An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology

Autor: Ernst, Oberortner, Robert, Evans, Xianwei, Meng, Sangeeta, Nath, Hector, Plahar, Lisa, Simirenko, Angela, Tarver, Samuel, Deutsch, Nathan J, Hillson, Jan-Fang, Cheng

Publikováno v: Methods in molecular biology (Clifton, N.J.). 2205

Biological computer-aided design and manufacturing (bioCAD/CAM) tools facilitate the design and build processes of engineering biological systems using iterative design-build-test-learn (DBTL) cycles. In this book chapter, we highlight some of the bi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::417ea1cbfd5a163b4a9ca6f0671e49b8
https://pubmed.ncbi.nlm.nih.gov/32809190

A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

Autor: Charless C Fowlkes, Kelly B Eckenrode, Meghan D Bragdon, Miriah Meyer, Zeba Wunderlich, Lisa Simirenko, Cris L Luengo Hendriks, Soile V E Keränen, Clara Henriquez, David W Knowles, Mark D Biggin, Michael B Eisen, Angela H DePace

Publikováno v: PLoS Genetics, Vol 7, Iss 10, p e1002346 (2011)

Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology

Externí odkaz: https://doaj.org/article/7df817c0d1ba41f1981d6ea5d2f6871a

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

Autor: Xiao-yong Li, Stewart MacArthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L Luengo Hendriks, Hou Cheng Chu, Nobuo Ogawa, William Inwood, Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E Celniker, David W Knowles, Tom Gingeras, Terence P Speed, Michael B Eisen, Mark D Biggin

Publikováno v: PLoS Biology, Vol 6, Iss 2, p e27 (2008)

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphoge

Externí odkaz: https://doaj.org/article/1c0cb54e3f884aad8d2824668852d428

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

Autor: Stewart MacArthur, Richard Weiszmann, Aaron Hechmer, David A. Nix, Venky N. Iyer, Mark D. Biggin, Mark Stapleton, Victor Sementchenko, Nobuo Ogawa, Terence P. Speed, Thomas R. Gingeras, Amy Beaton, Richard Bourgon, Susan E. Celniker, Daniel A. Pollard, David W. Knowles, Hou Cheng Chu, Michael B. Eisen, William Inwood, Xiao-Yong Li, Cris L. Luengo Hendriks, Lisa Simirenko

Publikováno v: PLoS Biology, Vol 6, Iss 2, p e27 (2008)
Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard; Nix, David; Pollard, Daniel A.; Iyer, Venky N.; et al.(2008). Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm. Lawrence Berkeley National Laboratory. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/1d584425
PLoS Biology

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphoge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bbf67bc24d65c3c986f7aec3fd1dda07
http://europepmc.org/articles/PMC2235902?pdf=render

Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline

Autor: Cris L, Luengo Hendriks, Soile V E, Keränen, Charless C, Fowlkes, Lisa, Simirenko, Gunther H, Weber, Angela H, DePace, Clara, Henriquez, David W, Kaszuba, Bernd, Hamann, Michael B, Eisen, Jitendra, Malik, Damir, Sudar, Mark D, Biggin, David W, Knowles

Publikováno v: Genome Biology

A suite of methods that provide the first quantitative three-dimensional description of gene expression and morphology with cellular resolution in whole Drosophila embryos is described.
Background To model and thoroughly understand animal transc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::620f365f5f4a60e2ac5ca4f5a6d3bf4d
https://pubmed.ncbi.nlm.nih.gov/17184546