Bokman, A.H., Levine, H.B. and M. Lusby (nee Riley): Glucose Catabolism in Malleomyces pseudomallei, J. Bact., 73:649-654 (1957).

Lusby, M. (nee Riley) and Levine, H.B.: An intracellular motality enhancing material from Malleomyces pseudomallei, J. Immunol., 80:446-453 (1958).

Riley, M., Pardee, A.B. Jacob, F. and Monod, J.: On the expression of a structural gene., J. Mol. Biol., 2:2l6-255 (1960).

Rushitzky, G.W., Riley, M., Prestidge, L.S. and Pardee, A.B.: Inactivation of enzyme formation by UV light. Biochim. Biophys., Acta, 45:70-76 (1960).

Riley, M. and Pardee, A.B.: Beta-galactosidase formation following decay of P32 in Escherichia coli zygotes., J. Mol. Biol., 5:63-75 (1962).

Riley, M. and Pardee, A.B.: Nutritional effects on frequencies of bacterial recombination., J. Bacteriol., 83:1332-1335 (1962).

Riley, M. and Pardee, A.B.: Gene expression: Its specificity and regulation., Ann. Rev. Microbiol., l3:l-34 (1962).

Gartner, T.K. and M. Riley: Genetic analysis of tryptophanase mutants of Escherichia coli, J. Bacteriol., 89:319-325 (1965).

Gartner, T.K. and Riley, M.: Isolation of mutants affecting tryptophanase production in Eschericha coli., J. Bacteriol., 89:3l3-3l8 (1965).

Oppenheim, A.B. and Riley, M.: Molecular recombination following conjugation in Escherichia coli., J. Mol. Biol., 20:33l-357 (1966).

Riley, M., Maling, B. and Chamberlin, M.J.: Physical and chemical characterization of two- and three-stranded adenine-thymine and adenine-uracil homopolymer complexes., J. Mol. Biol., 20:359-389 (1966).

Oppenheim, A.B. and Riley, M.: Covalent union of parental DNA's following conjugation in Escherichia coli., J. Mol. Biol., 28:503-511 (1967).

Riley, M. and Paul, A.V.: Two- and three-stranded complexes containing homopolymers polyriboadenylic acid and polyribobromouridylic acid., J. Mol. Biol., 50:439-455 (1970).

Riley, M. and Paul, A.V.: Properties of synthetic polydeoxyribonucleotide complexes containing adenine and bromouracil., Biochemistry, 10:3819-3825 (1971).

Ehrlich, M. and Riley, M.: Photolysis of polyribobromouridylic acid., Photochem. & Photobiol., 16:385-395 (1972).

Ehrlich, M. and Riley, M.: Oligonucleotide photoproducts formed by photolysis of polyribobromouridylic acid., Photochem. & Photobiol., 163:397-412 (1972).

Paul, A.V. and Riley, M.: Joint molecule formation following conjugation in wild type and mutant Escherichia coli recipients., J. Mol. Biol., 81:1-22 (1973).

Ehrlich, M. and Riley, M.: Effect of base sequence on the ultraviolet irradiation products of double stranded polynucleotides containing bromouracil and adenine., Photochem. & Photobiol., 20:159-165 (1974).

Zipkas, D. and Riley, M.: Proposal concerning mechanism of evolution of the genome of Escherichia coli, Proc. Natl. Acad. Sci. USA, 72:1354-1358 (1975).

Zipkas, D. and Riley, M.: Simplified method for interruption of conjugation in Escherichia coli., J. Bact., 126:559-560 (1976).

Anilionis, A. and Riley, M.: Conservation and variation of nucleotide sequences I. E. coli strains., J. Bacteriol., 143:355-365 (1978).

Riley, M. and Anilionis, A.: Evolution of the bacterial genome., Ann. Rev. Microbiol., 32:519-560 (1978).

Zipkas, D., Solomon, L. and Riley, M.: Relationship between gene function and gene location in Escherichia coli., J. Mol. Evol., 11:47-56 (1978).

Anilionis, A., Ostapchuk, M. and Riley, M. : Identification of a second cryptic lambdoid prophage in the E. coli K-12 genome., Mol. Gen. Genet. , 180:479-481 (1980).

Harshman L. and Riley, M.: Conservation and variation of nucleotide sequences in Escherichia coli strains isolated from nature, J. Bacteriol., 144:560-568 (1980).

Ostapchuk, M., Anilionis, A. and Riley, M.: Conserved genes in enteric bacteria are not identical., Mol. Gen. Genet., 180:475-477 (1980).

Riley, M.: Evolution of the bacterial genome., Stadler Genetics Symposium, 12:9-32 (1980).

Riley, M. and A. Anilionis: Conservation and variation of nucleotide sequences II. Enterobacteria., J. Bacteriol., 143:366-376 (1980).

Lampel, K. and Riley, M.: Discontinuity of homology of Escherichia coli and Salmonella typhimurium DNA in the lac region., Mol. Gen. Genet. , 186:82-86 (1982).

MacDonald, C. and Riley, M.: Cloning chromosomal lac genes of Klebsiella pneumoniae., Gene, 24:341-345 (1983).

Riley, M. and Glansdorff, N. : Cloning the Escherichia coli Kl2 argD gene specifying acetylornithine ?-transaminase., Gene, 24:335-339 (1983).

Buvinger, W.E., Lampel, K.A., Bojanowski, R.J. and Riley,M.: Location and analysis of nucleotide sequences at one end of a putative lac transposon in the Escherichia coli chromosome., J. Bacteriol, 159:618-623 (1984).

Riley, M.: Arrangement and rearrangement of bacterial genomes., in Microorganisms as Model Systems for Studying Evolution , ed. R.P. Mortlock, Plenum Press, N.Y., 285-315 (1984).

Riley, M., O'Reilly, C. and McConnell, D.: Physical map of Salmonella typhimurium LT2 DNA in the vicinity of the proA gene., J. Bacteriol, 157:655-657 (1984).

Buvinger, W.E. and Riley, M.: Nucleotide sequenceof Klebsiella pneumoniae lac genes., J. Bacteriol, 163:850-857 (1985).

Buvinger, W.E. and Riley, M.: Regulatory region of the divergent Klebsiella pneumoniae lac operon, J. Bacteriol., 163:858-862 (1985).

Riley, M.: Discontinuous processes in the evolution of the bacterial genome., in Evolutionary Biology, ed. M. Hecht, G. Prance, B. Wallace, Plenum Press, N.Y., 1-36 (1985).

Riley, M. and S. Krawiec: Genome organization, in Escherichia coli and Salmonella typhimurium, ed. J. Ingraham, K.B. Low, B. Magasanik, F. Neidhardt, M. Schaechter and H.E. Umbarger, American Society for Microbiology, Washington, D.C., 967-981 (1987).

Riley, M.: Constancy and change in bacterial genomes., in Bacteria in Nature, ed. J. Poindexter and E.R. Leadbetter, Plenum Press, N.Y., 359-388 (1989).

Drlica, K. and M. Riley: An historical introduction to the bacterial chromosome, (1990).

Riley, M. and K. Sanderson: Comparative genetics of Escherichia coli and Salmonella typhimurium., in The Bacterial Chromosome, ed. K. Drlica and M. Riley, American Society for Microbiology, Washington, D.C., 85-95 (1990).

Riley, M. and S. Krawiec: Organization of the bacterial chromosome., Microbiol. Rev., 54:502-539 (1990).

Riley, M.: The E. coli chromosome: A mosaic., in Perspectives in Cellular Regulation: Fr: Bacteria to Cancer, Marine Biol. Lab. Lecture Series, Wiley-Liss Publishing Co., New York, 3-15 (1991).

Riley. M.: Locations of bacterial genes., in Encyclopedia of Microbiology, ed. J. Lederberg, Academic Press, NY, 3758-3774 (1992).

Karp, P. and M. Riley : Representations of Metabolic Knowledge, in Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, ed. L. Hunter, D. Searls and J. Shavlik, AAI Publishers, Menlo Park, CA, (1993).

M. Riley: Functions of the gene products of E. coli., Microbiological Reviews, 57:862-952 (1993).

B. Labedan, M. Riley: Widespread protein sequence similarities: Origins of Escherichia coli genes., J. Bacteriol., 177:1585-1588 (1995).

B. Labedan, M. Riley: Gene products of Escherichia coli: Sequence comparisons and common ancestries., Mol. Biol. Evol., 12:980-987 (1995).

M. Riley and B. Labedan: E. coli gene products: Physiological functions and common ancestries., in Escherichia coli and Salmonella: Cellular and Molecular Biology, ed. F. Neidhardt, R. Curtiss,III, E.C.C. Lin, J. Ingraham, K. B. Low, B. Magasanik, , W. Reznikoff, M. R, ASM Press, Washington, D.C., 2118-2202 (1996).

M. Riley and D. Space: Genes and Proteins of Escherichia coli (GenProtEc)., Nucl. Acids Res., 24:40 (1996).

P. Karp, M. Riley, S. Paley, and A. Pellegrini-Toole: Ecocyc: Electronic encyclopedia of E. coli genes and metabolism., Nucl. Acids Res, 24:32-39 (1996).

Blattner, F. R., G. Plunkett III, C.A. Bloch, N.T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. Mayhew, J. Gregor, N. W. Davis, H.A. Kirkpatrick, M. Goeden, D. Rose, B. Mau, and Y. Shao: The complete genome sequence of Escherichia coli K-12, Science, 277(5331):1453-1462 (1997).

M. Riley: Genes and Proteins of Escherichia coli K-12 (GenProtEC)., Nucl. Acids Res., 25:51-52 (1997).

P. Karp, M. Riley, S. Paley, A. Pellegrini-Toole and M. Krummenacker: EcoCyc: Encyclopedia of Escherichia coli genes and metabolism., Nucleic Acids Res., 25:43-50 (1997).

Riley, M., B. Labedan: Protein evolution viewed through Escherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module, J. Mol. Biol., 268:857-868 (1997).

Karp, P.D., M. Riley, S.M. Paley, A. Pellegrini-Toole and M. Krummenacker: EcoCyc: Encyclopedia of Escherichi coli genes and metabolism, Nucl. Acids. Res., 26:50-53 (1998).

Moxon, E.R. and M. Riley: Editorial overview, Current Opinion in Microbiology, 1:559-561 (1998).

Riley, M.: Genes and proteins of Escherichia coli K-12 (GenProtEC), Nucl. Acids. Res., 26:54 (1998).

Riley, M.: E. coli genes: Ancestries and map locations, in Bacterial Genomes: Physical Structure and Analysis, ed. F.J. de Bruijn, J.R. Lupski and G. Weinstock, Chapman and Hall, New York, 187-195 (1998).

Riley, M.: Systems for categorizing functions of gene products, Current Opinion in Structural Biology, 8:388-392 (1998).

Karp, P.D., M. Riley, S.M. Paley, A. Pellegrini-Toole and M. Krummenacker: EcoCyc: Encyclopedia of Escherichia coli genes and metabolism, Nucl. Acids. Res., 27:55-58 (1999).

Labedan, B and M. Riley: Genetic inventory: Escherichia coli as a window on ancestral proteins, in Organization of the Prokaryotic Genome, ed. R. Charlebois, ASM Press, Washington, D.C., 311-329 (1999).

Riley, M.: Correlates of smallest sizes for microorganisms, in Size Limits of Very Small Organisms: Proceedings of a Workshop, National Academy of Sciences, Washington, D.D., 21-25 (1999).

Karp, P.D., M. Riley, M. Saier, I.T. Paulsen, S.M. Paley and A. Pellegrini-Toole: The EcoCyc and MetaCyc databases, Nucl. Acids. Res., 28:56-59 (2000).

Liang P., M. H. Serres and M. Riley: Genes and Proteins of Escherichia coli K-12 (GenProtEC), Nucl. Acids. Res., (2000). Link >>

Ng, W. V., S.P. Kennedy, G.G. Mahairas, B. Berquist, M. Pan, H.D. Shukla, S.R. Lasky, N.S. Baliga, V. Thorsson, J. Sbrogna, S. Swartzell, D. Weir, J. Hall, T.A. Dahl, R. Welti, Y.A. Goo, B. Leithauser, K. Keller, R. Cruz, M.J. Danson, D.W. Hough, D.G. Maddocks, P.E. Jablonski, M.P. Krebs, C.M. Angevine, H. Dale, T.A. Isenbarger, R.F. Peck, M. Pohlschroder, J.L. Spudich, K.W. Jung, M. Alam, T. Freitas, S. Hou, C.J. Daniels, P.P. Dennis, A.D. Omer, H. Ebhardt, T.M. Lowe, P. Liang, M. Riley, L. Hood, S. DasSarma: Genome sequence of Halobacterium species NRC-1, PNAS, 97:12176-12181 (2000).

Riley, M. and M. Serres: Genomics and Metabolism in Escherichia coli, in The Prokaryotes, Springer-Verlag, New York, (2000). Link >>

Serres, M. and M. Riley: Interim report on genomics of E. coli, Ann. Rev. Microbiol., 54:341-411 (2000).

Liang, P. and M. Riley : A comparative genomics approach for studying ancestral proteins and evolution, Advances in Applied Microbiology , 50:39-72 (2001).

Nahum, L. and M. Riley: Divergence of function in sequence-related groups of Escherichia coli proteins, Genome Research, 11:1375-1381 (2001).

Serres, M. and M. Riley : MultiFun, a multifunctional classification scheme for Escherichia coli K-12, Microbial and Comparative Genomics, 5(4):205-222 (2001).

Serres, M.H., M. Gopal, L. Nahum, T., P. Liang, T. Gaasterland and M. Riley : A functional update of the E. coli K-12 genome, Genome Biology , 2(9):research0035.1-0035.7. Data included in (2001). Link >>

Teichmann, S.A., S. Rison, J. Thornton, M. Riley, J. Gough and C. Chothia: The evolution and structural analtomy of the small molecule metabolic pathways in Escherichia coli, J. Mol. Biol., 311:693-708 (2001).

Teichmann, S.A., S. Rison, J. Thornton, M. Riley, J. Gough and C. Chothia: Small molecule metabolism: an enzyme mosaic, Trends in Biotechnology, 19:482-486 (2001).

Karp P.D., M. Riley, M. Saier, I.T. Paulsen, J. Collado-Vides, S.M. Paley, A. Pellegrini-Toole, C. Bonavides and S. Gama-Castro: The EcoCyc Database, Nucleic Acids Res., 30:56-58 (2002).

Karp P.D., M. Riley, S.M. Paley, A. Pellegrini-Toole: The MetaCyc Database, Nucleic Acids Res., 30:59-61 (2002).

Liang, P., B. Labedan and M. Riley : Physiological genomics of E. coli protein families, Physiological Genomics, 9:15-26 (2002).

Voit E.O. and M. Riley: Extending knowledge of Escherichia coli metabolism by modeling and experiment, Genome Biology, 4(11):235 (2003).

Serres M.H. and M. Riley: Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome, OMICS, 8:306-321 (2004).

Serres M.H., S. Goswami and M. Riley: GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins, Nucleic Acids Res., 32:D300-2 (2004).

Dhillon, A., S. Goswami, M. Riley, A. Teske, and M.L. Sogin: Domain Evolution and Functional Diversification of Sulfite Reductases, Astrobiology , 5(1):18-29 (2005).

Kolker E, A.F. Picone, M.Y. Galperin, M.F. Romine, R. Higdon, K.S. Makarova, N. Kolker, G.A. Anderson, X. Qiu, K.J. Auberry, G. Babnigg, A.S. Beliaev, P. Edlefsen, D.A. Elias, Y.A. Gorby, T. Holzman, J.A. Klappenbach, K.T. Konstantinidis, M.L. Land, M.S. Lipton, L.A. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, M.H. Serres, S. Tsapin, B.A. Zakrajsek, W. Zhu, J. Zhou, F.W. Larimer, C.E. Lawrence, M. Riley, F.R. Collart, J.R. Yates 3rd, R.D. Smith, C.S. Giometti, K.H. Nealson, J.K. Fredrickson, J.M. Tiedje: Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations, Proc Natl Acad Sci USA, 102:2099-2104 (2005).

Serres, M.H. and M. Riley: Gene fusions and gene duplications: relevance to genomic annotation and functional analysis, BMC Genomics, 6:33-40 (2005).

Riley M., Staley J.T., Danchin A., Wang T., Brettin T.S., Hauser L.J., Land M.L., Thompson L.S. Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics. 2008 May 6;9(1):210 PMID: 18460197.