![[Feedback]](/icons/banner/feedbackACT.gif){kind=icon}
![[For Subscribers]](/icons/banner/subscriberACT.gif){kind=icon}
![[Archive]](/icons/banner/archiveACT.gif){kind=icon}
![[Search]](/icons/banner/searchACT.gif){kind=icon}
![[Contents]](/icons/banner/tocACT.gif){kind=icon}
|
|
|
|
|
||
|
Vol. 10, Issue 9, 1304-1306, September 2000
REPORT
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
 |
|
  A. Tsirigos and I. Rigoutsos Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs Nucleic Acids Res., May 1, 2008; (2008) gkn155v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J.-H. Kim, P. N. Bogner, S.-H. Baek, N. Ramnath, P. Liang, H.-R. Kim, C. Andrews, and Y.-M. Park Up-Regulation of Peroxiredoxin 1 in Lung Cancer and Its Implication as a Prognostic and Therapeutic Target Clin. Cancer Res., April 15, 2008; 14(8): 2326 - 2333. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Huang, C. Zhu, H. Wang, E. Horvath, and E. A. Eklund The Interferon Consensus Sequence-binding Protein (ICSBP/IRF8) Represses PTPN13 Gene Transcription in Differentiating Myeloid Cells J. Biol. Chem., March 21, 2008; 283(12): 7921 - 7935. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Van Laer, E. Van Eyken, E. Fransen, J. R. Huyghe, V. Topsakal, J.-J. Hendrickx, S. Hannula, E. Maki-Torkko, M. Jensen, K. Demeester, et al. The grainyhead like 2 gene (GRHL2), alias TFCP2L3, is associated with age-related hearing impairment Hum. Mol. Genet., January 15, 2008; 17(2): 159 - 169. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Long and J. M. Miano Remote Control of Gene Expression J. Biol. Chem., June 1, 2007; 282(22): 15941 - 15945. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. G. Pezzolesi, K. M. Zbuk, K. A. Waite, and C. Eng Comparative genomic and functional analyses reveal a novel cis-acting PTEN regulatory element as a highly conserved functional E-box motif deleted in Cowden syndrome Hum. Mol. Genet., May 1, 2007; 16(9): 1058 - 1071. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Sosinsky, B. Honig, R. S. Mann, and A. Califano Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting PNAS, April 10, 2007; 104(15): 6305 - 6310. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Sabherwal, F. Bangs, R. Roth, B. Weiss, K. Jantz, E. Tiecke, G. K. Hinkel, C. Spaich, B. P. Hauffa, H. van der Kamp, et al. Long-range conserved non-coding SHOX sequences regulate expression in developing chicken limb and are associated with short stature phenotypes in human patients Hum. Mol. Genet., January 15, 2007; 16(2): 210 - 222. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. R. Morton and S. I. Wright Selective Constraints on Codon Usage of Nuclear Genes from Arabidopsis thaliana Mol. Biol. Evol., January 1, 2007; 24(1): 122 - 129. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Lamy, U. Rothbacher, D. Caillol, and P. Lemaire Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRP1/5 Development, August 1, 2006; 133(15): 2835 - 2844. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Rigoutsos, T. Huynh, K. Miranda, A. Tsirigos, A. McHardy, and D. Platt Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes PNAS, April 25, 2006; 103(17): 6605 - 6610. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Li, S. Zhong, and W. H. Wong Reliable prediction of transcription factor binding sites by phylogenetic verification PNAS, November 22, 2005; 102(47): 16945 - 16950. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Pearce, 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., November 11, 2005; 97(10): 1070 - 1076. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-P. Kim, B.-G. Kim, J. Letterio, and W. J. Leonard Smad-dependent Cooperative Regulation of Interleukin 2 Receptor {alpha} Chain Gene Expression by T Cell Receptor and Transforming Growth Factor-{beta} J. Biol. Chem., October 7, 2005; 280(40): 34042 - 34047. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Chi, P. K. Chatterjee, W. Wilson III, S.-X. Zhang, F. J. DeMayo, and R. J. Schwartz Complex cardiac Nkx2-5 gene expression activated by noggin-sensitive enhancers followed by chamber-specific modules PNAS, September 20, 2005; 102(38): 13490 - 13495. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. M. Cooper, E. A. Stone, G. Asimenos, NISC Comparative Sequencing Program, E. D. Green, S. Batzoglou, and A. Sidow Distribution and intensity of constraint in mammalian genomic sequence Genome Res., July 1, 2005; 15(7): 901 - 913. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. S. Pappu, 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, June 15, 2005; 132(12): 2895 - 2905. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K.-H. KANG and S.-H. IM Differential Regulation of the IL-10 Gene in Th1 and Th2 T Cells Ann. N.Y. Acad. Sci., June 1, 2005; 1050(1): 97 - 107. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Negre, 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., May 1, 2005; 15(5): 692 - 700. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J.-Y. Lee, 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, January 1, 2005; 17(1): 25 - 36. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-H. Im, A. Hueber, S. Monticelli, K.-H. Kang, and A. Rao Chromatin-level Regulation of the IL10 Gene in T Cells J. Biol. Chem., November 5, 2004; 279(45): 46818 - 46825. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Shnyreva, W. M. Weaver, M. Blanchette, S. L. Taylor, M. Tompa, D. R. Fitzpatrick, and C. B. Wilson Evolutionarily conserved sequence elements that positively regulate IFN-{gamma} expression in T cells PNAS, August 24, 2004; 101(34): 12622 - 12627. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. Frazer, C. M. Wade, D. A. Hinds, N. Patil, D. R. Cox, and M. J. Daly Segmental Phylogenetic Relationships of Inbred Mouse Strains Revealed by Fine-Scale Analysis of Sequence Variation Across 4.6 Mb of Mouse Genome Genome Res., August 1, 2004; 14(8): 1493 - 1500. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. J. Hatcher, N. Y.S.-G. Diman, M.-S. Kim, D. Pennisi, Y. Song, M. M. Goldstein, T. Mikawa, and C. T. Basson A role for Tbx5 in proepicardial cell migration during cardiogenesis Physiol Genomics, July 8, 2004; 18(2): 129 - 140. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. M.G. Smits, B. F.M. van Zutphen, R. H.A. Plasterk, and E. Cuppen Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains Genome Res., July 1, 2004; 14(7): 1285 - 1290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. Frazer, L. Pachter, A. Poliakov, E. M. Rubin, and I. Dubchak VISTA: computational tools for comparative genomics Nucleic Acids Res., July 1, 2004; 32(suppl_2): W273 - W279. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. P. Hardy and L. A. J. O'Neill The Murine Irak2 Gene Encodes Four Alternatively Spliced Isoforms, Two of Which Are Inhibitory J. Biol. Chem., June 25, 2004; 279(26): 27699 - 27708. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. W. Tullai, M. E. Schaffer, S. Mullenbrock, S. Kasif, and G. M. Cooper Identification of Transcription Factor Binding Sites Upstream of Human Genes Regulated by the Phosphatidylinositol 3-Kinase and MEK/ERK Signaling Pathways J. Biol. Chem., May 7, 2004; 279(19): 20167 - 20177. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. T. Dermitzakis, E. Kirkness, S. Schwarz, E. Birney, A. Reymond, and S. E. Antonarakis Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment Genome Res., May 1, 2004; 14(5): 852 - 859. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. B. Rankin, W. Xu, D. G. Silberg, and E. Suh Putative intestine-specific enhancers located in 5' sequence of the CDX1 gene regulate CDX1 expression in the intestine Am J Physiol Gastrointest Liver Physiol, May 1, 2004; 286(5): G872 - G880. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Hou, M. Eren, C. A. Painter, J. W. Covington, J. D. Dixon, J. A. Schoenhard, and D. E. Vaughan Tumor Necrosis Factor {alpha} Activates the Human Plasminogen Activator Inhibitor-1 Gene through a Distal Nuclear Factor {kappa}B Site J. Biol. Chem., April 30, 2004; 279(18): 18127 - 18136. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. J. Nelson, S. A. Duncan, and R. P. Misra Conserved Enhancer in the Serum Response Factor Promoter Controls Expression During Early Coronary Vasculogenesis Circ. Res., April 30, 2004; 94(8): 1059 - 1066. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. L. Abrams, J. Xu, C. Nativelle-Serpentini, S. Dabirshahsahebi, and M. B. Rogers An Evolutionary and Molecular Analysis of Bmp2 Expression J. Biol. Chem., April 16, 2004; 279(16): 15916 - 15928. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. E. Arking, S. S. Chugh, A. Chakravarti, and P. M. Spooner Genomics in Sudden Cardiac Death Circ. Res., April 2, 2004; 94(6): 712 - 723. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Sevetson, S. Taylor, and Y. Pan Cbfa1/RUNX2 Directs Specific Expression of the Sclerosteosis Gene (SOST) J. Biol. Chem., April 2, 2004; 279(14): 13849 - 13858. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. B. Yap and L. Pachter Identification of Evolutionary Hotspots in the Rodent Genomes Genome Res., April 1, 2004; 14(4): 574 - 579. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Brudno, A. Poliakov, A. Salamov, G. M. Cooper, A. Sidow, E. M. Rubin, V. Solovyev, S. Batzoglou, and I. Dubchak Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human Genome Res., April 1, 2004; 14(4): 685 - 692. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Ovcharenko, G. G. Loots, R. C. Hardison, W. Miller, and L. Stubbs zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles Genome Res., March 1, 2004; 14(3): 472 - 477. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. J. Langham, J. Walsh, M. Dunn, C. Ko, S. A. Goff, and M. Freeling Genomic Duplication, Fractionation and the Origin of Regulatory Novelty Genetics, February 1, 2004; 166(2): 935 - 945. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Clark, E. Linton, J. Messing, and J. F. Doebley Inaugural Article: Pattern of diversity in the genomic region near the maize domestication gene tb1 PNAS, January 20, 2004; 101(3): 700 - 707. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Zhang, P. Haws, and Q. Wu Multiple Variable First Exons: A Mechanism for Cell- and Tissue-Specific Gene Regulation Genome Res., January 1, 2004; 14(1): 79 - 89. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Berezikov, V. Guryev, R. H.A. Plasterk, and E. Cuppen CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting Genome Res., January 1, 2004; 14(1): 170 - 178. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Nobrega and L. A. Pennacchio Comparative genomic analysis as a tool for biological discovery J. Physiol., January 1, 2004; 554(1): 31 - 39. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Castronuevo, M. A. Thornton, L. E. McCarthy, J. Klimas, and B. P. Schick DNase I Hypersensitivity Patterns of the Serglycin Proteoglycan Gene in Resting and Phorbol 12-Myristate 13-Acetate-stimulated Human Erythroleukemia (HEL), CHRF 288-11, and HL-60 Cells Compared with Neutrophils and Human Umbilical Vein Endothelial Cells J. Biol. Chem., December 5, 2003; 278(49): 48704 - 48712. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. H. Margulies, M. Blanchette, NISC Comparative Sequencing Program, D. Haussler, and E. D. Green Identification and Characterization of Multi-Species Conserved Sequences Genome Res., December 1, 2003; 13(12): 2507 - 2518. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Negre, J. M. Ranz, F. Casals, M. Caceres, and A. Ruiz A New Split of the Hox Gene Complex in Drosophila: Relocation and Evolution of the Gene labial Mol. Biol. Evol., December 1, 2003; 20(12): 2042 - 2054. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. T. Dermitzakis, A. Reymond, N. Scamuffa, C. Ucla, E. Kirkness, C. Rossier, and S. E. Antonarakis Evolutionary Discrimination of Mammalian Conserved Non-Genic Sequences (CNGs) Science, November 7, 2003; 302(5647): 1033 - 1035. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. F. Kirkness, V. Bafna, A. L. Halpern, S. Levy, K. Remington, D. B. Rusch, A. L. Delcher, M. Pop, W. Wang, C. M. Fraser, et al. The Dog Genome: Survey Sequencing and Comparative Analysis Science, September 26, 2003; 301(5641): 1898 - 1903. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. C. Inada, A. Bashir, C. Lee, B. C. Thomas, C. Ko, S. A. Goff, and M. Freeling Conserved Noncoding Sequences in the Grasses Genome Res., September 1, 2003; 13(9): 2030 - 2041. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Mignone, G. Grillo, S. Liuni, and G. Pesole Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis Nucleic Acids Res., August 1, 2003; 31(15): 4639 - 4645. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. C.-C. Shih and W.-H. Li GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations Mol. Biol. Evol., August 1, 2003; 20(8): 1299 - 1309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. A. Lettice, S. J.H. 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., July 15, 2003; 12(14): 1725 - 1735. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Schwartz, L. Elnitski, M. Li, M. Weirauch, C. Riemer, A. Smit, N. C. S. Program, E. D. Green, R. C. Hardison, and W. Miller MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences Nucleic Acids Res., July 1, 2003; 31(13): 3518 - 3524. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. L. Hong, L. Hamaguchi, M. A. Busch, and D. Weigel Regulatory Elements of the Floral Homeotic Gene AGAMOUS Identified by Phylogenetic Footprinting and Shadowing PLANT CELL, June 1, 2003; 15(6): 1296 - 1309. [Abstract] [Full Text]
|
|
|
|
|
|
M. P. Hare and S. R. Palumbi High Intron Sequence Conservation Across Three Mammalian Orders Suggests Functional Constraints Mol. Biol. Evol., June 1, 2003; 20(6): 969 - 978. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Pozzoli, G. Elgar, R. Cagliani, L. Riva, G. P. Comi, N. Bresolin, A. Bardoni, and M. Sironi Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature Genome Res., May 1, 2003; 13(5): 764 - 772. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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. [Abstract] [Full Text]
|
|
|
|
|
|
M. Brudno, C. B. Do, G. M. Cooper, M. F. Kim, E. Davydov, N. C. S. Program, E. D. Green, A. Sidow, and S. Batzoglou LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA Genome Res., Apri |
