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in creator/contributor: "Biggin, Mark"

open access

A multi-channel gel electrophoresis and continuous fraction collection apparatus for high throughput protein separation and characterization

To facilitate a direct interface between protein separation by PAGE and protein identification by mass spectrometry, we developed a multichannel system that continuously collects fractions as protein bands migrate off the bottom of gel electrophoresis columns. The device was constructed using several short linear gel columns, each of a different percent acrylamide, to achieve a separation power similar to that of a long gradient gel. A Counter Free-Flow elution technique then allows continuous … more

Date: October 2, 2009

Creator: Choi, Megan; Nordmeyer, Robert A.; Cornell, Earl; Dong, Ming; Biggin, Mark D. & Jin, Jian

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Large-scale turnover of functional transcription factor bindingsites in Drosophila

The gain and loss of functional transcription-factor bindingsites has been proposed as a major source of evolutionary change incis-regulatory DNA and gene expression. We have developed an evolutionarymodel to study binding site turnover that uses multiple sequencealignments to assess the evolutionary constraint on individual bindingsites, and to map gain and loss events along a phylogenetic tree. Weapply this model to study the evolutionary dynamics of binding sites ofthe Drosophila melanogaste… more

Date: July 14, 2006

Creator: Moses, Alan M.; Pollard, Daniel A.; Nix, David A.; Iyer, VenkyN.; Li, Xiao-Yong; Biggin, Mark D. et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Large-Scale, Continuous-Flow Production of Stressed Biomass (Desulfovibrio vulgaris Hildenborough)

The Protein Complex Analysis Project (PCAP, http://pcap.lbl.gov/), focuses on high-throughput analysis of microbial protein complexes in the anaerobic, sulfate-reducing organism, DesulfovibriovulgarisHildenborough(DvH).Interest in DvHas a model organism for bioremediation of contaminated groundwater sites arises from its ability to reduce heavy metals. D. vulgarishas been isolated from contaminated groundwater of sites in the DOE complex. To understand the effect of environmental changes on the… more

Date: May 1, 2010

Creator: Geller, Jil T.; Borglin, Sharon E.; Fortney, Julian L.; Lam, Bonita R.; Hazen, Terry C. & Biggin, Mark D.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Quantitative Visualization of ChIP-chip Data by Using Linked Views

Most analyses of ChIP-chip in vivo DNA binding have focused on qualitative descriptions of whether genomic regions are bound or not. There is increasing evidence, however, that factors bind in a highly overlapping manner to the same genomic regions and that it is quantitative differences in occupancy on these commonly bound regions that are the critical determinants of the different biological specificity of factors. As a result, it is critical to have a tool to facilitate the quantitative visu… more

Date: November 5, 2010

Creator: Huang, Min-Yu; Weber, Gunther; Li, Xiao-Yong; Biggin, Mark & Hamann, Bernd

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Genome-wide analysis of Polycomb targets in Drosophila

Polycomb Group (PcG) complexes are multiprotein assemblages that bind to chromatin and establish chromatin states leading to epigenetic silencing. PcG proteins regulate homeotic genes in flies and vertebrates but little is known about other PcG targets and the role of the PcG in development, differentiation and disease. We have determined the distribution of the PcG proteins PC, E(Z) and PSC and of histone H3K27 trimethylation in the Drosophila genome. At more than 200 PcG target genes, binding… more

Date: April 1, 2006

Creator: Schwartz, Yuri B.; Kahn, Tatyana G.; Nix, David A.; Li,Xiao-Yong; Bourgon, Richard; Biggin, Mark et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Visually Relating Gene Expression and in vivo DNA Binding Data

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 resulting from this binding. Thus, there must be functional relationships between these two types of data. While visualization and data analysis tools exist for each data type alone, there is a lack of tools that can easily explore the relationship betwee… more

Date: September 20, 2011

Creator: Huang, Min-Yu; Mackey, Lester; Ker?; nen, Soile V. E.; Weber, Gunther H.; Jordan, Michael I. et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Zeste maintains repression of Ubx transgenes: Support for a new model of polycomb repression

During late embryogenesis, the expression domains of homeotic genes are maintained by two groups of ubiquitously expressed regulators: the Polycomb repressors and the Trithorax activators. It is not known how the activities of the two maintenance systems are initially targeted to the correct genes. Zeste and GAGA are sequence specific DNA binding proteins previously shown to be Trithorax group activators of the homeotic gene Ultrabithorax (Ubx). Here we demonstrate that Zeste and GAGA DNA bindi… more

Date: September 1, 2001

Creator: Hur, Man-Wook; Laney, Jeffrey D.; Jeon, Sang-Hack; Ali, Janann & Biggin, Mark D.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

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

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 resolution. The BDTNP team visualizes and analyzes Point-Cloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and com… more

Date: March 30, 2011

Creator: Ruebel, Oliver; Keranen, Soile V.E.; Biggin, Mark; Knowles, David W.; Weber, Gunther H.; Hagen, Hans et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

BACKGROUND: We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less … more

Date: May 15, 2009

Creator: MacArthur, Stewart; Li, Xiao-Yong; Li, Jingyi; Brown, James B.; Chu, Hou Cheng; Zeng, Lucy et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm

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 morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding … more

Date: January 10, 2008

Creator: Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard; Nix, David; Pollard, Daniel A.; Iyer, Venky N. et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-dimensional Scientific Data

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 presents tremendous challenges for effective data analysis and data exploration methods and tools. The combination and close integration of methods from scientific visualization, information visualization, automated data analysis, and other enabling techn… more

Date: June 8, 2010

Creator: Rubel, Oliver; Ahern, Sean; Bethel, E. Wes; Biggin, Mark D.; Childs, Hank; Cormier-Michel, Estelle et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

High Throughput Identification, Purification and Structural Characterization of Water Soluble Protein Complexes in Desulfovibrio vulgaris

Our scheme for the tagless purification of water soluble complexes. 10 g of protein from a crude bacterial extract is first fractionated by ammonium sulfate precipitation and then by a series of chromatographic steps: anion exchange (IEX), hydrophobic interaction (HIC), and finally size exclusion (Gel Filtration). Fractions from the last chromatography step are trypsin digested and peptides labeled with iTRAQ reagents to allow multiplexing and quantitation during mass spectrometric analysis. El… more

Date: May 17, 2010

Creator: Dong,, Ming; Han, Bong-Gyoon; Liu, Hui-Hai; Malik, J.; Geller, Jil; Yang, Li et al.

Item Type: Report

Partner: UNT Libraries Government Documents Department

open access

PointCloudExplore 2: Visual exploration of 3D gene expression

To better understand how developmental regulatory networks are defined inthe genome sequence, the Berkeley Drosophila Transcription Network Project (BDNTP)has developed a suite of methods to describe 3D gene expression data, i.e.,the output of the network at cellular resolution for multiple time points. To allow researchersto explore these novel data sets we have developed PointCloudXplore (PCX).In PCX we have linked physical and information visualization views via the concept ofbrushing (cell … more

Date: March 31, 2008

Creator: International Research Training Group Visualization of Large and Unstructured Data Sets, University of Kaiserslautern, Germany; Institute for Data Analysis and Visualization, University of California, Davis, CA; Computational Research Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA; Genomics Division, LBNL; Computer Science Department, University of California, Irvine, CA; Computer Science Division,University of California, Berkeley, CA et al.

Item Type: Report

Partner: UNT Libraries Government Documents Department

open access

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

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 present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex datasets. The interplay of data visualization and clustering-based data classification leads to improved vi… more

Date: May 12, 2008

Creator: Data Analysis and Visualization (IDAV) and the Department of Computer Science, University of California, Davis, One Shields Avenue, Davis CA 95616, USA,; nternational Research Training Group ``Visualization of Large and Unstructured Data Sets,'' University of Kaiserslautern, Germany; Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA; Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA; Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA,; Computer Science Division,University of California, Berkeley, CA, USA, et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department