ME, and Avramova Z (2013). Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. Accepted 19 Dec 2013. BMC Plant Biology 2013, 13:229  doi:10.1186/1471-2229-13-229
  16. Pashaj A, Yi X, Xia M, Canny S, Riethoven JJ, Moreau R. (2013) Characterization of genome-wide transcriptional changes in liver and adipose tissues of ZDF (fa/fa) rats fed R-α-lipoic acid by next-generation sequencing. Physiological Genomics PG-00138-2013R2. E-pub ahead of print 8 Oct 2013. doi: 10.1152/physiolgenomics.00138.2013
  17. N. N. Vellichirammal , A. J. Zera, R. J. Schilder, C. Wehrkamp, J-J. M. Riethoven, J. A. Brisson (2014). De novo transcriptome assembly and morph-specific gene expression profiling of the wing polymorphic cricket Gryllus firmus. PLoS One. 2014 Jan 8;9(1):e82129. doi: 10.1371/journal.pone.0082129
  18. Massilamany C, Gangaplara A, Jia T, Elowsky C, Kang G, Riethoven JJM, Li Q, Zhou Y, and Reddy J (2014). Direct staining with major histocompatibility complex class II dextramers permits detection of antigen-specific, autoreactive CD4 T cells in situ. PLoS ONE 9(1): e87519. doi:10.1371/journal.pone.0087519
  19. Tatineni S, Riethoven JJ, Graybosch RA, French R, Mitra A. (2014) Dynamics of small RNA profiles of virus and host origin in wheat cultivars synergistically infected by Wheat streak mosaic virus and Triticum mosaic virus: virus infection caused a drastic shift in the endogenous small RNA profile. PLoS One. 2014 Nov 3;9(11):e111577. doi: 10.1371/journal.pone.0111577
  20. Ding Y, Virlouvet L, Liu N, Riethoven JJM, Fromm M, and Avramova Z (2014) Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana. PLoS ONE 11/2014; 9(11):e111577. DOI:10.1371/journal.pone.0111577
  21. Blanc G, Mozar M, Agarkova IV, Gurnon JR, Yanai-Balser G, Rowe JM, Xia Y, Riethoven JJ, Dunigan DD, Van Etten JL (2014) Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1. PLoS One. 2014 Mar 7;9(3):e90989. doi: 10.1371/journal.pone.0090989. eCollection 2014.
  22. Massilamany C, Gangaplara A, Basavalingappa RH, Rajasekaran RA, Vu H, Riethoven JJ, Steffen D, Pattnaik AK, Reddy J. (2015) Mutations in the 5' NTR and the Non-Structural Protein 3A of the Coxsackievirus B3 Selectively Attenuate Myocarditogenicity. PLoS One. 2015 Jun 22;10(6):e0131052. doi: 10.1371/journal.pone.0131052 PMID 26098885
  23. Virdi KS, Laurie JD, Xu YZ, Yu J, Shao MR, Sanchez R, Kundariya H, Wang D, Riethoven JJ, Wamboldt Y, Arrieta-Montiel MP, Shedge V, Mackenzie SA. (2015) Arabidopsis MSH1 mutation alters the epigenome and produces heritable changes in plant growth. Nat Commun. 2015 Feb 27;6:6386. doi: 10.1038/ncomms7386
  24. Zhen Wang, Juan Armando Casas-Mollano, Jianping Xu, Jean-Jack M. Riethoven, Chi Zhang, and Heriberto Cerutti (2015) Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of Arabidopsis thaliana. PNAS (e-pub ahead of print) doi: 10.1073/pnas.1423325112
  25. Vellichirammal NN, Wang H, Eyun S, Moriyama EN, Coates BS, Miller NJ, Siegfried BD (2015) Transcriptional analysis of susceptible and resistant European corn borer strains and their response to Cry1F protoxin. BMC Genomics 16:558
  26. Wei HH, Rowe M, Riethoven JJ, Grove R, Adamec J, Jikumaru Y, Staswick P. Overaccumulation of γ-Glutamylcysteine in a Jasmonate-Hypersensitive Arabidopsis Mutant Causes Jasmonate-Dependent Growth Inhibition.  Plant Physiol. 2015 Oct;169(2):1371-81. doi:0.1104/pp.15.00999. Epub 2015 Aug 17. PMID: 26282239
  27. Nguyen, A., Beyersdorf, J., Riethoven, J.-J. and Pannier, A. K. (2016), High-throughput screening of clinically approved drugs that prime polyethylenimine transfection reveals modulation of mitochondria dysfunction response improves gene transfer efficiencies. Bioengineering & Translational Medicine. doi:10.1002/btm2.10017
  28. Basavalingappa RH, Massilamany C, Krishnan B, Gangaplara A, Kang G, Khalilzad-Sharghi V, Han Z, Othman S, Li Q, Riethoven JJ, Sobel RA, Steffen D, Reddy J (2016). Identification of an Epitope from Adenine Nucleotide Translocator 1 That Induces Inflammation in Heart in A/J Mice. Am J Pathol. 2016 Dec;186(12):3160-3175. doi: 10.1016/j.ajpath.2016.08.005. PMID: 27876151
  29. Jia, Q., G. Li, T. G. Kollner, J. Fu, X. Chen, W. Xiong, B. J. Crandall-Stotler, J. L. Bowman, D. J. Weston, Y. Zhang, L. Chen, Y. Xie, F. W. Li, C. J. Rothfels, A. Larsson, S. W. Graham, D. W. Stevenson, G. K. Wong, J. Gershenzon and F. Chen (2016). "Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants." Proc Natl Acad Sci U S A 113(43): 12328-12333.
  30. Chen, X., T. G. Kollner, Q. Jia, A. Norris, B. Santhanam, P. Rabe, J. S. Dickschat, G. Shaulsky, J. Gershenzon and F. Chen (2016). "Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae." Proc Natl Acad Sci U S A 113(43): 12132-12137.
  31. Kumar, S., C. Kempinski, X. Zhuang, A. Norris, S. Mafu, J. Zi, S. A. Bell, S. E. Nybo, S. E. Kinison, Z. Jiang, S. Goklany, K. B. Linscott, X. Chen, Q. Jia, S. D. Brown, J. L. Bowman, P. C. Babbitt, R. J. Peters, F. Chen and J. Chappell (2016). "Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha." Plant Cell 28(10): 2632-2650.
  32. Yuan Z, Kang G, Ma F, Lu W, Fan W, Fennessey CM, Keele BF, Li Q (2016). Recapitulating Cross-Species Transmission of Simian Immunodeficiency Virus SIVcpz to Humans by Using Humanized BLT Mice. J Virol. 2016 Aug 12;90(17):7728-39. doi: 10.1128/JVI.00860-16. Print 2016 Sep 1.
  33. Basavalingappa RH, Massilamany C, Krishnan B, Gangaplara A, Kang G, Khalilzad-Sharghi V, Han Z, Othman S, Li Q, Riethoven JJ, Sobel RA, Steffen D, Reddy J (2016). Identification of an Epitope from Adenine Nucleotide Translocator 1 That Induces Inflammation in Heart in A/J Mice. Am J Pathol. 2016 Dec;186(12):3160-3175. doi: 10.1016/j.ajpath.2016.08.005. PMID: 27876151
  34. Eyun S, Soh HY, Posavi M, Munro J, Remfert J, Hughes DST, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneli H, Worley KC, Muzny DM, Park EO, Silva JC, Richards S, Gibbs RA, Lee CE (2017) Evolutionary history of chemosensory-related gene families across the Arthropoda. Molecular Biology and Evolution, Volume 34, Issue 8, pp 1838–1862, https://doi.org/10.1093/molbev/msx147
  35. Eyun, S. (2017) Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evolutionary Biology 17:23 https://doi.org/10.1186/s12862-017-0883-5
  36. Wang H, Eyun S, Arora K, Tan SY, Gandra P, Moriyama E, Khajuria C, Jurzenski J, Li H, Donahue M, Narva K, Siegfried B (2017) Patterns of Gene Expression in Western Corn Rootworm (Diabrotica virgifera virgifera) Neonates, Challenged with Cry34Ab1, Cry35Ab1 and Cry34/35Ab1, Based on Next-Generation Sequencing. Toxins 2017, 9(4), 124; doi:10.3390/toxins9040124
  37. Quispe, C. F., A. Esmael, O. Sonderman, M. McQuinn, I. Agarkova, M. Battah, G. A. Duncan, D. D. Dunigan, T. P. Smith, C. De Castro, I. Speciale, F. Ma and J. L. Van Etten (2017). "Characterization of a new chlorovirus type with permissive and non-permissive features on phylogenetically related algal strains." Virology 500: 103-113
  38. Nissimov, J. I., A. Pagarete, F. Ma, S. Cody, D. D. Dunigan, S. A. Kimmance and M. J. Allen (2017). "Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery." Viruses 9(3): 52
  39. Yuan, Z., F. Ma, A. J. Demers, D. Wang, J. Xu, M. G. Lewis and Q. Li (2017). "Characterization of founder viruses in very early SIV rectal transmission." Virology 502: 97-105.
  40. Lu, W., Y. Wan, F. Ma, R. P. Johnson and Q. Li (2017). "Distinct transcriptome profiles of Gag-specific CD8+ T cells temporally correlated with the protection elicited by SIVΔnef live attenuated vaccine." PloS one 12(3): e0173929.
  41. Wijesena HR, Lents CA, Trenhaile-Grannemann MD, Riethoven JJ, Keel BN, Thorson JF, Miller PS, Johnson RK, Spangler ML, Kachman SD and Ciobanu DC (2017) Using Genomic Approaches to Uncover Sources of Variation in Age at Puberty and Reproductive Longevity in Sows. Journal of Animal Science 2017 95: supplement2: 12-12. doi:10.2527/asasmw.2017.027. Epub ahead of print Apr 2017.
  42. Krishnan B, Massilaman C, Basavalingappa R, Gangaplara A, Kang G, Li Q, Uzal F, Strande J, Delhon G, Riethoven JJ, Steffen D, Reddy J (2017) Branched chain α-ketoacid dehydrogenase kinase 111-130, a T cell epitope that induces both autoimmune myocarditis and hepatitis in A/J mice. Immun Inflamm Dis. 2017 Dec;5(4):421-434. doi: 10.1002/iid3.177. Epub 2017 Jun 9.
  43. Basavalingappa, R. H., C. Massilamany, B. Krishnan, A. Gangaplara, R. A. Rajasekaran, M. Z. Afzal, J.-J. Riethoven, J. L. Strande, D. Steffen and J. Reddy (2017). β1-Adrenergic Receptor Contains Multiple IAk and IEk Binding Epitopes That Induce T Cell Responses with Varying Degrees of Autoimmune Myocarditis in A/J Mice. Frontiers in Immunology 8(1567). https://doi.org/10.3389/fimmu.2017.01567
  44. Krishnan, B., C. Massilamany, R. H. Basavalingappa, A. Gangaplara, R. A. Rajasekaran, M. Z. Afzal, V. Khalilzad-Sharghi, Y. Zhou, J. J. Riethoven, S. S. Nandi, P. K. Mishra, R. A. Sobel, J. L. Strande, D. Steffen and J. Reddy (2018). "Epitope Mapping of SERCA2a Identifies an Antigenic Determinant That Induces Mainly Atrial Myocarditis in A/J Mice." J Immunol 200(2): 523-537. DOI: https://doi.org/10.4049/jimmunol.1701090
  45. Sinha R, Clarke J, Riethoven J. Metabolic Syndrome, Gut Microbiome and Dietary Bioactive Peptides, an Unexplored Triad. Diabesity, v. 4, n. 1, p. 1-4, jan. 2018. ISSN 2369-0569. doi:http://dx.doi.org/10.15562/diabesity.2018.45.
  46. Kopf JC; Suhr MJ; Clarke J; Eyun S; Riethoven JJM; Ramer-Tait AE; Rose DJ (2018) Role of whole grains versus fruits and vegetables in reducing subclinical inflammation and promoting gastrointestinal health in individuals affected by overweight and obesity: a randomized controlled trial. Nutrition Journal 2018 17:72 https://doi.org/10.1186/s12937-018-0381-7
  47. Manca, S., C. P. Frisbie, C. A. LaGrange, C. A. Casey, J.-J. M. Riethoven and A. Petrosyan (2018). "The Role of Alcohol-induced Golgi Fragmentation for Androgen Receptor Signaling in Prostate Cancer." Molecular Cancer Research. DOI: 10.1158/1541-7786.MCR-18-0577
  48. Hovde, B. T., E. R. Hanschen, C. R. Steadman Tyler, C.-C. Lo, Y. Kunde, K. Davenport, H. Daligault, J. Msanne, S. Canny, S.-i. Eyun, J.-J. M. Riethoven, J. Polle and S. R. Starkenburg (2018). "Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)." Algal Research 35: 449-461. https://doi.org/10.1016/j.algal.2018.09.012
  49. Petrosyan A, Frisbie C, Lushnikov A, Krasnoslobodtsev A, Stepchenkova S, Riethoven JJM, Clarke J (2019) Post-ER stress biogenesis of Golgi is governed by giantin. Cells 2019, 8(12), 1631; https://doi.org/10.3390/cells8121631
  50. Jia, Q., Chen, X., Köllner, T.G. et al. Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi. Sci Rep 9, 9223 (2019). https://doi.org/10.1038/s41598-019-45532-1
  51. Arumugam R, Yalaka B, Massilamany C, Haider Ali MSS, Lasrado N, Jayaraja S, Riethoven JJ, Sun X, Reddy J. An evidence for surface expression of an immunogenic epitope of sarcoplasmic/endoplasmic reticulum calcium-ATPase2a on antigen-presenting cells from naive mice in the mediation of autoimmune myocarditis. Immunobiology. 2020 Mar;225(2):151896. doi: 10.1016/j.imbio.2019.12.005.
  52. Jayeshbhai Chaudhari; Chia-Sin Liew; Aspen Workman; Jean-Jack Riethoven; David Steffen; Sarah Sillman; Hiep Vu. Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain. 2020, 12, 817 . https://doi.org/10.3390/v12080817
  53. Basavalingappa RH, Arumugam R, Lasrado N, Yalaka B, Massilamany C, Gangaplara A, Riethoven JJ, Xiang SH, Steffen D, Reddy J. Viral myocarditis involves the generation of autoreactive T cells with multiple antigen specificities that localize in lymphoid and non-lymphoid organs in the mouse model of CVB3 infection. Mol Immunol. 2020 Aug;124:218-228. doi: 10.1016/j.molimm.2020.06.017. Epub 2020 Jun 29. PMID: 32615275; PMCID: PMC7363587.
  54. Hiruni R Wijesena, Stephen D Kachman, Clay A Lents, Jean-Jack Riethoven, Melanie D Trenhaile-Grannemann, Tim J Safranski, Matthew L Spangler, Daniel C Ciobanu, Fine mapping genetic variants associated with age at puberty and sow fertility using SowPro90 genotyping array, Journal of Animal Science, Volume 98, Issue 10, October 2020, skaa293, https://doi.org/10.1093/jas/skaa293
  55. Liew, C., Courtney, S., de Lange, P. J. & Pelser, P. B. (2021). Taxonomic realignment of Senecio glaucophyllus (Asteraceae; Senecioneae) necessitates a new name for a widespread New Zealand species. New Zealand Journal of Botany, DOI: 10.1080/0028825X.2020.1866030.
  56. Chaudhari J, Liew CS, Riethoven JM, Sillman S, Vu HLX. Porcine Reproductive and Respiratory Syndrome Virus Infection Upregulates Negative Immune Regulators and T-Cell Exhaustion Markers. J Virol. 2021 Oct 13;95(21):e0105221. doi: 10.1128/JVI.01052-21. Epub 2021 Aug 11. PubMed PMID: 34379512; PubMed Central PMCID: PMC8513478.
  57. Khan AL, Asaf S, Numan M, AbdulKareem NM, Imran M, Riethoven JM, Kim HY, Al-Harrasi A, Schachtman DP, Al-Rawahi A, Lee IJ. Transcriptomics of tapping and healing process in frankincense tree during resin production. Genomics. 2021 Nov;113(6):4337-4351. doi: 10.1016/j.ygeno.2021.11.020. Epub 2021 Nov 16. PubMed PMID: 34798281.
  58. Pachikov AN, Gough RR, Christy CE, Morris ME, Casey CA, LaGrange CA, Bhat G, Kubyshkin AV, Fomochkina II, Zyablitskaya EY, Makalish TP, Golubinskaya EP, Davydenko KA, Eremenko SN, Riethoven JM, Maroli AS, Payne TS, Powers R, Lushnikov AY, Macke AJ, Petrosyan A. The non-canonical mechanism of ER stress-mediated progression of prostate cancer. J Exp Clin Cancer Res. 2021 Sep 14;40(1):289. doi: 10.1186/s13046-021-02066-7. PubMed PMID: 34521429; PubMed Central PMCID: PMC8439065.
  59. Abid, M.S.R., Qiu, H., Tripp, B.A., de Lima Leite, A., Roth, H.E., Adamec, J., Powers, R., Checco, J.W. Peptidomics analysis reveals changes in small urinary peptides in patients with interstitial cystitis/bladder pain syndrome. Sci Rep 12, 8289 (2022). https://doi.org/10.1038/s41598-022-12197-2
  60. Wang P, Lopes LD, Lopez-Guerrero MG, van Dijk K, Alvarez S, Riethoven JJ, Schachtman DP. Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes. J Exp Bot. 2022 May 11:erac202. doi: 10.1093/jxb/erac202. Epub ahead of print. PMID: 35552399.
  61. Khan AL, Al-Harrasi A, Wang J, Asaf S, Riethoven JJM, Shehzad T, Liew C, Song X, Schachtman DP, et al. Genome Structure and Evolutionary History of Frankincense producing Boswellia sacra. iScience: 104574 2022. doi: 10.1016/j.isci.2022.104574
  62. Yun Zhang, Katherine M. Weh, Connor L. Howard, Jean-Jack Riethoven, Jennifer L. Clarke, Kiran H. Lagisetty, Jules Lin, Rishindra M. Reddy, Andrew C. Chang, David G. Beer, Laura A. Kresty, Characterizing Isoform Switching Events in Esophageal Adenocarcinoma, Molecular Therapy - Nucleic Acids, 2022, ISSN 2162-2531, https://doi.org/10.1016/j.omtn.2022.08.018.
  63. Shafieifini M, Sun Y, Staley ZR, Riethoven JJ, Li X. Effects of Nutrient Level and Growth Rate on the Conjugation Process That Transfers Mobile Antibiotic Resistance Genes in Continuous Cultures. Appl Environ Microbiol. 2022 Sep 12:e0112122. doi: 10.1128/aem.01121-22. Epub ahead of print. PMID: 36094214.
  64. de Lange, P. J., Pelser, P. B., Liew, C.-S., & Marshall, A. J. (2022). Senecio pokohinuensis (Asteraceae), a new combination for an endemic species of Mokohinau Islands, Hauraki Gulf (Tikapa Moana o Hauraki), northern Te Ika a Maui/North Island, Aotearoa/New Zealand. Ukrainian Botanical Journal, 79(3), 125-129. https://doi.org/10.15407/ukrbotj79.125
  65. Walker, K., Kalra, D.., Lowdon, R.., …, Liew, C.-S., …, Busby, B. (2022) The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms [version 1; peer review: 1 approved, 3 approved with reservations]. F1000Research, 11:530. https://doi.org/10.12688/f1000research.110194.1
  66. Mousavi S, Qiu H, Heinis FI, Abid MSR, Andrews MT, Checco JW. Short-Term Administration of Common Anesthetics Does Not Dramatically Change the Endogenous Peptide Profile in the Rat Pituitary. ACS Chem Neurosci. 2022 Sep 20. doi: 10.1021/acschemneuro.2c00359. Epub ahead of print. PMID: 36126283.
  67. Salomon JD, Qiu H, Feng D, Owens J, Khailova L, Lujan SO, Iguidbashian J, Chhonker YS, Murry DJ, Riethoven JJ, Lindsey ML, Singh AB, Davidson JA. Piglet cardiopulmonary bypass induces intestinal dysbiosis and barrier dysfunction associated with systemic inflammation. Dis Model Mech. 2022 Nov 25:dmm.049742. doi: 10.1242/dmm.049742. Epub ahead of print. PMID: 36426663.
  68. Rasquinha MT, Lasrado N, Sur M, Mone K, Qiu H, Riethoven J-J, Sobel RA, Reddy J. A Monovalent Mt10-CVB3 Vaccine Prevents CVB4-Accelerated Type 1 Diabetes in NOD Mice. Vaccines. 2023; 11(1):76. https://doi.org/10.3390/vaccines11010076
  69. Sakallioglu IT, Tripp B, Kubik J, Casey CA, Thomes P, Powers R. Multiomics Approach Captures Hepatic Metabolic Network Altered by Chronic Ethanol Administration. Biology. 2023; 12(1):28. https://doi.org/10.3390/biology12010028
  70. Mousavi S, Qiu H, Andrews MT*, Checco JW*. “Peptidomic analysis reveals seasonal neuropeptide and peptide hormone changes in the hypothalamus and pituitary of a hibernating mammal” ACS Chem. Neurosci. (2023) Article ASAP. DOI:10.1021/acschemneuro.3c00268
  71. Macke AJ, Pachikov AN, Divita TE, Morris ME, LaGrange CA, Holzapfel MS, Kubyshkin AV, Zyablitskaya EY, Makalish TP, Eremenko SN, Qiu H, Riethoven JM, Hemstreet GP, Petrosyan A. Targeting the ATF6-mediated ER stress response and autophagy blocks integrin-driven prostate cancer progression. Mol Cancer Res. 2023 Jun 14:MCR-23-0108. doi: 10.1158/1541-7786.MCR-23-0108. Epub ahead of print. PMID: 37314749.
  72. VanOrmer M, Thompson M, Thoene M, Riethoven J-J, Natarajan SK, Hanson C, et al. (2024) The impact of iron supplementation on the preterm neonatal gut microbiome: A pilot study. PLoS ONE 19(2): e0297558. https://doi.org/10.1371/journal.pone.0297558
  73. Sun Y, Staley ZR, Woodbury B, Riethoven J-J, Li X. Composting reduces the risks of resistome in beef cattle manure at the transcriptional level. Appl Environ Microbiol. 2024 Apr 17;90(4):e0175223. doi: 10.1128/aem.01752-23. Epub 2024 Mar 6. PMID: 38445903; PMCID: PMC11022583.
  74. Abid, M.S.R., Qiu, H., Checco, J.W. (2024). Label-Free Quantitation of Endogenous Peptides. In: Schrader, M., Fricker, L.D. (eds) Peptidomics. Methods in Molecular Biology, vol 2758. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3646-6_7
  75. Cheng X, Baki VB, Moran M, Liu B, Yu J, Zhao M, Li Q, Riethoven JJ, Gurumurth CB, Harris EN, Sun X. (2024) Liver Matrin-3 Protects Mice Against Hepatic Steatosis and Stress Response via Constitutive Androstane Receptor. Mol Metab. 86:2024:101977. https://doi.org/10.1016/j.molmet.2024.101977. PMID: 38936659.

BIOINFORMATICS