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2019

Allele-specific enhancer interaction at the Peg3 imprinted domain

Kim, J., Frey, W. D., Sharma, K., Ghimire, S., Teruyama, R. & Stubbs, L., 2019, In : PloS one. 14, 10, e0224287.

Research output: Contribution to journalArticle

Open Access

A mouse mutation that dysregulates neighboring GALNT17 and AUTS2 genes is associated with phenotypes related to the human AUTS2 syndrome

Weisner, P. A., Chen, C. Y., Sun, Y., Yoo, J., Kao, W. C., Zhang, H., Baltz, E. T., Troy, J. M. & Stubbs, L., Nov 1 2019, In : G3: Genes, Genomes, Genetics. 9, 11, p. 3891-3906 16 p.

Research output: Contribution to journalArticle

Open Access

An extended regulatory landscape drives Tbx18 activity in a variety of prostate-associated cell lineages

Negi, S., Bolt, C. C., Zhang, H. & Stubbs, L., Feb 15 2019, In : Developmental Biology. 446, 2, p. 180-192 13 p.

Research output: Contribution to journalArticle

Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge

Saul, M. C., Blatti, C., Yang, W., Bukhari, S. A., Shpigler, H. Y., Troy, J. M., Seward, C. H., Sloofman, L., Chandrasekaran, S., Bell, A. M., Stubbs, L., Robinson, G. E., Zhao, S. D. & Sinha, S., Jan 2019, In : Genes, Brain and Behavior. 18, 1, p. e12502 e12502.

Research output: Contribution to journalArticle

Honey bee neurogenomic responses to affiliative and agonistic social interactions

Shpigler, H. Y., Saul, M. C., Murdoch, E. E., Corona, F., Cash-Ahmed, A. C., Seward, C. H., Chandrasekaran, S., Stubbs, L. J. & Robinson, G. E., Jan 2019, In : Genes, Brain and Behavior. 18, 1, e12509.

Research output: Contribution to journalArticle

2017

Behavioral, transcriptomic and epigenetic responses to social challenge in honey bees

Shpigler, H. Y., Saul, M. C., Murdoch, E. E., Cash-Ahmed, A. C., Seward, C. H., Sloofman, L., Chandrasekaran, S., Sinha, S., Stubbs, L. J. & Robinson, G. E., Jul 2017, In : Genes, Brain and Behavior. 16, 6, p. 579-591 13 p.

Research output: Contribution to journalArticle

Comparative analysis of weighted gene coexpression networks in human and mouse

Eidsaa, M., Stubbs, L. & Almaas, E., Nov 2017, In : PloS one. 12, 11, e0187611.

Research output: Contribution to journalArticle

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks

Bukhari, S. A., Saul, M. C., Seward, C. H., Zhang, H., Bensky, M., James, N., Zhao, S. D., Chandrasekaran, S., Stubbs, L. & Bell, A. M., Jul 2017, In : PLoS genetics. 13, 7, e1006840.

Research output: Contribution to journalArticle

Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice

Saul, M. C., Seward, C. H., Troy, J. M., Zhang, H., Sloofman, L. G., Lu, X., Weisner, P. A., Caetano-Anolles, D., Sun, H., Zhao, S. D., Chandrasekaran, S., Sinha, S. & Stubbs, L., Jun 2017, In : Genome Research. 27, 6, p. 959-972 14 p.

Research output: Contribution to journalArticle

2016

Tbx18 regulates the differentiation of periductal smooth muscle stroma and the maintenance of epithelial integrity in the prostate

Bolt, C. C., Negi, S., Guimarães-Camboa, N., Zhang, H., Troy, J. M., Lu, X., Kispert, A., Evans, S. M. & Stubbs, L., Apr 2016, In : PloS one. 11, 4, e0154413.

Research output: Contribution to journalArticle

ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression

Sun, Y., Zhang, H., Kazemian, M., Troy, J. M., Seward, C., Lu, X. & Stubbs, L., Jan 1 2016, In : Oncotarget. 7, 45, p. 72571-72592 22 p.

Research output: Contribution to journalArticle

2015

Roles of progesterone receptor A and B isoforms during human endometrial decidualization

Kaya, H. S., Hantak, A. M., Stubbs, L. J., Taylor, R. N., Bagchi, I. C. & Bagchi, M. K., Jun 1 2015, In : Molecular Endocrinology. 29, 6, p. 882-895 14 p.

Research output: Contribution to journalArticle

2014

A distant downstream enhancer directs essential expression of Tbx18 in urogenital tissues

Bolt, C. C., Elso, C. M., Lu, X., Pan, F., Kispert, A. & Stubbs, L., Aug 15 2014, In : Developmental Biology. 392, 2, p. 483-493 11 p.

Research output: Contribution to journalArticle

Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies

Liu, H., Chang, L. H., Sun, Y., Lu, X. & Stubbs, L., Mar 2014, In : Genome biology and evolution. 6, 3, p. 510-525 16 p.

Research output: Contribution to journalArticle

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Rittschof, C. C., Bukhari, S. A., Sloofman, L. G., Troy, J. M., Caetano-Anollés, D., Cash-Ahmed, A., Kent, M., Lu, X., Sanogo, Y. O., Weisner, P. A., Zhang, H., Bell, A. M., Ma, J., Sinha, S., Robinson, G. E. & Stubbs, L., Dec 16 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 50, p. 17929-17934 6 p.

Research output: Contribution to journalArticle

2013

A reciprocal translocation dissects roles of Pax6 alternative promoters and upstream regulatory elements in the development of pancreas, brain, and eye

Elso, C., Lu, X., Weisner, P. A., Thompson, H. L., Skinner, A., Carver, E. & Stubbs, L., Sep 1 2013, In : Genesis. 51, 9, p. 630-646 17 p.

Research output: Contribution to journalArticle

2011

Function and evolution of C2H2 zinc finger arrays

Stubbs, L., Sun, Y. & Caetano-Anolles, D., Jan 1 2011, In : Sub-Cellular Biochemistry. 52, p. 75-94 20 p.

Research output: Contribution to journalArticle

Gain, loss and divergence in primate Zinc-Finger genes: A rich resource for evolution of gene regulatory differences between species

Nowick, K., Fields, C., Gernat, T., Caetano-Anolles, D., Kholina, N. & Stubbs, L., Jul 1 2011, In : PloS one. 6, 6, e21553.

Research output: Contribution to journalArticle

2010

Lineage-specific transcription factors and the evolution of gene regulatory networks

Nowick, K. & Stubbs, L., Jan 16 2010, In : Briefings in Functional Genomics and Proteomics. 9, 1, p. 65-78 14 p., elp056.

Research output: Contribution to journalArticle

Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes

Nowick, K., Hamilton, A. T., Zhang, H. & Stubbs, L., Nov 1 2010, In : Molecular biology and evolution. 27, 11, p. 2606-2617 12 p.

Research output: Contribution to journalArticle

2009

Lineage-specific biology revealed by a finished genome assembly of the mouse

Church, D. M., Goodstadt, L., Hillier, L. W., Zody, M. C., Goldstein, S., She, X., Bult, C. J., Agarwala, R., Cherry, J. L., DiCuccio, M., Hlavina, W., Kapustin, Y., Meric, P., Maglott, D., Birtle, Z., Marques, A. C., Graves, T., Zhou, S., Teague, B., Potamousis, K. & 155 others, Churas, C., Place, M., Herschleb, J., Runnheim, R., Forrest, D., Amos-Landgraf, J., Schwartz, D. C., Cheng, Z., Lindblad-Toh, K., Eichler, E. E., Ponting, C. P., Muzny, D. M., Dugan-Rocha, S., Ding, Y., Scherer, S. E., Buhay, C. J., Cree, A., Hernandez, J., Holder, M., Hume, J., Jackson, L. R., Kovar, C., Lee, S. L., Lewis, L. R., Metzker, M. L., Narareth, L. V., Sabo, A., Sodergren, E., Gibbs, R. A., FitzGerald, M., Cook, A., Jaffe, D. B., Garber, M., Zimmer, A. R., Pirun, M., Russell, L., Sharpe, T., Chaturvedi, M. K. K., Wilkinson, J., LaButti, K., Yang, X., Bessette, D., Allen, N. R., Nguyen, C., Nguyen, T., Dunbar, C., Lubonja, R., Matthews, C., Liu, X., Benamara, M., Negash, T., Lokyitsang, T., Decktor, K., Piqani, B., Munson, G., Tenzin, P., Stone, S., Macdonald, P., Arachchi, H., Abouelleil, A., Lui, A., Priest, M., Gearin, G., Brown, A., Aftuck, L., Shea, T., Sykes, S., Berlin, A., Chu, J., Dooley, K., Hagopian, D., Hall, J., Hafez, N., Smith, C. L., Olandt, P., Miller, K., Ventkataraman, V., Rachupka, A., Dorris, L., Ayotte, L., Mabbitt, R., Erickson, J., Horn, A., An, P., Naylor, J. W., Settipalli, S., Lander, E. S., Wilson, R. K., Graves, T. A., Fulton, R. S., Rock, S. M., Chinwalla, A. T., Bernard, K., Courtney, L. P., Fronick, C., Fulton, L. L., O'Laughlin, M., Kremitzki, C. L., Minx, P. J., Nelson, J. O., Schatzkamer, K. L., Strong, C., Wollam, A. M., Weinstock, G. M., Yang, S. P., Rogers, J., Grafham, D., Humphray, S., Nicholson, C., Bird, C., Brown, A. J., Burton, J., Clee, C., Hunt, A., Jones, M. C., Lloyd, C., Matthews, L., Mclaren, K., Mclaren, S., McLay, K., Palmer, S. A., Plumb, R., Shownkeen, R., Sims, S., Quail, M. A., Whitehead, S. L., Willey, D. L., Deschamps, S., Kenton, S., Song, L., Do, T., Roe, B., Bouffard, G. G., Blakesley, R. W., Green, E. D., Kucherlapati, R., Grills, G., Li, L., Montgomery, K. T., Kramer, M., Speigel, L., McCombie, W. R., Lucas, S., Terry, A., Gordon, L., Stubbs, L., Denny, P., Brown, S. D. M., Mallon, A. M., Campbell, R. D., Botherby, M. R. M., Jackson, I. J., Rubenfield, M. J., Rogosin, A. M. & Smith, D. R., May 2009, In : PLoS biology. 7, 5, e1000112.

Research output: Contribution to journalArticle

2008

Germline translocations in mice: Unique tools for analyzing gene function and long-distance regulatory mechanisms

Elso, C., Lu, X., Morrison, S., Tarver, A., Thompson, H., Thurkow, H., Yamada, N. A. & Stubbs, L., Sep 25 2008, In : Journal of the National Cancer Institute - Monographs. 39, p. 91-95 5 p.

Research output: Contribution to journalArticle

2007

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Gordon, L., Yang, S., Tran-Gyamfi, M., Baggott, D., Christensen, M., Hamilton, A., Crooijmans, R., Groenen, M., Lucas, S., Ovcharenko, I. & Stubbs, L., Nov 1 2007, In : Genome Research. 17, 11, p. 1603-1613 11 p.

Research output: Contribution to journalArticle

Extent of linkage disequilibrium in chicken

Aerts, J., Megens, H. J., Veenendaal, T., Ovcharenko, I., Crooijmans, R., Gordon, L., Stubbs, L. & Groenen, M., Jul 1 2007, In : Cytogenetic and Genome Research. 117, 1-4, p. 338-345 8 p.

Research output: Contribution to journalArticle

Genomic organization and imprinting of the Peg3 domain in bovine

Kim, J., Bergmann, A., Choo, J. H. & Stubbs, L., Jul 1 2007, In : Genomics. 90, 1, p. 85-92 8 p.

Research output: Contribution to journalArticle

YY1 as a controlling factor for the Peg3 and Gnas imprinted domains

Do Kim, J., Hinz, A. K., Ha Choo, J., Stubbs, L. & Kim, J., Feb 1 2007, In : Genomics. 89, 2, p. 262-269 8 p.

Research output: Contribution to journalArticle

2006

A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors

Huntley, S., Baggott, D. M., Hamilton, A. T., Tran-Gyamfi, M., Yang, S., Kim, J., Gordon, L., Branscomb, E. & Stubbs, L., May 2006, In : Genome Research. 16, 5, p. 669-677 9 p.

Research output: Contribution to journalArticle

Allele-specific deposition of macroH2A1 in imprinting control regions

Choo, J. H., Kim, J. D., Chung, J. H., Stubbs, L. & Kim, J., Mar 1 2006, In : Human molecular genetics. 15, 5, p. 717-724 8 p.

Research output: Contribution to journalArticle

Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes

Hamilton, A. T., Huntley, S., Tran-Gyamfi, M., Baggott, D. M., Gordon, L. & Stubbs, L., May 1 2006, In : Genome Research. 16, 5, p. 584-594 11 p.

Research output: Contribution to journalArticle

Identification of clustered YY1 binding sites in imprinting control regions

Kim, J. D., Hinz, A. K., Bergmann, A., Huang, J. M., Ovcharenko, I., Stubbs, L. & Kim, J., Jul 10 2006, In : Genome Research. 16, 7, p. 901-911 11 p.

Research output: Contribution to journalArticle

Rapid evolution of a recently retroposed transcription factor YY2 in mammalian genomes

Luo, C., Lu, X., Stubbs, L. & Kim, J., Mar 1 2006, In : Genomics. 87, 3, p. 348-355 8 p.

Research output: Contribution to journalArticle

2005

A mutation in NFkB interacting protein 1 results in cardiomyopathy and abnormal skin development in wa3 mice

Herron, B. J., Rao, C., Liu, S., Laprade, L., Richardson, J. A., Oliveri, E., Semsarian, C., Millar, S. E., Stubbs, L. & Beier, D. R., Mar 1 2005, In : Human molecular genetics. 14, 5, p. 667-677 11 p.

Research output: Contribution to journalArticle

Evolution and functional classification of vertebrate gene deserts

Ovcharenko, I., Loots, G. G., Nobrega, M. A., Hardison, R. C., Miller, W. & Stubbs, L., Jan 2005, In : Genome Research. 15, 1, p. 137-145 9 p.

Research output: Contribution to journalArticle

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Ovcharenko, I., Loots, G. G., Giardine, B. M., Hou, M., Ma, J., Hardison, R. C., Stubbs, L. & Miller, W., Jan 2005, In : Genome Research. 15, 1, p. 184-194 11 p.

Research output: Contribution to journalArticle

Two reciprocal translocations provide new clues to the high mutability of the Grid2 locus

Robinson, K. O., Petersen, A. M., Morrison, S. N., Elso, C. M. & Stubbs, L., Jan 1 2005, In : Mammalian Genome. 16, 1, p. 32-40 9 p.

Research output: Contribution to journalArticle

2004

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

Wong, G. K. S., Liu, B., Wang, J., Zhang, Y., Yang, X., Zhang, Z., Meng, Q., Zhou, J., Li, D., Zhang, J., Ni, P., Li, S., Ran, L., Li, H., Zhang, J., Li, R., Li, S., Zheng, H., Lin, W., Li, G. & 94 others, Wang, X., Zhao, W., Li, J., Ye, C., Dai, M., Ruan, J., Zhou, Y., Li, Y., He, X., Zhang, Y., Wang, J., Huang, X., Tong, W., Chen, J., Ye, J., Chen, C., Wei, N., Li, G., Dong, L., Lan, F., Sun, Y., Zhang, Z., Yang, Z., Yu, Y., Huang, Y., He, D., Xi, Y., Wei, D., Qi, Q., Li, W., Shi, J., Wang, M., Xie, F., Wang, J., Zhang, X., Wang, P., Zhao, Y., Li, N., Yang, N., Dong, W., Hu, S., Zeng, C., Zheng, W., Hao, B., Hillier, L. D. W., Yang, S. P., Warren, W. C., Wilson, R. K., Brandström, M., Ellegren, H., Crooijmans, R. P. M. A., van der Poel, J. J., Bovenhuis, H., Groenen, M. A. M., Ovcharenko, I., Gordon, L., Stubbs, L., Lucas, S., Glavina, T., Aerts, A., Kaiser, P., Rothwell, L., Young, J. R., Rogers, S., Walker, B. A., van Hateren, A., Kaufman, J., Bumstead, N., Lamont, S. J., Zhou, H., Hocking, P. M., Morrice, D., de Koning, D. J., Law, A., Bartley, N., Burt, D. W., Hunt, H., Cheng, H. H., Gunnarsson, U., Wahlberg, P., Andersson, L., Kindlund, E., Tammi, M. T., Andersson, B., Webber, C., Ponting, C. P., Overton, I. M., Boardman, P. E., Tang, H., Hubbard, S. J., Wilson, S. A., Yu, J., Wang, J. & Yang, H. M., Dec 9 2004, In : Nature. 432, 7018, p. 717-722 6 p.

Research output: Contribution to journalArticle

ECR Browser: A tool for visualizing and accessing data from comparisons of multiple vertebrate genomes

Ovcharenko, I., Nobrega, M. A., Loots, G. G. & Stubbs, L., Jul 1 2004, In : Nucleic acids research. 32, WEB SERVER ISS., p. W280-W286

Research output: Contribution to journalArticle

Finishing the euchromatic sequence of the human genome

International Human Genome Sequencing Consortium, Oct 21 2004, In : Nature. 431, 7011, p. 931-945 15 p.

Research output: Contribution to journalArticle

Open Access

Heightened susceptibility to chronic gastritis, hyperplasia and metaplasia in Kcnq1 mutant mice

Elso, C. M., Lu, X., Culiat, C. T., Rutledge, J. C., Cacheiro, N. L. A., Generoso, W. M. & Stubbs, L. J., Nov 15 2004, In : Human molecular genetics. 13, 22, p. 2813-2821 9 p.

Research output: Contribution to journalArticle

Interpreting mammalian evolution using Fugu genome comparisons

Ovcharenko, I., Stubbs, L. & Loots, G. G., Nov 1 2004, In : Genomics. 84, 5, p. 890-895 6 p.

Research output: Contribution to journalArticle

Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2

Kim, J., Bergmann, A., Lucas, S., Stone, R. & Stubbs, L., Jul 1 2004, In : Genomics. 84, 1, p. 47-58 12 p.

Research output: Contribution to journalArticle

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium, Dec 9 2004, In : Nature. 432, 7018, p. 695-716 22 p.

Research output: Contribution to journalArticle

Open Access

The DNA sequence and biology of human chromosome 19

Grimwood, J., Gordon, L. A., Olsen, A., Terry, A., Schmutz, J., Lamerdin, J., Hellsten, U., Goodstein, D., Couronne, O., Tran-Gyamil, M., Aerts, A., Altherr, M., Ashworth, L., Bajorek, E., Black, S., Branscomb, E., Caenepeel, S., Carrano, A., Caoile, C., Chan, Y. M. & 78 others, Christensen, M., Cleland, C. A., Copeland, A., Dalin, E., Dehal, P., Denys, M., Detter, J. C., Escobar, J., Flowers, D., Fotopolus, D., Garcia, C., Georgescu, A. M., Glavina, T., Gomez, M., Gonzales, E., Groza, M., Hammon, N., Hawkins, T., Haydu, L., Ho, I., Huang, W., Israni, S., Jett, J., Kadner, K., Kimball, H., Kobayashi, A., Larionov, V., Leem, S. H., Lopez, F., Lou, Y., Lowry, S., Malfatti, S., Martinez, D., McCready, P., Medina, C., Morgan, J., Nelson, K., Nolan, M., Ovcharenko, I., Pitluck, S., Pollard, M., Popkie, A. P., Predki, P., Quan, G., Ramirez, L., Rash, S., Retterer, J., Rodriguez, A., Rogers, S., Salamov, A., Salazar, A., She, X., Smith, D., Slezak, T., Solovyev, V., Thayer, N., Tice, H., Tsai, M., Ustaszewska, A., Vo, N., Wagner, M., Wheeler, J., Wu, K., Xie, G., Yang, J., Dubchak, I., Furey, T. S., DeJong, P., Dickson, M., Gordon, D., Eichler, E. E., Pennacchio, L. A., Richardson, P., Stubbs, L., Rokhsar, D. S., Myers, R. M., Rubin, E. M. & Lucas, S. M., Apr 1 2004, In : Nature. 428, 6982, p. 529-535 7 p.

Research output: Contribution to journalArticle

zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles

Ovcharenko, I., Loots, G. G., Hardison, R. C., Miller, W. & Stubbs, L., Mar 1 2004, In : Genome Research. 14, 3, p. 472-477 6 p.

Research output: Contribution to journalArticle

2003

Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters

Shannon, M., Hamilton, A. T., Gordon, L., Branscomb, E. & Stubbs, L., Jun 1 2003, In : Genome Research. 13, 6 A, p. 1097-1110 14 p.

Research output: Contribution to journalArticle

Lineage-specific expansion of KRAB zinc-finger transcription factor genes: Implications for the evolution of vertebrate regulatory networks

Hamilton, A. T., Huntley, S., Kim, J., Branscomb, E. & Stubbs, L., Jan 1 2003, In : Cold Spring Harbor symposia on quantitative biology. 68, p. 131-140 10 p.

Research output: Contribution to journalArticle

2002

A new mouse model for autosomal recessive polycystic kidney disease

Chittenden, L., Lu, X., Cacheiro, N. L. A., Cain, K. T., Generoso, W., Bryda, E. C. & Stubbs, L., Jan 1 2002, In : Genomics. 79, 4, p. 499-504 6 p.

Research output: Contribution to journalArticle

Characterization of the region containing the jcpkPKD gene on mouse Chromosome 10

Price, S. J., Chittenden, L. R., Flaherty, L., O'Dell, B., Guay-Woodford, L. M., Stubbs, L. J. & Bryda, E. C., Dec 1 2002, In : Cytogenetic and Genome Research. 98, 1, p. 61-66 6 p.

Research output: Contribution to journalArticle

EMR4, a novel epidermal growth factor (EGF)-TM7 molecule up-regulated in activated mouse macrophages, binds to a putative cellular ligand on B lymphoma cell line A20.

Stacey, M., Chang, G. W., Sanos, S. L., Chittenden, L. R., Stubbs, L., Gordon, S. & Lin, H. H., Aug 9 2002, In : The Journal of biological chemistry. 277, 32, p. 29283-29293 11 p.

Research output: Contribution to journalArticle