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Publications

Peer-Reviewed Publications

  1. Bennett CJ, Aramayo R. A Re-Analysis of an Existing Drosophila melanogaster Dataset Reveals a New Set of Genes Involved in Post-Mating Response. bioRxiv. 2024:2024.04.10.588867. doi: 10.1101/2024.04.10.588867.
  2. Aramayo R. Evaluating the impact of sequence duplications on the measurement of transcriptional profiling in the Human genome.2024;In Preparation.
  3. Aramayo R, Nan B. De Novo Assembly and Annotation of the Complete Genome Sequence of Myxococcus xanthus DZ2. Microbiol Resour Announc. 2022;11(5):e0107421. Epub 20220406. doi: 10.1128/mra.01074-21. PubMed PMID: 35384715; PMCID: PMC9119067.
  4. Gerth M, Martinez-Montoya H, Ramirez P, Masson F, Griffin JS, Aramayo R, Siozios S, Lemaitre B, Mateos M, Hurst GDD. Rapid molecular evolution of Spiroplasma symbionts of Drosophila. Microb Genom. 2021;7(2). doi: 10.1099/mgen.0.000503. PubMed PMID: 33591248; PMCID: PMC8208695.
  5. Maitra N, He C, Blank HM, Tsuchiya M, Schilling B, Kaeberlein M, Aramayo R, Kennedy BK, Polymenis M. Translational control of methionine and serine metabolic pathways underpin the paralog-specific phenotypes of Rpl22 ribosomal protein mutants in cell division and replicative longevity. bioRxiv. 2020.
  6. Maitra N, He C, Blank HM, Tsuchiya M, Schilling B, Kaeberlein M, Aramayo R, Kennedy BK, Polymenis M. Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity. Elife. 2020;9:e53127. Epub 20200520. doi: 10.7554/eLife.53127. PubMed PMID: 32432546; PMCID: PMC7263821.
  7. Mateos M, Silva NO, Ramirez P, Higareda-Alvear VM, Aramayo R, Erickson JW. Effect of heritable symbionts on maternally-derived embryo transcripts. Sci Rep. 2019;9(1):8847. Epub 20190620. doi: 10.1038/s41598-019-45371-0. PubMed PMID: 31222094; PMCID: PMC6586653.
  8. Stavrianakou M, Perez R, Wu C, Sachs MS, Aramayo R, Harlow M. Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ. BMC Genomics. 2017;18(1):611. Epub 20170814. doi: 10.1186/s12864-017-3890-4. PubMed PMID: 28806931; PMCID: PMC5557070.
  9. Li H, Wu C, Aramayo R, Sachs MS, Harlow ML. Synaptic vesicles isolated from the electric organ of Torpedo californica and from the central nervous system of Mus musculus contain small ribonucleic acids (sRNAs). Genom Data. 2017;12:52-3. Epub 20170308. doi: 10.1016/j.gdata.2017.02.015. PubMed PMID: 28367405; PMCID: PMC5361766.
  10. Clanton RM, Wu G, Akabani G, Aramayo R. Control of seizures by ketogenic diet-induced modulation of metabolic pathways. Amino Acids. 2017;49(1):1-20. Epub 20160928. doi: 10.1007/s00726-016-2336-7. PubMed PMID: 27683025.
  11. Blank HM, Perez R, He C, Maitra N, Metz R, Hill J, Lin Y, Johnson CD, Bankaitis VA, Kennedy BK, Aramayo R, Polymenis M. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. EMBO J. 2017;36(4):487-502. Epub 20170105. doi: 10.15252/embj.201695050. PubMed PMID: 28057705; PMCID: PMC5694946.
  12. Aramayo R, Polymenis M. Ribosome profiling the cell cycle: lessons and challenges. Curr Genet. 2017;63(6):959-64. Epub 20170427. doi: 10.1007/s00294-017-0698-3. PubMed PMID: 28451847; PMCID: PMC5790165.
  13. Sauceda DJ AR, Youssef S, Dima A, chaudhary N, Karaman I, Perez R, Aramayo R., editor. Data and Tools for Materials Discovery and Design. Data and Tools for Materials Discovery and Design Materials Science & Technology 2015; 2015 October 4; Columbus, OH, USA Columbus, OH: Conference Tools for Materials Science & Technology 2015; c2015; 2015.
  14. Polymenis M, Aramayo R. Translate to divide: small es, Cyrillicontrol of the cell cycle by protein synthesis. Microb Cell. 2015;2(4):94-104. Epub 20150320. doi: 10.15698/mic2015.04.198. PubMed PMID: 28357283; PMCID: PMC5348972.
  15. Li H, Wu C, Aramayo R, Sachs MS, Harlow ML. Synaptic vesicles contain small ribonucleic acids (sRNAs) including transfer RNA fragments (trfRNA) and microRNAs (miRNA). Sci Rep. 2015;5(1):14918. Epub 20151008. doi: 10.1038/srep14918. PubMed PMID: 26446566; PMCID: PMC4597359.
  16. Ilori MO, Picardal FW, Aramayo R, Adebusoye SA, Obayori OS, Benedik MJ. Catabolic plasmid specifying polychlorinated biphenyl degradation in Cupriavidus sp. strain SK-4: mobilization and expression in a pseudomonad. J Basic Microbiol. 2015;55(3):338-45. Epub 20130621. doi: 10.1002/jobm.201200807. PubMed PMID: 23787897.
  17. Aramayo R, Selker EU. Neurospora crassa, a model system for epigenetics research. Cold Spring Harb Perspect Biol. 2013;5(10):a017921. Epub 20131001. doi: 10.1101/cshperspect.a017921. PubMed PMID: 24086046; PMCID: PMC3783048.
  18. Wajid B AR, Serpedin E., editor. Exploring Minimum Description Length and Probabilistic Distributions of the Reference Sequences for Comparative Assembly of Genomes. In: Cristea P, editor Proceedings of the International Conference International Conference on Genomic Signal Processing; 2011.
  19. Lee DW, Millimaki R, Aramayo R. QIP, a component of the vegetative RNA silencing pathway, is essential for meiosis and suppresses meiotic silencing in Neurospora crassa. Genetics. 2010;186(1):127-33.
  20. Borkovich K, Ebbole DJ. Cellular and molecular biology of filamentous fungi. American Society for Microbiology Press; 2010.
  21. Aramayo R, Pratt RJ. Meiotic trans‐Sensing and Silencing in Neurospora. Cellular and Molecular Biology of Filamentous Fungi. 2010:132-44.
  22. Lee DW, Freitag M, Selker EU, Aramayo R. A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans. PloS one. 2008;3(6):e2531.
  23. Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Kihara D, Knight TF, Jr., Pico AR, Siegele DA, Wanner BL, Welch RD. The emerging world of wikis. Science. 2008;320(5881):1289-90. doi: 10.1126/science.320.5881.1289b. PubMed PMID: 18535227.
  24. Ng DW, Wang T, Chandrasekharan MB, Aramayo R, Kertbundit S, Hall TC. Plant SET domain-containing proteins: structure, function and regulation. Biochim Biophys Acta. 2007;1769(5-6):316-29. Epub 20070412. doi: 10.1016/j.bbaexp.2007.04.003. PubMed PMID: 17512990; PMCID: PMC2794661.
  25. Kelly WG, Aramayo R. Meiotic silencing and the epigenetics of sex. Chromosome Res. 2007;15(5):633-51. doi: 10.1007/s10577-007-1143-0. PubMed PMID: 17674151; PMCID: PMC4090689.
  26. Pratt RJ, Lee DW, Aramayo R. DNA methylation affects meiotic trans-sensing, not meiotic silencing, in Neurospora. Genetics. 2004;168(4):1925-35.
  27. Lee DW, Seong KY, Pratt RJ, Baker K, Aramayo R. Properties of unpaired DNA required for efficient silencing in Neurospora crassa. Genetics. 2004;167(1):131-50. doi: 10.1534/genetics.167.1.131. PubMed PMID: 15166142; PMCID: PMC1470857.
  28. Freitag M, Lee DW, Kothe GO, Pratt RJ, Aramayo R, Selker EU. DNA methylation is independent of RNA interference in Neurospora. Science. 2004;304(5679):1939-.
  29. Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev. 2004;68(1):1-108. doi: 10.1128/MMBR.68.1.1-108.2004. PubMed PMID: 15007097; PMCID: PMC362109.
  30. Bogomolnaya LM, Pathak R, Guo J, Cham R, Aramayo R, Polymenis M. Hym1p affects cell cycle progression in Saccharomyces cerevisiae. Curr Genet. 2004;46(4):183-92. Epub 20040910. doi: 10.1007/s00294-004-0527-3. PubMed PMID: 15365764.
  31. Lee DW, Pratt RJ, McLaughlin M, Aramayo R. An argonaute-like protein is required for meiotic silencing. Genetics. 2003;164(2):821.
  32. Lee DW, Haag JR, Aramayo R. Construction of strains for rapid homokaryon purification after integration of constructs at the histidine-3 (his-3) locus of Neurospora crassa. Current genetics. 2003;43(1):17-23.
  33. Kutil BL, Seong K-Y, Aramayo R. Unpaired genes do not silence their paired neighbors. Current genetics. 2003;43(6):425-32.
  34. JR H, R A. Construction of a his-3 integration vector capable of performing GATEWAY™ recombinational cloning for high-throughput analysis of Neurospora crassa. Fungal Genetics Newsletter. 2003;50:6-8.
  35. Han BK, Aramayo R, Polymenis M. The G1 cyclin Cln3p controls vacuolar biogenesis in Saccharomyces cerevisiae. Genetics. 2003;165(2):467-76. doi: 10.1093/genetics/165.2.467. PubMed PMID: 14573462; PMCID: PMC1462773.
  36. Haag JR, Lee DW, Aramayo R. A GATEWAY™ Destination Vector For High-Throughput Construction of Neurospora crassa histidine-3 Gene Replacement Plasmids. Fungal Genetics Newsletter. 2003:6-8.
  37. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 2003;422(6934):859-68. doi: 10.1038/nature01554. PubMed PMID: 12712197.
  38. Pratt RJ, Aramayo R. Improving the efficiency of gene replacements in Neurospora crassa: a first step towards a large-scale functional genomics project. Fungal Genet Biol. 2002;37(1):56-71. doi: 10.1016/s1087-1845(02)00032-4. PubMed PMID: 12223190.
  39. DiDomenico B, Aramayo R. Pathogenesis In Fungi. Encyclopedia of Molecular Biology. 2002.
  40. DiDomenico B, Aramayo R. Circadian Rhythms and Clocks in Fungi. Encyclopedia of Molecular Biology. 2002.
  41. DiDomenico B, Aramayo R. Mating In Fungi. Encyclopedia of Molecular Biology. 2002.
  42. DiDomenico B, Aramayo R. Filamentous Fungi. Encyclopedia of Molecular Biology. 2002(10.1002/047120918X.emb0564).
  43. Chang P YJ, Bhatnagar D, Cotty P, Keller N, Aramayo R, Roe B, Kupfer D, Cleveland T. Aspergillus EST Databases Provide Insights into Aflatoxin Biosynthesis Research. Mycopathologia. 2002;155(1-2).
  44. Aramayo R, Bennett J. The importance of fungal genomics. AMER SOC MICROBIOLOGY 1325 MASSACHUSETTS AVENUE, NW, WASHINGTON, DC 20005-4171; 1997. p. 176-7.
  45. Peleg Y, Aramayo R, Kang S, Hall JG, Metzenberg RL. NUC-2, a component of the phosphate-regulated signal transduction pathway inNeurospora crassa, is an ankyrin repeat protein. Molecular and General Genetics MGG. 1996;252(6):709-16.
  46. Peleg Y, Aramayo R, Bleeker A, Metzenberg R. A gas emitted by Neurospora crassa. Fungal Genetics Reports. 1996;43(1):41-2.
  47. Peleg Y, Addison R, Aramayo R, Metzenberg RL. Translocation of Neurospora crassa Transcription Factor NUC-1 into the Nucleus Is Induced by Phosphorus Limitation. Fungal Genetics and Biology. 1996;20(3):185-91.
  48. Bruno KS, Aramayo R, Minke PF, Metzenberg RL, Plamann M. Loss of growth polarity and mislocalization of septa in a Neurospora mutant altered in the regulatory subunit of cAMP-dependent protein kinase. EMBO J. 1996;15(21):5772-82. PubMed PMID: 8918454; PMCID: PMC452324.
  49. Aramayo R, Peleg Y, Addison R, Metzenberg R. Asm-1+, a Neurospora crassa gene related to transcriptional regulators of fungal development. Genetics. 1996;144(3):991-1003. doi: 10.1093/genetics/144.3.991. PubMed PMID: 8913744; PMCID: PMC1207638.
  50. Aramayo R, Metzenberg RL. Meiotic transvection in fungi. Cell. 1996;86(1):103-13. doi: 10.1016/s0092-8674(00)80081-1. PubMed PMID: 8689677.
  51. Aramayo R, Metzenberg R. Gene replacements at the his-3 locus of Neurospora crassa. Fungal Genetics Reports. 1996;43(5):9-13.
  52. Aramayo R. Construction of a Cosmid library of Neurospora crassa DNA sequences from a Mating Type a strain. Catalogue of Strains Supplement of the Fungal Genetics Newsletter. 1996;43:5.
  53. Aramayo R, Timberlake WE. The Aspergillus nidulans yA gene is regulated by abaA. The EMBO Journal. 1993;12(5):2039-48.
  54. Aramayo R, Timberlake WE. Construction of a 24-h developmental cDNA library from Aspergillus nidulans. Fungal Genetics Newsletter. 1990;40(11):103.
  55. Aramayo R, Timberlake WE. Sequence and molecular structure of the Aspergillus nidulans yA (laccase I) gene. Nucleic Acids Res. 1990;18(11):3415. doi: 10.1093/nar/18.11.3415. PubMed PMID: 2192364; PMCID: PMC330968.
  56. Aramayo R, Adams T, Timberlake W. A large cluster of highly expressed genes is dispensable for growth and development in Aspergillus nidulans. Genetics. 1989;122(1):65-71.
  57. de Castro LL, Z. Aramayo, R. Sampaio, M. Gander, E. Evidence for a precursor molecule of Brazil nut 2S seed proteins from biosynthesis and cDNA analysis. Molecular and General Genetics MGG. 1987;206(02):338-43.
  58. Aramayo R CL. Isolation and characterization of a peptide from Bacillus subtilis (Ehrenberg) Cohn, T41, with antibiotic activity against phytopathogenic fungi. Fitopatología Brasileira. 1986;11.

Electronic Publications

  1. Aramayo R. Fasta_GFF3_Equalizer_Bash. In: https://doi.org/10.5281/zenodo.11396812, editor. Zenodo. v1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  2. Aramayo R. Assessing the Influence of Sequence Duplications and Genome Annotations on Transcriptional Profiling Measurements. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  3. Aramayo R. Busco_Plot. In: https://doi.org/10.5281/zenodo.10945685, editor. Zenodo. v1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  4. Aramayo R. Fasta_Seq_Prepare_Bash. In: https://zenodo.org/doi/10.5281/zenodo.10905863, editor. Zenodo. v1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  5. Aramayo R. Fasta_Seq_Plot_Bash. In: https://zenodo.org/doi/10.5281/zenodo.10892498, editor. Zenodo. v1.0.2 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  6. Aramayo R. PepStats_Tables_Python. In: https://zenodo.org/doi/10.5281/zenodo.10889791, editor. Zenodo. v1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  7. Aramayo R. PepStats_Tables_Bash. In: https://zenodo.org/doi/10.5281/zenodo.10888521, editor. Zenodo. v1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  8. Gallucci JL, Aramayo R. Do Public Databases Need Higher Standards for Next-Generation Data Submissions? In: https://zenodo.org/doi/10.5281/zenodo.7943044, editor. Zenodo. DOI: 10.5281/zenodo.7943045 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2023.
  9. Aramayo R. Computational_Genomics. In: https://zenodo.org/doi/10.5281/zenodo.6625427, editor. Zenodo. v2023-1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2023.
  10. Aramayo R. Compara_lists. In: https://zenodo.org/doi/10.5281/zenodo.6582472, editor. Zenodo. v1.0.1 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2022.
  11. Aramayo R. Bioinformatics_Fall_2021. In: https://zenodo.org/doi/10.5281/zenodo.6618284, editor. Zenodo. v2021-1.0.2 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2022.
  12. Aramayo R. Computational_Genomics. In: https://doi.org/10.5281/zenodo.6628964, editor. Zenodo. v2023-1.0.2 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2022.
  13. Aramayo R. Teaching Computational Genomics: A Tale of Tables and Tests. In: https://zenodo.org/doi/10.5281/zenodo.6634706, editor. Zenodo. v1 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2022.
  14. Aramayo R. A Re-Analysis of an Existing Drosophila melanogaster Dataset Reveals a New Set of Genes Involved in Post-Mating Response. In: https://zenodo.org/doi/10.5281/zenodo.6685976, editor. Zenodo. v2022-09-06 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2022.
  15. Aramayo R. Digital_Biology. In: https://zenodo.org/doi/10.5281/zenodo.6626235, editor. Zenodo. v2022-1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2022.
  16. Aramayo R. Myxococcus xanthus DZ2 Genome Assembly. In: https://zenodo.org/doi/10.5281/zenodo.6359693, editor. Zenodo. v1.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2022.