BIOINFORMATICS ORIGINAL PAPER (2009)
Genome Analysis, Pan Du, Warren A. Kibbe, Simon M. Lin
doi:10.1093/bioinformatics/btl355 Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
Julie A. Dickerson, Daniel Berleant, Pan Du, Jing Ding, Carol M, Ling Li, ...
Key words: fuzzy logic, microarray analysis, gene expression networks, fuzzy cognitive
Du, Pan, Feng, Gang, Flatow, Jared, Song, Jie, Holko, Michelle, Kibbe, Warren A., ...
Subjective methods have been reported to adapt a general-purpose ontology for a specific application. For example, Gene Ontology (GO) Slim was created from GO to generate a highly aggregated report...
Lukas, Thomas J, Miao, Haixi, Chen, Lin, Riordan, Sean M, Li, Wenjun, Crabb, Andrea M, ...
Abstract Background Epidemiological and genetic studies indicate that ethnic/genetic background plays an important role in susceptibility to primary open angle glaucoma (POAG). POAG is more prevalent...
Pan Du, Warren A. Kibbe, Simon M. Lin
Motivation: A major problem for current peak detection algorithms is that noise in Mass Spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially...
Pan Du, Warren A. Kibbe, Simon M. Lin
Motivation: A major problem for current peak detection algorithms is that noise in Mass Spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially...
SMCB-E-06072004-0293 Modeling Gene Expression Networks using Fuzzy Logic (2008)
Pan Du, Jian Gong, Eve Syrkin Wurtele, Julie A. Dickerson
Abstract—Gene regulatory networks model regulation in living organisms. Fuzzy logic can effectively model gene regulation and interaction to accurately reflect the underlying biology. A new...
Du, Pan, Zhou, Bo, Cai, Chenxin
A novel glucose biosensor based on the electrocatalytic reduction of H2O2 generated by the enzymatic reaction was developed by employing single-walled carbon nanotube/nile blue A as an enzyme...
Model-based variance-stabilizing transformation for Illumina microarray data (2008)
Lin, Simon M., Du, Pan, Huber, Wolfgang, Kibbe, Warren A.
Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of...
lumi: a pipeline for processing Illumina microarray (2008)
Du, Pan, Kibbe, Warren A., Lin, Simon M.
Summary: Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray...
Du, Pan, Kibbe, Warren A, Lin, Simon M
Abstract Background Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and...
Du, Pan, Kibbe, Warren A., Lin, Simon M.
Motivation: A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially...
Multi-scale genetic network inference based on time series gene expression profiles / (2005)
This work integrates multi-scale clustering and short-time correlation to estimate genetic networks with different time resolutions and detail levels. Gene expression data are noisy and large scale....
Multi-scale genetic network inference based on time series gene expression profiles / (2005)
Thesis (Ph.D.)--Iowa State University, 2005.
Model-based variance-stabilizing transformation for Illumina microarray data
Lin, Simon M., Du, Pan, Huber, Wolfgang, Kibbe, Warren A.
Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of...
Lukas, Thomas J, Miao, Haixi, Chen, Lin, Riordan, Sean M, Li, Wenjun, Crabb, Andrea M, ...
Comparison of gene expression in normal and glaucomatous eyes from Caucasian American and African American donors reveals differences that might reflect different susceptibility to glaucoma.
Correlated Mutation Analysis on the Catalytic Domains of Serine/Threonine Protein Kinases
Xu, Feng, Du, Pan, Shen, Hongbo, Hu, Hairong, Wu, Qi, Xie, Jun, ...
Du, Pan, Feng, Gang, Flatow, Jared, Song, Jie, Holko, Michelle, Kibbe, Warren A., ...
Subjective methods have been reported to adapt a general-purpose ontology for a specific application. For example, Gene Ontology (GO) Slim was created from GO to generate a highly aggregated report...
Fang, Feng, Flegler, Ayanna J., Du, Pan, Lin, Simon, Clevenger, Charles V.
Cyclophilin B (CypB) is a 21-kDa protein with peptidyl-prolyl cis-trans isomerase activity that functions as a transcriptional inducer for Stat5 and as a ligand for CD147. To better understand the...
Xu, Feng, Du, Pan, Shen, Hongbo, Hu, Hairong, Wu, Qi, Xie, Jun, ...
Lin, Simon, Du, Pan, Jafari, Nadereh, Ouchi, Toru
Whole-genome array Comparative Genomics Hybridization (aCGH) can be used to scan chromosomes for deletions and amplifications. Because of the increased accessibility of many commercial platforms, a...