Department of Genetics

2008

Trends in metabolic syndrome and gene networks in human and rodent models

Kraja, A. T., Province, M. A., Huang, P., Jarvis, J. P., Rice, T., Cheverud, J. M. & Rao, D. C., Sep 2008, In: Endocrine, Metabolic and Immune Disorders - Drug Targets. 8, 3, p. 198-207 10 p.

Research output: Contribution to journal › Review article › peer-review

14 Scopus citations

Ultraconserved elements in the Olig2 promoter

Chen, C. T. L., Gottlieb, D. I. & Cohen, B. A., Dec 16 2008, In: PloS one. 3, 12, e3946.

Research output: Contribution to journal › Article › peer-review

Open Access

14 Scopus citations

Variants in nicotinic receptors and risk for nicotine dependence

Bierut, L. J., Stitzel, J. A., Wang, J. C., Hinrichs, A. L., Grucza, R. A., Xuei, X., Saccone, N. L., Saccone, S. F., Bertelsen, S., Fox, L., Horton, W. J., Breslau, N., Budde, J., Cloninger, C. R., Dick, D. M., Foroud, T., Hatsukami, D., Hesselbrock, V., Johnson, E. O., Kramer, J., & 13 othersKuperman, S., Madden, P. A. F., Mayo, K., Nurnberger, J., Pomerleau, O., Porjesz, B., Reyes, O., Schuckit, M., Swan, G., Tischfield, J. A., Edenberg, H. J., Rice, J. P. & Goate, A. M., Sep 2008, In: American Journal of Psychiatry. 165, 9, p. 1163-1171 9 p.

Research output: Contribution to journal › Article › peer-review

514 Scopus citations

Vestigial expression in the Drosophila embryonic central nervous system

Guss, K. A., Mistry, H. & Skeath, J. B., Sep 2008, In: Developmental Dynamics. 237, 9, p. 2483-2489 7 p.

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Whole-genome sequencing and variant discovery in C. elegans

Hillier, L. D. W., Marth, G. T., Quinlan, A. R., Dooling, D., Fewell, G., Barnett, D., Fox, P., Glasscock, J. I., Hickenbotham, M., Huang, W., Magrini, V. J., Richt, R. J., Sander, S. N., Stewart, D. A., Stromberg, M., Tsung, E. F., Wylie, T., Schedl, T., Wilson, R. K. & Mardis, E. R., Feb 2008, In: Nature Methods. 5, 2, p. 183-188 6 p.

Research output: Contribution to journal › Article › peer-review

344 Scopus citations

2007

Abrogation of nuclear receptors Nr4a3 andNr4a1 leads to development of acute myeloid leukemia

Mullican, S. E., Zhang, S., Konopleva, M., Ruvolo, V., Andreeff, M., Milbrandt, J. & Conneely, O. M., Jun 2007, In: Nature medicine. 13, 6, p. 730-735 6 p.

Research output: Contribution to journal › Article › peer-review

246 Scopus citations

A cis-regulatory logic simulator

Zeigler, R. D., Gertz, J. & Cohen, B. A., Jul 27 2007, In: BMC bioinformatics. 8, 272.

Research output: Contribution to journal › Article › peer-review

Open Access

A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments

Zhou, Y., Cras-Méneur, C., Ohsugi, M., Stormo, G. D. & Permutt, M. A., Aug 15 2007, In: Bioinformatics. 23, 16, p. 2073-2079 7 p.

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Altered axonal mitochondrial transport in the pathogenesis of Charcot-Marie-Tooth disease from mitofusin 2 mutations

Baloh, R. H., Schmidt, R. E., Pestronk, A. & Milbrandt, J., Jan 10 2007, In: Journal of Neuroscience. 27, 2, p. 422-430 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

351 Scopus citations

An investigation of the effects of lipid-lowering medications: Genome-wide linkage analysis of lipids in the HyperGEN study

Wu, J., Province, M. A., Coon, H., Hunt, S. C., Eckfeldt, J. H., Arnett, D. K., Heiss, G., Lewis, C. E., Ellison, R. C., Rao, D. C., Rice, T. & Kraja, A. T., Sep 10 2007, In: BMC genetics. 8, 60.

Research output: Contribution to journal › Article › peer-review

Open Access

43 Scopus citations

An iterative method for selecting degenerate multiplex PCR primers

Souvenir, R., Buhler, J., Stormo, G. & Zhang, W., Aug 2 2007, PCR Primer Design. Yuryev, A. (ed.). p. 245-267 23 p. (Methods in Molecular Biology; vol. 402).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

10 Scopus citations

A novel method combining linkage disequilibrium information and imputed functional knowledge for tagSNP selection

Rochat, R. H., De Las Fuentes, L., Stormo, G., Davila-Roman, V. G. & Charles Gu, C., Jul 2007, In: Human heredity. 64, 4, p. 243-249 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

A revised nomenclature for the human and rodent α-tubulin gene family

Khodiyar, V. K., Maltais, L. J., Sneddon, K. M. B., Smith, J. R., Shimoyama, M., Cabral, F., Dumontet, C., Dutcher, S. K., Harvey, R. J., Lafanechère, L., Murray, J. M., Nogales, E., Piquemal, D., Stanchi, F., Povey, S. & Lovering, R. C., Aug 2007, In: Genomics. 90, 2, p. 285-289 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

50 Scopus citations

A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples

Leparc, G. G. & Mitra, R. D., Dec 2007, In: Nucleic acids research. 35, 21, e146.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Bedraggled, a putative transporter, influences the tissue polarity complex during the R3/R4 fate decision in the Drosophila eye

Rawls, A. S., Schultz, S. A., Mitra, R. D. & Wolff, T., Sep 2007, In: Genetics. 177, 1, p. 313-328 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Caenorhabditis elegans prom-1 is required for meiotic prophase progression and homologous chromosome pairing

Jantsch, V., Tang, L., Pasierbek, P., Penkner, A., Nayak, S., Baudrimont, A., Schedl, T., Gartner, A. & Loidl, J., Dec 2007, In: Molecular biology of the cell. 18, 12, p. 4911-4920 10 p.

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

Calling cards for DNA-binding proteins

Wang, H., Johnston, M. & Mitra, R. D., 2007, In: Genome research. 17, 8, p. 1202-1209 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

27 Scopus citations

Characteristics Affecting Expression and Solubilization of Yeast Membrane Proteins

White, M. A., Clark, K. M., Grayhack, E. J. & Dumont, M. E., Jan 19 2007, In: Journal of Molecular Biology. 365, 3, p. 621-636 16 p.

Research output: Contribution to journal › Article › peer-review

37 Scopus citations

Characterizing the cancer genome in lung adenocarcinoma

Weir, B. A., Woo, M. S., Getz, G., Perner, S., Ding, L., Beroukhim, R., Lin, W. M., Province, M. A., Kraja, A., Johnson, L. A., Shah, K., Sato, M., Thomas, R. K., Barletta, J. A., Borecki, I. B., Broderick, S., Chang, A. C., Chiang, D. Y., Chirieac, L. R., Cho, J., & 50 othersFujii, Y., Gazdar, A. F., Giordano, T., Greulich, H., Hanna, M., Johnson, B. E., Kris, M. G., Lash, A., Lin, L., Lindeman, N., Mardis, E. R., McPherson, J. D., Minna, J. D., Morgan, M. B., Nadel, M., Orringer, M. B., Osborne, J. R., Ozenberger, B., Ramos, A. H., Robinson, J., Roth, J. A., Rusch, V., Sasaki, H., Shepherd, F., Sougnez, C., Spitz, M. R., Tsao, M. S., Twomey, D., Verhaak, R. G. W., Weinstock, G. M., Wheeler, D. A., Winckler, W., Yoshizawa, A., Yu, S., Zakowski, M. F., Zhang, Q., Beer, D. G., Wistuba, I. I., Watson, M. A., Garraway, L. A., Ladanyi, M., Travis, W. D., Pao, W., Rubin, M. A., Gabriel, S. B., Gibbs, R. A., Varmus, H. E., Wilson, R. K., Lander, E. S. & Meyerson, M., Dec 6 2007, In: Nature. 450, 7171, p. 893-898 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

944 Scopus citations

Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs

Saccone, S. F., Hinrichs, A. L., Saccone, N. L., Chase, G. A., Konvicka, K., Madden, P. A. F., Breslau, N., Johnson, E. O., Hatsukami, D., Pomerleau, O., Swan, G. E., Goate, A. M., Rutter, J., Bertelsen, S., Fox, L., Fugman, D., Martin, N. G., Montgomery, G. W., Wang, J. C., Ballinger, D. G., & 2 othersRice, J. P. & Bierut, L. J., Jan 1 2007, In: Human molecular genetics. 16, 1, p. 36-49 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

674 Scopus citations

Comparison of quantitative methods for cell-shape analysis

Pincus, Z. & Theriot, J. A., Aug 2007, In: Journal of Microscopy. 227, 2, p. 140-156 17 p.

Research output: Contribution to journal › Article › peer-review

205 Scopus citations

Complex genetic changes in strains of Saccharomyces cerevisiae derived by selection in the laboratory

Witten, J. T., Chen, C. T. L. & Cohen, B. A., Sep 2007, In: Genetics. 177, 1, p. 449-456 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Computational identification and functional validation of regulatory motifs in cartilage-expressed genes

Davies, S. R., Chang, L. W., Patra, D., Xing, X., Posey, K., Hecht, J., Stormo, G. D. & Sandell, L. J., Oct 2007, In: Genome research. 17, 10, p. 1438-1447 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

27 Scopus citations

Conditional ablation of GFRα1 in postmigratory eneric neurons triggers unconventional neuronal death in the colon and causes Hirschsprungs's disease phenotype

Uesaka, T., Jain, S., Yonemura, S., Uchiyama, Y., Milbrandt, J. & Enomoto, H., Jun 2007, In: Development. 134, 11, p. 2171-2181 11 p.

Research output: Contribution to journal › Article › peer-review

113 Scopus citations

Contribution of the orphan nuclear receptor Nur77 to the apoptotic action of IGFBP-3

Lee, K. W., Cobb, L. J., Paharkova-Vatchkova, V., Liu, B., Milbrandt, J. & Cohen, P., Aug 2007, In: Carcinogenesis. 28, 8, p. 1653-1658 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

38 Scopus citations

Deciphering adaptor specificity in GFL-dependent RET-mediated proliferation and neurite outgrowth

Gustin, J. A., Yang, M., Johnson, E. M. & Milbrandt, J., Aug 2007, In: Journal of Neurochemistry. 102, 4, p. 1184-1194 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

DNA-protein interactions: Integrating structure, sequence, and function

Bulyk, M. L., Hartemink, A. J., Fraenkel, E. & Stormo, G., Dec 1 2007, Pacific Symposium on Biocomputing 2007, PSB 2007. p. 470-471 2 p. (Pacific Symposium on Biocomputing 2007, PSB 2007).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Do inflammation and procoagulation biomarkers contribute to the metabolic syndrome cluster?

Kraja, A. T., Province, M. A., Arnett, D., Wagenknecht, L., Tang, W., Hopkins, P. N., Djoussé, L. & Borecki, I. B., 2007, In: Nutrition and Metabolism. 4, 28.

Research output: Contribution to journal › Article › peer-review

Open Access

57 Scopus citations

Early-onset subicular microvascular amyloid and neuroinflammation correlate with behavioral deficits in vasculotropic mutant amyloid β-protein precursor transgenic mice

Xu, F., Grande, A. M., Robinson, J. K., Previti, M. L., Vasek, M., Davis, J. & Van Nostrand, W. E., Apr 25 2007, In: Neuroscience. 146, 1, p. 98-107 10 p.

Research output: Contribution to journal › Article › peer-review

75 Scopus citations

Emergence of large-scale cell morphology and movement from local actin filament growth dynamics

Lacayo, C. I., Pincus, Z., VanDuijn, M. M., Wilson, C. A., Fletcher, D. A., Gertler, F. B., Mogilner, A. & Theriot, J. A., Sep 2007, In: PLoS biology. 5, 9, p. 2035-2052 18 p.

Research output: Contribution to journal › Article › peer-review

Open Access

148 Scopus citations

Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach

Zhao, G., Chang, K. Y., Varley, K. & Stormo, G. D., Feb 28 2007, In: PloS one. 2, 2, e262.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

Evidence of QTL on 15q21 for high-density lipoprotein cholesterol: The National Heart, Lung, and Blood Institute Family Heart Study (NHLBI FHS)

Feitosa, M. F., Province, M. A., Heiss, G., Arnett, D. K., Myers, R. H., Pankow, J. S., Hopkins, P. N. & Borecki, I. B., Jan 2007, In: Atherosclerosis. 190, 1, p. 232-237 6 p.

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Evolutionary and biomedical insights from the rhesus macaque genome

Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., Batzer, M. A., Bustamante, C. D., Eichler, E. E., Hahn, M. W., Hardison, R. C., Makova, K. D., Miller, W., Milosavljevic, A., Palermo, R. E., Siepel, A., & 156 othersSikela, J. M., Attaway, T., Bell, S., Bernard, K. E., Buhay, C. J., Chandrabose, M. N., Dao, M., Davis, C., Delehaunty, K. D., Ding, Y., Dinh, H. H., Dugan-Rocha, S., Fulton, L. A., Gabisi, R. A., Garner, T. T., Godfrey, J., Hawes, A. C., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S. N., Joshi, V., Khan, Z. M., Kirkness, E. F., Cree, A., Fowler, R. G., Lee, S., Lewis, L. R., Li, Z., Liu, Y. S., Moore, S. M., Muzny, D., Nazareth, L. V., Dinh, N. N., Okwuonu, G. O., Pai, G., Parker, D., Paul, H. A., Pfannkoch, C., Pohl, C. S., Rogers, Y. H., Ruiz, S. J., Sabo, A., Santibanez, J., Schneider, B. W., Smith, S. M., Sodergren, E., Svatek, A. F., Utterback, T. R., Vattathil, S., Warren, W., White, C. S., Chinwalla, A. T., Feng, Y., Halpern, A. L., Hillier, L. D. W., Huang, X., Minx, P., Nelson, J. O., Pepin, K. H., Qin, X., Sutton, G. G., Venter, E., Walenz, B. P., Wallis, J. W., Worley, K. C., Yang, S. P., Jones, S. M., Marra, M. A., Rocchi, M., Schein, J. E., Baertsch, R., Clarke, L., Csürös, M., Glasscock, J., Harris, R. A., Havlak, P., Jackson, A. R., Jiang, H., Liu, Y., Messina, D. N., Shen, Y., Song, H. X. Z., Wylie, T., Zhang, L., Birney, E., Han, K., Konkel, M. K., Lee, J., Smit, A. F. A., Ullmer, B., Wang, H., Xing, J., Burhans, R., Cheng, Z., Karro, J. E., Ma, J., Raney, B., She, X., Cox, M. J., Demuth, J. P., Dumas, L. J., Han, S. G., Hopkins, J., Karimpour-Fard, A., Kim, Y. H., Pollack, J. R., Vinar, T., Addo-Quaye, C., Degenhardt, J., Denby, A., Hubisz, M. J., Indap, A., Kosiol, C., Lahn, B. T., Lawson, H. A., Marklein, A., Nielsen, R., Vallender, E. J., Clark, A. G., Ferguson, B., Hernandez, R. D., Hirani, K., Kehrer-Sawatzki, H., Kolb, J., Patil, S., Pu, L. L., Ren, Y., Smith, D. G., Wheeler, D. A., Schenck, I., Ball, E. V., Chen, R., Cooper, D. N., Giardine, B., Hsu, F., Kent, W. J., Lesk, A., Nelson, D. L., O'Brien, W. E., Prüfer, K., Stenson, P. D., Wallace, J. C., Ke, H., Liu, X. M., Wang, P., Xiang, A. P., Yang, F., Barber, G. P., Haussler, D., Karolchik, D., Kern, A. D., Kuhn, R. M., Smith, K. E. & Zwieg, A. S., Apr 13 2007, In: Science. 316, 5822, p. 222-234 13 p.

Research output: Contribution to journal › Review article › peer-review

1063 Scopus citations

Familial Parkinsonism and ophthalmoplegia from a mutation in the mitochondrial DNA helicase twinkle

Baloh, R. H., Salavaggione, E., Milbrandt, J. & Pestronk, A., Jul 2007, In: Archives of neurology. 64, 7, p. 998-1000 3 p.

Research output: Contribution to journal › Article › peer-review

85 Scopus citations

Fenofibrate effect on triglyceride and postprandial response of apolipoprotein A5 variants: The GOLDN study

Lai, C. Q., Arnett, D. K., Corella, D., Straka, R. J., Tsai, M. Y., Peacock, J. M., Adiconis, X., Parnell, L. D., Hixson, J. E., Province, M. A. & Ordovas, J. M., Jun 2007, In: Arteriosclerosis, thrombosis, and vascular biology. 27, 6, p. 1417-1425 9 p.

Research output: Contribution to journal › Article › peer-review

111 Scopus citations

Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

King, D. C., Taylor, J., Zhang, Y., Cheng, Y., Lawson, H. A., Martin, J., Chiaromonte, F., Miller, W. & Hardison, R. C., Jun 2007, In: Genome research. 17, 6, p. 775-786 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

66 Scopus citations

Finding treasures in frozen cells: New centriole intermediates

Dutcher, S. K., Jul 2007, In: BioEssays. 29, 7, p. 630-634 5 p.

Research output: Contribution to journal › Review article › peer-review

24 Scopus citations

Functional variants in TAS2R38 and TAS2R16 influence alcohol consumption in high-risk families of African-American origin

Wang, J. C., Hinrichs, A. L., Bertelsen, S., Stock, H., Budde, J. P., Dick, D. M., Bucholz, K. K., Rice, J., Saccone, N., Edenberg, H. J., Hesselbrock, V., Kuperman, S., Schuckit, M. A., Bierut, L. J. & Goate, A. M., Feb 2007, In: Alcoholism: Clinical and Experimental Research. 31, 2, p. 209-215 7 p.

Research output: Contribution to journal › Article › peer-review

99 Scopus citations

Genetic control of dorsoventral patterning and neuroblast specification in the Drosophila Central Nervous System

Zhao, G., Wheeler, S. R. & Skeath, J. B., 2007, In: International Journal of Developmental Biology. 51, 2, p. 107-115 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

19 Scopus citations

Genotype-by-sex interaction on fasting insulin concentration: The HyperGEN study

North, K. E., Franceschini, N., Borecki, I. B., Gu, C. C., Heiss, G., Province, M. A., Arnett, D. K., Lewis, C. E., Miller, M. B., Myers, R. H., Hunt, S. C. & Freedman, B. I., Jan 2007, In: Diabetes. 56, 1, p. 137-142 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

Glutamate receptor activation evokes calpain-mediated degradation of Sp3 and Sp4, the prominent Sp-family transcription factors in neurons

Mao, X., Yang, S. H., Simpkins, J. W. & Barger, S. W., Mar 2007, In: Journal of Neurochemistry. 100, 5, p. 1300-1314 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

43 Scopus citations

HC-Pro protein of Potato virus Y can interact with three Arabidopsis 20S proteasome subunits in planta

Jin, Y., Ma, D., Dong, J., Jin, G., Li, D., Deng, C. & Wang, T., Dec 2007, In: Journal of virology. 81, 23, p. 12881-12888 8 p.

Research output: Contribution to journal › Article › peer-review

66 Scopus citations

Identification of muscle-specific regulatory modules in Caenorhabditis elegans

Zhao, G., Schriefer, L. A. & Stormo, G. D., Mar 2007, In: Genome research. 17, 3, p. 348-357 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

35 Scopus citations

Identification of photoreceptor genes affected by PRPF31 mutations associated with autosomal dominant retinitis pigmentosa

Mordes, D., Yuan, L., Xu, L., Kawada, M., Molday, R. S. & Wu, J. Y., May 2007, In: Neurobiology of Disease. 26, 2, p. 291-300 10 p.

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

Inactive full-length p53 mutants lacking dominant wild-type p53 inhibition highlight loss of heterozygosity as an important aspect of p53 status in human cancers

Dearth, L. R., Qian, H., Wang, T., Baroni, T. E., Zeng, J., Chen, S. W., Yi, S. Y. & Brachmann, R. K., Feb 2007, In: Carcinogenesis. 28, 2, p. 289-298 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

103 Scopus citations

Irritable bowel syndrome: A co-twin control analysis

Wojczynski, M. K., North, K. E., Pedersen, N. L. & Sullivan, P. F., Oct 2007, In: American Journal of Gastroenterology. 102, 10, p. 2220-2229 10 p.

Research output: Contribution to journal › Article › peer-review

35 Scopus citations

Keeping an eye on I1:I1 Dynein as a model for flagellar dynein assembly and regulation

Wirschell, M., Hendrickson, T. & Sale, W. S., Aug 2007, In: Cell Motility and the Cytoskeleton. 64, 8, p. 569-579 11 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

76 Scopus citations

Linking pattern formation to cell-type specification: Dichaete and Ind directly repress achaete gene expression in the Drosophila CNS

Zhao, G., Boekhoff-Falk, G., Wilson, B. A. & Skeath, J. B., Mar 6 2007, In: Proceedings of the National Academy of Sciences of the United States of America. 104, 10, p. 3847-3852 6 p.

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Mice lacking sister chromatid cohesion protein PDS5B exhibit developmental abnormalities reminiscent of Cornelia de Lange syndrome

Zhang, B., Jain, S., Song, H., Fu, M., Heuckeroth, R. O., Erlich, J. M., Jay, P. Y. & Milbrandt, J., Sep 2007, In: Development. 134, 17, p. 3191-3201 11 p.

Research output: Contribution to journal › Article › peer-review

88 Scopus citations

Misexpression of Pou3f1 results in peripheral nerve hypomyelination and axonal loss

Ryu, E. J., Wang, J. Y. T., Le, N., Baloh, R. H., Gustin, J. A., Schmidt, R. E. & Milbrandt, J., Oct 24 2007, In: Journal of Neuroscience. 27, 43, p. 11552-11559 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

48 Scopus citations

Department of Genetics

Research output

Search results