Simon Lin

Energy landscape paving for X-ray structure determination of organic molecules.

Evolution and structure formation of the distribution of partition function zeros: triangular type Ising lattices with cell decoration.

Applications of Tree-Maps to hierarchical biological data.

Microarray analysis: a comparative approach.

A complexity reduction algorithm for analysis and annotation of large genomic sequences.

QA/QC as a pressing need for microarray analysis: meeting report from CAMDA'02.

Transcriptional profiling of the Sonic hedgehog response: a critical role for N-myc in proliferation of neuronal precursors.

Data mining issues and opportunities for building nursing knowledge.

MedlineR: an open source library in R for Medline literature data mining.

Impaired cell adhesion and apoptosis in a novel CLN9 Batten disease variant.

RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells.

Loss of patched and disruption of granule cell development in a pre-neoplastic stage of medulloblastoma.

Differential cardiac gene expression during cardiopulmonary bypass: ischemia-independent upregulation of proinflammatory genes.

Heterogeneity of Flt3-expressing multipotent progenitors in mouse bone marrow.

Irrational exuberance in clinical proteomics.

What is mzXML good for?

Molecular profile and partial functional analysis of novel endothelial cell-derived growth factors that regulate hematopoiesis.

Gene expression profiles of the rat brain both immediately and 3 months following acute sarin exposure.

Improved prediction of treatment response using microarrays and existing biological knowledge.

Partition functions and finite-size scalings of Ising model on helical tori.

Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.

Grid-enabled high-throughput in silico screening against influenza A neuraminidase.

Master equation approach to folding kinetics of lattice polymers based on conformation networks.

Other riffs on cooperation are already showing how well a wiki could work.

nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays.

The New York City Palliative Care Quality Improvement Collaborative.

Gene expression analysis of frontotemporal lobar degeneration of the motor neuron disease type with ubiquitinated inclusions.

Interpreting microarray results with gene ontology and MeSH.

Model-based variance-stabilizing transformation for Illumina microarray data.

Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).

Self-similarity in the classification of finite-size scaling functions for toroidal boundary conditions.

lumi: a pipeline for processing Illumina microarray.

Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors.

Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal African Americans and Caucasian Americans donors.

Expression of cyclophilin B is associated with malignant progression and regulation of genes implicated in the pathogenesis of breast cancer.

Overexpression of RhoA induces preneoplastic transformation of primary mammary epithelial cells.

Intragraft TNF receptor signaling contributes to activation of innate and adaptive immunity in a renal allograft model.

BALB/c mice genetically susceptible to proteoglycan-induced arthritis and spondylitis show colony-dependent differences in disease penetrance.

Genomics of human intracranial aneurysm wall.

Characterising phase variations in MALDI-TOF data and correcting them by peak alignment.

From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.

Annotating the human genome with Disease Ontology.

GATA-2 reinforces megakaryocyte development in the absence of GATA-1.

Using Free and Open-Source Bioconductor Packages to Analyze Array Comparative Genomics Hybridization (aCGH) Data.

Visual annotation of the gene database.

2009 and beyond: the decade of personalised medicine.

A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays.

A collection of bioconductor methods to visualize gene-list annotations.

L-methionine-induced alterations in molecular signatures in MCF-7 and LNCaP cancer cells.

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.

Suppression by L-methionine of cell cycle progression in LNCaP and MCF-7 cells but not benign cells.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Visual presentation as a welcome alternative to textual presentation of gene annotation information.

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis.

Epithelial regulation of mesenchymal tissue behavior.

Ultrastructural, immunofluorescence, and RNA evidence support the hypothesis of a "new" virus associated with Kawasaki disease.

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 responses.

Gene expression variation between African Americans and whites is associated with coronary artery calcification: the multiethnic study of atherosclerosis.

Activated TLR signaling in atherosclerosis among women with lower Framingham risk score: the multi-ethnic study of atherosclerosis.

Gene expression changes in retinal Müller (glial) cells exposed to elevated pressure.

Egr-1 induces a profibrotic injury/repair gene program associated with systemic sclerosis.

Improved Statistical Analysis for Array CGH-Based DNA Copy Number Aberrations.

PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011.

Using the bioconductor GeneAnswers package to interpret gene lists.

Mining the Gene Wiki for functional genomic knowledge.

Genomic sequencing in clinical trials.

Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma.

Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae.

Opportunities in systems biology to discover mechanisms and repurpose drugs for CNS diseases.

DNA methylation alterations in response to pesticide exposure in vitro.

Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro.

Technical reproducibility of genotyping SNP arrays used in genome-wide association studies.

A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.

The Disease and Gene Annotations (DGA): an annotation resource for human disease.

A framework for annotating human genome in disease context.

Inspired by intricacy. Interviewed by Elizabeth Gardner.

Linezolid Exerts Greater Bacterial Clearance but No Modification of Host Lung Gene Expression Profiling: A Mouse MRSA Pneumonia Model.

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics.

Transcriptional events during the recovery from MRSA lung infection: a mouse pneumonia model.

Some experiences and opportunities for big data in translational research.

In vitro evaluation of novel inhibitors against the NS2B-NS3 protease of dengue fever virus type 4.

Rodriguez syndrome with SF3B4 mutation: a severe form of Nager syndrome?

Patients surviving six months in hospice care: who are they?

Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA.

A google glass application to support shoppers with dietary management of diabetes.

Phenome-wide association studies demonstrating pleiotropy of genetic variants within FTO with and without adjustment for body mass index.

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

SeqHBase: a big data toolset for family based sequencing data analysis.

Enabling online studies of conceptual relationships between medical terms: developing an efficient web platform.

A fuzzy-match search engine for physician directories.

The cell cycle regulator ecdysoneless cooperates with H-Ras to promote oncogenic transformation of human mammary epithelial cells.

Application of clinical text data for phenome-wide association studies (PheWASs).

Efficiently mining Adverse Event Reporting System for multiple drug interactions.

Opportunities for drug repositioning from phenome-wide association studies.

WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data.

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

Collecting and Analyzing Patient Experiences of Health Care From Social Media.

Context-Sensitive Spelling Correction of Consumer-Generated Content on Health Care.

A Practical Guide for Exploring Opportunities of Repurposing Drugs for CNS Diseases in Systems Biology.

A conceptual model for translating omic data into clinical action.

Practical considerations in genomic decision support: The eMERGE experience.

A Review on Genomics APIs.

Computerized "Learn-As-You-Go" classification of traumatic brain injuries using NEISS narrative data.

MD-CTS: An integrated terminology reference of clinical and translational medicine.

Privacy in Pharmacogenetics: An End-to-End Case Study of Personalized Warfarin Dosing.

'RE:fine drugs': an interactive dashboard to access drug repurposing opportunities.

The health care and life sciences community profile for dataset descriptions.

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.

MYPT1 isoforms expressed in HEK293T cells are differentially phosphorylated after GTPγS treatment.

Patient-centered design criteria for wearable seizure detection devices.