Brunner, S., Pea, G. and Rafalski, A.
Origins, Genetic Organization and Transcription of a Family of Non-Autonomous Helitron Elements in Maize 
Plant J. 2005 Sep;43(6):799-810.

Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A.
Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize.
Nat Genet. 2005 Sep;37(9):997-1002. Epub 2005 Jul 31.

Stephan Brunner, Kevin Fengler, Michele Morgante, Scott Tingey, and Antoni Rafalski
Evolution of DNA Sequence Nonhomologies among Maize Inbreds
Plant Cell;17 (2005) 343-360.

Jung, M; Ching, A; Bhattramakki, D; Dolan, M; Tingey, S; Morgante, M; Rafalski, A
Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm
Theoretical and Applied Genetics 109 (2004) 681-689

Palaisa, K, Morgante, M., Tingey, S. and Rafalski, A.
Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep.
Proc. Natl. Acad. Sci. USA, 101 (2004) 9885-9890.

Rafalski, A. and Morgante, M.
Corn and humans: recombination and linkage disequilibrium in two genomes of similar size.
Trends in Genetics, 20 (2004) 103-111.

Palaisa, K, Morgante, M., Williams, M. and Rafalski, A.
Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci.
The Plant Cell 15 (2003) 1795-1806.

Ching, A and Rafalski, A.
Rapid Genetic Mapping of ESTs Using SNP Pyrosequencing and Indel Analysis
Cellular and Molecular Biology Letters 7 (2002) 803-810

J.-M. Lee, M.E. Williams, S.V. Tingey and J.A. Rafalski
DNA Array Profiling of Gene Expression Changes During Maize Embryo Development
Functional and Integrative Genomics 2 (2002) 13-27

Ching, A and Rafalski, A
Rapid EST Mapping and SNP Genotyping of Individuals Using Pyrosequencing
Maize Genetics Newsletter 76 (2001) paper 29.
http://www.agron.missouri.edu/mnl/76/29ching.html

Rafalski, A
Book Review: Molecular techniques in crop improvement. Pant Science 163 (2002) 1073

Rafalski, A.
Book Review: PCR Cloning Protocols. Plant Science 163 (2002) 1073

Rafalski, A.
Applications of Single Nucleotide Polymorphisms in Crop Plant Genetics
Current Opinion in Plant Biology 5(2002) 94-100.

Rafalski, A.
Plant Genomics: Present State and A Perspective on Future Developments
Briefings in Functional Genomics and Proteomics 1 (2002) 80-94.

Rafalski, A.
Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Science 162 (2002) 329-333.

Ching, A., Caldwell, K., Jung, M., Dolan, M., Smith, H., Tingey, S., Morgante, M. and Rafalski, A.
SNP frequency and haplotype structure of 18 maize genes. BMC Genetics 2002, 3:19 (7Oct2002)

Bhattramakki, D., Dolan, M., Hanafey, M., Wineland, R., Vaske, D., Register III, J.C., Tingey, S.V. and Rafalski, A.
Insertion-Deletion Polymorphisms in 3’-Regions of Maize Genes Occur Frequently and Can Be Used as Highly Informative Genetic Markers. Plant Mol.Biol. 48 (2002) 539-547.

Rafalski, A.
Book Review: Plant’s Fingerprints - Plant Genotyping, The DNA Fingerprinting of Plants. R.J. Henry, Ed. CABI Publishing 2001, Trends in Biotechnology 20 (2002) 133

Rafalski, A.
Book Review: DNA –based Markers in Plants, 2nd Edition,  Plant Science 161 (2001) 1039-1040.

Van Dyk, T. K., G. E. Gonye M. J. G. Reeve, E. J. DeRose, M. Dolan, M. K. Hanafey, Y. Wei, J. A. Rafalski, and R. A. LaRossa. 2001. Genome-wide expression profiling with luxCDABE gene fusions, p. 461-464. In J. Case, P. Herring, B. Robison, S. Haddock, L. Kricka, and P. Stanely (ed.), Proceedings of the 11th International Symposium on Bioluminescence and Chemiluminescence. World Scientific, Singapore.

Bhattramakki, D. and Rafalski, A.
Discovery and application of single nucleotide polymorphism markers in plants. In: Plant Genotyping: The DNA Fingerprinting of Plants. R. J. Henry, Ed. CABI Publishing, Wallingford Oxon, UK, 2001.

Van Dyk TK, Wei Y, Hanafey MK, Dolan M, Reeve MJ, Rafalski JA, Rothman-Denes LB, LaRossa RA. A genomic approach to gene fusion technology. Proc Natl Acad Sci U S A. 2001, 98, 2555-60.

Wei, Y, Lee, J.-M., Richmond, C., Blattner, F.R., Rafalski, J.A. and LaRossa, R.A.
High Density Microarray-Mediated Gene Expression Profiling of Escherichia coli
J.Bact. 2001, 183, 545-556.

Tarchini, R., Biddle, P., Wineland, R., Tingey, S. and Rafalski, A.
The Complete Sequence of 340 kb of DNA around the Rice Adh1-Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4
The Plant Cell 2000, 12, 381-391.

Jia MH, Larossa RA, Lee JM, Rafalski A, Derose E, Gonye G, Xue Z.
Global expression profiling of yeast treated with an inhibitor of amino acid
biosynthesis, sulfometuron methyl.
Physiol Genomics. 2000 Aug 9;3(2):83-92.

deBarros EG,Tingey S,Rafalski JA
Sequence characterization of hypervariable regions in the soybean genome: leucine-rich repeats and simple sequence repeats.
Genet. Mol. Biol. 2000; 23, 411-415

Rafalski JA, Hanafey M, Miao GH, Ching A, Lee JM, Dolan M, Tingey S.
New experimental and computational approaches to the analysis of gene
expression.
Acta Biochim Pol. 1998;45(4):929-34. Review.

Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A.
Cross-species amplification of soybean (Glycine max) simple sequence repeats
(SSRs) within the genus and other legume genera: implications for the
transferability of SSRs in plants.
Mol Biol Evol. 1998 Oct;15(10):1275-87.

Morgante M, Jurman I, Shi L, Zhu T, Keim P, Rafalski JA.
The STR120 satellite DNA of soybean: organization, evolution and chromosomal
specificity.
Chromosome Res. 1997 Sep;5(6):363-73.

Powell W, Morgante M, Doyle JJ, McNicol JW, Tingey SV, Rafalski AJ.
Genepool variation in genus Glycine subgenus Soja revealed by polymorphic
nuclear and chloroplast microsatellites.
Genetics. 1996 Oct;144(2):793-803.

Shi L, Zhu T, Morgante M, Rafalski JA, Keim P.
Soybean chromosome painting: a strategy for somatic cytogenetics.
J Hered. 1996 Jul-Aug;87(4):308-13.

Powell W, Morgante M, Andre C, McNicol JW, Machray GC, Doyle JJ, Tingey SV,
Rafalski JA.
Hypervariable microsatellites provide a general source of polymorphic DNA
markers for the chloroplast genome.
Curr Biol. 1995 Sep 1;5(9):1023-9.

Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA.
Polymorphic simple sequence repeat regions in chloroplast genomes: applications
to the population genetics of pines.
Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7759-63.

Morgante M, Rafalski A, Biddle P, Tingey S, Olivieri AM.
Genetic mapping and variability of seven soybean simple sequence repeat loci.
Genome. 1994 Oct;37(5):763-9.

Zietkiewicz E, Rafalski A, Labuda D.
Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain
reaction amplification.
Genomics. 1994 Mar 15;20(2):176-83.

Rafalski JA, Tingey SV.
Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines.
Trends Genet. 1993 Aug;9(8):275-80. Review.

Williams JG, Hanafey MK, Rafalski JA, Tingey SV.
Genetic analysis using random amplified polymorphic DNA markers.
Methods Enzymol. 1993;218:704-40. No abstract available.

Reiter RS, Williams JG, Feldmann KA, Rafalski JA, Tingey SV, Scolnik PA.
Global and local genome mapping in Arabidopsis thaliana by using recombinant
inbred lines and random amplified polymorphic DNAs.
Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1477-81.

Williams, JGK, Kubelik, AR, Livak KJ, Rafalski JA, Tingey SV
DNA Polymorphisms Amplified by Arbitrary Primers Are Useful as Genetic Markers
Nucleic Acids Res. 1990 18: 6531-6535