RICHEST - a web server for richness estimation in biological data

RICHEST - a web server for richness estimation in biological data

Date: February 27, 2009
Creator: Durden, Chris & Dong, Qunfeng
Description: Article discussing a web server for richness estimation in biological data called RICHness ESTimator (RICHEST).
Contributing Partner: UNT College of Arts and Sciences
Using WebGBrowse to Visualize Genome Annotation on GBrowse

Using WebGBrowse to Visualize Genome Annotation on GBrowse

Date: March 2010
Creator: Podicheti, Ram & Dong, Qunfeng
Description: Article discussing using WebGBrowse to visualize genome annotation on GBrowse.
Contributing Partner: UNT College of Arts and Sciences
WebGBrowse 2.1 - A Web Server Supporting Multiple Versions of the Generic Genome Browser for Customizable Genome Annotation Display

WebGBrowse 2.1 - A Web Server Supporting Multiple Versions of the Generic Genome Browser for Customizable Genome Annotation Display

Date: April 2011
Creator: Podicheti, Ram; Revanna, Kashi V. & Dong, Qunfeng
Description: In this book, the authors discuss WebGBrowse 2.1, one of the most popular genome browsers used by the research community.
Contributing Partner: UNT College of Arts and Sciences
Tracembler - software for in-silico chromosome walking in unassembled genomes

Tracembler - software for in-silico chromosome walking in unassembled genomes

Date: May 2007
Creator: Dong, Qunfeng; Wilkerson, Matthew D. & Brendel, Volker
Description: Article discussing Tracembler, a software for in-silico chromosome walking in unassembled genomes.
Contributing Partner: UNT College of Arts and Sciences
xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features

xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features

Date: November 20, 2006
Creator: Schlueter, Shannon D.; Wilkerson, Matthew D.; Dong, Qunfeng & Brendel, Volker
Description: Article discussing the eXtensible Genome Data Broker (xGDB) and an open-source computational infrastructure for the integrated evaluation and anlysis of genome features.
Contributing Partner: UNT College of Arts and Sciences
GSV: a web-based genome synteny viewer for customized data

GSV: a web-based genome synteny viewer for customized data

Date: 2011
Creator: Revanna, Kashi V.; Chiu, Chi-Chen; Bierschank, Ezekiel & Dong, Qunfeng
Description: Article discussing the genome synteny viewer (GSV), a web-based viewer providing a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser.
Contributing Partner: UNT College of Arts and Sciences
Enabling Large Scale Scientific Computations for Expressed Sequence Tag Sequencing over Grid and Cloud Computing Clusters

Enabling Large Scale Scientific Computations for Expressed Sequence Tag Sequencing over Grid and Cloud Computing Clusters

Date: September 2009
Creator: Pallickara, Sangmi Lee; Pierce, Marlon; Dong, Qunfeng & Kong, ChinHua
Description: This paper discusses expressed sequence tag sequencing over grid and cloud computing clusters, specifically for biological applications. In this paper, the authors propose a Web service framework for high-level job scheduling that is developed for scientific applications.
Contributing Partner: UNT College of Arts and Sciences
Investigation of the Effect of Type 2 Diabetes Mellitus on Subgingival Plaque Microbiota by High-Throughput 16S rDNA Pyrosequencing

Investigation of the Effect of Type 2 Diabetes Mellitus on Subgingival Plaque Microbiota by High-Throughput 16S rDNA Pyrosequencing

Date: April 22, 2013
Creator: Zhou, Mi; Rong, Ruichen; Munro, Daniel; Zhu, Chunxia; Gao, Xiang; Zhang, Qi et al.
Description: Article discussing the bacterial composition of subgingival plaque among diabetic and non-diabetic subjects to determine the effect that diabetes mellitus has on dental health.
Contributing Partner: UNT College of Arts and Sciences
Draft Genome Sequence of the Cyanide-Utilizing Bacterium Pseudomonas fluorescens Strain NCIMB 11764

Draft Genome Sequence of the Cyanide-Utilizing Bacterium Pseudomonas fluorescens Strain NCIMB 11764

Date: 2012
Creator: Vilo, Claudia A.; Benedik, Michael J.; Kunz, Daniel A. & Dong, Qunfeng
Description: Article discussing the draft genome sequence of the cyanide-utilizing bacterium 'Pseudomonas fluorescens' strain NCIMB 11764.
Contributing Partner: UNT College of Arts and Sciences
Genome-wide mutagenesis of Zea mays L. using RescueMu transposons

Genome-wide mutagenesis of Zea mays L. using RescueMu transposons

Date: 2004
Creator: Fernandes, John; Dong, Qunfeng; Schneider, Bret; Morrow, Darren J.; Nan, Guo-Ling; Brendel, Volker et al.
Description: This article discusses genome-wide mutagenesis of Zea mays L. using RescueMu transposons.
Contributing Partner: UNT College of Arts and Sciences
ESTPiper - a web-based analysis pipeline for expressed sequence tags

ESTPiper - a web-based analysis pipeline for expressed sequence tags

Date: April 21, 2009
Creator: Tang, Zuojian; Choi, Jeong-Hyeon; Hemmerich, Chris; Sarangi, Ankita; Colbourne, John K. & Dong, Qunfeng
Description: Article discussing ESTPiper, a web interface that streamlines the expressed sequence tags (EST) analysis process.
Contributing Partner: UNT College of Arts and Sciences
BOV - a web-based BLAST output visualization tool

BOV - a web-based BLAST output visualization tool

Date: September 15, 2008
Creator: Gollapudi, Rajesh; Revanna, Kashi V.; Hemmerich, Chris; Schaack, Sarah & Dong, Qunfeng
Description: Article discussing research on BOV, a web-based BLAST output visualization tool.
Contributing Partner: UNT College of Arts and Sciences
A web-based multi-genome synteny viewer for customized data

A web-based multi-genome synteny viewer for customized data

Date: August 2, 2012
Creator: Revanna, Kashi V.; Munro, Daniel; Gao, Alvin; Chiu, Chi-Chen; Pathak, Anil & Dong, Qunfeng
Description: This article discusses a web-based multi-genome synteny viewer for customized data.
Contributing Partner: UNT College of Arts and Sciences
TableMaker: An ad hoc Query Tool for Relational Databases

TableMaker: An ad hoc Query Tool for Relational Databases

Date: July 2008
Creator: Lushbough, Carol; Duvick, Jon; Dong, Qunfeng; Jennewein, Douglas; Reynoldson, Joe & Brendel, Volker
Description: This paper discusses an ad hoc query tool for relational databases. Most Web servers hosting biological data limit users to a defined set of search options and output formats that are short of the whole range of options available to users with direct database access. However, to make full use of the wealth of data in the database resource, it is desirable to have an intermediate solution that provides a broad range of flexible query and output options through a Web portal.
Contributing Partner: UNT College of Arts and Sciences
Multiple domains in MtENOD8 protein including the signal peptide target it to the symbiosome

Multiple domains in MtENOD8 protein including the signal peptide target it to the symbiosome

Date: May 2012
Creator: Meckfessel, Matthew H.; Blancaflor, Elison B.; Plunkett, Michael; Dong, Qunfeng & Dickstein, Rebecca
Description: Article presenting evidence from GFP fusion experiments that the MtENOD8 protein contains at least three symbiosome targeting domains, including its N-terminal signal peptide (SP).
Contributing Partner: UNT College of Arts and Sciences
Draft Genome Sequence of Cupriavidus sp. Strain SK-3, a 4-Chlorobiphenyl- and 4-Clorobenzoic Acid-Degrading Bacterium

Draft Genome Sequence of Cupriavidus sp. Strain SK-3, a 4-Chlorobiphenyl- and 4-Clorobenzoic Acid-Degrading Bacterium

Date: June 10, 2014
Creator: Vilo, Claudia A.; Benedik, Michael J.; Ilori, Matthew Olusoji & Dong, Qunfeng
Description: Article on the draft genome sequence of Cupriavidus sp. strain SK-3, a 4-chlorobiphenyl- and 4-clorobenzoic acid-degrading bacterium.
Contributing Partner: UNT College of Arts and Sciences
Draft Genome Sequence of Cupriavidus sp. Strain SK-4, a di-ortho-Substituted Biphenyl-Utilizing Bacterium Isolated from Polychlorinated Biphenyl-Contaminated Sludge

Draft Genome Sequence of Cupriavidus sp. Strain SK-4, a di-ortho-Substituted Biphenyl-Utilizing Bacterium Isolated from Polychlorinated Biphenyl-Contaminated Sludge

Date: May 1, 2014
Creator: Vilo, Claudia A.; Benedik, Michael J.; Ilori, Matthew Olusoji & Dong, Qunfeng
Description: Article on the draft genome sequence of Cupriavidus sp. strain SK-4, a di-ortho-substituted biphenyl-utilizing bacterium isolated from polychlorinated biphenyl-contaminated sludge.
Contributing Partner: UNT College of Arts and Sciences
Bacterial Community Profiling of Milk Samples as a Means to Understand Culture-Negative Bovine Clinical Mastitis

Bacterial Community Profiling of Milk Samples as a Means to Understand Culture-Negative Bovine Clinical Mastitis

Date: April 25, 2013
Creator: Kuehn, Joanna S.; Gorden, Patrick J.; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J. et al.
Description: Article discussing a study that was conducted to understand the basis of a bacterial infection that is common among dairy cows.
Contributing Partner: UNT College of Arts and Sciences
Comparative Plant Genomics Resources at Plant GDB

Comparative Plant Genomics Resources at Plant GDB

Date: October 2005
Creator: Dong, Qunfeng; Lawrence, Carolyn J.; Schlueter, Shannon D.; Wilkerson, Matthew D.; Kurtz, Stefan; Brendel, Volker et al.
Description: Article on comparative plant genomics resources at plant GDB.
Contributing Partner: UNT College of Arts and Sciences
The Microbial Communities in Male First Catch Urine Are Highly Similar to Those in Paired Urethral Swab Specimens

The Microbial Communities in Male First Catch Urine Are Highly Similar to Those in Paired Urethral Swab Specimens

Date: May 13, 2011
Creator: Dong, Qunfeng; Nelson, David E.; Toh, Evelyn; Diao, Lixia; Gao, Xiang; Fortenberry, J. Dennis et al.
Description: Article discussing the microbial communities in male first catch urine and how these are highly similar to those paired in urethral swab specimens.
Contributing Partner: UNT College of Arts and Sciences
Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets

Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets

Date: March 13, 2012
Creator: Hughes, Adam; Ruan, Yang; Ekanayake, Saliya; Bae, Seung-Hee; Dong, Qunfeng; Rho, Mina et al.
Description: This article discusses interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets.
Contributing Partner: UNT College of Arts and Sciences
Evidence of Uncultivated Bacteria in the Adult Female Bladder

Evidence of Uncultivated Bacteria in the Adult Female Bladder

Date: January 25, 2012
Creator: Wolfe, Alan J.; Toh, Evelyn; Shibata, Noriko; Rong, Ruichen; Kenton, Kimberly S.; FitzGerald, MaryPat et al.
Description: Article on evidence of uncultivated bacteria in the adult female bladder.
Contributing Partner: UNT College of Arts and Sciences
Diversity of Bacteria at Healthy Human Conjunctiva

Diversity of Bacteria at Healthy Human Conjunctiva

Date: July 2011
Creator: Dong, Qunfeng; Brulc, Jennifer M.; Iovieno, Alfonso; Bates, Brandon; Garoutte, Aaron; Miller, Darlene et al.
Description: Article on the diversity of bacteria at healthy human conjunctiva.
Contributing Partner: UNT College of Arts and Sciences
Characteristic Male Urine Microbiomes Associate with Asymptomatic Sexually Transmitted Infection

Characteristic Male Urine Microbiomes Associate with Asymptomatic Sexually Transmitted Infection

Date: November 2010
Creator: Nelson, David E.; Van Der Pol, Barbara; Dong, Qunfeng; Revanna, Kashi V.; Fan, Baochang; Easwaran, Shraddha et al.
Description: Article discussing research on characteristic male urine microbiomes associated with asymptomatic sexually transmitted infection.
Contributing Partner: UNT College of Arts and Sciences
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