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18 papers found.
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The Dkk3 gene encodes a vital intracellular regulator of cell proliferation

. Leonard, Deborah M. Leonard, Scot A. Wolfe, Karl J. Simin. Data curation: Jack L. Leonard, Deborah M. Leonard, Jilin Liu, Kate L. Liebmann. 22 / 27 Formal analysis: Jack L. Leonard, Deborah M. Leonard ... , Scot A. Wolfe, Jaime Rivera, Karl J. Simin. Funding acquisition: Jack L. Leonard. Investigation: Jack L. Leonard, Deborah M. Leonard, Jilin Liu, Jaime Rivera, Michelle Yang, Ryan T. Leonard, Jacob P

Targeted germ line disruptions reveal general and species-specific roles for paralog group 1 hox genes in zebrafish

Scot A Wolfe 1 Charles G Sagerstrm 0 0 Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , 364 Plantation St./LRB815, Worcester, MA 01605-2324 , USA 1

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal...

Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells

The identification of the trans-acting factors and cis-regulatory modules that are involved in human pluripotent stem cell (hPSC) maintenance and differentiation is necessary to dissect the operating regulatory networks in these processes and thereby identify nodes where signal input will direct desired cell fate decisions in vitro or in vivo. To deconvolute these networks, we...

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

ChIP-based genome-wide assays of transcription factor (TF) occupancy have emerged as a powerful, high-throughput method to understand transcriptional regulation, especially on a global scale. This has led to great interest in the underlying biochemical mechanisms that direct TF-DNA binding, with the ultimate goal of computationally predicting a TF's occupancy profile in any...

Recognition models to predict DNA-binding specificities of homeodomain proteins

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 computational biology. There has been some progress in constructing useful models, especially for C2H2 zinc finger proteins, but it remains a...

An improved predictive recognition model for Cys2-His2 zinc finger proteins

Cys2-His2 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 ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred...

A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity

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 sequencing a small subset of the selected clones. We can obtain even more accurate binding models using a modified version of B1H...

Using defined finger–finger interfaces as units of assembly for constructing zinc-finger nucleases

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 part because of potential finger–finger incompatibility generated on assembly of modules into zinc-finger arrays (ZFAs). Herein, we...

Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases

also be addressed to Scot A. Wolfe. Tel: 508 856 3953; Fax: 508 856 5460; Email: Present address: Xiangdong Meng, Sangamo BioSciences, 501 Canal Blvd, Richmond, CA 94804, USA. The Author(s) 2010

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

Specificity data for groups of transcription factors (TFs) in a common regulatory network can be used to computationally identify the location of cis-regulatory modules in a genome. The primary limitation for this type of analysis is the paucity of specificity data that is available for the majority of TFs. We describe an omega-based bacterial one-hybrid system that provides a...

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

. Celniker Sudhir Kumar Scot A. Wolfe Michael H. Brodsky Saurabh Michael B. Eisen, University of California Berkeley, United States of America Cis-regulatory modules that drive precise spatial-temporal

Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish

. Giraldez 6 A. Thomas Look 3 Jonathan A. Epstein 1 Nathan D. Lawson ( 4 Scot A. Wolfe ) 4 5 0 Present address: Max-Planck Institute for Molecular Biomedicine, Laboratory for Cardiovascular Patterning

Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method

The C2H2 zinc finger is the most commonly utilized framework for engineering DNA-binding domains with novel specificities. Many different selection strategies have been developed to identify individual fingers that possess a particular DNA-binding specificity from a randomized library. In these experiments, each finger is selected in the context of a constant finger framework...

Zebrafish neurofibromatosis type 1 genes have redundant functions in tumorigenesis and embryonic development

Jimann Shin Arun Padmanabhan Eric D. de Groh Jeong-Soo Lee Sam Haidar Suzanne Dahlberg Feng Guo Shuning He Marc A. Wolman Michael Granato Nathan D. Lawson Scot A. Wolfe Seok-Hyung Kim Lilianna

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

FlyFactorSurvey ( 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 recognition motifs and position weight matrices for over 200 TFs, including many unpublished motifs. Search tools and flat file...