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Research Output 1978 2019

2019

Allele-specific enhancer interaction at the Peg3 imprinted domain

Kim, J., Frey, W. D., Sharma, K., Ghimire, S., Teruyama, R. & Stubbs, L., Jan 1 2019, In : PloS one. 14, 10, e0224287.

Research output: Contribution to journalArticle

Open Access
Conformations
Brain
Animals
Genes
Alleles

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 5 2019, In : G3 (Bethesda, Md.). 9, 11, p. 3891-3906 16 p.

Research output: Contribution to journalArticle

Open Access
Homozygote
Phenotype
Mutation
N-Acetylgalactosaminyltransferases
Pathology

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

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

Research output: Contribution to journalArticle

Cell Lineage
Chromatin
Prostate
Essential Genes
Ureter

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. p. e12502

Research output: Contribution to journalArticle

Systems Analysis
Synaptic Transmission
Genetic Phenomena
Genes
Smegmamorpha

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

Honey
Bees
Interpersonal Relations
Nursing
Mushroom Bodies
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

Honey
Bees
Epigenomics
Mushroom Bodies
Transcription Factors

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

Gene Regulatory Networks
Genes
mice
genes
Gene Ontology

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

Smegmamorpha
Gasterosteidae
Interpersonal Relations
plasticity
chromatin

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

Chromatin
Frontal Lobe
Amygdala
Energy Metabolism
Hypothalamus
2016

A Hox-Embedded Long Noncoding RNA: Is It All Hot Air?

Selleri, L., Bartolomei, M. S., Bickmore, W. A., He, L., Stubbs, L., Reik, W. & Barsh, G. S., Dec 2016, In : PLoS genetics. 12, 12, e1006485.

Research output: Contribution to journalComment/debate

Long Noncoding RNA
RNA
Air
air
non-coding RNA

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., Jan 1 2016, In : PloS one. 11, 4, p. e0154413

Research output: Contribution to journalArticle

smooth muscle
Smooth Muscle
Muscle
Prostate
sinuses

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

RNA Polymerase III
Primates
Transfer RNA
Genes
Cell Cycle
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

Protein Isoforms
Progesterone Receptors
Stromal Cells
Cell Differentiation
Pregnancy
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. J., Aug 15 2014, In : Developmental Biology. 392, 2, p. 483-493 11 p.

Research output: Contribution to journalArticle

Homozygote
Phenotype
Mutation
Inner Ear
Point Mutation

Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies

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

Research output: Contribution to journalArticle

zinc finger motif
Zinc Fingers
Vertebrates
vertebrate
Transcription Factors

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

Smegmamorpha
Honey
Bees
Fishes
Energy Metabolism
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. J., Sep 1 2013, In : Genesis. 51, 9, p. 630-646 17 p.

Research output: Contribution to journalArticle

Pancreas
Phenotype
Brain
Lacrimal Apparatus
Retinal Ganglion Cells
2012

Editorial

Stubbs, L. J., May 1 2012, In : Briefings in Functional Genomics. 11, 3, 1 p., els021.

Research output: Contribution to journalEditorial

DNA-Binding Proteins
DNA Replication
Animals
DNA
2011

Function and evolution of C2H2 zinc finger arrays

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

Research output: Contribution to journalArticle

Zinc
Transcription Factors
Nucleotide Motifs
Proteins
DNA

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

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

Research output: Contribution to journalArticle

zinc finger motif
Zinc Fingers
Regulator Genes
regulator genes
Primates
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

Gene Regulatory Networks
Transcription Factors
Genes
Gene Expression
Proteins

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. J., Nov 1 2010, In : Molecular biology and evolution. 27, 11, p. 2606-2617 12 p.

Research output: Contribution to journalArticle

zinc finger motif
Zinc Fingers
primate
Primates
zinc
2009
Pan troglodytes
Transcription Factors
Gene Expression
Brain
Genes

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 1 2009, In : PLoS biology. 7, 5, e1000112.

Research output: Contribution to journalArticle

genome assembly
Genes
Genome
Biological Sciences
mice
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

Regulator Genes
Radiation
Genes
Mutation
Inborn Genetic Diseases
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

Vertebrates
Chickens
Chromosomes
CpG Islands
Genes

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

Linkage Disequilibrium
Chickens
Chromosomes, Human, Pair 10
Chromosomes
Quantitative Trait Loci

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

Genomic Imprinting
Genes
Proteins
Brain
Names

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

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

Research output: Contribution to journalArticle

Up-Regulation
Binding Sites
DNA Methylation
RNA Interference
Epigenomics
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 1 2006, In : Genome Research. 16, 5, p. 669-677 9 p.

Research output: Contribution to journalArticle

Zinc Fingers
History
Genes
Proteins
Mammals

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

Alleles
X Chromosome
CpG Islands
DNA Methylation
Epigenomics

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. J., May 1 2006, In : Genome Research. 16, 5, p. 584-594 11 p.

Research output: Contribution to journalArticle

Zinc Fingers
Primates
Genes
Platyrrhini
Cercopithecidae

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

Binding Sites
Genomic Imprinting
Alleles
Transcription Factors
Genes

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

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

Research output: Contribution to journalArticle

Peptide Hydrolases
Transcription Factors
Genome
Mammals
Membranes
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

Cardiomyopathies
Skin
Mutation
Skin Abnormalities
Proteins

Evolution and functional classification of vertebrate gene deserts

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

Research output: Contribution to journalArticle

Vertebrates
Genes
Human Genome
Genetic Drift
Gene Ontology

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 1 2005, In : Genome Research. 15, 1, p. 184-194 11 p.

Research output: Contribution to journalArticle

Sequence Alignment
Genome
Transcription Factors
Binding Sites
Genes

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. J., Jan 1 2005, In : Mammalian Genome. 16, 1, p. 32-40 9 p.

Research output: Contribution to journalArticle

Mutation
Introns
Genes
Gait Ataxia
Chlorambucil
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

Single Nucleotide Polymorphism
Chickens
Domestic Animals
Poultry
Nucleotides

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. J., Jul 1 2004, In : Nucleic acids research. 32, WEB SERVER ISS.

Research output: Contribution to journalArticle

Vertebrates
Genome
Sequence Alignment
Genetic Association Studies
Human Genome

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

Metaplasia
Gastritis
Hyperplasia
Helicobacter Infections
Mucins

Interpreting mammalian evolution using Fugu genome comparisons

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

Research output: Contribution to journalArticle

Takifugu
Genome
Transcriptional Regulatory Elements
Human Genome
Mammals

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

Zinc Fingers
Exons
Genes
Testis
Mammals

Photon scanning tunneling microscopy of unstained mammalian cells and chromosomes

Meriaudeau, F., Stubbs, L., Parks, J. E., Jacobson, K. B., Goudonnet, J. P. & Ferrell, T. L., Dec 1 2004, In : Proceedings of SPIE - The International Society for Optical Engineering. 2782, p. 828-835 8 p.

Research output: Contribution to journalConference article

chromosomes
Scanning tunneling microscopy
Chromosomes
Microscopy
Chromosome

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

Chromosomes, Human, Pair 19
Human Chromosomes
Genes
Chromosomes
Takifugu

zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles

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

Research output: Contribution to journalArticle

Binding Sites
Genome
Molecular Sequence Annotation
Sequence Alignment
Sequence Analysis
2003

A rule-based framework for gene regulation pathways discovery

Wilczyński, B., Hvidsten, T., Kryshtafovych, A., Stubbs, L., Komorowski, J. & Fidelis, K., Jan 1 2003, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., p. 435-436 2 p. 1227361. (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Gene expression
Transcription factors
Genes
Binding sites
Learning systems

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

Zinc Fingers
Multigene Family
Transcription Factors
Genes
Primates

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. J., Jan 1 2003, In : Cold Spring Harbor symposia on quantitative biology. 68, p. 131-140 10 p.

Research output: Contribution to journalArticle

Zinc
Transcription Factors
Genes

Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3

Kim, J., Kollhoff, A., Bergmann, A. & Stubbs, L., Feb 1 2003, In : Human molecular genetics. 12, 3, p. 233-245 13 p.

Research output: Contribution to journalReview article

YY1 Transcription Factor
Methylation
Binding Sites
Genes
Alleles