Výsledky vyhledávání - "Soile V.E. Keranen"

Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy

Autor: Clara Henriquez, Hamutal Arbel, Mark D. Biggin, Susan E. Celniker, Kenneth H. Wan, James B. Brown, Sumanta Basu, Soo Park, Peter J. Bickel, Richard Weiszmann, Benjamin W. Booth, Ann S. Hammonds, Omid Shams Solari, William W. Fisher, Soile V.E. Keranen

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America, vol 116, iss 3
Proceedings of the National Academy of Sciences of the United States of America
Arbel, H; Basu, S; Fisher, WW; Hammonds, AS; Wan, KH; Park, S; et al.(2019). Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. Proceedings of the National Academy of Sciences of the United States of America, 116(3), 900-908. doi: 10.1073/pnas.1808833115. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/6jt200hj

Significance We demonstrate a high-accuracy method for predicting enhancers genome-wide with >85% precision as validated by transgenic reporter assays in Drosophila embryos. This accuracy in a metazoan system enables us to predict with high confidenc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0a35a0f230f22332bdb66c91afb2e914
https://escholarship.org/uc/item/6jt200hj

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Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy

Autor: Richard Weiszmann, Soo Park, Clara Henriquez, Hamutal Arbel, Peter J. Bickel, Omid Shams Solari, Susan E. Celniker, Kenneth H. Wan, Mark D. Biggin, James B. Brown, Soile V.E. Keranen, William W. Fisher, Ann S. Hammonds

Identifying functional enhancers elements in metazoan systems is a major challenge. For example, large-scale validation of enhancers predicted by ENCODE reveal false positive rates of at least 70%. Here we use the pregrastrula patterning network ofDr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e815b9560030612aff673afc2fac389d

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Simulation study on effects of signaling network structure on the developmental increase in complexity

Autor: Soile V.E. Keranen

Publikováno v: Keranen, Soile V.E.(2003). Simulation study on effects of signaling network structure on the developmental increase in complexity. Lawrence Berkeley National Laboratory. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/3031b30z

The developmental increase in structural complexity in multicellular lifeforms depends on local, often non-periodic differences in gene expression. These, in turn, depend on a network of gene-gene interactions coded within the organismal genome. To s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1da8203ac45add5361ed8bc6ce732620
https://doi.org/10.1016/j.jtbi.2004.03.021

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Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data

Publikováno v: ICCS

Knowledge discovery from large and complex scientific data is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the growing number of data dimensions and data objects presen

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3657053460c196ca7bf0933de6579709
https://pubmed.ncbi.nlm.nih.gov/23762211

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Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data

Autor: Bernd Hamann, Mark D. Biggin, Oliver Rubel, Hans Hagen, David W. Knowles, Gunther H. Weber, Soile V.E. Keranen, E. Wes Bethel

Publikováno v: Mathematics and Visualization ISBN: 9783642216077
Visualization in Medicine and Life Sciences II

Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila Transcription Network Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::d58b945817696059642dc0eca795f689
https://doi.org/10.1007/978-3-642-21608-4_15

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Visually Relating Gene Expression and in vivo DNA Binding Data

Autor: Soile V.E. Keranen, Min-Yu Huang, Michael I. Jordan, David W. Knowles, Lester Mackey, Gunther H. Weber, Mark D. Biggin, Bernd Hamann

Publikováno v: BIBM

Gene expression and in vivo DNA binding data provide important information for understanding gene regulatory networks: in vivo DNA binding data indicate genomic regions where transcription factors are bound, and expression data show the output result

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::30053d9347187b574806a023a2a297fa
https://doi.org/10.1109/bibm.2011.85

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Nonparametric identification of regulatory interactions from spatial and temporal gene expression data

Autor: Claire J. Tomlin, Peter J. Bickel, Mark D. Biggin, James B. Brown, Soile V.E. Keranen, Anil Aswani, Charless C. Fowlkes, David W. Knowles

Publikováno v: BMC Bioinformatics
Aswani, Anil; Keränen, Soile VE; Brown, James; Fowlkes, Charless C; Knowles, David W; Biggin, Mark D; et al.(2010). Nonparametric identification of regulatory interactions from spatial and temporal gene expression data. BMC Bioinformatics, 11(1), 413. doi: http://dx.doi.org/10.1186/1471-2105-11-413. Retrieved from: http://www.escholarship.org/uc/item/01k390bj
BMC Bioinformatics, Vol 11, Iss 1, p 413 (2010)

Background The correlation between the expression levels of transcription factors and their target genes can be used to infer interactions within animal regulatory networks, but current methods are limited in their ability to make correct predictions

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::887bdbc777be713c72d1d875601a2576
https://pubmed.ncbi.nlm.nih.gov/20684787

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Integrating data clustering and visualization for the analysis of 3D gene expression data

Autor: Bernd Hamann, E.W. Bethel, Oliver Rubel, Michael B. Eisen, Jitendra Malik, David W. Knowles, Hans Hagen, Gunther H. Weber, C.L. Luengo Hendriks, Soile V.E. Keranen, Min-Yu Huang, Charless C. Fowlkes, Mark D. Biggin

Publikováno v: IEEE/ACM transactions on computational biology and bioinformatics. 7(1)

The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ea1b9bdb83b568ef954c4e3dd42fd372
https://pubmed.ncbi.nlm.nih.gov/20150669

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Automatic channel unmixing for high-throughput quantitative analysis of fluorescence images

Autor: DavidW. Knowles, Cris L. Luengo Hendriks, Soile V.E. Keranen, Mark D. Biggin

Publikováno v: Optics express. 15(19)

Laser-scanning microscopy allows rapid acquisition of multi-channel data, paving the way for high-throughput, high-content analysis of large numbers of images. An inherent problem of using multiple fluorescent dyes is overlapping emission spectra, wh

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::320115be07d128925c73b9340747d7b5
https://pubmed.ncbi.nlm.nih.gov/19547599

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