Publications

Journal and book articles written.

Robert Settlage
2022-06-01
Angenstein, Frank, Anne M. Evans, Shuo-Chien Ling, Robert E. Settlage, Scott Ficarro, Franklin A. Carrero-Martinez, Jeffrey Shabanowitz, Donald F. Hunt, and William T. Greenough. 2005. “Proteomic Characterization of Messenger Ribonucleoprotein Complexes Bound to Nontranslated or Translated Poly(a) mRNAs in the Rat Cerebral Cortex.” Journal of Biological Chemistry 280 (8): 6496–6503. https://doi.org/10.1074/jbc.m412742200.
Angenstein, Frank, Anne M. Evans, Robert E. Settlage, Stewart T. Moran, Shuo-Chien Ling, Anna Y. Klintsova, Jeffrey Shabanowitz, Donald F. Hunt, and William T. Greenough. 2002. “A Receptor for Activated c Kinase Is Part of Messenger Ribonucleoprotein Complexes Associated with PolyA-mRNAs in Neurons.” The Journal of Neuroscience 22 (20): 8827–37. https://doi.org/10.1523/jneurosci.22-20-08827.2002.
Ates, Kristin M., Tong Wang, Trevor Moreland, Rajalakshmi Veeranan-Karmegam, Manxiu Ma, Chelsi Jeter, Priya Anand, et al. 2020. “Deficiency in the Endocytic Adaptor Proteins PHETA1/2 Impair Renal and Craniofacial Development.” Disease Models and Mechanisms, January. https://doi.org/10.1242/dmm.041913.
Baginsky, S., A. Shteiman-Kotler, V. Liveanu, S. Yehudai-Resheff, M. Bellaoui, R. E. Settlage, J. Shabanowitz, D. F. Hunt, G. Schuster, and W. Gruissem. 2001. “Chloroplast PNPase exists as a homo-multimer enzyme complex that is distinct from the Escherichia coli degradosome.” RNA 7 (10): 1464–75.
Bavarva, Jasmin H., Hongseok Tae, Robert E. Settlage, and Harold R. Garner. 2013. “Characterizing the Genetic Basis for Nicotine Induced Cancer Development: A Transcriptome Sequencing Study.” Edited by Emmanuel Dias-Neto. PLoS ONE 8 (6): e67252. https://doi.org/10.1371/journal.pone.0067252.
Bishop, Barney M., Melanie L. Juba, Paul S. Russo, Megan Devine, Stephanie M. Barksdale, Shaylyn Scott, Robert Settlage, et al. 2017. “Discovery of Novel Antimicrobial Peptides from Varanus Komodoensis (Komodo Dragon) by Large-Scale Analyses and de-Novo-Assisted Sequencing Using Electron-Transfer Dissociation Mass Spectrometry.” Journal of Proteome Research 16 (4): 1470–82. https://doi.org/10.1021/acs.jproteome.6b00857.
Borer, L. L., J. G. Russell, R. E. Settlage, and R. G. Bryant. 2002. “Experiments with Tris(ethylenediamine)cobalt(III) Compounds: 59Co NMR and the Resolution of Enantiomeric [Co(en)3]3 Ion and Analysis by Formation of Diastereomeric Ion Pairs.” Journal of Chemical Education 79 (4): 494. https://doi.org/10.1021/ed079p494.
Castaneda-Guzman, Mariana, Gabriel Mantilla-Saltos, Kris A. Murray, Robert Settlage, and Luis E. Escobar. 2021. “A Database of Global Coastal Conditions.” Scientific Data 8 (1). https://doi.org/10.1038/s41597-021-01081-9.
Castro, Ryan, Thomas Taetzsch, Sydney K Vaughan, Kerilyn Godbe, John Chappell, Robert E Settlage, and Gregorio Valdez. 2020. “Specific Labeling of Synaptic Schwann Cells Reveals Unique Cellular and Molecular Features.” eLife 9 (June). https://doi.org/10.7554/elife.56935.
Compton, Austin, Jiangtao Liang, Chujia Chen, Varvara Lukyanchikova, Yumin Qi, Mark Potters, Robert Settlage, et al. 2020. “The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere.” G3 Genes\(\vert\)Genomes\(\vert\)Genetics 10 (10): 3811–19. https://doi.org/10.1534/g3.120.401654.
Crotzer, Victoria L., Robert E. Christian, Jill M. Brooks, Jeffrey Shabanowitz, Robert E. Settlage, Jarrod A. Marto, Forest M. White, Alan B. Rickinson, Donald F. Hunt, and Victor H. Engelhard. 2000. “Immunodominance Among EBV-Derived Epitopes Restricted by HLA-B27 Does Not Correlate with Epitope Abundance in EBV-Transformed b-Lymphoblastoid Cell Lines.” The Journal of Immunology 164 (12): 6120–29. https://doi.org/10.4049/jimmunol.164.12.6120.
Dalloul, Rami A., Aleksey V. Zimin, Robert E. Settlage, Sungwon Kim, and Kent M. Reed. 2014. “Next-Generation Sequencing Strategies for Characterizing the Turkey Genome.” Poultry Science 93 (2): 479–84. https://doi.org/10.3382/ps.2013-03560.
Davis, Mary, Renee Jessee, Matthew Close, Xiangping Fu, Robert Settlage, Guoqing Wang, Mark A. Cline, and Elizabeth R. Gilbert. 2015. “Fasting for 21 Days Leads to Changes in Adipose Tissue and Liver Physiology in Juvenile Checkered Garter Snakes ( Thamnophis Marcianus ).” Comparative Biochemistry and Physiology Part A: Molecular and Integrative Physiology 190 (December): 68–74. https://doi.org/10.1016/j.cbpa.2015.09.001.
Ding, Jingzhong, Lindsay M. Reynolds, Tanja Zeller, Christian Müller, Kurt Lohman, Barbara J. Nicklas, Stephen B. Kritchevsky, et al. 2015. “Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease.” Diabetes 64 (10): 3464–74. https://doi.org/10.2337/db14-1314.
Dragon, François, Jennifer E. G. Gallagher, Patricia A. Compagnone-Post, Brianna M. Mitchell, Kara A. Porwancher, Karen A. Wehner, Steven Wormsley, et al. 2002. “A Large Nucleolar U3 Ribonucleoprotein Required for 18s Ribosomal RNA Biogenesis.” Nature 417 (6892): 967–70. https://doi.org/10.1038/nature00769.
Engelhard, Victor H. 2007. “The Contributions of Mass Spectrometry to Understanding of Immune Recognition by t Lymphocytes.” International Journal of Mass Spectrometry 259 (1-3): 32–39. https://doi.org/10.1016/j.ijms.2006.08.009.
Friedman, David B., Tracy M. Andacht, Maureen K. Bunger, Allis S. Chien, David H. Hawke, Jeroen Krijgsveld, William S. Lane, et al. 2011. “The ABRF Proteomics Research Group Studies: Educational Exercises for Qualitative and Quantitative Proteomic Analyses.” PROTEOMICS 11 (8): 1371–81. https://doi.org/10.1002/pmic.201000736.
Gioeli, Daniel, Scott B. Ficarro, Jesse J. Kwiek, David Aaronson, Mathew Hancock, Andrew D. Catling, Forest M. White, et al. 2002. “Androgen Receptor Phosphorylation.” Journal of Biological Chemistry 277 (32): 29304–14. https://doi.org/10.1074/jbc.m204131200.
Gleason, Claire B., Robert E. Settlage, Linda M. Beckett, and Robin R. White. 2021. “Characterizing Effects of Ingredients Differing in Ruminally Degradable Protein and Fiber Supplies on the Ovine Rumen Microbiome Using Next-Generation Sequencing.” Frontiers in Animal Science 2 (October). https://doi.org/10.3389/fanim.2021.745848.
Hendrickson, Ronald C., Anita Y. H. Lee, Qinghua Song, Andy Liaw, Matt Wiener, Cloud P. Paweletz, Jeffrey L. Seeburger, et al. 2015. “High Resolution Discovery Proteomics Reveals Candidate Disease Progression Markers of Alzheimer’s Disease in Human Cerebrospinal Fluid.” Edited by Stephen D Ginsberg. PLOS ONE 10 (8): e0135365. https://doi.org/10.1371/journal.pone.0135365.
Hoek, Monique L. van, M. Dennis Prickett, Robert E. Settlage, Lin Kang, Pawel Michalak, Kent A. Vliet, and Barney M. Bishop. 2019. “The Komodo Dragon (Varanus Komodoensis) Genome and Identification of Innate Immunity Genes and Clusters.” BMC Genomics 20 (1). https://doi.org/10.1186/s12864-019-6029-y.
Ji, Xu, Huili Tong, Robert Settlage, Wen Yao, and Honglin Jiang. 2021. “Establishment of a Bovine Rumen Epithelial Cell Line.” Journal of Animal Science 99 (10). https://doi.org/10.1093/jas/skab273.
Jiang, Xiaofang, Ashley Peery, A Brantley Hall, Atashi Sharma, Xiao-Guang Chen, Robert M Waterhouse, Aleksey Komissarov, et al. 2014. “Genome Analysis of a Major Urban Malaria Vector Mosquito, Anopheles Stephensi.” Genome Biology 15 (9). https://doi.org/10.1186/s13059-014-0459-2.
Kang, Lin, Robert Settlage, Wyatt McMahon, Katarzyna Michalak, Hongseok Tae, Harold R. Garner, Elizabeth A. Stacy, Donald K. Price, and Pawel Michalak. 2016. “Genomic Signatures of Speciation in Sympatric and Allopatric Hawaiian Picture-Winged Drosophila.” Genome Biology and Evolution 8 (5): 1482–88. https://doi.org/10.1093/gbe/evw095.
Lee, Anita Y. H., Cloud P. Paweletz, Roy M. Pollock, Robert E. Settlage, Jonathan C. Cruz, J. Paul Secrist, Thomas A. Miller, et al. 2008. “Quantitative Analysis of Histone Deacetylase-1 Selective Histone Modifications by Differential Mass Spectrometry.” Journal of Proteome Research 7 (12): 5177–86. https://doi.org/10.1021/pr800510p.
Leng, Xinyan, Xu Ji, Yuguo Hou, Robert Settlage, and Honglin Jiang. 2019. “Roles of the Proteasome and Inhibitor of DNA Binding 1 Protein in Myoblast Differentiation.” The FASEB Journal 33 (6): 7403–16. https://doi.org/10.1096/fj.201800574rr.
Liao, Xiaofeng, Song Li, Robert E. Settlage, Sha Sun, Jingjing Ren, Alec M. Reihl, Husen Zhang, et al. 2015. “Cutting Edge: Plasmacytoid Dendritic Cells in Late-Stage Lupus Mice Defective in Producing IFN-\(\alpha\).” The Journal of Immunology 195 (10): 4578–82. https://doi.org/10.4049/jimmunol.1501157.
Lyu, Pengcheng, Robert Settlage, and Honglin Jiang. 2021. “192 Identification of Fos and FosB as Transcriptional Regulators of Bovine Satellite Cell Differentiation.” Journal of Animal Science 99 (Supplement_3): 103–3. https://doi.org/10.1093/jas/skab235.186.
Mattison, Christopher P., Ruhi Rai, Robert E. Settlage, Doug J. Hinchliffe, Crista Madison, John M. Bland, Suzanne Brashear, et al. 2017. “RNA-Seq Analysis of Developing Pecan (Carya Illinoinensis) Embryos Reveals Parallel Expression Patterns Among Allergen and Lipid Metabolism Genes.” Journal of Agricultural and Food Chemistry 65 (7): 1443–55. https://doi.org/10.1021/acs.jafc.6b04199.
Monson, Melissa S., Robert E. Settlage, Kevin W. McMahon, Kristelle M. Mendoza, Sumit Rawal, Hani S. El-Nezami, Roger A. Coulombe, and Kent M. Reed. 2014. “Response of the Hepatic Transcriptome to Aflatoxin B1 in Domestic Turkey (Meleagris Gallopavo).” Edited by Huaijun Zhou. PLoS ONE 9 (6): e100930. https://doi.org/10.1371/journal.pone.0100930.
Monson, Melissa S., Robert E. Settlage, Kristelle M. Mendoza, Sumit Rawal, Hani S. El-Nezami, Roger A. Coulombe, and Kent M. Reed. 2015. “Modulation of the Spleen Transcriptome in Domestic Turkey (Meleagris Gallopavo) in Response to Aflatoxin B1 and Probiotics.” Immunogenetics 67 (3): 163–78. https://doi.org/10.1007/s00251-014-0825-y.
Nichols, Anne E. C., Robert E. Settlage, Stephen R. Werre, and Linda A. Dahlgren. 2018. “Novel Roles for Scleraxis in Regulating Adult Tenocyte Function.” BMC Cell Biology 19 (1). https://doi.org/10.1186/s12860-018-0166-z.
Patel, P. A., C. Liang, A. Arora, S. Vijayan, S. Ahuja, P. K. Wagley, R. Settlage, et al. 2020. “Haploinsufficiency of x-Linked Intellectual Disability Gene CASK Induces Post-Transcriptional Changes in Synaptic and Cellular Metabolic Pathways.” Experimental Neurology 329 (July): 113319. https://doi.org/10.1016/j.expneurol.2020.113319.
Paweletz, Cloud P., Matthew C. Wiener, Andrey Y. Bondarenko, Nathan A. Yates, Qinghua Song, Andy Liaw, Anita Y. H. Lee, et al. 2010. “Application of an End-to-End Biomarker Discovery Platform to Identify Target Engagement Markers in Cerebrospinal Fluid by High Resolution Differential Mass Spectrometry.” Journal of Proteome Research 9 (3): 1392–1401. https://doi.org/10.1021/pr900925d.
Pestic-Dragovich, Lidija, Ljuba Stojiljkovic, Anatoly A. Philimonenko, Grzegorz Nowak, Yunbo Ke, Robert E. Settlage, Jeffrey Shabanowitz, Donald F. Hunt, Pavel Hozak, and Primal de Lanerolle. 2000. “A Myosin i Isoform in the Nucleus.” Science 290 (5490): 337–41. https://doi.org/10.1126/science.290.5490.337.
Pieper, Rembert, Robert E. Christian, Monica I. Gonzales, Michael I. Nishimura, Gaorav Gupta, Robert E. Settlage, Jeffrey Shabanowitz, Steven A. Rosenberg, Donald F. Hunt, and Suzanne L. Topalian. 1999. “Biochemical Identification of a Mutated Human Melanoma Antigen Recognized by CD4 t Cells.” Journal of Experimental Medicine 189 (5): 757–66. https://doi.org/10.1084/jem.189.5.757.
Radakovits, Randor, Robert E. Jinkerson, Susan I. Fuerstenberg, Hongseok Tae, Robert E. Settlage, Jeffrey L. Boore, and Matthew C. Posewitz. 2012. “Draft Genome Sequence and Genetic Transformation of the Oleaginous Alga Nannochloropsis Gaditana.” Nature Communications 3 (1). https://doi.org/10.1038/ncomms1688.
Rajamohan, Srijith, and Robert E. Settlage. 2020. “Informing the on/Off-Prem Cloud Discussion in Higher Education.” In Practice and Experience in Advanced Research Computing. ACM. https://doi.org/10.1145/3311790.3396627.
Reed, Kent M, Kristelle M Mendoza, and Robert E Settlage. 2016. “Targeted Capture Enrichment and Sequencing Identifies Extensive Nucleotide Variation in the Turkey MHC-b.” Immunogenetics 68 (3): 219–29. https://doi.org/10.1007/s00251-015-0893-7.
Reed, Kent M., and Robert E. Settlage. 2021. “Major Histocompatibility Complex Genes and Locus Organization in the Komodo Dragon (Varanus Komodoensis).” Immunogenetics 73 (5): 405–17. https://doi.org/10.1007/s00251-021-01217-6.
Settlage, Robert E., Paul S. Russo, Jeffrey Shabanowitz, and Donald F. Hunt. 1998. “A Novel \(\mu\)-ESI Source for Coupling Capillary Electrophoresis and Mass Spectrometry: Sequence Determination of Tumor Peptides at the Attomole Level.” Journal of Microcolumn Separations 10 (3): 281–85. https://doi.org/10.1002/(sici)1520-667x(1998)10:3<281::aid-mcs7>3.0.co;2-c.
Settlage, Robert, Alan Chalker, Eric Franz, Doug Johnson, Steve Gallo, Edgar Moore, and David Hudak. 2019. “Open OnDemand: HPC for Everyone.” In Lecture Notes in Computer Science, 504–13. Springer International Publishing. https://doi.org/10.1007/978-3-030-34356-9_38.
Settlage, Robert, Srijith Rajamohan, Kevin Lahmers, Alan Chalker, Eric Franz, Steve Gallo, and David Hudak. 2020. “Portals for Interactive Steering of HPC Workflows.” In Communications in Computer and Information Science, 179–89. Springer International Publishing. https://doi.org/10.1007/978-3-030-44728-1_11.
Sheehan, Lauren M., James A. Budnick, Jaquille Fyffe-Blair, Kellie A. King, Robert E. Settlage, and Clayton C. Caswell. 2020. “The Endoribonuclease RNase e Coordinates Expression of mRNAs and Small Regulatory RNAs and Is Critical for the Virulence of Brucella Abortus.” Edited by Laurie E. Comstock. Journal of Bacteriology 202 (20). https://doi.org/10.1128/jb.00240-20.
Tae, Hongseok, Dong-Yun Kim, John McCormick, Robert E. Settlage, and Harold R. Garner. 2013. “Discretized Gaussian Mixture for Genotyping of Microsatellite Loci Containing Homopolymer Runs.” Bioinformatics 30 (5): 652–59. https://doi.org/10.1093/bioinformatics/btt595.
Tae, Hongseok, Robert E. Settlage, Shamira Shallom, Jasmin H. Bavarva, Dale Preston, Gregory N. Hawkins, L. Garry Adams, and Harold R. Garner. 2012. “Improved Variation Calling via an Iterative Backbone Remapping and Local Assembly Method for Bacterial Genomes.” Genomics 100 (5): 271–76. https://doi.org/10.1016/j.ygeno.2012.07.015.
Tae, Hongseok, Shamira Shallom, Robert Settlage, Dale Preston, L. Garry Adams, and Harold R. Garner. 2011. “Revised Genome Sequence of Brucella Suis 1330.” Journal of Bacteriology 193 (22): 6410–10. https://doi.org/10.1128/jb.06181-11.
Taetzsch, Thomas, Dillon Shapiro, Randa Eldosougi, Tracey Myers, Robert E. Settlage, and Gregorio Valdez. 2020. “The microRNA miR-133b Functions to Slow Duchenne Muscular Dystrophy Pathogenesis.” The Journal of Physiology 599 (1): 171–92. https://doi.org/10.1113/jp280405.
Thompson, Lee W., Kevin T. Hogan, Jennifer A. Caldwell, Richard A. Pierce, Ronald C. Hendrickson, Donna H. Deacon, Robert E. Settlage, et al. 2004. “Preventing the Spontaneous Modification of an HLA-A2-Restricted Peptide at an n-Terminal Glutamine or an Internal Cysteine Residue Enhances Peptide Antigenicity.” Journal of Immunotherapy 27 (3): 177–83. https://doi.org/10.1097/00002371-200405000-00001.
Todd, S. Michelle, Robert E. Settlage, Kevin K. Lahmers, and Daniel J. Slade. 2018. “Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction.” Edited by Sarah E. F. DOrazio. mSphere 3 (4). https://doi.org/10.1128/msphere.00269-18.
Wang, Zheng, Dagmar H. Leary, Jinny Liu, Robert E. Settlage, Kenan P. Fears, Stella H. North, Anahita Mostaghim, et al. 2015. “Molt-Dependent Transcriptomic Analysis of Cement Proteins in the Barnacle Amphibalanus Amphitrite.” BMC Genomics 16 (1). https://doi.org/10.1186/s12864-015-2076-1.
Yang, Ching-Hui, Jacek Szeliga, Jeremy Jordan, Shawn Faske, Zvjezdana Sever-Chroneos, Bre Dorsett, Robert E. Christian, et al. 2005. “Identification of the Surfactant Protein a Receptor 210 as the Unconventional Myosin 18a.” Journal of Biological Chemistry 280 (41): 34447–57. https://doi.org/10.1074/jbc.m505229200.
Yang, Xin-She, Simon Sherratt, Nilanjan Dey, and Amit Joshi, eds. 2022. Proceedings of Sixth International Congress on Information and Communication Technology. Springer Singapore. https://doi.org/10.1007/978-981-16-1781-2.
Yates, Nathan A., Ekaterina G. Deyanova, Wayne Geissler, Matthew C. Wiener, Jeffrey R. Sachs, Kenny K. Wong, Nancy A. Thornberry, Ranabir Sinha Roy, Robert E. Settlage, and Ronald C. Hendrickson. 2007. “Identification of Peptidase Substrates in Human Plasma by FTMS Based Differential Mass Spectrometry.” International Journal of Mass Spectrometry 259 (1-3): 174–83. https://doi.org/10.1016/j.ijms.2006.09.020.
Zalenskaya, Irina A., Theresa Joseph, Jasmin Bavarva, Nazita Yousefieh, Suzanne S. Jackson, Titilayo Fashemi, Hidemi S. Yamamoto, Robert Settlage, Raina N. Fichorova, and Gustavo F. Doncel. 2015. “Gene Expression Profiling of Human Vaginal Cells in Vitro Discriminates Compounds with Pro-Inflammatory and Mucosa-Altering Properties: Novel Biomarkers for Preclinical Testing of HIV Microbicide Candidates.” Edited by J. Gerardo Garcia-Lerma. PLOS ONE 10 (6): e0128557. https://doi.org/10.1371/journal.pone.0128557.
Zhang, Husen, Joshua B Sparks, Saikumar V Karyala, Robert Settlage, and Xin M Luo. 2014. “Host Adaptive Immunity Alters Gut Microbiota.” The ISME Journal 9 (3): 770–81. https://doi.org/10.1038/ismej.2014.165.
Zhang, Wei, Sungwon Kim, Robert Settlage, Wyatt McMahon, Lindsay H. Sumners, Paul B. Siegel, Benjamin J. Dorshorst, Mark A. Cline, and Elizabeth R. Gilbert. 2015. “Hypothalamic Differences in Expression of Genes Involved in Monoamine Synthesis and Signaling Pathways After Insulin Injection in Chickens from Lines Selected for High and Low Body Weight.” Neurogenetics 16 (2): 133–44. https://doi.org/10.1007/s10048-014-0435-8.
Zhao, Xuemei, Ekaterina G. Deyanova, Laura S. Lubbers, Pete Zafian, Jenny J. Li, Andy Liaw, Qinghua Song, et al. 2008. “Differential Mass Spectrometry of Rat Plasma Reveals Proteins That Are Responsive to 17\(\beta\)-Estradiol and a Selective Estrogen Receptor Modulator PPT.” Journal of Proteome Research 7 (10): 4373–83. https://doi.org/10.1021/pr800309z.

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Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/rsettlage/rsettlage.github.io, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".