Simon Lin

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 4	2016

Other Publications

Article	Year
Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic acids research\| PubMed ID: 18178591	2008
Energy landscape paving for X-ray structure determination of organic molecules. Acta crystallographica. Section A, Foundations of crystallography\| PubMed ID: 11961287	2002
Evolution and structure formation of the distribution of partition function zeros: triangular type Ising lattices with cell decoration. Physical review. E, Statistical, nonlinear, and soft matter physics\| PubMed ID: 12188800	2002
Applications of Tree-Maps to hierarchical biological data. Bioinformatics (Oxford, England)\| PubMed ID: 12217926	2002
Microarray analysis: a comparative approach. Molecular cancer therapeutics\| PubMed ID: 12467218	2002
A complexity reduction algorithm for analysis and annotation of large genomic sequences. Genome research\| PubMed ID: 12566410	2003
QA/QC as a pressing need for microarray analysis: meeting report from CAMDA'02. BioTechniques\| PubMed ID: 12664687	2003
Transcriptional profiling of the Sonic hedgehog response: a critical role for N-myc in proliferation of neuronal precursors. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12777630	2003
Data mining issues and opportunities for building nursing knowledge. Journal of biomedical informatics\| PubMed ID: 14643734	2003
MedlineR: an open source library in R for Medline literature data mining. Bioinformatics (Oxford, England)\| PubMed ID: 15284107	2004
Impaired cell adhesion and apoptosis in a novel CLN9 Batten disease variant. Annals of neurology\| PubMed ID: 15349861	2004
RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells. Molecular cancer\| PubMed ID: 15353001	2004
Loss of patched and disruption of granule cell development in a pre-neoplastic stage of medulloblastoma. Development (Cambridge, England)\| PubMed ID: 15843415	2005
Differential cardiac gene expression during cardiopulmonary bypass: ischemia-independent upregulation of proinflammatory genes. The Journal of thoracic and cardiovascular surgery\| PubMed ID: 16077395	2005
Heterogeneity of Flt3-expressing multipotent progenitors in mouse bone marrow. Journal of immunology (Baltimore, Md. : 1950)\| PubMed ID: 16210604	2005
Irrational exuberance in clinical proteomics. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 16299224	2005
What is mzXML good for? Expert review of proteomics\| PubMed ID: 16307524	2005
Molecular profile and partial functional analysis of novel endothelial cell-derived growth factors that regulate hematopoiesis. Stem cells (Dayton, Ohio)\| PubMed ID: 16373696	2006
Gene expression profiles of the rat brain both immediately and 3 months following acute sarin exposure. Biochemical pharmacology\| PubMed ID: 16376859	2006
Improved prediction of treatment response using microarrays and existing biological knowledge. Pharmacogenomics\| PubMed ID: 16610959	2006
Partition functions and finite-size scalings of Ising model on helical tori. Physical review. E, Statistical, nonlinear, and soft matter physics\| PubMed ID: 16802982	2006
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics (Oxford, England)\| PubMed ID: 16820428	2006
Grid-enabled high-throughput in silico screening against influenza A neuraminidase. IEEE transactions on nanobioscience\| PubMed ID: 17181029	2006
Master equation approach to folding kinetics of lattice polymers based on conformation networks. The Journal of chemical physics\| PubMed ID: 17430067	2007
Other riffs on cooperation are already showing how well a wiki could work. Nature\| PubMed ID: 17443163	2007
nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. Biology direct\| PubMed ID: 17540033	2007
The New York City Palliative Care Quality Improvement Collaborative. Joint Commission journal on quality and patient safety\| PubMed ID: 17566540	2007
Gene expression analysis of frontotemporal lobar degeneration of the motor neuron disease type with ubiquitinated inclusions. Acta neuropathologica\| PubMed ID: 17569064	2007
Interpreting microarray results with gene ontology and MeSH. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 17634620	2007
Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 18314582	2007
Self-similarity in the classification of finite-size scaling functions for toroidal boundary conditions. Physical review. E, Statistical, nonlinear, and soft matter physics\| PubMed ID: 18351807	2008
lumi: a pipeline for processing Illumina microarray. Bioinformatics (Oxford, England)\| PubMed ID: 18467348	2008
Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors. Genome biology\| PubMed ID: 18613964	2008
Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal African Americans and Caucasian Americans donors. PloS one\| PubMed ID: 18716680	2008
Expression of cyclophilin B is associated with malignant progression and regulation of genes implicated in the pathogenesis of breast cancer. The American journal of pathology\| PubMed ID: 19056847	2009
Overexpression of RhoA induces preneoplastic transformation of primary mammary epithelial cells. Cancer research\| PubMed ID: 19147561	2009
Intragraft TNF receptor signaling contributes to activation of innate and adaptive immunity in a renal allograft model. Transplantation\| PubMed ID: 19155971	2009
BALB/c mice genetically susceptible to proteoglycan-induced arthritis and spondylitis show colony-dependent differences in disease penetrance. Arthritis research & therapy\| PubMed ID: 19220900	2009
Genomics of human intracranial aneurysm wall. Stroke\| PubMed ID: 19228845	2009
Characterising phase variations in MALDI-TOF data and correcting them by peak alignment. Cancer informatics\| PubMed ID: 19305630	2005
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics (Oxford, England)\| PubMed ID: 19478018	2009
Annotating the human genome with Disease Ontology. BMC genomics\| PubMed ID: 19594883	2009
GATA-2 reinforces megakaryocyte development in the absence of GATA-1. Molecular and cellular biology\| PubMed ID: 19620289	2009
Using Free and Open-Source Bioconductor Packages to Analyze Array Comparative Genomics Hybridization (aCGH) Data. Current genomics\| PubMed ID: 19721812	2009
Visual annotation of the gene database. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference\| PubMed ID: 19964623	2009
2009 and beyond: the decade of personalised medicine. International journal of computational biology and drug design\| PubMed ID: 20063461	2008
A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays. International journal of computational biology and drug design\| PubMed ID: 20063464	2008
A collection of bioconductor methods to visualize gene-list annotations. BMC research notes\| PubMed ID: 20180973	2010
L-methionine-induced alterations in molecular signatures in MCF-7 and LNCaP cancer cells. Journal of cancer research and clinical oncology\| PubMed ID: 20454975	2011
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC bioinformatics\| PubMed ID: 20459804	2010
Suppression by L-methionine of cell cycle progression in LNCaP and MCF-7 cells but not benign cells. Anticancer research\| PubMed ID: 20651330	2010
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature biotechnology\| PubMed ID: 20676074	2010
Visual presentation as a welcome alternative to textual presentation of gene annotation information. Advances in experimental medicine and biology\| PubMed ID: 20865558	2010
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC bioinformatics\| PubMed ID: 21118553	2010
Epithelial regulation of mesenchymal tissue behavior. The Journal of investigative dermatology\| PubMed ID: 21228814	2011
Ultrastructural, immunofluorescence, and RNA evidence support the hypothesis of a "new" virus associated with Kawasaki disease. The Journal of infectious diseases\| PubMed ID: 21402552	2011
The early growth response gene Egr2 (Alias Krox20) is a novel transcriptional target of transforming growth factor-β that is up-regulated in systemic sclerosis and mediates profibrotic respo... The American journal of pathology\| PubMed ID: 21514423	2011
Gene expression variation between African Americans and whites is associated with coronary artery calcification: the multiethnic study of atherosclerosis. Physiological genomics\| PubMed ID: 21521779	2011
Activated TLR signaling in atherosclerosis among women with lower Framingham risk score: the multi-ethnic study of atherosclerosis. PloS one\| PubMed ID: 21698167	2011
Gene expression changes in retinal Müller (glial) cells exposed to elevated pressure. Current eye research\| PubMed ID: 21780925	2011
Egr-1 induces a profibrotic injury/repair gene program associated with systemic sclerosis. PloS one\| PubMed ID: 21931594	2011
Improved Statistical Analysis for Array CGH-Based DNA Copy Number Aberrations. Cancer informatics\| PubMed ID: 22084565	2011
PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011. PLoS computational biology\| PubMed ID: 22125481	2011
Using the bioconductor GeneAnswers package to interpret gene lists. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 22130876	2012
Mining the Gene Wiki for functional genomic knowledge. BMC genomics\| PubMed ID: 22165947	2011
Genomic sequencing in clinical trials. Journal of translational medicine\| PubMed ID: 22206293	2011
Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma. PloS one\| PubMed ID: 22428009	2012
Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. RNA (New York, N.Y.)\| PubMed ID: 22539527	2012
Opportunities in systems biology to discover mechanisms and repurpose drugs for CNS diseases. Drug discovery today\| PubMed ID: 22750722	2012
DNA methylation alterations in response to pesticide exposure in vitro. Environmental and molecular mutagenesis\| PubMed ID: 22847954	2012
Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro. Environmental toxicology and pharmacology\| PubMed ID: 22964155	2012
Technical reproducibility of genotyping SNP arrays used in genome-wide association studies. PloS one\| PubMed ID: 22970228	2012
A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads. PloS one\| PubMed ID: 23049702	2012
The Disease and Gene Annotations (DGA): an annotation resource for human disease. Nucleic acids research\| PubMed ID: 23197658	2013
A framework for annotating human genome in disease context. PloS one\| PubMed ID: 23251346	2012
Inspired by intricacy. Interviewed by Elizabeth Gardner. Health data management\| PubMed ID: 23638605	2013
Linezolid Exerts Greater Bacterial Clearance but No Modification of Host Lung Gene Expression Profiling: A Mouse MRSA Pneumonia Model. PloS one\| PubMed ID: 23826353	2013
An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. Studies in health technology and informatics\| PubMed ID: 23920613	2013
Transcriptional events during the recovery from MRSA lung infection: a mouse pneumonia model. PloS one\| PubMed ID: 23936388	2013
Some experiences and opportunities for big data in translational research. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 24008998	2013
In vitro evaluation of novel inhibitors against the NS2B-NS3 protease of dengue fever virus type 4. Molecules (Basel, Switzerland)\| PubMed ID: 24352016	2013
Rodriguez syndrome with SF3B4 mutation: a severe form of Nager syndrome? American journal of medical genetics. Part A\| PubMed ID: 24715698	2014
Patients surviving six months in hospice care: who are they? Journal of palliative medicine\| PubMed ID: 24933676	2014
Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA. BioMed research international\| PubMed ID: 24995327	2014
A google glass application to support shoppers with dietary management of diabetes. Journal of diabetes science and technology\| PubMed ID: 25015954	2014
Phenome-wide association studies demonstrating pleiotropy of genetic variants within FTO with and without adjustment for body mass index. Frontiers in genetics\| PubMed ID: 25177340	2014
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nature communications\| PubMed ID: 25254650	2014
SeqHBase: a big data toolset for family based sequencing data analysis. Journal of medical genetics\| PubMed ID: 25587064	2015
Enabling online studies of conceptual relationships between medical terms: developing an efficient web platform. JMIR medical informatics\| PubMed ID: 25600290	2014
A fuzzy-match search engine for physician directories. JMIR medical informatics\| PubMed ID: 25601050	2014
The cell cycle regulator ecdysoneless cooperates with H-Ras to promote oncogenic transformation of human mammary epithelial cells. Cell cycle (Georgetown, Tex.)\| PubMed ID: 25616580	2015
Application of clinical text data for phenome-wide association studies (PheWASs). Bioinformatics (Oxford, England)\| PubMed ID: 25657332	2015
Efficiently mining Adverse Event Reporting System for multiple drug interactions. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science\| PubMed ID: 25717411	2014
Opportunities for drug repositioning from phenome-wide association studies. Nature biotechnology\| PubMed ID: 25850054	2015
WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data. Computers in biology and medicine\| PubMed ID: 25890833	2016
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome biology\| PubMed ID: 26109056	2015
Collecting and Analyzing Patient Experiences of Health Care From Social Media. JMIR research protocols\| PubMed ID: 26137885	2015
Context-Sensitive Spelling Correction of Consumer-Generated Content on Health Care. JMIR medical informatics\| PubMed ID: 26232246	2015
A Practical Guide for Exploring Opportunities of Repurposing Drugs for CNS Diseases in Systems Biology. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 26235090	2016
A conceptual model for translating omic data into clinical action. Journal of pathology informatics\| PubMed ID: 26430534	2015
Practical considerations in genomic decision support: The eMERGE experience. Journal of pathology informatics\| PubMed ID: 26605115	2015
A Review on Genomics APIs. Computational and structural biotechnology journal\| PubMed ID: 26702340	2016
Computerized "Learn-As-You-Go" classification of traumatic brain injuries using NEISS narrative data. Accident; analysis and prevention\| PubMed ID: 26851618	2016
MD-CTS: An integrated terminology reference of clinical and translational medicine. Computational and structural biotechnology journal\| PubMed ID: 27069559	2016
Privacy in Pharmacogenetics: An End-to-End Case Study of Personalized Warfarin Dosing. Proceedings of the ... USENIX Security Symposium. UNIX Security Symposium\| PubMed ID: 27077138	2014
'RE:fine drugs': an interactive dashboard to access drug repurposing opportunities. Database : the journal of biological databases and curation\| PubMed ID: 27189611	2016
The health care and life sciences community profile for dataset descriptions. PeerJ\| PubMed ID: 27602295	2016
Associations of blood mercury, inorganic mercury, methyl mercury and bisphenol A with dental surface restorations in the U.S. population, NHANES 2003-2004 and 2010-2012. Ecotoxicology and environmental safety\| PubMed ID: 27639196	2016
MYPT1 isoforms expressed in HEK293T cells are differentially phosphorylated after GTPγS treatment. Journal of smooth muscle research = Nihon Heikatsukin Gakkai kikanshi\| PubMed ID: 27725371	2016
Patient-centered design criteria for wearable seizure detection devices. Epilepsy & behavior : E&B\| PubMed ID: 27741462	2016