The Institute for Systems Biology Publications

ELECTRONIC/SOFTWARE PUBLICATIONS

Jurka J, Smit AFA.
"Reference collections of human and rodent repetitive elements." URL: http://www.girinst.org/
Co-editor of the mammalian databases. (1994-2005)

Smit AFA.
"RepeatMasker."
URL: http://www.repeatmasker.org
(1996-2005)

JOURNALS

2005

Churakov G, Smit AF, Brosius J, and Schmitz J.
"A Novel Abundant Family of Transposable Elements (DAS-SINEs) in The Nine-Banded Armadillo (Dasypus novemcinctus)."
Mol Biol Evol. 22:886-93. (2005)

The Chimpanzee Sequencing and Analysis Consortium
"Initial sequence of the chimpanzee genome and comparison with the human genome."
Nature 437 (7055), 69-87. (2005)

Khan H, Smit AF, and Boissinot S.
"Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates."
Genome Res 15, in press (2005)

2004

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, and Miller W.
"Aligning multiple genomic sequences with the threaded blockset aligner."
Genome Res 14: 708-15. (2004)

Hillier LW, Miller W, Birney E, Warren W, Hardison R, Ponting CP, Bork P, Burt DW,? Pevzner PA, Smit AF, Fulton, LA, Mardis ER, and Wilson, RK.
"Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution."
Nature 432: 695-716. (2004)

Yang, S., A.F. Smit, S. Schwartz, F. Chiaromonte, K.M. Roskin, D. Haussler, W. Miller, and R.C. Hardison.;
"Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes."
Genome Res 14: 517-527. (2004)

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren E.J, Scherer S, Scott G, Worley KC, et al.
"Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
Nature 428: 493-521. (2004)

2003

Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, ? De Jong PJ, Lawrence CE., Smit AF, Chakravarti A, Haussler D, Green P, Miller W, and Green ED.
"Comparative analyses of multi-species sequences from targeted genomic regions."
Nature 424: 788-93. (2003)

Schwartz, S., W.J. Kent, A. Smit, Z. Zhang, R. Baertsch, R.C. Hardison, D. Haussler, and W. Miller.
"Human-mouse alignments with BLASTZ."
Genome Res 13: 103-107. (2003b)

Schwartz, S., L. Elnitski, M. Li, M. Weirauch, C. Riemer, A. Smit, E.D. Green, R.C. Hardison, and W. Miller.
"MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences."
Nucleic Acids Res 31: 3518-3524. (2003a)

Hardison, R.C., K.M. Roskin, S. Yang, M. Diekhans, W.J. Kent, R. Weber, L. Elnitski, J. Li, M. O'Connor, D. Kolbe, S. Schwartz, T.S. Furey, S. Whelan, N. Goldman, A. Smit, W. Miller, F. Chiaromonte, and D. Haussler.
"Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution."
Genome Res 13: 13-26. (2003)

2002

Waterston, RH, et al.
"Initial sequencing and comparative analysis of the mouse genome."
Nature. 420(6915):5 20-62. (2002)

Aparicio, S, et al.
"Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes."
Science 297(5585): 1301-10. (2002)

Smit AFA
"Initial survey of interspersed repeats in Takifugu rubripes."
RepBase Reports 1(2). (2002)

Lane RP, Roach JC, Lee IY, Boysen C, Smit AF, Trask BJ, and Hood L.
"Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor alpha/delta loci."
Genome Res 12(1): 81-7. (2002)

2001

Glusman G, Rowen L, Lee I, Boysen C, Roach JC, Smit AF, Wang K, Koop BF, and Hood L.
"Comparative genomics of the human and mouse T cell receptor loci."
Immunity 15(3): 337-49. (2001)

Lander E.S, et al.
"Initial sequencing and analysis of the human genome."
Nature 409(6822): 860-921. (2001)

2000

Smit AFA, Mushegian AR.
"Biosynthesis of terpenoids via mevalonate in archaea: the lost pathway."
Genome Res. 10(10) 1468-84. (2000)

Schwartz S, Zhang Z, Frazer K, Smit AFA, Riemer C., Bouck J, Gibbs R, Hardison R, Miller W.
"Pipmaker - a web server for aligning two genomic DNA sequences."
Genome Res.: 10(4) 577-586.. (2000)

1999

Moore R, Lee IY, Silverman G, Harrison PM, Strome R, Heinrich C, Karunaratne A,et al.
"Ataxia in prion protein (PrP) deficient mice associated with upregulation of the novel PrP-like protein doppel."
J. Mol. Biol.: 292 (4) 797-817. (1999)

Smit AFA.
"Interspersed repeats and other mementos of transposable elements in the human genome."
Curr. Opin. Genet. Devel.: 9 (6), 657-63. (1999)

Smit, A. F.
"Interspersed repeats and other mementos of transposable elements in mammalian genomes."
Curr Opin Genet Dev 9: 657-63. (1999)

1998

Lee, I. Y., Westaway, D., Smit, A. F., Wang, K., Seto, J., Chen, L., Acharya, C., Ankener, M., Baskin, D., Cooper, C., Yao, H., Prusiner, S. B., and Hood, L. E.
"Complete genomic sequence and analysis of the prion protein gene region from three mammalian species."
Genome Res 8: 1022-37. (1998)

1997

Jurka J, Kapitonov V, Klonowski, P, Walichiewicz J, Smit AFA
"Identification of new medium reiteration frequency repeats in the human, rodent and rabbit genomes."
Genetica: 98 (3) 235-247. (1997)

1996

Smit, A. F.
"The origin of interspersed repeats in the human genome."
Curr Opin Genet Dev 6: 743-8. (1996)

Smit, A. F., and Riggs, A. D.
"Tiggers and other DNA transposon fossils in the human genome."
Proc Natl Acad Sci USA 93: 1443-8. (1996)

1995

Smit, A. F., Toth, G., Riggs, A. D., and Jurka, J.;
"Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences.";
J Mol Biol 246: 401-417. (1995)

Smit AFA, Riggs AD.
"MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation."
Nucleic Acids Res.: 23(1), 98-102. (1995)

1993

Smit A.F.A.;
"Identification of a new, abundant superfamily of mammalian LTR-transposons";
Nucleic Acids Res 21: p. 1863-72 (1993)

Institute for Systems Biology
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