A. Mira. Why is Meiosis Arrested?. Journal of Theoretical Biology. 1998.
  D. Krakauer, A. Mira. Mutation, mitochondria and atresia. Nature, 1999
  A. Mira. Exuviae eating: a nitrogen meal?. Journal of Insect Physiology, 1999
  D. Krakauer, A. Mira. Mitochondria and the death of oocytes. Nature, 2000
  A. Mira, H. Ochman, N. A. Moran. Deletional bias and the evolution of bacterial genomes. Trends in Genetics, 2001
  N. A. Moran, A. Mira. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biology, 2001
  A. Mira, E.A. Bernays. Trade-offs in host use by Manduca sexta: host characters vs natural enemies. Oikos, 2002
  A. Mira, N.A. Moran. Estimating population size and transmisión bottlenecks in maternally-transmitted endosymbionts. Microbial Ecology, 2002
  A. Mira, H.Ochman. Gene location and bacterial sequence divergence. Molecular Biology and Evolution, 2002.
  A. Mira, D. Raubenheimer. Divergent nutrition-related adaptations in two cockroach populations inhabiting different environments. Physiological Entomology, 2002.
  A. Mira, L. Klasson,S.G.E. Andersson. Microbial genome evolution: sources of variability. Current Opinión in Microbiology, 2002.
  S.G.E. Andersson, C. Alsmark, B. Canback, W. Davids, C. Frank, O. Karlberg, L. Klasson, A. Mira and I. Tamas. Comparative Genomics of microbial pathogens and symbionts. Bioinformatics, 2003.
  Pushker R., A. Mira, F. Rodríguez Valera. Comparative genomics of gene family size in closely related bacteria. Genome Biology , 2004.
  A. Mira, R. Pushker, B.A. Legault, D. Moreira, F. Rodríguez Valera. Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evolutionary Biology, 2004.
  H. Lindroos, A. Mira, D. Repsilber, O. Vinnere, M. Dehio, K. Näslund, C. Dehio, S.G.E. Andersson. Characterization of the genome composition of Bartonella koehlerae by microarray CGH profiling. Journal of Bacteriology, 2005.
  A. Mira, R. Pushker. The silencing of pseudogenes. Molecular Biology and Evolution, 2005.
  D. Repsilber, A. Mira, H. Lindroos, K. Näslund, S.G.E. Andersson. Data-rotation improves genomotyping efficiency. Biometrical Journal, 2005.
  A. Mira, R. Pushker, F. Rodriguez-Valera. The Neolithic revolution of bacterial genomes. Trends in Microbiology 14: 200-206, 2006.
  A. Mira, R. Pushker. Genome architecture and the evolution of bacterial pathogens. In: ?Introduction to Evolutionary Biology of Bacterial and Fungal Pathogens? (F. Baquero, C. Nombela, G.H. Cassell and J.A. Gutiérrez, Eds.). ASM Press. Chapter 13, 2007.
  H. Lindroos, Olga Vinnere, Alex Mira, Dirk Repsilber, Alix Boulouis, Kristina Näslund, Siv G.E. Andersson. Genome Rearrangements, Deletions and Amplifications in the Natural Population of Bartonella henselae. Journal of Bacteriology, 2006.
  A. Mira. Horizontal gene transfer in oral bacteria. In: ?Oral Molecular Microbiology? (A.H. Rogers, editor). Horizon Scientific Press. Chapter 3. 2007.
  López-López A., Benlloch, S, Rodríguez-Valera, F., Alex Mira. Intragenomic 16S rRNA divergence in Haloarcula marismortui is an adaptation to different environmental conditions. J Molecular Evolution, 2007.
  G. Sanchez-Perez*, A. Mira*, G. Nyiro, L. Pasic and F. Rodriguez-Valera. Adapting to environmental changes by specialized paralogs. Trends in Genetics, 2008.
  Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME Journal, 2008.
  J. Tamames, A. Mira. Horizontal Gene Transfer in Natural Communities. In: ?Metagenomics: Theory, Methods, and Applications? (D. Marco, editor). Horizon Press. Chapter 4, 2009.
  Rodriguez-Valera, A.B. Martín-Cuadrado, B. Rodríguez-Brito, F. Thingstad, F. Rohwer and A. Mira. Explaning bacterial population genomics through phage predation. Nature Reviews Microbiology, 2009.
  Diana L Williams, Richard A Slayden, Amol Amin, Alejandra N Martinez, Tana L Pittman, Alex Mira, Anirban Mitra, Valakunja Nagaraja, Norman Morrison, Milton Moraes and Thomas P. Gillis. Implications of high level pseudogene transcription in Mycobacterium leprae. BMC Genomics, 2009.
  Beltran Rodriguez-Brito, LinLin Li, Linda Wegley, Mike Furlan, Florent Angly, Mya Breitbart, John Buchanan, Christelle Desnues, Elizabeth Dinsdale, Robert Edwards, Ben Felts, Dana Willner, Matthew Haynes, Hong Liu, David Lipson, Joseph Mahaffy, Anna Belen Martin-Cuadrado, Alex Mira, Jim Nulton, Lejla Pasic, Steve Rayhawk, Jennifer Rodriguez-Mueller, Francisco Rodriguez-Valera, Peter Salamon, Shailaja Srinagesh, Tron Frede Thingstad, Tuong Tran, Rebecca Vega Thurber, Merry Youle, Forest Rohwer.Viral and microbial community dynamics in four aquatic environments. ISME Journal 4(6): 739-751, 2010.
  Pasic L, Rodriguez-Mueller B, Martin-Cuadrado AB, Mira A, Rohwer F, Rodriguez-Valera F. Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. BMC Genomics 10:570, 2009.
  Zilm P.S., Mira A., C.J. Bagley, Rogers A.H. The effect of alkaline growth pH on the expression of cell envelope proteins in Fusobacterium nucleatum. Microbiology SGM 156 (6): 1786-1794, 2009.
  R. Ghai, A.B. Martin-Cuadrado, A. Gonzaga-Molto, I. García-Heredia, R. Cabrera, J. Martin, M. Verdú, P. Deschamps, D. Moreira, P. López-García, A. Mira, F. Rodriguez-Valera. The deep chlorophyll maximum of the Mediterranean metagenome studied by direct and fosmid library 454 pyrosequencing. ISME Journal 4(9): 1154-1166, 2010.
  Alex Mira, A.B. Martin-Cuadrado, G. D'Auria, F. Rodriguez-Valera. The microbial pan-genome: A new paradigm in Microbiology. International Microbiology 13: 45-57, 2010.