Extracting knowledge from gene expression data: A case study of Batten Disease. - Simon M. Lin; Sumeer Dhar; Rose-Mary N. Boustany (BIOKDD, 2001)

Critical Assessment of Microarray Data Analysis: the 2001 challenge. - Kimberly F. Johnson; Simon M. Lin (Bioinform., 2001)

ICA and PLS modeling for functional analysis and drug sensitivity for DNA microarray signals. - Xuejun Liao; Nilanjan Dasgupta; Simon M. Lin; Lawrence Carin (ICASSP, 2002)

Applications of Tree-Maps to hierarchical biological data. - Patrick McConnell; Kimberly F. Johnson; Simon M. Lin (Bioinform., 2002)

Sequential modeling for identifying CpG island locations in human genome. - Nilanjan Dasgupta; Simon M. Lin; Lawrence Carin (IEEE Signal Process. Lett., 2002)

MedlineR: an open source library in R for Medline literature data mining. - Simon M. Lin; Patrick McConnell; Kimberly F. Johnson; Jennifer Shoemaker (Bioinform., 2004)

Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. - Pan Du 004; Warren A. Kibbe; Simon M. Lin (Bioinform., 2006)

Application of Wavelet Transform to the MS-based Proteomics Data Preprocessing. - Pan Du 004; Simon M. Lin; Warren A. Kibbe; Haihui Wang (BIBE, 2007)

lumi: a pipeline for processing Illumina microarray. - Pan Du 004; Warren A. Kibbe; Simon M. Lin (Bioinform., 2008)

2009 and beyond: the decade of personalised medicine. - Pan Du; Simon M. Lin; Mary Qu Yang; Jack Y. Yang (Int. J. Comput. Biol. Drug Des., 2008)

A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays. - Chia-Ju Lee; Dong Fu; Pan Du 004; Hongmei Jiang; Simon M. Lin; Warren A. Kibbe (Int. J. Comput. Biol. Drug Des., 2008)

From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. - Pan Du 004; Gang Feng; Jared Flatow; Jie Song; Michelle Holko; Warren A. Kibbe; Simon M. Lin (Bioinform., 2009)

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. - Pan Du 004; Xiao Zhang; Chiang-Ching Huang; Nadereh Jafari; Warren A. Kibbe; Lifang Hou; Simon M. Lin (BMC Bioinform., 2010)

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. - Lihua Julie Zhu; Claude Gazin; Nathan D. Lawson; Hervé Pagès; Simon M. Lin; David S. Lapointe; Michael R. Green (BMC Bioinform., 2010)

PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011. - Pedro Madrigal; Noa Sela; Simon M. Lin (PLoS Comput. Biol., 2011)

An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics. - Matthias Samwald; Robert R. Freimuth; Joanne S. Luciano; Simon M. Lin; Robert L. Powers; M. Scott Marshall; Klaus-Peter Adlassnig; Michel Dumontier; Richard D. Boyce (MedInfo, 2013)

The disease and gene annotations (DGA): an annotation resource for human disease. - Kai Peng 001; Wei Xu 038; Jianyong Zheng; Kegui Huang; Huisong Wang; Jiansong Tong; Zhifeng Lin; Jun Liu; Wenqing Cheng; Dong Fu; Pan Du 004; Warren A. Kibbe; et al. (Nucleic Acids Res., 2013)

Mining massive SNP data for identifying associated SNPs and uncovering gene relationships. - Amy Webb; Aaron Albin; Zhan Ye; Majid Rastegar-Mojarad; Kun Huang 001; Jeffrey D. Parvin; Wolfgang Sadee; Lang Li 001; Simon M. Lin; Yang Xiang (BCB, 2014)

Privacy in Pharmacogenetics: An End-to-End Case Study of Personalized Warfarin Dosing. - Matthew Fredrikson; Eric Lantz; Somesh Jha; Simon M. Lin; David Page; Thomas Ristenpart (USENIX Security Symposium, 2014)

Application of clinical text data for phenome-wide association studies (PheWASs). - Scott J. Hebbring; Majid Rastegar-Mojarad; Zhan Ye; John Mayer; Crystal Jacobson; Simon M. Lin (Bioinform., 2015)

Investigating properties of a family of quantum Rényi divergences. - Simon M. Lin; Marco Tomamichel (Quantum Inf. Process., 2015)

Evaluation of a Machine Learning Method to Rank PubMed Central Articles For Clinical Relevancy: NCH at TREC 2016 Clinical Decision Support Track. - Wei Chen; Soheil Moosavinasab; Steve Rust; Yungui Huang; Simon M. Lin; Anna Zemke; Ariana Prinzbach (TREC, 2016)

'RE: fine drugs': an interactive dashboard to access drug repurposing opportunities. - Soheil Moosavinasab; Jeremy A. Patterson; Robert Strouse; Majid Rastegar-Mojarad; Kelly Regan; Philip R. O. Payne; Yungui Huang; Simon M. Lin (Database J. Biol. Databases Curation, 2016)

WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data. - Zhan Ye; Christopher Kadolph; Robert Strenn; Daniel Wall; Elizabeth McPherson; Simon M. Lin (Comput. Biol. Medicine, 2016)

Vitals Risk Index: A Simplified Pediatric Early Warning Index that Relies Solely on Objective Measures. - Tyler Gorham; Steven W. Rust; Jing Yang; James Lin; Richard Hoyt; Swan Bee Liu; Jeffrey Hoffman; Tensing Maa; Yungui Huang; Simon M. Lin (AMIA, 2017)

Genome Dashboard: An Interactive Tool for the Exploration of Human Genomic Variants and Phenotypic Associations. - Katherine Miller; Rajeswari Swaminathan; Soheil Moosavinasab; Robert Strouse; Matthew Bailey 002; Yungui Huang; Simon M. Lin (AMIA, 2017)

DeepSuggest: Query Expansion for Clinical Notes by Deep Learning. - Emre Sezgin; Koushik Jinna; Tran Bourgeois; Soheil Moosavinasab; Yungui Huang; Simon M. Lin (AMIA, 2017)

Sharing exome sequencing data between Clinical Sequencing Labs and Healthcare Providers. - Rajeswari Swaminathan; Yungui Huang; Katherine Miller; Matthew Pastore; Sayaka Hashimoto; Theodora Jacobson; Danielle Mouhlas; Simon M. Lin (AMIA, 2017)

Clinical exome sequencing reports: current informatics practice and future opportunities. - Rajeswari Swaminathan; Yungui Huang; Caroline Astbury; Sara Fitzgerald-Butt; Katherine Miller; Justin Cole; Christopher W. Bartlett; Simon M. Lin (J. Am. Medical Informatics Assoc., 2017)

Simplified Readability Metric Drives Improvement of Radiology Reports: an Experiment on Ultrasound Reports at a Pediatric Hospital. - Wei Chen; Claire Durkin; Yungui Huang; Brent Adler; Steve Rust; Simon M. Lin (J. Digit. Imaging, 2017)

Variation in After-hours EHR Usage among Ambulatory Care Physicians. - Selasi Attipoe; Yungui Huang; Sharon B. Schweikhart; Simon M. Lin (AMIA, 2018)

Char2Vec: Learning the Semantic Embedding of Rare and Unseen Words in the Biomedical Literature. - Syed-Amad A. Hussain; Soheil Moosavinasab; Emre Sezgin; Yungui Huang; Simon M. Lin (AMIA, 2018)

A roadmap of transition to health independence: A patient-centered study of self-management and digital-health solutions among teens with chronic conditions. - Emre Sezgin; Monica Weiler; Anthony Weiler; Simon M. Lin (AMIA, 2018)

DeepChild: Hospitalization Prediction via Neural Network. - Xianlong Zeng; Soheil Moosavinasab; Enju Lin; Yungui Huang; Chang Liu 028; Simon M. Lin (AMIA, 2018)

Prediction of Clinical Outcomes of Spinal Muscular Atrophy Using Motion Tracking Data and Elastic Net Regression. - David Chen; Steve Rust; En-Ju D. Lin; Simon M. Lin; Leslie Nelson; Lindsay Alfano; Linda P. Lowes (BCB, 2018)

Phrase2VecGLM: Neural generalized language model-based semantic tagging for complex query reformulation in medical IR. - Manirupa Das; Eric Fosler-Lussier; Simon M. Lin; Soheil Moosavinasab; David Chen; Steve Rust; Yungui Huang; Rajiv Ramnath (BioNLP, 2018)

Identifying Candidates for Medical Coding Audits: Demonstration of a Data Driven Approach to Improve Medicare Severity Diagnosis-Related Group Coding Compliance. - Yunyi Feng; Simon M. Lin; Enju Lin; Lesley Farley; Yungui Huang; Chang Liu 028 (HIS, 2019)

SurfCon: Synonym Discovery on Privacy-Aware Clinical Data. - Zhen Wang 041; Xiang Yue; Soheil Moosavinasab; Yungui Huang; Simon M. Lin; Huan Sun 001 (KDD, 2019)

Device-free Sleep Stage Recognition through Bed Frame Vibration Sensing. - Zhizhang Hu; Emre Sezgin; Simon M. Lin; Pei Zhang 001; Hae Young Noh; Shijia Pan (DFHS@BuildSys, 2019)

Distributed representation of patients and its use for medical cost prediction. - Xianlong Zeng; Soheil Moosavinasab; En-Ju D. Lin; Simon M. Lin; Razvan C. Bunescu; Chang Liu 028 (CoRR, 2019)

Sequence-to-Set Semantic Tagging: End-to-End Multi-label Prediction using Neural Attention for Complex Query Reformulation and Automated Text Categorization. - Manirupa Das; Juanxi Li; Eric Fosler-Lussier; Simon M. Lin; Soheil Moosavinasab; Steve Rust; Yungui Huang; Rajiv Ramnath (CoRR, 2019)

Transcending Dimensions: a Comparative Analysis of Cloaca Imaging in Advancing the Surgeon's Understanding of Complex Anatomy. - Alessandra C. Gasior; Carlos Reck; Victoria Lane; Richard J. Wood; Jeremy A. Patterson; Robert Strouse; Simon M. Lin; Jennifer N. Cooper; D. Gregory Bates; Marc A. Levitt (J. Digit. Imaging, 2019)

Rationalizing Medical Relation Prediction from Corpus-level Statistics. - Zhen Wang 041; Jennifer Lee; Simon M. Lin; Huan Sun 001 (ACL, 2020)

Tasks Associated With Extreme After-hours EHR Use Among Ambulatory Care Pediatricians. - Selasi Attipoe; Yungui Huang; Sharon B. Schweikhart; Jennifer L. Hefner; Daniel M. Walker; Steven W. Rust; Jeffrey Hoffman; Simon M. Lin (AMIA, 2020)

Clinical Phrase Mining with Language Models. - Kaushik Mani; Xiang Yue; Bernal Jimenez Gutierrez; Yungui Huang; Simon M. Lin; Huan Sun 001 (BIBM, 2020)

Sequence-to-Set Semantic Tagging for Complex Query Reformulation and Automated Text Categorization in Biomedical IR using Self-Attention. - Manirupa Das; Juanxi Li; Eric Fosler-Lussier; Simon M. Lin; Steve Rust; Yungui Huang; Rajiv Ramnath (BioNLP, 2020)

Multilevel Self-Attention Model and Its Use on Medical Risk Prediction. - Xianlong Zeng; Yunyi Feng; Soheil Moosavinasab; Deborah Lin; Simon M. Lin; Chang Liu 028 (PSB, 2020)

Graph embedding on biomedical networks: methods, applications and evaluations. - Xiang Yue; Zhen Wang 041; Jingong Huang; Srinivasan Parthasarathy 001; Soheil Moosavinasab; Yungui Huang; Simon M. Lin; Wen Zhang 008; Ping Zhang 016; Huan Sun 001 (Bioinform., 2020)

COUGH: A Challenge Dataset and Models for COVID-19 FAQ Retrieval. - Xinliang Frederick Zhang; Heming Sun; Xiang Yue; Emmett Jesrani; Simon M. Lin; Huan Sun 001 (CoRR, 2020)

Transformer-based unsupervised patient representation learning based on medical claims for risk stratification and analysis. - Xianlong Zeng; Simon M. Lin; Chang Liu 028 (BCB, 2021)

CliniQG4QA: Generating Diverse Questions for Domain Adaptation of Clinical Question Answering. - Xiang Yue; Xinliang Frederick Zhang; Ziyu Yao 002; Simon M. Lin; Huan Sun 001 (BIBM, 2021)

COUGH: A Challenge Dataset and Models for COVID-19 FAQ Retrieval. - Xinliang Frederick Zhang; Heming Sun; Xiang Yue; Simon M. Lin; Huan Sun 001 (EMNLP (1), 2021)

Pre-training transformer-based framework on large-scale pediatric claims data for downstream population-specific tasks. - Xianlong Zeng; Simon M. Lin; Chang Liu 028 (CoRR, 2021)

Multi-View Deep Learning Framework for Predicting Patient Expenditure in Healthcare. - Xianlong Zeng; Simon M. Lin; Chang Liu 028 (IEEE Open J. Comput. Soc., 2021)