Annotating the human genome with Disease Ontology (2009)
Osborne, John D, Flatow, Jared, Holko, Michelle, Lin, Simon M, Kibbe, Warren A, Zhu, Lihua, ...
Abstract Background The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. Results We used the Unified...
Farkas, Balint, Boldizsar, Ferenc, Tarjanyi, Oktavia, Laszlo, Anna, Lin, Simon M, Hutas, Gabor, ...
Abstract Introduction The major histocompatibility complex (H-2d) and non-major histocompatibility complex genetic backgrounds make the BALB/c strain highly susceptible to inflammatory arthritis and...
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
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...
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...
Characterising phase variations in MALDI-TOF data and correcting (2005)
Simon M Lin, Richard P Haney, Michael J Campa, Michael C Fitzgerald, Edward F Patz, Jr
Abstract: The use of MALDI-TOF mass spectrometry as a means of analyzing the proteome has been evaluated extensively in recent years. One of the limitations of this technique that has impeded the...
Characterising phase variations in MALDI-TOF data and correcting (2005)
Simon M Lin, Richard P Haney, Michael J Campa, Michael C Fitzgerald, Edward F Patz, Jr
Abstract: The use of MALDI-TOF mass spectrometry as a means of analyzing the proteome has been evaluated extensively in recent years. One of the limitations of this technique that has impeded the...
Penalva, Luiz OF, Burdick, Michael D, Lin, Simon M, Sutterluety, Hedwig, Keene, Jack D
Abstract Background Tumors and complex tissues consist of mixtures of communicating cells that differ significantly in their gene expression status. In order to understand how different cell types...
MedlineR: an open source library in R for Medline literature data mining (2004)
Lin, Simon M., McConnell, Patrick, Johnson, Kimberly F., Shoemaker, Jennifer
Summary: We describe an open source library written in the R programming language for Medline literature data mining. This MedlineR library includes programs to query Medline through the NCBI PubMed...
MedlineR: an open source library in R for Medline literature data mining (2004)
Lin, Simon M., McConnell, Patrick, Johnson, Kimberly F., Shoemaker, Jennifer
Summary: We describe an open source library written in the R programming language for Medline literature data mining. This MedlineR library includes programs to query Medline through the NCBI PubMed...
MedlineR: an open source library in R for Medline literature data mining (2004)
Lin, Simon M., McConnell, Patrick, Johnson, Kimberly F., Shoemaker, Jennifer
Summary: We describe an open source library written in the R programming language for Medline literature data mining. This MedlineR library includes programs to query Medline through the NCBI PubMed...
Critical Assessment of Microarray Data Analysis: the 2001 challenge (2001)
Johnson, Kimberly F., Lin, Simon M.
Summary: We initiated the Critical Assessment of Microarray Data Analysis (CAMDA) conference to stimulate and evaluate the development of advanced data analysis techniques for microarrays. A standard...
Oliver, Trudy G., Grasfeder, Linda L., Carroll, Audra L., Kaiser, Constanze, Gillingham, Christine L., Lin, Simon M., ...
Cerebellar granule cells are the most abundant neurons in the brain, and granule cell precursors (GCPs) are a common target of transformation in the pediatric brain tumor medulloblastoma....
Oliver, Trudy G., Grasfeder, Linda L., Carroll, Audra L., Kaiser, Constanze, Gillingham, Christine L., Lin, Simon M., ...
Cerebellar granule cells are the most abundant neurons in the brain, and granule cell precursors (GCPs) are a common target of transformation in the pediatric brain tumor medulloblastoma....
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.
Characterising phase variations in MALDI-TOF data and correcting them by peak alignment
Lin, Simon M, Haney, Richard P, Campa, Michael J, Fitzgerald, Michael C, Patz, Edward F
The use of MALDI-TOF mass spectrometry as a means of analyzing the proteome has been evaluated extensively in recent years. One of the limitations of this technique that has impeded the development...
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...