Publications
List of Publications
2009
Text-mining approach to evaluate terms for ontology development.
LC Tsoi and R Patel and W Zhao and WJ Zheng
J Biomed Inform, (2009). [url]
Evaluation of genome-wide association study results through development of ontology fingerprints.
LC Tsoi and M Boehnke and RL Klein and WJ Zheng
Bioinformatics, 10: 25, (2009). [url]
GOGrapher: A Python library for GO graph representation and analysis
B Muller and AJ Richards and B Jin and X Lu
BMC Research Notes, 2, (2009). [url]
iQuantitator: A tool for protein expression inference using iTRAQ.
JH Schwacke and EG Hill and EL Krug and S Comte-Walters and KL Schey
BMC Bioinformatics, 1: 10, (2009). [url]
Quantification of protein expression changes in the aging left ventricle of Rattus norvegicus.
JE Grant and AD Bradshaw and JH Schwacke and CF Baicu and MR Zile and KL Schey
J Proteome Res, 9: 8, (2009). [url]
2008
In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen
D Plouffe and A Brinker and C McNamara and K Henson and N Kato and K Kuhen and A Nagle and F Adrian and JT Matzen and P Anderson and T Nam and NS Gray and A Chatterjee and J Janes and SF Yan and R Trager and JS Caldwell and PG Schultz and Y Zhou and EA Win
Proceedings of the National Academy of Sciences, 26: 105, (2008). [url]
Comparing methods for the assessment of reproductive activity in adult male loggerhead sea turtles Caretta caretta at Cape Canaveral, Florida
G Blanvillain and AP Pease and AL Segars and DC Rostal and AJ Richards and DW Owens
Endang Spec Res, 1: 6, (2008). [url]
Development of the philometrids Philometra overstreeti and philometroides paralichthydis in the experimentally infected copepod Oithona colcarva.
TP Bryan and LC Tsoi and I de Buron
Folia Parasitol (Praha), 4: 55, (2008).
A statistical model for iTRAQ data analysis.
EG Hill and JH Schwacke and S Comte-Walters and EH Slate and AL Oberg and JE Eckel-PassowE and TM Therneau and KL Schey
J Proteome Res, 8: 7, (2008). [url]
Multi-label literature classification based on the Gene Ontology graph
B Jin and B Muller and C Zhai and X Lu
BMC Bioinformatics, 9, (2008). [url]
Use artificial neural network to align biological ontologies.
J Huang and J Dang and MN Huhns and WJ Zheng
BMC Genomics, 9 Suppl 2, (2008). [url]
Mathematical modeling of pathogenicity of Cryptococcus neoformans.
J Garcia and J Shea and F Alvarez-Vasquez and A Qureshi and C Luberto and EO Voit and M Del Poeta
Mol Syst Biol, 4, (2008). [url]
A role for Fli-1 in B cell proliferation: Implications for SLE pathogenesis.
S Bradshaw and WJ Zheng and LC Tsoi and G Gilkeson and XK Zhang
Clin Immunol, (2008). [url]
Dynamic of Positional Enrichment: Theoretical Development and Application to Carbon Labeling in Zymomonas mobilis.
F Alvarez-Vasquez and EO Voit and YA Hannun
Biochemical Engineering Journal, 1: 40, (2008). [url]
2007
The potential for signal integration and processing in interacting MAP kinase cascades
JH Schwacke and EO Voit
J Theor Biol, 4: 246, (2007).
A guide to biochemical systems modeling of sphingolipids for the biochemist.
KJ Sims and F Alvarez-Vasquez and EO Voit and YA Hannun
Methods Enzymol, 432, (2007).
Coordination of the dynamics of yeast sphingolipid metabolism during the diauxic shift.
F Alvarez-Vasquez and KJ Sims and EO Voit and YA Hannun
Theor Biol Med Model, 1: 4, (2007). [url]
Concentration-dependent effects on the rapid and efficient activation of the MAP kinase signaling cascade
JH Schwacke and EO Voit
Proteomics, 6: 7, (2007).
A method of microarray data storage using array data type.
LC Tsoi and WJ Zheng
Comput Biol Chem, 2: 31, (2007).
Novel metrics for evaluating the functional coherence of protein groups via protein-semantic-network.
B Zheng and X Lu
Genome Biol, 7: 8, (2007). [url]
2006
Long-term ERG analysis in the partially light-damaged mouse retina reveals regressive and compensatory changes.
AJ Richards and AA Emondi and B Rohrer
Vis Neurosci, 1: 23, (2006). [url]
Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.
L Mao and WJ Zheng
BMC Bioinformatics, 7 Suppl 4, (2006).
Engineering Approaches Toward Biological Information Integration at the Systems Level.
WJ Zheng
Current Bioinformatics, 1: 1, (2006). [url]
Enhancing text categorization with semantic-enriched representation and training data augmentation.
X Lu and B Zheng and A Velivelli and C Zhai
J Am Med Inform Assoc, 5: 13, (2006). [url]
A multivariate prediction model for microarray cross-hybridization.
YA Chen and CC Chou and X Lu and EH Slate and K Peck and W Xu and EO Voit and JS Almeida
BMC Bioinformatics, 7, (2006).
Identifying biological concepts from a protein-related corpus with a probabilistic topic model.
B Zheng and DC McLean and X Lu
BMC Bioinformatics, 7, (2006). [url]
Necessary role for the Lag1p motif in (dihydro)ceramide synthase activity.
S Spassieva and JG Seo and JC Jiang and J Bielawski and F Alvarez-Vasquez and SM Jazwinski and YA Hannun and LM Obeid
J Biol Chem, 45: 281, (2006). [url]
Distinct roles for de novo versus hydrolytic pathways of sphingolipid biosynthesis in Saccharomyces cerevisiae.
LA Cowart and Y Okamoto and X Lu and YA Hannun
Biochem J, Pt 3: 393, (2006). [url]
2005
ArrayQuest: a web resource for the analysis of DNA microarray data.
GL Argraves and S Jani and JL Barth and WS Argraves
BMC Bioinformatics, 6, (2005). [url]
Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae.
F Alvarez-Vasquez and KJ Sims and LA Cowart and Y Okamoto and EO Voit and YA Hannun
Nature, 7024: 433, (2005). [url]
Computation and analysis of time-dependent sensitivities in Generalized Mass Action systems
JH Schwacke and EO Voit
J Theor Biol, 1: 236, (2005).
Object-oriented biological system integration: a SARS coronavirus example.
D Shegogue and WJ Zheng
Bioinformatics, 10: 21, (2005). [url]
Integration of the Gene Ontology into an object-oriented architecture.
D Shegogue and WJ Zheng
BMC Bioinformatics, 6, (2005). [url]
Capturing biological information with class-responsibility-collaboration cards.
D Shegogue and WJ Zheng
Bioinformatics, 3: 21, (2005). [url]
2004
Improved methods for the mathematically controlled comparison of biochemical systems
JH Schwacke and EO Voit
Theor Biol Med Model, 1, (2004).
A study of statistical methods for function prediction of protein motifs.
T Tao and CX Zhai and X Lu and H Fang
Appl Bioinformatics, 2-3: 3, (2004).
Analysis of dynamic labeling data.
EO Voit and F Alvarez-Vasquez and KJ Sims
Math Biosci, 1: 191, (2004).
A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction.
WJ Zheng and VZ Spassov and L Yan and PK Flook and S Szalma
Comput Biol Chem, 4: 28, (2004).
Yeast sphingolipid metabolism: clues and connections.
KJ Sims and SD Spassieva and EO Voit and LM Obeid
Biochem Cell Biol, 1: 82, (2004).
Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models.
F Alvarez-Vasquez and KJ Sims and YA Hannun and EO Voit
J Theor Biol, 3: 226, (2004).
Modeling cellular processes with variational Bayesian cooperative vector quantizer.
X Lu and M Hauskrecht and RS Day
Pac Symp Biocomput, (2004).
2003
The MUSC DNA Microarray Database.
GL Argraves and JL Barth and WS Argraves
Bioinformatics, 18: 19, (2003). [url]
Unexpected mobility variation among individual secretory vesicles produces an apparent refractory neuropeptide pool.
YK Ng and X Lu and A Gulacsi and W Han and MJ Saxton and ES Levitan
Biophys J, 6: 84, (2003).
Calcium requirements for exocytosis do not delimit the releasable neuropeptide pool.
X Lu and GC Ellis-Davies and ES Levitan
Cell Calcium, 4: 33, (2003).
2002
Modeling, optimization and experimental assessment of continuous L-(-)-carnitine production by Escherichia coli cultures.
F Alvarez-Vasquez and M Canovas and JL Iborra and NV Torres
Biotechnology and Bioengineering, 7: (2002).
Physical mobilization of secretory vesicles facilitates neuropeptide release by nerve growth factor-differentiated PC12 cells.
YK Ng and X Lu and ES Levitan
J Physiol, Pt 2: 542, (2002).
Efficient Boolean implementation of universal sequence maps (bUSM)
JH Schwacke and JS Almeida
BMC Bioinformatics, 3, (2002).
Nerve growth factor-induced differentiation changes the cellular organization of regulated Peptide release by PC12 cells.
YK Ng and X Lu and SC Watkins and GC Ellis-Davies and ES Levitan
J Neurosci, 10: 22, (2002).
2000
Cloning of human Ca2+ homoeostasis endoplasmic reticulum protein (CHERP): regulated expression of antisense cDNA depletes CHERP, inhibits intracellular Ca2+ mobilization and decreases cell proliferation.
JM Laplante and F ORourke and X Lu and A Fein and A Olsen and MB Feinstein
Biochem J, 348 Pt 1, (2000).
TRH regulates Kv1.5 gene expression through a Galphaq-mediated PLC-independent pathway.
TT Zhang and R Gealy and X Lu and LE Heasley and K Takimoto and ES Levitan
Mol Cell Endocrinol, 1-2: 165, (2000).
Metabolism of citric acid production by Aspergillus niger: Model definition, Steady state analysis and Constrained Optimization of citric acid production rate.
F Alvarez-Vasquez and C Gonzalez-Alcon and N Torres
Biotechnol Bioeng., 1: 70, (2000).
1999
Immunohistochemical localization of the INsP4 receptor GTPase-activating protein GAP1IP4BP in the rat brain.
AP Signore and F ORourke and X Lu and MB Feinstein and HH Yeh
J Neurosci Res, 3: 55, (1999).