Publications

Genetics, Genomics, Rare Diseases

• Genetic Diagnosis on Patients with Previously Undiagnosed Disease
• Tissues affected in rare genetic disease
• Genetic misdiagnosis and health disparities
• Pathogemic vs penetrance of genetic variants
• Best practices in clinical interpretation of human genomes
• Phenome-genome network
• Conservation of pluripotentiality signature across cancers.
• Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers
• Gene regulation and DNA damage in the ageing human brain
• sing EHR to drive discovery in disease genomics
• Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers
• Mutual information relevance networks for functional genomics clustering

Artificial Intelligence/Machine Learning

• A review in NEJM about Machine Learning in Medicine
• Adversarial attacks in medical machine learning
• Framing the challenge in medical AI
• Machine Learning/Big Data
• Longitudinal histories as predictors of future diagnoses of domestic abuse
• A unified inference procedure for a class of measures to assess improvement in risk prediction systems with survival data
• Unsupervised learning from EHRs
• EHR data biased by physician behavior
• Prediction of chronic obstructive pulmonary disease (COPD) in asthma patients using EHRs
• Bayesian approach to discovering pathogenic SNPs in conserved protein domains
• Computer 'fuzzy' controlled weaning of infants off ventilators
• Medical trend diagnosis
• Temporal reasoning in medical expert systems

Clinical Informatics

• Probabilistic Linkage Across Databases
• SMART/FHIR API for EHR
• Overdose risk from opiates after surgery
• Lightly supervised deep phenotyping
• Phenotyping Insomnia in the EHR
• Missing link for big biomedical data
• Math vs medicine (PPV)
• A translational engine at the national scale: imtegrating biology and the bedside (i2b2)
• First paper on the SMART platform for EHR apps
• Personal Internetworked Notary and Guardian
• SHRINE: Enabling Nationally Scalable Multi-Site Disease Studies
• Building national EHR via WWW (1995 3 hospital demo)

Autism

• Immunological expression signatiure in mouse FMR1 model of autism.
• Autism recurrence risk from claims databases
• Shared innate immune expression across autism + comorbities
• Model for shared dyregulation in IBD and ASD
• Diagnosing autism with auditory screening at birth
• NLP for the autism phenotype
• Inflammatory bowel disease overrepresented in patients with autism
• Precision medicine case history in autism
• Finding diverse autisms through comorbidity profiling
• Can we measure autism?
• Outliers in autism (gene expression)
• RNA editing dysregulated in autism
• Differences in blood gene expression between probands and sibs
• Predictive value of blood transcriptome in autism

Therapeutics

• R Package for drug repositioning
• Computational drug repositioning for vestibular schwannoma
• Case history of generic just as good as brand drug
• Drug target-gene signatures that predict teratogenicity are enriched for developmentally related genes
• Real-time detection of cardiotoxity for hypoglycemic agents from EHR data
• Discovering functional relationships between gene expression and chemotherapeutic sensibility
• Post-hoc detection of Vioxx effect using hospital data