Tools for Comparative Genomics

Selected studies that used the VISTA tools

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Earlier citations

Alternative splicing, gene families

I Kleino, RM Ortiz, APJ Huovila.
ADAM15 gene structure and differential alternative exon use in human tissues
BMC Mol Biol. 2007, 8(1):90

Ayoub NA, Garb JE, Tinghitella RM, Collin MA, Hayashi CY.
Blueprint for a high-performance biomaterial: full-length spider dragline silk genes.
PLoS ONE. 2007. 2(6):e514.

Caspersen CS, Reznik B, Weldy PL, Abildskov KM, Stark RI, Garland M.
Molecular cloning of the baboon UDP-glucuronosyltransferase 1A gene family: evolution of the primate UGT1 locus and relevance for models of human drug metabolism.
Pharmacogenet Genomics. 2007. 17(1):11-24

Greger IH, Ziff EB, Penn AC.
Molecular determinants of AMPA receptor subunit assembly.
Trends Neurosci. 2007. 30(8):407-16.

Leonardi R, Zhang YM, Lykidis A, Rock CO, Jackowski S.
Localization and regulation of mouse pantothenate kinase 2.
FEBS Lett. 2007. 581(24):4639-44.

Kim K-H, ChoY, La Rota M, Cramer RA AND Lawrence CB.
Functional analysis of the Alternaria brassicicola non-ribosomal peptide synthetase gene AbNPS2 reveals a role in conidial cell wall construction
Molecular Plant Pathology, 2007. 8:1-137

Hardy, M.P. and L.A. O'Neill,
The murine IRAK2 gene encodes four alternatively spliced isoforms, two of which are inhibitory.
J Biol Chem, 2004. 279(26): p. 27699-708.

Kim, J. and J.D. Lauderdale
Analysis of Pax6 expression using a BAC transgene reveals the presence of a paired-less isoform of Pax6 in the eye and olfactory bulb.
Dev Biol, 2006. 292(2): p. 486-505.

Lundquist, A.L., C.L. Turner, L.Y. Ballester, and A.L. George, Jr.
Expression and transcriptional control of human KCNE genes.
Genomics, 2006. 87(1): p. 119-28.

Martinez, P. and C.T. Amemiya
Genomics of the HOX gene cluster.
Comp Biochem Physiol B Biochem Mol Biol, 2002. 133(4): p. 571-80.

Mulley, J.F., C.H. Chiu, and P.W. Holland
Breakup of a homeobox cluster after genome duplication in teleosts.
Proc Natl Acad Sci U S A, 2006. 103(27): p. 10369-72.

Nakabayashi, K., L. Bentley, M.P. Hitchins, K. Mitsuya, M. Meguro, S. Minagawa, J.S. Bamforth, P. Stanier, M. Preece, R. Weksberg, M. Oshimura, G.E. Moore, and S.W. Scherer
Identification and characterization of an imprinted antisense RNA (MESTIT1) in the human MEST locus on chromosome 7q32.
Hum Mol Genet, 2002. 11(15): p. 1743-56.

Parent, S.A., T. Zhang, G. Chrebet, J.A. Clemas, D.J. Figueroa, B. Ky, R.A. Blevins, C.P. Austin, and H. Rosen
Molecular characterization of the murine SIGNR1 gene encoding a C-type lectin homologous to human DC-SIGN and DC-SIGNR.
Gene, 2002. 293(1-2): p. 33-46.

Philipps, D.L., J.W. Park, and B.R. Graveley
A computational and experimental approach toward a priori identification of alternatively spliced exons.
Rna, 2004. 10(12): p. 1838-44.

Premzl, M., J.E. Gready, L.S. Jermiin, T. Simonic, and J.A. Marshall Graves
Evolution of vertebrate genes related to prion and Shadoo proteins--clues from comparative genomic analysis.
Mol Biol Evol, 2004. 21(12): p. 2210-31.

Streb, J.W., C.M. Kitchen, I.H. Gelman, and J.M. Miano
Multiple promoters direct expression of three AKAP12 isoforms with distinct subcellular and tissue distribution profiles.
J Biol Chem, 2004. 279(53): p. 56014-23.

Csiszar, A., M. Ahmad, K.E. Smith, N. Labinskyy, Q. Gao, G. Kaley, J.G. Edwards, M.S. Wolin, and Z. Ungvari
Bone morphogenetic protein-2 induces proinflammatory endothelial phenotype.
Am J Pathol, 2006. 168(2): p. 629-38.

Gong, T.W., L. Huang, S.J. Warner, and M.I. Lomax
Characterization of the human UBE3B gene: structure, expression, evolution, and alternative splicing.
Genomics, 2003. 82(2): p. 143-52.

Genetic studies

Del Mastro RG, Turenne L, Giese H, Keith TP, Van Eerdewegh P, May KJ
Little RD. Mechanistic role of a disease-associated genetic variant within the ADAM33 asthma susceptibility gene.
BMC Med Genet. 2007 Jul 17;8:46.

Bernig, T., W. Breunis, N. Brouwer, A. Hutchinson, R. Welch, D. Roos, T. Kuijpers, and S. Chanock
An analysis of genetic variation across the MBL2 locus in Dutch Caucasians indicates that 3' haplotypes could modify circulating levels of mannose-binding lectin.
Hum Genet, 2005. 118(3-4): p. 404-15.

Bernig, T., J.G. Taylor, C.B. Foster, B. Staats, M. Yeager, and S.J. Chanock
Sequence analysis of the mannose-binding lectin (MBL2) gene reveals a high degree of heterozygosity with evidence of selection.
Genes Immun, 2004. 5(6): p. 461-76.

Carlson, C.S., S.F. Aldred, P.K. Lee, R.P. Tracy, S.M. Schwartz, M. Rieder, K. Liu, O.D. Williams, C. Iribarren, E.C. Lewis, M. Fornage, E. Boerwinkle, M. Gross, C. Jaquish, D.A. Nickerson, R.M. Myers, D.S. Siscovick, and A.P. Reiner
Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels.
Am J Hum Genet, 2005. 77(1): p. 64-77.

Emison, E.S., A.S. McCallion, C.S. Kashuk, R.T. Bush, E. Grice, S. Lin, M.E. Portnoy, D.J. Cutler, E.D. Green, and A. Chakravarti
A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk.
Nature, 2005. 434(7035): p. 857-63.

Taylor, M.S., R.S. Devon, J.K. Millar, and D.J. Porteous
Evolutionary constraints on the Disrupted in Schizophrenia locus.
Genomics, 2003. 81(1): p. 67-77.

Krishnaswamy, S., Q. Hao, A. Al-Rohaimi, L.M. Hesse, L.L. von Moltke, D.J. Greenblatt, and M.H. Court
UDP glucuronosyltransferase (UGT) 1A6 pharmacogenetics: I. Identification of polymorphisms in the 5'-regulatory and exon 1 regions, and association with human liver UGT1A6 gene expression and glucuronidation.
J Pharmacol Exp Ther, 2005. 313(3): p. 1331-9.

Nurmi, E.L., T. Amin, L.M. Olson, M.M. Jacobs, J.L. McCauley, A.Y. Lam, E.L. Organ, S.E. Folstein, J.L. Haines, and J.S. Sutcliffe
Dense linkage disequilibrium mapping in the 15q11-q13 maternal expression domain yields evidence for association in autism.
Mol Psychiatry, 2003. 8(6): p. 624-34, 570.

Pals, P., S. Lincoln, J. Manning, M. Heckman, L. Skipper, M. Hulihan, M. Van den Broeck, T. De Pooter, P. Cras, J. Crook, C. Van Broeckhoven, and M.J. Farrer
alpha-Synuclein promoter confers susceptibility to Parkinson's disease.
Ann Neurol, 2004. 56(4): p. 591-5.

Pearce, E., D.A. Tregouet, A. Samnegard, A.R. Morgan, C. Cox, A. Hamsten, P. Eriksson, and S. Ye
Haplotype effect of the matrix metalloproteinase-1 gene on risk of myocardial infarction.
Circ Res, 2005. 97(10): p. 1070-6.

Peterson, K.A., B.L. King, A. Hagge-Greenberg, J.J. Roix, C.J. Bult, and T.P. O'Brien
Functional and comparative genomic analysis of the piebald deletion region of mouse chromosome 14.
Genomics, 2002. 80(2): p. 172-84.

Savage, S.A., B.J. Stewart, A. Eckert, M. Kiley, J.S. Liao, and S.J. Chanock
Genetic variation, nucleotide diversity, and linkage disequilibrium in seven telomere stability genes suggest that these genes may be under constraint.
Hum Mutat, 2005. 26(4): p. 343-50.

Zeng, W., T. Gillis, M. Hakky, L. Djousse, R.H. Myers, M.E. MacDonald, and J.F. Gusella
Genetic analysis of the GRIK2 modifier effect in Huntington's disease.
BMC Neurosci, 2006. 7: p. 62.

Palsson, A., A. Rouse, R. Riley-Berger, I. Dworkin, and G. Gibson
Nucleotide variation in the Egfr locus of Drosophila melanogaster.
Genetics, 2004. 167(3): p. 1199-212.

Wen, G., S.K. Mahata, P. Cadman, M. Mahata, S. Ghosh, N.R. Mahapatra, F. Rao, M. Stridsberg, D.W. Smith, P. Mahboubi, N.J. Schork, D.T. O'Connor, and B.A. Hamilton
Both rare and common polymorphisms contribute functional variation at CHGA, a regulator of catecholamine physiology.
Am J Hum Genet, 2004. 74(2): p. 197-207.

Wong, C., N.R. Mahapatra, S. Chitbangonsyn, P. Mahboubi, M. Mahata, S.K. Mahata, and D.T. O'Connor
The angiotensin II receptor (Agtr1a): functional regulatory polymorphisms in a locus genetically linked to blood pressure variation in the mouse.
Physiol Genomics, 2003. 14(1): p. 83-93.

Non-coding conservation, regulatory sequences

Abbasi AA, Paparidis Z, Malik S, Goode DK, Callaway H, Elgar G, Grzeschik KH.
Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers.
PLoS ONE. 2007. 2(4):e366

Cleynen I, Huysmans C, Sasazuki T, Shirasawa S, Van de Ven W, Peeters K.
Transcriptional control of the human high mobility group A1 gene: basal and oncogenic Ras-regulated expression.
Cancer Res. 2007. 67(10):4620-9

van Deursen D, Botma GJ, Jansen H, Verhoeven AJ.
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.
BMC Genomics. 2007. 8:99.

Lanier J, Quina LA, Eng SR, Cox E, Turner EE.
Brn3a target gene recognition in embryonic sensory neurons.
Dev Biol. 2007. 302(2):703-16.

Gunasekera AM, Myrick A, Militello KT, Sims JS, Dong CK, Gierahn T, Le Roch K, Winzeler E, Wirth DF.
Regulatory motifs uncovered among gene expression clusters in Plasmodium falciparum.
Mol Biochem Parasitol. 2007. 153(1):19-30.

Anguita, E., J.A. Sharpe, J.A. Sloane-Stanley, C. Tufarelli, D.R. Higgs, and W.G. Wood
Deletion of the mouse alpha-globin regulatory element (HS -26) has an unexpectedly mild phenotype.
Blood, 2002. 100(10): p. 3450-6.

Bielinska, B., J. Lu, D. Sturgill, and B. Oliver
Core promoter sequences contribute to ovo-B regulation in the Drosophila melanogaster germline.
Genetics, 2005. 169(1): p. 161-72.

Brown, N.L., S.L. Dagenais, C.M. Chen, and T. Glaser
Molecular characterization and mapping of ATOH7, a human atonal homolog with a predicted role in retinal ganglion cell development.
Mamm Genome, 2002. 13(2): p. 95-101.

Chapman, M.A., F.J. Charchar, S. Kinston, C.P. Bird, D. Grafham, J. Rogers, F. Grutzner, J.A. Graves, A.R. Green, and B. Gottgens
Comparative and functional analyses of LYL1 loci establish marsupial sequences as a model for phylogenetic footprinting.
Genomics, 2003. 81(3): p. 249-59.

Crisponi, L., M. Uda, M. Deiana, A. Loi, R. Nagaraja, F. Chiappe, D. Schlessinger, A. Cao, and G. Pilia
FOXL2 inactivation by a translocation 171 kb away: analysis of 500 kb of chromosome 3 for candidate long-range regulatory sequences.
Genomics, 2004. 83(5): p. 757-64.

de la Calle-Mustienes, E., C.G. Feijoo, M. Manzanares, J.J. Tena, E. Rodriguez-Seguel, A. Letizia, M.L. Allende, and J.L. Gomez-Skarmeta
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts.
Genome Res, 2005. 15(8): p. 1061-72.

Denarier, E., R. Forghani, H.F. Farhadi, S. Dib, N. Dionne, H.C. Friedman, P. Lepage, T.J. Hudson, R. Drouin, and A. Peterson
Functional organization of a Schwann cell enhancer.
J Neurosci, 2005. 25(48): p. 11210-7.

Goode, D.K., P. Snell, and G. Elgar
Comparative analysis of vertebrate Shh genes identifies novel conserved non-coding sequence.
Mamm Genome, 2003. 14(3): p. 192-201.

Grice, E.A., E.S. Rochelle, E.D. Green, A. Chakravarti, and A.S. McCallion
Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer.
Hum Mol Genet, 2005. 14(24): p. 3837-45.

Griffin, C., D.A. Kleinjan, B. Doe, and V. van Heyningen
New 3' elements control Pax6 expression in the developing pretectum, neural retina and olfactory region.
Mech Dev, 2002. 112(1-2): p. 89-100.

Hardy, M.P., P.J. Hertzog, and C.M. Owczarek
Multiple regions within the promoter of the murine Ifnar-2 gene confer basal and inducible expression.
Biochem J, 2002. 365(Pt 2): p. 355-67.

Kaelin, C.B., A.W. Xu, X.Y. Lu, and G.S. Barsh
Transcriptional regulation of agouti-related protein (Agrp) in transgenic mice.
Endocrinology, 2004. 145(12): p. 5798-806.

Koster, M.I., S. Kim, J. Huang, T. Williams, and D.R. Roop
TAp63alpha induces AP-2gamma as an early event in epidermal morphogenesis.
Dev Biol, 2006. 289(1): p. 253-61.

Landry, J.R., S. Kinston, K. Knezevic, I.J. Donaldson, A.R. Green, and B. Gottgens
Fli1, Elf1, and Ets1 regulate the proximal promoter of the LMO2 gene in endothelial cells.
Blood, 2005. 106(8): p. 2680-7.

Lee, D.U., O. Avni, L. Chen, and A. Rao
A distal enhancer in the interferon-gamma (IFN-gamma) locus revealed by genome sequence comparison.
J Biol Chem, 2004. 279(6): p. 4802-10.

Ludwig, M.Z., A. Palsson, E. Alekseeva, C.M. Bergman, J. Nathan, and M. Kreitman
Functional evolution of a cis-regulatory module.
PLoS Biol, 2005. 3(4): p. e93.

Mantel, P.Y., N. Ouaked, B. Ruckert, C. Karagiannidis, R. Welz, K. Blaser, and C.B. Schmidt-Weber
Molecular mechanisms underlying FOXP3 induction in human T cells.
J Immunol, 2006. 176(6): p. 3593-602.

Pappu, K.S., E.J. Ostrin, B.W. Middlebrooks, B.T. Sili, R. Chen, M.R. Atkins, R. Gibbs, and G. Mardon
Dual regulation and redundant function of two eye-specific enhancers of the Drosophila retinal determination gene dachshund.
Development, 2005. 132(12): p. 2895-905.

Pauler, F.M., S.H. Stricker, K.E. Warczok, and D.P. Barlow
Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements.
Genome Res, 2005. 15(10): p. 1379-87.

Pickell, L., P. Tran, D. Leclerc, J. Hiscott, and R. Rozen
Regulatory studies of murine methylenetetrahydrofolate reductase reveal two major promoters and NF-kappaB sensitivity.
Biochim Biophys Acta, 2005. 1731(2): p. 104-14.

Premzl, M., M. Delbridge, J.E. Gready, P. Wilson, M. Johnson, J. Davis, E. Kuczek, and J.A. Marshall Graves
The prion protein gene: identifying regulatory signals using marsupial sequence.
Gene, 2005. 349: p. 121-34.

Remaley, A.T., S. Bark, A.D. Walts, L. Freeman, S. Shulenin, T. Annilo, E. Elgin, H.E. Rhodes, C. Joyce, M. Dean, S. Santamarina-Fojo, and H.B. Brewer, Jr.
Comparative genome analysis of potential regulatory elements in the ABCG5-ABCG8 gene cluster.
Biochem Biophys Res Commun, 2002. 295(2): p. 276-82.

Spitz, F., F. Gonzalez, and D. Duboule
A global control region defines a chromosomal regulatory landscape containing the HoxD cluster.
Cell, 2003. 113(3): p. 405-17.

Teunissen, B.E., S.C. van Amersfoorth, T. Opthof, H.J. Jongsma, and M.F. Bierhuizen
Sp1 and Sp3 activate the rat connexin40 proximal promoter .
Biochem Biophys Res Commun, 2002. 292(1): p. 71-8.

Touchman, J.W., A. Dehejia, O. Chiba-Falek, D.E. Cabin, J.R. Schwartz, B.M. Orrison, M.H. Polymeropoulos, and R.L. Nussbaum
Human and mouse alpha-synuclein genes: comparative genomic sequence analysis and identification of a novel gene regulatory element.
Genome Res, 2001. 11(1): p. 78-86.

Tyas, D.A., T.I. Simpson, C.B. Carr, D.A. Kleinjan, V. van Heyningen, J.O. Mason, and D.J. Price
Functional conservation of Pax6 regulatory elements in humans and mice demonstrated with a novel transgenic reporter mouse.
BMC Dev Biol, 2006. 6: p. 21.

Ghislain, J., C. Desmarquet-Trin-Dinh, M. Jaegle, D. Meijer, P. Charnay, and M. Frain
Characterisation of cis-acting sequences reveals a biphasic, axon-dependent regulation of Krox20 during Schwann cell development.
Development, 2002. 129(1): p. 155-66.

Saraiva, M., J.R. Christensen, A.V. Tsytsykova, A.E. Goldfeld, S.C. Ley, D. Kioussis, and A. O'Garra
Identification of a macrophage-specific chromatin signature in the IL-10 locus. J Immunol, 2005. 175(2): p. 1041-6.

Chen, C.H., C.J. Cretekos, J.J.t. Rasweiler, and R.R. Behringer
Hoxd13 expression in the developing limbs of the short-tailed fruit bat, Carollia perspicillata.
Evol Dev, 2005. 7(2): p. 130-41.

Wang, Z.Y., H. Sato, S. Kusam, S. Sehra, L.M. Toney, and A.L. Dent
Regulation of IL-10 gene expression in Th2 cells by Jun proteins.
J Immunol, 2005. 174(4): p. 2098-105.

Abrams, K.L., J. Xu, C. Nativelle-Serpentini, S. Dabirshahsahebi, and M.B. Rogers
An evolutionary and molecular analysis of Bmp2 expression.
J Biol Chem, 2004. 279(16): p. 15916-28.

Amarger, V., R. Erlandsson, G. Pielberg, J.T. Jeon, and L. Andersson
Comparative sequence analysis of the PRKAG3 region between human and pig: evolution of repetitive sequences and potential new exons.
Cytogenet Genome Res, 2003. 102(1-4): p. 163-72.

Bak, M., C. Hansen, K.F. Henriksen, L. Hansen, H. Pakkenberg, H. Eiberg, and N. Tommerup
Mutation analysis of the Sonic hedgehog promoter and putative enhancer elements in Parkinson's disease patients.
Brain Res Mol Brain Res, 2004. 126(2): p. 207-11.

Dayal, S., T. Kiyama, J.T. Villinski, N. Zhang, S. Liang, and W.H. Klein
Creation of cis-regulatory elements during sea urchin evolution by co-option and optimization of a repetitive sequence adjacent to the spec2a gene.
Dev Biol, 2004. 273(2): p. 436-53.

Kleinjan, D.A., A. Seawright, A.J. Childs, and V. van Heyningen
Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription.
Dev Biol, 2004. 265(2): p. 462-77.

Hogan, P.G., L. Chen, J. Nardone, and A. Rao
Transcriptional regulation by calcium, calcineurin, and NFAT.
Genes Dev, 2003. 17(18): p. 2205-32.

Lettice, L.A., S.J. Heaney, L.A. Purdie, L. Li, P. de Beer, B.A. Oostra, D. Goode, G. Elgar, R.E. Hill, and E. de Graaff
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly.
Hum Mol Genet, 2003. 12(14): p. 1725-35.

Teunissen, B.E., A.T. Jansen, S.C. van Amersfoorth, T.X. O'Brien, H.J. Jongsma, and M.F. Bierhuizen
Analysis of the rat connexin 43 proximal promoter in neonatal cardiomyocytes.
Gene, 2003. 322: p. 123-36.

Plant genomes

Tang C, Toomajian C, Sherman-Broyles S, Plagnol V, Guo YL, Hu TT, Clark RM, Nasrallah JB, Weigel D, Nordborg M.
The evolution of selfing in Arabidopsis thaliana.
Science. 2007 Aug 24;317(5841):1070-2.

Zhang S, Gu YQ, Singh J, Coleman-Derr D, Brar DS, Jiang N, Lemaux PG.
New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification.
Plant Mol Biol. 2007. 64(5):589-600.

Schlueter JA, et al.
The FAD2 Gene Family of Soybean: Insights into the Structural and Functional Divergence of a Paleopolyploid Genome.
Crop Sci 47:14-26 (2007)

Ishikawa G, Yonemaru J, Saito M, Nakamura T.
PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes.
BMC Genomics. 2007, 8:135

Bomblies, K. and J.F. Doebley
Molecular evolution of FLORICAULA/LEAFY orthologs in the Andropogoneae (Poaceae).
Mol Biol Evol, 2005. 22(4): p. 1082-94.

Clark, R.M., E. Linton, J. Messing, and J.F. Doebley
Pattern of diversity in the genomic region near the maize domestication gene tb1.
Proc Natl Acad Sci U S A, 2004. 101(3): p. 700-7.

Federico, M.L., F.L. Iniguez-Luy, R.W. Skadsen, and H.F. Kaeppler
Spatial and temporal divergence of expression in duplicated barley germin-like protein-encoding genes.
Genetics, 2006. 174(1): p. 179-90.

Lee, J.Y., S.F. Baum, J. Alvarez, A. Patel, D.H. Chitwood, and J.L. Bowman
Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis.
Plant Cell, 2005. 17(1): p. 25-36.

H. Guo and S. P. Moose
Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution.
PLANT CELL, May 1, 2003; 15(5): 1143 - 1158.

Regulatory VISTA (rVISTA) - transcription factor binding sites database search with a comparative sequence analysis

Chatterjee, B., A.J. Chin, G. Valdimarsson, C. Finis, J.M. Sonntag, B.Y. Choi, L. Tao, K. Balasubramanian, C. Bell, A. Krufka, D.J. Kozlowski, R.G. Johnson, and C.W. Lo
Developmental regulation and expression of the zebrafish connexin43 gene.
Dev Dyn, 2005. 233(3): p. 890-906.

Deal, K.K., V.A. Cantrell, R.L. Chandler, T.L. Saunders, D.P. Mortlock, and E.M. Southard-Smith
Distant regulatory elements in a Sox10-beta GEO BAC transgene are required for expression of Sox10 in the enteric nervous system and other neural crest-derived tissues.
Dev Dyn, 2006. 235(5): p. 1413-32.

Kaelin, C.B., L. Gong, A.W. Xu, F. Yao, K. Hockman, G.J. Morton, M.W. Schwartz, G.S. Barsh, and R.G. MacKenzie
Signal transducer and activator of transcription (stat) binding sites but not stat3 are required for fasting-induced transcription of agouti-related protein messenger ribonucleic acid.
Mol Endocrinol, 2006. 20(10): p. 2591-602.

Machinis, K. and S. Amselem
Functional relationship between LHX4 and POU1F1 in light of the LHX4 mutation identified in patients with pituitary defects.
J Clin Endocrinol Metab, 2005. 90(9): p. 5456-62.

Napal, L., P.F. Marrero, and D. Haro
An intronic peroxisome proliferator-activated receptor-binding sequence mediates fatty acid induction of the human carnitine palmitoyltransferase 1A.
J Mol Biol, 2005. 354(4): p. 751-9.

Seki, T., K.H. Hong, J. Yun, S.J. Kim, and S.P. Oh
Isolation of a regulatory region of activin receptor-like kinase 1 gene sufficient for arterial endothelium-specific expression.
Circ Res, 2004. 94(8): p. e72-7.

Tian, B., D.E. Nowak, and A.R. Brasier
A TNF-induced gene expression program under oscillatory NF-kappaB control.
BMC Genomics, 2005. 6: p. 137.

Vazquez-Padron, R.I., S.M. Pham, M. Pang, S. Li, and A. Aitouche
Molecular dissection of mouse soluble guanylyl cyclase alpha1 promoter.
Biochem Biophys Res Commun, 2004. 314(1): p. 208-14.

Synteny and rearrangements

Frank N. Martin
Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae
Curr Genet (2007) 51:285296

Goode, D.K., P. Snell, S.F. Smith, J.E. Cooke, and G. Elgar
Highly conserved regulatory elements around the SHH gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3.
Genomics, 2005. 86(2): p. 172-81.

Negre, B., S. Casillas, M. Suzanne, E. Sanchez-Herrero, M. Akam, M. Nefedov, A. Barbadilla, P. de Jong, and A. Ruiz
Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex.
Genome Res, 2005. 15(5): p. 692-700.

Wong, M.L., A. Islas-Trejo, and J.F. Medrano
Structural characterization of the mouse high growth deletion and discovery of a novel fusion transcript between suppressor of cytokine signaling-2 (Socs-2) and viral encoded semaphorin receptor (Plexin C1).
Gene, 2002. 299(1-2): p. 153-63.

Owczarek, C.M., K.J. Portbury, M.P. Hardy, D.A. O'Leary, J. Kudoh, K. Shibuya, N. Shimizu, I. Kola, and P.J. Hertzog
Detailed mapping of the ERG-ETS2 interval of human chromosome 21 and comparison with the region of conserved synteny on mouse chromosome 16.
Gene, 2004. 324: p. 65-77.

Xie, T., L. Rowen, B. Aguado, M.E. Ahearn, A. Madan, S. Qin, R.D. Campbell, and L. Hood
Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse.
Genome Res, 2003. 13(12): p. 2621-36.

Viral genomes

Urisman, A., R.J. Molinaro, N. Fischer, S.J. Plummer, G. Casey, E.A. Klein, K. Malathi, C. Magi-Galluzzi, R.R. Tubbs, D. Ganem, R.H. Silverman, and J.L. DeRisi
Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant.
PLoS Pathog, 2006. 2(3): p. e25.