Publications

  1. Zhu, J., Wang, J., Chen, X., Tsompana, M., Gaile, D., Buck, M., & Ren, X. (2017). A Time-Series Analysis of Altered Histone H3 Acetylation and Gene Expression during the Course of MMAIII-Induced Malignant Transformation of Urinary Bladder Cells. Carcinogenesis. doi:10.1093/carcin/bgx011
  2. Narla, S. T., Lee, Y. W., Benson, C. A., Sarder, P., Brennand, K. J., Stachowiak, E. K., & Stachowiak, M. K. (2017). Common developmental genome deprogramming in schizophrenia – Role of Integrative Nuclear FGFR1 Signaling (INFS). Schizophr Res. doi:10.1016/j.schres.2016.12.012
  3. Hefti, E., Bard, J., & Blanco, J. G. (2017). Analysis of Heteroplasmic Variants in the Cardiac Mitochondrial Genome of Individuals with Down Syndrome. Hum Mutat, 38(1), 48-54. doi:10.1002/humu.23071
  4. Yang, S., Cai, Q., Vethanayagam, R. R., Wang, J., Yang, W., & Hu, B. H. (2016). Immune defense is the primary function associated with the differentially expressed genes in the cochlea following acoustic trauma. Hear Res, 333, 283-294. doi:10.1016/j.heares.2015.10.010
  5. Tylee, D. S., Espinoza, A. J., Hess, J. L., Tahir, M. A., McCoy, S. Y., Rim, J. K., . . . Glatt, S. J. (2016). RNA sequencing of transformed lymphoblastoid cells from siblings discordant for autism spectrum disorders reveals transcriptomic and functional alterations: Evidence for sex-specific effects. Autism Res. doi:10.1002/aur.1679
  6. Tomov, M. L., Olmsted, Z. T., Dogan, H., Gongorurler, E., Tsompana, M., Otu, H. H., . . . Paluh, J. L. (2016). Distinct and Shared Determinants of Cardiomyocyte Contractility in Multi-Lineage Competent Ethnically Diverse Human iPSCs. Sci Rep, 6, 37637. doi:10.1038/srep37637
  7. Smith, C., Stringer, A. M., Mao, C., Palumbo, M. J., & Wade, J. T. (2016). Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion. MBio, 7(5). doi:10.1128/mBio.01024-16
  8. Singh, N., Bubunenko, M., Smith, C., Abbott, D. M., Stringer, A. M., Shi, R., . . . Wade, J. T. (2016). SuhB Associates with Nus Factors To Facilitate 30S Ribosome Biogenesis in Escherichia coli. MBio, 7(2), e00114. doi:10.1128/mBio.00114-16
  9. Simpson, R. M., Bruno, A. E., Bard, J. E., Buck, M. J., & Read, L. K. (2016). High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing. Rna, 22(5), 677-695. doi:10.1261/rna.055160.115
  10. Sankari, S., & O’Brian, M. R. (2016). The Bradyrhizobium japonicum Ferrous Iron Transporter FeoAB Is Required for Ferric Iron Utilization in Free Living Aerobic Cells and for Symbiosis. J Biol Chem, 291(30), 15653-15662. doi:10.1074/jbc.M116.734129
  11. Rizzo, J. M., Oyelakin, A., Min, S., Smalley, K., Bard, J., Luo, W., . . . Romano, R. A. (2016). DeltaNp63 regulates IL-33 and IL-31 signaling in atopic dermatitis. Cell Death Differ, 23(6), 1073-1085. doi:10.1038/cdd.2015.162
  12. Hui-Yuen, J. S., Zhu, L., Wong, L. P., Jiang, K., Chen, Y., Liu, T., & Jarvis, J. N. (2016). Chromatin landscapes and genetic risk in systemic lupus. Arthritis Res Ther, 18(1), 281. doi:10.1186/s13075-016-1169-9
  13. Gluck, C., Min, S., Oyelakin, A., Smalley, K., Sinha, S., & Romano, R. A. (2016). RNA-seq based transcriptomic map reveals new insights into mouse salivary gland development and maturation. BMC Genomics, 17(1), 923. doi:10.1186/s12864-016-3228-7
  14. Zheng, W., Tsompana, M., Ruscitto, A., Sharma, A., Genco, R., Sun, Y., & Buck, M. J. (2015). An accurate and efficient experimental approach for characterization of the complex oral microbiota. Microbiome, 3(1), 48. doi:10.1186/s40168-015-0110-9
  15. Yang, S., Cai, Q., Bard, J., Jamison, J., Wang, J., Yang, W., & Hu, B. H. (2015). Variation analysis of transcriptome changes reveals cochlear genes and their associated functions in cochlear susceptibility to acoustic overstimulation. Hearing research, 330(0 0), 78-89. doi:10.1016/j.heares.2015.04.010
  16. Wang, J., Rennie, W., Liu, C., Carmack, C. S., Prevost, K., Caron, M. P., . . . Wade, J. T. (2015). Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Res, 43(21), 10308-10320. doi:10.1093/nar/gkv1158
  17. Tsompana, M., Valiyaparambil, S., Bard, J., Marzullo, B., Nowak, N., & Buck, M. J. (2015). An automated method for efficient, accurate and reproducible construction of RNA-seq libraries. BMC Research Notes, 8, 124. doi:10.1186/s13104-015-1089-9
  18. Terranova, C., Narla, S. T., Lee, Y.-W., Bard, J., Parikh, A., Stachowiak, E. K., . . . Stachowiak, M. K. (2015). Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1). PLoS One, 10(4), e0123380. doi:10.1371/journal.pone.0123380
  19. Sabharwal, A., Liao, Y. C., Lin, H. H., Haase, E. M., & Scannapieco, F. A. (2015). Draft genome sequences of 18 oral streptococcus strains that encode amylase-binding proteins. Genome Announc, 3(3). doi:10.1128/genomeA.00510-15
  20. Rizzo, J. M., Romano, R. A., Bard, J., & Sinha, S. (2015). RNA-seq studies reveal new insights into p63 and the transcriptomic landscape of the mouse skin. J Invest Dermatol, 135(2), 629-632. doi:10.1038/jid.2014.384
  21. Puri, S., Li, R., Ruszaj, D., Tati, S., & Edgerton, M. (2015). Iron binding modulates candidacidal properties of salivary histatin 5. J Dent Res, 94(1), 201-208. doi:10.1177/0022034514556709
  22. Paul, E., Zhu, Z. I., Landsman, D., & Morse, R. H. (2015). Genome-wide association of mediator and RNA polymerase II in wild-type and mediator mutant yeast. Mol Cell Biol, 35(1), 331-342. doi:10.1128/mcb.00991-14
  23. Paul, E., Tirosh, I., Lai, W., Buck, M. J., Palumbo, M. J., & Morse, R. H. (2015). Chromatin mediation of a transcriptional memory effect in yeast. G3 (Bethesda), 5(5), 829-838. doi:10.1534/g3.115.017418
  24. Minkah, N., Macaluso, M., Oldenburg, D. G., Paden, C. R., White, D. W., McBride, K. M., & Krug, L. T. (2015). Absence of the uracil DNA glycosylase of murine gammaherpesvirus 68 impairs replication and delays the establishment of latency in vivo. J Virol, 89(6), 3366-3379. doi:10.1128/jvi.03111-14
  25. Mechtler, P., Singhal, R., Kichina, J. V., Bard, J. E., Buck, M. J., & Kandel, E. S. (2015). MicroRNA analysis suggests an additional level of feedback regulation in the NF-kappaB signaling cascade. Oncotarget, 6(19), 17097-17106. doi:10.18632/oncotarget.4005
  26. Lott, K., Mukhopadhyay, S., Li, J., Wang, J., Yao, J., Sun, Y., . . . Read, L. K. (2015). Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome. Nucleic Acids Res, 43(11), 5501-5523. doi:10.1093/nar/gkv428
  27. Kapoor, S., Zhu, L., Froyd, C., Liu, T., & Rusche, L. N. (2015). Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin. Proc Natl Acad Sci U S A, 112(39), 12139-12144. doi:10.1073/pnas.1508749112
  28. Jiang, K., Zhu, L., Buck, M. J., Chen, Y., Carrier, B., Liu, T., & Jarvis, J. N. (2015). Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells. Arthritis Rheumatol, 67(7), 1966-1977. doi:10.1002/art.39135
  29. Hoffman, E. A., McCulley, A., Haarer, B., Arnak, R., & Feng, W. (2015). Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription. Genome Res, 25(3), 402-412. doi:10.1101/gr.180497.114
  30. Haycocks, J. R., Sharma, P., Stringer, A. M., Wade, J. T., & Grainger, D. C. (2015). The molecular basis for control of ETEC enterotoxin expression in response to environment and host. PLoS Pathog, 11(1), e1004605. doi:10.1371/journal.ppat.1004605
  31. Haase, E. M., Feng, X., Pan, J., Miecznikowski, J. C., & Scannapieco, F. A. (2015). Dynamics of the Streptococcus gordonii Transcriptome in Response to Medium, Salivary alpha-Amylase, and Starch. Appl Environ Microbiol, 81(16), 5363-5374. doi:10.1128/aem.01221-15
  32. Fitzgerald, D. M., Bonocora, R. P., & Wade, J. T. (2015). Correction: Comprehensive Mapping of the Escherichia coli Flagellar Regulatory Network. PLoS Genet, 11(9), e1005456. doi:10.1371/journal.pgen.1005456
  33. Chandler, C. H., Badawi, M., Moumen, B., Greve, P., & Cordaux, R. (2015). Multiple Conserved Heteroplasmic Sites in tRNA Genes in the Mitochondrial Genomes of Terrestrial Isopods (Oniscidea). G3 (Bethesda), 5(7), 1317-1322. doi:10.1534/g3.115.018283
  34. Adelaiye, R., Ciamporcero, E., Miles, K. M., Sotomayor, P., Bard, J., Tsompana, M., . . . Pili, R. (2015). Sunitinib dose-escalation overcomes transient resistance in clear cell renal cell carcinoma and is associated with epigenetic modifications. Molecular cancer therapeutics, 14(2), 513-522. doi:10.1158/1535-7163.MCT-14-0208
  35. Zhu, L., Liu, W., Alkhouri, R., Baker, R. D., Bard, J. E., Quigley, E. M., & Baker, S. S. (2014). Structural changes in the gut microbiome of constipated patients. Physiol Genomics, 46(18), 679-686. doi:10.1152/physiolgenomics.00082.2014
  36. Tsompana, M., & Buck, M. J. (2014). Chromatin accessibility: a window into the genome. Epigenetics & Chromatin, 7, 33. doi:10.1186/1756-8935-7-33
  37. Stringer, A. M., Currenti, S., Bonocora, R. P., Baranowski, C., Petrone, B. L., Palumbo, M. J., . . . Wade, J. T. (2014). Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon. J Bacteriol, 196(3), 660-671. doi:10.1128/jb.01007-13
  38. Sethi, I., Sinha, S., & Buck, M. J. (2014). Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes. BMC Genomics, 15, 1042. doi:10.1186/1471-2164-15-1042
  39. Sapkota, D., Chintala, H., Wu, F., Fliesler, S. J., Hu, Z., & Mu, X. (2014). Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development. Proc Natl Acad Sci U S A, 111(39), E4086-4095. doi:10.1073/pnas.1405354111
  40. Rizzo, J. M., & Sinha, S. (2014). Analyzing the global chromatin structure of keratinocytes by MNase-seq. Methods Mol Biol, 1195, 49-59. doi:10.1007/7651_2014_77
  41. Puri, S., Lai, W. K., Rizzo, J. M., Buck, M. J., & Edgerton, M. (2014). Iron-responsive chromatin remodelling and MAPK signalling enhance adhesion in Candida albicans. Mol Microbiol, 93(2), 291-305. doi:10.1111/mmi.12659
  42. Novikova, O., Smith, D., Hahn, I., Beauregard, A., & Belfort, M. (2014). Interaction between conjugative and retrotransposable elements in horizontal gene transfer. PLoS Genet, 10(12), e1004853. doi:10.1371/journal.pgen.1004853
  43. Li, R., Wu, F., Ruonala, R., Sapkota, D., Hu, Z., & Mu, X. (2014). Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells. PLoS One, 9(3), e92105. doi:10.1371/journal.pone.0092105
  44. Hohle, T. H., & O’Brian, M. R. (2014). Magnesium-dependent processes are targets of bacterial manganese toxicity. Mol Microbiol, 93(4), 736-747. doi:10.1111/mmi.12687
  45. Frangou, C., Li, Y. W., Shen, H., Yang, N., Wilson, K. E., Blijlevens, M., . . . Zhang, J. (2014). Molecular profiling and computational network analysis of TAZ-mediated mammary tumorigenesis identifies actionable therapeutic targets. Oncotarget, 5(23), 12166-12176. doi:10.18632/oncotarget.2570
  46. Chandler, C. H. (2014). Parallel genome-wide fixation of ancestral alleles in partially outcrossing experimental populations of Caenorhabditis elegans. G3 (Bethesda), 4(9), 1657-1665. doi:10.1534/g3.114.012914
  47. Cai, Q., Vethanayagam, R. R., Yang, S., Bard, J., Jamison, J., Cartwright, D., . . . Hu, B. H. (2014). Molecular profile of cochlear immunity in the resident cells of the organ of Corti. J Neuroinflammation, 11, 173. doi:10.1186/s12974-014-0173-8
  48. Buck, M. J., Raaijmakers, L. M., Ramakrishnan, S., Wang, D., Valiyaparambil, S., Liu, S., . . . Pili, R. (2014). Alterations in chromatin accessibility and DNA methylation in clear cell renal cell carcinoma. Oncogene, 33(41), 4961-4965. doi:10.1038/onc.2013.455
  49. Ballinger, M. J., Bruenn, J. A., Hay, J., Czechowski, D., & Taylor, D. J. (2014). Discovery and evolution of bunyavirids in arctic phantom midges and ancient bunyavirid-like sequences in insect genomes. J Virol, 88(16), 8783-8794. doi:10.1128/jvi.00531-14
  50. Taylor, D. J., Ballinger, M. J., Bowman, S. M., & Bruenn, Jeremy A. (2013). Virus-host co-evolution under a modified nuclear genetic code. PeerJ, 1, e50. doi:10.7717/peerj.50
  51. Singhal, R., Bard, J. E., Nowak, N. J., Buck, M. J., & Kandel, E. S. (2013). FOXO1 regulates expression of a microRNA cluster on X chromosome. Aging (Albany NY), 5(5), 347-356. doi:10.18632/aging.100558
  52. Patel, M., Hu, Z., Bard, J., Jamison, J., Cai, Q., & Hu, B. H. (2013). Transcriptome characterization by RNA-Seq reveals the involvement of the complement components in noise-traumatized rat cochleae. Neuroscience, 248, 1-16. doi:10.1016/j.neuroscience.2013.05.038
  53. Liu, X., Hu, Q., Liu, S., Tallo, L. J., Sadzewicz, L., Schettine, C. A., . . . Ionov, Y. (2013). Serum Antibody Repertoire Profiling Using In Silico Antigen Screen. PLoS One, 8(6), e67181. doi:10.1371/journal.pone.0067181
  54. Kuo, S. M., Wang, L. Y., Yu, S., Campbell, C. E., Valiyaparambil, S. A., Rance, M., & Blumenthal, K. M. (2013). The N-terminal basolateral targeting signal unlikely acts alone in the differential trafficking of membrane transporters in MDCK cells. Biochemistry, 52(30), 5103-5116. doi:10.1021/bi4005914
  55. Garcia, H., Miecznikowski, J. C., Safina, A., Commane, M., Ruusulehto, A., Kilpinen, S., . . . Gurova, K. V. (2013). Facilitates chromatin transcription complex is an “accelerator” of tumor transformation and potential marker and target of aggressive cancers. Cell Rep, 4(1), 159-173. doi:10.1016/j.celrep.2013.06.013
  56. Dolan, J. M., Meng, H., Sim, F. J., & Kolega, J. (2013). Differential gene expression by endothelial cells under positive and negative streamwise gradients of high wall shear stress. Am J Physiol Cell Physiol, 305(8), C854-866. doi:10.1152/ajpcell.00315.2012
  57. Rizzo, J. M., Bard, J. E., & Buck, M. J. (2012). Standardized collection of MNase-seq experiments enables unbiased dataset comparisons. BMC Mol Biol, 13, 15. doi:10.1186/1471-2199-13-15
  58. Lai, W. K., Bard, J. E., & Buck, M. J. (2012). ArchTEx: accurate extraction and visualization of next-generation sequence data. Bioinformatics, 28(7), 1021-1023. doi:10.1093/bioinformatics/bts063
  59. Kos, V. N., Desjardins, C. A., Griggs, A., Cerqueira, G., Van Tonder, A., Holden, M. T., . . . Gilmore, M. S. (2012). Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States. MBio, 3(3). doi:10.1128/mBio.00112-12
  60. Hu, B. H., Cai, Q., Hu, Z., Patel, M., Bard, J., Jamison, J., & Coling, D. (2012). Metalloproteinases and their associated genes contribute to the functional integrity and noise-induced damage in the cochlear sensory epithelium. J Neurosci, 32(43), 14927-14941. doi:10.1523/jneurosci.1588-12.2012
  61. Givens, R. M., Lai, W. K., Rizzo, J. M., Bard, J. E., Mieczkowski, P. A., Leatherwood, J., . . . Buck, M. J. (2012). Chromatin architectures at fission yeast transcriptional promoters and replication origins. Nucleic Acids Res, 40(15), 7176-7189. doi:10.1093/nar/gks351
  62. Dolan, J. M., Sim, F. J., Meng, H., & Kolega, J. (2012). Endothelial cells express a unique transcriptional profile under very high wall shear stress known to induce expansive arterial remodeling. Am J Physiol Cell Physiol, 302(8), C1109-1118. doi:10.1152/ajpcell.00369.2011
  63. Baxter, J. C., & Sutton, M. D. (2012). Evidence for roles of the Escherichia coli Hda protein beyond regulatory inactivation of DnaA. Mol Microbiol, 85(4), 648-668. doi:10.1111/j.1365-2958.2012.08129.x
  64. Naka, H., Dias, G. M., Thompson, C. C., Dubay, C., Thompson, F. L., & Crosa, J. H. (2011). Complete genome sequence of the marine fish pathogen Vibrio anguillarum harboring the pJM1 virulence plasmid and genomic comparison with other virulent strains of V. anguillarum and V. ordalii. Infect Immun, 79(7), 2889-2900. doi:10.1128/iai.05138-11
  65. Madhusoodanan, J., Seo, K. S., Remortel, B., Park, J. Y., Hwang, S. Y., Fox, L. K., . . . Gill, S. R. (2011). An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis. J Bacteriol, 193(8), 1854-1862. doi:10.1128/jb.00162-10
  66. Kvist, S., Narechania, A., Oceguera-Figueroa, A., Fuks, B., & Siddall, M. E. (2011). Phylogenomics of Reichenowia parasitica, an alphaproteobacterial endosymbiont of the freshwater leech Placobdella parasitica. PLoS One, 6(11), e28192. doi:10.1371/journal.pone.0028192
  67. Hsu, Y. C., Osinski, J., Campbell, C. E., Litwack, E. D., Wang, D., Liu, S., . . . Gronostajski, R. M. (2011). Mesenchymal nuclear factor I B regulates cell proliferation and epithelial differentiation during lung maturation. Dev Biol, 354(2), 242-252. doi:10.1016/j.ydbio.2011.04.002
  68. Davie, J. J., Earl, J., de Vries, S. P., Ahmed, A., Hu, F. Z., Bootsma, H. J., . . . Campagnari, A. A. (2011). Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates. BMC Genomics, 12, 70. doi:10.1186/1471-2164-12-70
  69. Sukumaran, S., Xue, B., Jusko, W. J., Dubois, D. C., & Almon, R. R. (2010). Circadian variations in gene expression in rat abdominal adipose tissue and relationship to physiology. Physiol Genomics, 42a(2), 141-152. doi:10.1152/physiolgenomics.00106.2010
  70. Nagarajan, P., Chin, S. S., Wang, D., Liu, S., Sinha, S., & Garrett-Sinha, L. A. (2010). Ets1 blocks terminal differentiation of keratinocytes and induces expression of matrix metalloproteases and innate immune mediators. J Cell Sci, 123(Pt 20), 3566-3575. doi:10.1242/jcs.062240
  71. Escamilla-Hernandez, R., Chakrabarti, R., Romano, R. A., Smalley, K., Zhu, Q., Lai, W., . . . Sinha, S. (2010). Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland. BMC Mol Biol, 11, 68. doi:10.1186/1471-2199-11-68
  72. Sanders, L. H., Sudhakaran, J., & Sutton, M. D. (2009). The GO system prevents ROS-induced mutagenesis and killing in Pseudomonas aeruginosa. FEMS Microbiol Lett, 294(1), 89-96. doi:10.1111/j.1574-6968.2009.01550.x
  73. Adams, M. D., Goglin, K., Molyneaux, N., Hujer, K. M., Lavender, H., Jamison, J. J., . . . Gill, S. R. (2008). Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii. J Bacteriol, 190(24), 8053-8064. doi:10.1128/jb.00834-08