* indicates an undergraduate co-author.
  1. Karnovsky NJ, Brown ZW, Weicker J, Harding AMA, Walkusz W, Cavalcanti ARO, Harding J, Kitaysky A, Gabrielsen G, Gemillet D (2011) Inter-colony comparison of diving behavior of an Arctic top predator: implications for warming in the Greenland Sea. Marine Ecology Progress Series. 440: 229-240. doi: 10.3354/meps09351
  2. Koire AM*, Cavalcanti ARO (2011) A fusion of the subunits _ and _ of succinyl-CoA synthetase as a phylogenetic marker for Pezizomycotina fungi. Genetics and Molecular Biology, 34(4): 669-675.
  3. Salim HMW*, Koire AM*, Stover NA, Cavalcanti ARO (2011) Detection of Fused Genes in Eukaryotic Genomes using Gene deFuser: Analysis of the Tetrahymena thermophila genome. BMC Bioinformatics 12 (1): 279.
  4. Stover NA, Dixon TA*, Cavalcanti ARO (2011) Multiple Independent Fusions of Glucose-6-Phosphate Dehydrogenase with Enzymes in the Pentose Phosphate Pathway. PLoS ONE 6(8): e22269. doi:10.1371/journal.pone.0022269
  5. Salim HMW*, Negritto MC, Cavalcanti ARO (2009) 1+1=3: A Fusion of 2 Enzymes in the Methionine Salvage Pathway of Tetrahymena thermophila Creates a Trifunctional Enzyme That Catalyzes 3 Steps in the Pathway. PLoS Genet 5(10):e1000701.
  6. Adachi M*, Cavalcanti ARO (2009) Tandem stop codons in ciliates that reassign stop codons. J Mol Evol. 68(4):424-31.
  7. Möllenbeck M, Zhou Y, Cavalcanti ARO, Jönsson F, Chang WJ, Juranek S, Doak TG, Rozenberg G, Lipps HJ, Landweber LF (2008). The pathway for detangling a scrambled gene. PLOS ONE 3(6):e2330.
  8. Ring KL*, Cavalcanti ARO (2008) Consequences of Stop Codon Reassignment on Protein Evolution in Ciliates with Alternative Genetic Codes. Mol Biol Evol, 25(1): 179-186.
  9. Salim HMW*, Ring KL*, Cavalcanti ARO (2008) Patterns of codon usage in two ciliates that reassign the genetic code: Tetrahymena thermophila and Paramecium tetraurelia. Protist 159(2): 283-298.
  10. Salim HMW*, Cavalcanti ARO (2008) Factors Influencing Codon Usage Bias in Genomes. J Braz Chem Soc, 19: 257-262.
  11. Mollenbeck M, Cavalcanti ARO, Jonsson F, Lipps H, Landweber LF (2006) Interconversion of germline-limited and somatic DNA in a scrambled gene. J Mol Evol. 63(1):69-73.
  12. Cavalcanti ARO, Stover NA, Landweber LF (2006) On the paucity of duplicated genes in Caenorhabditis elegans operons. J Mol Evol. 62(6):765-771.
  13. Stover NA, Kaye MS*, Cavalcanti ARO (2006) Quick Guide: Spliced leader trans-splicing. Curr Biol. 16: R8-R9.
  14. Stover NA, Cavalcanti ARO, Li AJ*, Richardson BC, Landweber LF (2005) Reciprocal fusions of two genes in the formaldehyde detoxification pathway in ciliates and diatoms. Mol Biol Evol. 22: 1539-1542.
  15. Cavalcanti ARO, Clarke TH*, Landweber LF (2005) MDS_IES_DB: A Database of Macronuclear and Micronuclear Genes in Spirotrichous Ciliates. Nucleic Acids Res. 33(Database issue): D396-398.
  16. Liang H, Cavalcanti ARO, Landweber LF (2005) Conservation of tandem stop codons in yeasts. Genome Biol. 6: R31.
  17. Liang H, Wong J*, Bao Q, Cavalcanti ARO, and Landweber LF (2005) Decoding the decoding region: analysis of the eukaryotic release factor (eRF1) stop codon-binding residues. J Mol Evol. 60: 337-344.
  18. Cavalcanti ARO , Stover N, Orecchia L*, Doak TG, Landweber LF (2004) Properties of Oxytricha trifallax nanochromosomes: analysis of a pilot genome project. Chromosoma 113 (2): 69 –76.
  19. Cavalcanti ARO , Doak TG, Landweber LF (2004) Sequence features of Oxytricha trifallax (class Spirotrichia) macronuclear telomeric and subtelomeric sequences. Protist 155: 311–322.
  20. Cavalcanti ARO , Leite ES*, Neto BB, Ferreira R (2004) On the classes of Aminoacyl-tRNA Syntethases, amino acids and the genetic code . Orig Life Evol Biosph 34 (4): 407–420.
  21. Cavalcanti ARO , Landweber LF (2004) Gene Unscrambler – A Program to Study Scrambled Genes in Ciliates. Bioinformatics 20 (5): 800–802.
  22. Cavalcanti ARO , Chang W (2004) Book Review: Computation in Living Cells: Gene Assembly in Ciliates. J Euk Microbiol 51 (4): 459.
  23. Cavalcanti ARO , Landweber LF (2004) Quick Guide: Genetic Code. Curr Biol 14 (4): R147.
  24. Cavalcanti ARO , Landweber LF (2003) Genetic code: what nature missed. Curr Biol 13 (22): R884–885.
  25. Doak TG, Cavalcanti ARO, Stover NA, Dunn DM, Weiss R, Herrick G, Landweber LF (2003) Sequencing the Oxytricha trifallax macronuclear genome: a pilot project. Trends Genet 19 (11): 603–607.
  26. Li WH, Gu Z, Cavalcanti ARO, Nekrutenko A (2003) Detection of gene duplications and block duplications in eukaryotic genomes. J Struct Funct Genomics 3 (1-4): 27–34.
  27. Cavalcanti ARO , Gu Z, Ferreira R, Li WH (2003) Patterns of Gene Duplication in Yeast and Worm. J Mol Evol 56 (1): 28–37.
  28. Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH ( 2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19 (3): 256–262 .
  29. Cavalcanti ARO , Ferreira R (2001) On the Relative Content of G,C Bases in Codons of Amino Acids Corresponding to Class I and II tRNA Synthetases. Orig Life Evol Biosph 31 : 257–269.
  30. Cavalcanti ARO , Neto BB, Ferreira R (2000) On the Classes of Aminoacyl-tRNA Synthetases and the Error Minimization in the Genetic Code. J Theor Biol 204: 15–20.
  31. Cavalcanti ARO , Ferreira R (1998) On the Relative Content of C,G Bases in Codons Corresponding to the Two Classes of Aminoacyl-tRNA Synthetases. An Acad Bras Ci 70 (4): 899–904.
  32. Ferreira R, Cavalcanti ARO (1997) Vestiges of Early Molecular Processes Leading to the Emergence of the Genetic Code. Orig Life Evol Biosph 27: 397–403.
  33. Cavalcanti ARO* , Ferreira R (1995) On the Statistical Distribution of Amino Acid Residues in Randomly Synthesized Peptides. An Acad Bras Ci 67 (4): 401–402.

  35. Stover NA, Cavalcanti ARO (2011) Using NCBI BLAST . In Current Protocols Essential Laboratory Techniques. John Wiley & Sons, Inc. Hoboken, NJ.
  36. Stover NA, Cavalcanti ARO (2009) Using NCBI BLAST. In Current Protocols in Essential Laboratory Techniques, Online supplement. Wiley.
  37. Cavalcanti ARO, Landweber LF (2005) Insights into a biological computer: Detangling scrambled genes in ciliates. in Chen J, Jonoska N, Rozenberg G (Eds.), Nanotechnology: Science and Computation (pp. 349-360). Berlin: Springer-Verlag.

  39. Cavalcanti ARO* , Souza Jr MB (1996) Biological Processes Modeled by Neural Networks. An SINAFERM 11 (a).
  40. Cavalcanti ARO* , Ferreira R (1995) Sobre a Distribuição Estatística de Resíduos de Amino Ácidos em Peptídeos Sintetizados Aleatoriamente. An Acad Bras Ci 67 (3): 396 (in Portuguese).