Zobrazeno 1 - 10
of 11
pro vyhledávání: '"Ryan G. Christensen"'
Autor:
Adam Richards, Susan E. Celniker, Jianhong Ou, Hannah Pham, Metewo Selase Enuameh, Charles Blatti, Ryan G. Christensen, Scot A. Wolfe, Majid Kazemian, Qiong Cheng, Gary D. Stormo, Jessie A. Brasefield, Victoria L. Hall, Matthew D. Basciotta, Lihua Julie Zhu, Joseph C. McNulty, Saurabh Sinha, Michael H. Brodsky, Yuna Asriyan, Cong Zhu
Publikováno v:
Genome Research. 23:928-940
Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aae5a0687c364994d35b670314e32a31
https://doi.org/10.1101/gr.151472.112
https://doi.org/10.1101/gr.151472.112
Autor:
Gary D. Stormo, Cong Zhu, Abirami Lakshmanan, Amy L. Rayla, Ankit Gupta, Benjamin Dake, Victoria L. Hall, Scot A. Wolfe, Charlotte Kuperwasser, Ryan G. Christensen
Publikováno v:
Nucleic Acids Research
Zinc-finger nucleases (ZFNs) have been used for genome engineering in a wide variety of organisms; however, it remains challenging to design effective ZFNs for many genomic sequences using publicly available zinc-finger modules. This limitation is in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0733d7171f07a4dd64b3a9742f042fd3
http://europepmc.org/articles/PMC3575815
http://europepmc.org/articles/PMC3575815
Autor:
Metewo Selase Enuameh, Gary D. Stormo, Marcus B. Noyes, Scot A. Wolfe, Ryan G. Christensen, Michael H. Brodsky
Publikováno v:
Bioinformatics
Motivation: Recognition models for protein-DNA interactions, which allow the prediction of specificity for a DNA-binding domain based only on its sequence or the alteration of specificity through rational design, have long been a goal of computationa
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::00e5f1bd2437e6cbdac136f883c21536
https://doi.org/10.1093/bioinformatics/bts202
https://doi.org/10.1093/bioinformatics/bts202
Autor:
Matthew D. Basciotta, Michael H. Brodsky, Yuna Asriyan, Cong Zhu, Ryan G. Christensen, David S. Lapointe, Lihua Julie Zhu, Metewo Selase Enuameh, Christopher J. Hull, Saurabh Sinha, Scot A. Wolfe, Jessie A. Brasefield, Majid Kazemian
Publikováno v:
Nucleic Acids Research
FlyFactorSurvey (http://pgfe.umassmed.edu/TFDBS/) is a database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system. The database provides community access to over 400 rec
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fc7f669da7ef19a6d408954296614dbd
https://doi.org/10.1093/nar/gkq858
https://doi.org/10.1093/nar/gkq858
Autor:
Gary D. Stormo, Marcus B. Noyes, Ryan G. Christensen, Scot A. Wolfe, Michael H. Brodsky, Atsuya Wakabayashi
Publikováno v:
Cell. 133:1277-1289
SummaryWe describe the comprehensive characterization of homeodomain DNA-binding specificities from a metazoan genome. The analysis of all 84 independent homeodomains from D. melanogaster reveals the breadth of DNA sequences that can be specified by
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::52bdb72ed4676f825faf6c3363cfbcd3
https://doi.org/10.1016/j.cell.2008.05.023
https://doi.org/10.1016/j.cell.2008.05.023
Autor:
Gary D. Stormo, Scot A. Wolfe, Abirami Lakshmanan, Ankit Gupta, Amy L. Rayla, Ryan G. Christensen
Publikováno v:
Nature methods
The widespread use of zinc finger nucleases (ZFNs) for genome engineering is hampered by the fact that only a subset of sequences can be efficiently recognized using published finger archives. We describe a set of validated two-finger modules that co
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ddc86d46de8437fd8f66574b52abe33f
https://doi.org/10.1038/nmeth.1994
https://doi.org/10.1038/nmeth.1994
Autor:
Ryan G. Christensen, Ankit Gupta, Metewo Selase Enuameh, Gary D. Stormo, Mathew J. Goodwin, J. Keith Joung, Manishi Pandey, Stacey Thibodeau-Beganny, Ronak Y. Patel, Michael H. Brodsky, Cong Zhu, Scot A. Wolfe, Heather A. Bell, Amy L. Rayla
Publikováno v:
Nucleic Acids Research
Cys(2)-His(2) zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d5d889cc318ff09d08f1d3e672887e2d
https://pubmed.ncbi.nlm.nih.gov/24523353
https://pubmed.ncbi.nlm.nih.gov/24523353
Autor:
Zhiping Weng, Gary D. Stormo, Marcus B. Noyes, Scot A. Wolfe, Ryan G. Christensen, Brian G. Pierce, Stephanie W. Chu, Lihua Julie Zhu
Publikováno v:
Genome research. 22(10)
The recognition potential of most families of DNA-binding domains (DBDs) remains relatively unexplored. Homeodomains (HDs), like many other families of DBDs, display limited diversity in their preferred recognition sequences. To explore the recogniti
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2ee661c975775c34546aad6da9e3531f
https://pubmed.ncbi.nlm.nih.gov/22539651
https://pubmed.ncbi.nlm.nih.gov/22539651
Autor:
Zheng Zuo, Lawrence A. Schriefer, Ankit Gupta, Ryan G. Christensen, Scot A. Wolfe, Gary D. Stormo
Publikováno v:
Nucleic Acids Research
We examine the use of high-throughput sequencing on binding sites recovered using a bacterial one-hybrid (B1H) system and find that improved models of transcription factor (TF) binding specificity can be obtained compared to standard methods of seque
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::86077605d8dffa29783ab3273bddc250
https://pubmed.ncbi.nlm.nih.gov/21507886
https://pubmed.ncbi.nlm.nih.gov/21507886
Autor:
Keith A, Crandall, Marcos, Pérez-Losada, Ryan G, Christensen, David A, McClellan, Raphael P, Viscidi
Publikováno v:
Advances in experimental medicine and biology. 577
We provide in this chapter an overview of the basic steps to reconstruct evolutionary relationships through standard phylogeny estimation approaches as well as network approaches for sequences more closely related. We discuss the importance of sequen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::af1f804afbb61378427654e7f8eacca3
https://pubmed.ncbi.nlm.nih.gov/16626026
https://pubmed.ncbi.nlm.nih.gov/16626026