The Institute for Systems Biology Related Publications


Surya Saha, Susan Bridges, Zenaida V. Magbanua, Daniel G. Peterson
"Empirical comparison of ab initio repeat finding programs"
Nucleic Acids Research 2008 Feb

Surya Saha, Susan Bridges, Zenaida V. Magbanua, Daniel G. Peterson
"Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences"
Tropical Plant Biology 2008 Feb


Bergman CM, Quesneville H.
"Discovering and detecting transposable elements in genome sequences"
Briefings in Bioinformatics 2007 Nov, 8(6):382-92


Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA.
"Identifying repeat domains in large genomes"
Genome Biol: 7(1):R7 (2006)


Alkes L. Price, Neil C. Jones, Pavel A. Pevzner
"De novo identification of repeat families in large genomes"
Bioinformatics: Vol 21, Suppl 1, i351-i358 (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)


Benjamin Raphael, Degui Zhi, Haixu Tang, and Pavel Pezner;
"A novel method for multiple alignments of sequences with repeated and shuffled elements"
Genome Research 14: 2336-2346 (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)

Nagashima, T., H. Matsuda, D.G. Silva, N. Petrovsky, A. Konagaya, C. Schonbach, T. Kasukawa, T. Arakawa, P. Carninci, J. Kawai, and Y. Hayashizaki.
"FREP: a database of functional repeats in mouse cDNAs."
Nucleic Acids Res 32 Database issue: D471-475. (2004)

Rat Genome Sequencing Consortium.
"Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
Nature 428: 493-521. (2004)

Schonbach, C.
"From masking repeats to identifying functional repeats in the mouse transcriptome."
Brief Bioinform 5: 107-117. (2004)

Juretic, N., T.E. Bureau, and R.M. Bruskiewich.
"Transposable element annotation of the rice genome."
Bioinformatics 20: 155-160. (2004)


Robert C. Edgar, Eugene W. Myers.
"PILER: identification and classification of genomic repeats"
Bioinformatics: Vol 1., No 1 (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)

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)

Thomas, J.W., et al.
"Comparative analyses of multi-species sequences from targeted genomic regions."
Nature 424: 788-793. (2003)

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)

Cawley, S., L. Pachter, and M. Alexandersson.
"SLAM web server for comparative gene finding and alignment."
Nucleic Acids Res 31: 3507-3509. (2003)


Zhirong Bao, Sean R. Eddy;
"Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes"; Genome Research: Vol. 12, Issue 8 1269-1276 (2002) Full Text

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)

Vieux, E.F., P.Y. Kwok, and R.D. Miller.
"Primer design for PCR and sequencing in high-throughput analysis of SNPs."
Biotechniques Suppl: 28-30, 32. (2002)

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., and Haussler, D.
"The human genome browser at UCSC."
Genome Res 12: 996-1006. (2002)

Kashuk, C., S. SenGupta, E. Eichler, and A. Chakravarti.
"ViewGene: a graphical tool for polymorphism visualization and characterization."
Genome Res 12: 333-338. (2002)

Aparicio, S., et al.
"Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes."
Science 297: 1301-1310. (2002)

Mouse Genome Sequencing Consortium.
"Initial sequencing and comparative analysis of the mouse genome."
Nature 420: 520-562. (2002)


Glusman, G., and Lancet, D.
"Visualizing large-scale genomic sequences."
IEEE Eng Med Biol Mag 20: 49-54. (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)

International Human Genome Sequencing Consortium
"Initial sequencing and analysis of the human genome. "
Nature 409: 860-921. (2001)

Gemund, C., C. Ramu, B. Altenberg-Greulich, and T.J. Gibson.
"Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries."
Nucleic Acids Res 29: 1272-1277. (2001)

Makalowska, I., J.F. Ryan, and A.D. Baxevanis.
"GeneMachine: gene prediction and sequence annotation."
Bioinformatics 17: 843-844. (2001)

Yeh, R. F., Lim, L. P., and Burge, C. B.
"Computational inference of homologous gene structures in the human genome."
Genome Res 11: 803-16. (2001)


Arnaud, P., Goubely, C., Pelissier, T., and Deragon, J. M.
"SINE retroposons can be used in vivo as nucleation centers for de novo methylation."
Mol Cell Biol 20: 3434-41. (2000)

Bedell, J. A., Korf, I., and Gish, W.
"MaskerAid: a performance enhancement to RepeatMasker."
Bioinformatics 16: 1040-1. (2000)

Esnault, C., Maestre, J., and Heidmann, T.
"Human LINE retrotransposons generate processed pseudogenes."
Nat Genet 24: 363-7. (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)

Glusman, G., and Lancet, D.
"GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses."
Bioinformatics 16: 482-3. (2000)

Jareborg, N. and R. Durbin.
"Alfresco--a workbench for comparative genomic sequence analysis. "
Genome Res 10: 1148-1157. (2000)

Jurka, J.
"Repbase update: a database and an electronic journal of repetitive elements."
Trends Genet 16: 418-20. (2000)

Shedlock, A. M., and Okada, N.
"SINE insertions: powerful tools for molecular systematics."
Bioessays 22: 148-60. (2000)

Pusch, C. M., Bachmann, L., Broghammer, M., and Scholz, M.
"Internal Alu-polymerase chain reaction: a sensitive contamination monitoring protocol for DNA extracted from prehistoric animal bones."
Anal Biochem 284: 408-11. (2000)


Deininger, P. L., and Batzer, M. A.
"Alu repeats and human disease."
Mol Genet Metab 67: 183-93. (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)

Kazazian, H. H., Jr.
"An estimated frequency of endogenous insertional mutations in humans."
Nat Genet 22: 130. (1999)

Kapitonov, V. V., and Jurka, J.
"Molecular paleontology of transposable elements from Arabidopsis thaliana."
Genetica 107: 27-37. (1999)

Petrov, D. A., and Hartl, D. L.
"Patterns of nucleotide substitution in Drosophila and mammalian genomes."
Proc Natl Acad Sci U S A 96: 1475-9. (1999)

Moran, J. V., DeBerardinis, R. J., and Kazazian, H. H., Jr.
"Exon shuffling by L1 retrotransposition."
Science 283: 1530-4. (1999)

Nikaido, M., Rooney, A. P., and Okada, N.
"Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales."
Proc Natl Acad Sci U S A 96: 10261-6. (1999)

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


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)


Burge, C., and Karlin, S.
"Prediction of complete gene structures in human genomic DNA."
J Mol Biol 268: 78-94. (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)


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 DNA transposon fossils in the human genome."
Proc Natl Acad Sci USA 93: 1443-8. (1996)

Jurka, J., Klonowski, P., Dagman, V., and Pelton, P.
"CENSOR--a program for identification and elimination of repetitive elements from DNA sequences."
Comput Chem 20: 119-21. (1996)


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)

Labuda, D., Zietkiewicz, E., and Mitchel, M.
"The impact of short interspersed elements (SINEs) on the host genome."
(R. J. Maraia, Ed.), RG Landes Com., Springer, Austin, Texas. (1995)


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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