High Content and High Throughput Based Discovery Platform

• A machine to make a future. (2005 pdf)
• The first commercial genomic database - DoubleTwist. (1999 pdf)
• Urine peptidomics for clinical biomarker discovery (2010 pdf)
• Proteomics and biomarkers in neonatology (2011 pdf)
• Method for the discovery of biomarkers 08/07/2007. Attorney docket: S07-242
• Proteomics studies in breast cancer (2012 pdf)
• High throughput screening informatics (2008 pdf)
• Cloud-based solution to identify statistically significant MS peaks differentiating sample categories (2013 pdf)
• FDR made easy in differential feature discovery and correlation analyses (2009 pdf); and tutorials: local FDR; Global FDR; FDR analysis
• Virtual Pharmacist: A Platform for Pharmacogenomics (2015 pdf)
• Significance Analysis and Multiple Pharmacophore Models for Differentiating P-Glycoprotein Substrates (2007 pdf)

• Kawasaki disease

  • A machine-learning algorithm for diagnosis of multisystem inflammatory syndrome in children and Kawasaki disease in the USA: a retrospective model development and validation study (2022) pdf)
  • Multicenter Validation of a Machine Learning Algorithm for Diagnosing Pediatric Patients with Multisystem Inflammatory Syndrome and Kawasaki Disease (2022) pdf)
  • Single center blind testing of a US multi-center validated diagnostic algorithm for Kawasaki disease in Asia (2022) pdf)
  • Multicentre validation of a computer-based tool for differentiation of acute Kawasaki disease from clinically similar febrile illnesses (2020 pdf)
  • Unique Molecular Patterns Uncovered in Kawasaki Disease Patients with Elevated Serum Gamma Glutamyl Transferase Levels: Implications for Intravenous Immunoglobulin Responsiveness (2016 pdf)
  • A Classification Tool for Differentiation of Kawasaki Disease from Other Febrile Illnesses. (2016; pdf)
  • A Novel Truncated Form of Serum Amyloid A in Kawasaki Disease. (2016; pdf)
  • Urinary colorimetric sensor array and algorithm to distinguish Kawasaki disease from other febrile illnesses. (2016; pdf)
  • Novel data-mining approach identifies biomarkers for diagnosis of Kawasaki disease. (2015; pdf)
  • An Improved Point-of-care Differentiation Of Kawasaki Disease From Other Febrile Illnesses. Circulation. 2015; 131: AO32. Oral presentations. IKDS 2015.
  • Point-of-Care Differentiation of Kawasaki Disease from Other Febrile Illnesses (2012 pdf);
  • A diagnostic algorithm combining clinical andmolecular data distinguishes Kawasaki diseasefrom other febrile illnesses (2011 pdf)
  • Methods for diagnosis of Kawasaki disease 7/10/2013. Attorney docket: S09-260, US patent publicaiton US2013/0316921A1, US 13/910,817, a CON of PCT/US2012/023739 02/03/2012, 61/567,321 12/06/2011, 61/444,735 02/20/2011.
  • Methods for diagnosis of Kawasaki disease 6/25/2014. Attorney docket: S14-075, provisional application 62/016,706.
  • Discrimination of Kawasaki disease from other febrile illnesses with a urinary colorimetric sensor array 8/2014. Attorney docket: S14-303.
  • Novel KD diagnostic algorithm with both "cloud" and smartphone based prediction software 12/2011. Attorney docket: S11-457.

• Pregnancy baseline

  • Gestational Dating by Urine Metabolic Profile at High Resolution Weekly Sampling Timepoints: Discovery and Validation (2022 pdf)
  • Integrated trajectories of the maternal metabolome, proteome, and immunome predict labor onset (2021 pdf)
  • Towards personalized medicine in maternal and child health: integrating biologic and social determinants (2021 pdf)
  • High-throughput quantitation of serological ceramides/dihydroceramides by LC/MS/MS: Pregnancy baseline biomarkers and potential metabolic messengers (2021 pdf, website)

• Preeclampsia disease

  • Development of a Urine Metabolomics Biomarker-Based Prediction Model for Preeclampsia during Early Pregnancy (2023 pdf)
  • Early prediction and longitudinal modeling of preeclampsia from multiomics (2022 pdf)
  • Proteomic signatures predict preeclampsia in individual cohorts but not across cohorts - implications for clinical biomarker studies. (2022 pdf)
  • Early-pregnancy prediction of risk for pre-eclampsia using maternal blood leptin/ceramide ratio: discovery and confirmation. (2021 pdf)
  • Changes in pregnancy-related serum biomarkers early in gestation are associated with later development of preeclampsia (2020 pdf)
  • Precision test for precision medicine opportunities, challenges and perspectives regarding pre-eclampsia as an intervention window for future cardiovascular disease (2016 web)
  • Integrating multiple 'omics' analyses identifies serological protein biomarkers for preeclampsia (2013 pdf)
  • Methods and compositions for providing a preeclampsia assessment 11/14/2013. Attorney docket: S11-499 (STAN-939PRV2),International publication (WO2013169751),US61/731,640, PCT/US2013/039918. 
  • Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia (2013 pdf)
  • Methods of predicting preeclampsia 3/14/2013. Attorney docket: S12-310 STAN-983PRV, US provisional application 61/783,450, PCT/US2014/026124, TIPO 092160 Ntc of Riken, Japan, Stanford, US)
• Preterm birth
  • Understanding how biologic and social determinants affect disparities in preterm birth and outcomes of preterm infants in the NICU (2021 pdf)
  • Maternal metabolic profiling to assess fetal gestational age and predict preterm delivery: a two-centre retrospective cohort study in the US (2020 journal site; pdf)
  • Plasma biomarkers in a mouse model of preterm labor (2009 pdf)
  • Investigation of maternal environmental exposures in association with self-reported preterm birth (2014 pdf)
  • Serological Targeted Analysis of an ITIH4 Peptide Isoform: A Preterm Birth Biomarker and Its Associated SNP Implications (2015 pdf)
  • SNP for predicting effectness of preterm birth diagnostic test 5/5/2014. Attorney docket: S12-344. U.S. Provisional No. 61/974,114 filed 2/23/2014.
• Neonatal diseases
  • Progressive Metabolic Abnormalities Associated with the Development of Neonatal Bronchopulmonary Dysplasia (2022 pdf)
• Necrotizing Enterocolitis
  • Progressive Metabolic Dysfunction and Nutritional Variability Precedes Necrotizing Enterocolitis (2020 pdf)
  • Urine protein biomarkers for the diagnosis and prognosis of necrotizing enterocolitis in infants (2014 pdf)
  • A novel urine peptide biomarker-based algorithmfor the prognosis of necrotising enterocolitisin human infants (2013 pdf)
  • Biomarkers for NEC and sepsis 12/20/2012. Attorney docket: S10-302 STAN-788PRV (WO 2012/174129 Al US61/496,684)
  • Parallel Analysis of serum EpCAM and MMP7 to discriminate sepsis, Necrotizing enterocolitis and normal control patients 8/15/2014. Attorney docket: S13-331,US provisional application 61/919,459.
  • A data-driven algorithm integrating clinical and laboratory features for the diagnosis and prognosis of necrotizing enterocolitis (2014, pdf)
• Renal diseases
  • Estimating One-Year Risk of Incident Chronic Kidney Disease Retrospective Development and Validation Study Using Electronic Medical Record \ Data From the State of Maine (2017, pdf)
  • Integrative Urinary Peptidomics in Renal Transplantation Identifies Biomarkers for Acute Rejection (2010 pdf)
  • Biomarkers for the diagnosis of kidney graft rejection 7/1/2014. Attorney docket: S09-365 STAN-707, International publication number (WO2011066380A1), US patent application 13/508,013.
  • Urinary peptidomic analysis identifies potential biomarkers for acute rejection of renal transplantation (2009 pdf)
• Systemic Juvenile Idiopathic Arthritis SJIA
  • Plasma profiles in active systemic juvenile idiopathicarthritis: Biomarkers and biological implications (2010 pdf) 
  • Methods for diagnosing systemic juvenile idiopathic arthritis 2/28/2013. Attorney docket: S09-405, US patent application (2013/0052665A1), related US provisional application 61/527,533 8/25/2011.
  • Urine peptidomic and targeted plasma protein analysesin the diagnosis and monitoring of Systemic JuvenileIdiopathic Arthritis (2010 pdf)
  • Methods for diagnosing systemic juvenile idiopathic arthritis 1/27/2012. Attorney docket: S07-246, US patent application 61/593,791
  • Correlation analyses of clinical and molecularfindings identify candidate biological pathways insystemic juvenile idiopathic arthritis (2012 pdf)
• Heart disease
  • Utility of smart watches for identifying arrhythmias in children(2023, pdf).
  • Exploring the feasibility of using long-term stored newborn dried blood spots to identify metabolic features for congenital heart disease screening(2023, pdf).
  • Machine Learning for Pediatric Echocardiographic Mitral Regurgitation Detection.(2022, pdf).
  • Multi-Omics Signatures Link to Ticagrelor Effects on Vascular Function in Patients With Acute Coronary Syndrome (2022, pdf).
  • Electronic Health Record-Based Prediction of 1-Year Risk of Incident Cardiac Dysrhythmia: Prospective Case-Finding Algorithm Development and Validation Study (2021, pdf).
  • Identification of patients at risk of new onset heart failure: Utilizing a large statewide health information exchange to train and validate a risk prediction model (2021, pdf).
  • Validation of a novel automated signal analysis tool for ablation of Wolff-Parkinson- White Syndrome (2019, pdf).
  • Exploring the role of polycythemia in patients with cyanosis after palliative congenital heart surgery. (2016, pdf)
  • Exploring Value in Congenital Heart Disease: An Evaluation of Inpatient Admissions. (2015, pdf)
  • Utility of Clinical Biomarkers to Predict Central Line Associated Bloodstream Infections After Congenital Heart Surgery. (2014, PMID: 25232780, pdf)
• Diabetes
  • Serological Phenotyping Analysis Uncovers a Unique Metabolomic Pattern Associated With Early Onset of Type 2 Diabetes Mellitus (2022, pdf)
  • Defining and characterizing the critical transition state prior to the type 2 diabetes disease (2017, pdf)
• Hypertension
  • Prospective prediction of incident hypertension within the next year using statewide electronic health records and machine learning (2018, pdf)
  • Prehypertension during normotensive pregnancy and postpartum clustering of cardiometabolic risk factors: A prospective cohort study. (2016, pdf)
• Cancer
  • Global metabolomics revealed deviations from the metabolic aging clock in colorectal cancer patients (2024,pdf)
  • High-throughput quantitation of amino acids and acylcarnitine in cerebrospinal fluid: identification of PCNSL biomarkers and potential metabolic messengers (2023, pdf)
  • Altered expression of the L-arginine/nitric oxide pathway in ovarian cancer: metabolic biomarkers and biological implications (2023, pdf)
  • Deviation from the precisely timed phenomic ageotypes can assist in early CRC screening and reveal underlying pathophysiology. (2020)
  • A proteomic clock for malignant gliomas: The role of the environment in tumorigenesis at the presymptomatic stage (2019)
  • Improved detection of prostate cancer using a magneto-nanosensor assay for serum circulating autoantibodies (2019)
  • Prediction of the 1-Year Risk of Incident Lung Cancer: Prospective Study Using Electronic Health Records from the State of Maine. (2019)
  • Cerebrospinal fluid protein dynamic driver network: at the crossroads of brain tumorigenesis. (2015, pdf)
  • Biomarker for ovarian cancer. Worldwide patent WO2015/042115. Attorney docket: S13-086 (STAN-1022PRV), US provisional application 61/879,051, 9/17/2013.
  • A novel serum biomarker panel for the early detection of colorectal cancer. Attorney docket: S14-001 STAN-1094PRV, US provisional application 61/979,889.
  • Proteomics studies in breast cancer (review) 2012
  • Cancer biomarker discovery via targeted profiling of multiclass tumor tissue-derived proteomes (2009 pdf)
  • Tumor associated proteome and peptidome derived serum biomarkers 9/2009. Attorney docket: S09-159, US patent application publication (US20110224101A1)
  • Multiclass cancer classification and biomarker discovery using GA-based algorithms (2005 pdf)

• Integrating multiple "omics" analyses, on a triage concept, for effective case selection followed by diagnostic colonoscopy. (2020)
• Expression of antibody-drug conjugates (ADC) biomarkers in colorectal cancer. (2020)
• Proteomic profiling to identify therapeutics targets in glioblastoma (GBM). (2020)

• Kinetics of SARS-CoV-2 Positivity of Infected and Recovered Patients: A Single Center COVID-19 Experience and Potential Implications. (2020, report)

• Industry news update by Chris Dickey, DrPH, Editor in chief www.dddmag.com - Non-overlapping gene sets in the primary human genome assemblies and RefSeq. (2003 pdf)
• A comparative analysis of HGSC and Celera human genome assemblies and gene sets (2003 pdf)
• Comparative Analysis of Human Genome Assemblies Reveals Genome-Level Differences (2001 pdf)

• An Engineered Living Intestinal Muscle Patch Produces Macroscopic Contractions that can Mix and Break Down Artificial Intestinal Contents (2023 pdf)
• Unique Molecular Patterns Uncovered in Kawasaki Disease Patients with Elevated Serum Gamma Glutamyl Transferase Levels: Implications for Intravenous Immunoglobulin Responsiveness (2016 pdf)
• PRC17, a Novel Oncogene Encoding a Rab GTPase-activating Protein, Is Amplified in Prostate Cancer (2002 pdf)
• DIAN: a novel algorithm for genome ontological classification. (2001 pdf)

• Improved detection of prostate cancer using a magneto-nanosensor assay for serum circulating autoantibodies (2019)
• Urinary colorimetric sensor array and algorithm to distinguish Kawasaki disease from other febrile illnesses. (2016; pdf)
• Pilot application of magnetic nanoparticle-based biosensor for necrotizing enterocolitis (2013 pdf)
• Ultrasensitive protein biomarker sensor U.S. Application Serial No. 14/576,967 (6/26/2015 US Patent and trademark office docketed)

Big data based health care business intelligence

• Identification of patients at risk of new onset heart failure: Utilizing a large statewide health information exchange to train and validate a risk prediction model (2021, pdf).
• Predicting 1-year mortality of acute kidney injury: a risk model using electronic health records (2021, pdf).
• Electronic Health Record-Based Prediction of 1-Year Risk of Incident Cardiac Dysrhythmia: Prospective Case-Finding Algorithm Development and Validation Study (2021, pdf).
• Identification of elders at higher risk for fall with statewide electronic health records and a machine learning algorithm (2020, pdf).
• Development of an early-warning system for high-risk patients for suicide attempt using deep learning and electronic health records (2020, pdf).
• Validation of a novel automated signal analysis tool for ablation of Wolff-Parkinson- White Syndrome (2019, pdf).
• Prediction of the 1-Year Risk of Incident Lung Cancer: Prospective Study Using Electronic Health Records from the State of Maine. (2019)
• A Real-Time Early Warning System for Monitoring Inpatient Mortality Risk: Prospective Study Using Electronic Medical Record Data. (2019)
• Preliminary Evaluation of a Deep Learning Approach for Echocardiographic Screening for Rheumatic Heart Disease. (2019)
• Shorten Bipolarity Checklist for the Differentiation of Subtypes of Bipolar Disorder Using Machine Learning (2019)
• Assessing Statewide All-Cause Future One-Year Mortality: Prospective Study With Implications for Quality of Life, Resource Utilization, and Medical Futility (2018, pdf)
• Prospective prediction of incident hypertension within the next year using statewide electronic health records and machine learning (2018, pdf)
• Estimating One-Year Risk of Incident Chronic Kidney Disease Retrospective Development and Validation Study Using Electronic Medical Record Data From the State of Maine (2017, pdf)
• Defining and characterizing the critical transition state prior to the type 2 diabetes disease (2017, pdf)
• Web-based Real-Time Case Finding for the Population Health Management of Patients With Diabetes Mellitus: A Prospective Validation of the Natural Language Processing–Based Algorithm With Statewide Electronic Medical Records (2016, pdf)
• Prospective stratification of patients at risk for emergency department revisit: resource utilization and population management strategy implications (2016, pdf)
• Prehypertension during normotensive pregnancy and postpartum clustering of cardiometabolic risk factors: A prospective cohort study. (2016, pdf)
• Development, validation and deployment of a real time 30 day hospital readmission risk assessment tool in the Maine Healthcare Information Exchange (2015, pdf)
• Online Prediction of health care utilization in the next six months based on electronic health record information: A cohort and validation study (2015, JMIR site, pdf)
• Exploring value in congenital heart disease: an evaluation of inpatient admissions. (2015, pdf)
• NLP based congestive heart failure case finding: A prospective analysis on statewide electronic medical records. (2015, pdf)
• Real-time web-based assessment of total population risk of future emergency department utilization: statewide prospective active case finding study. (2015, pdf)
• Risk prediction of stroke: A prospective statewide study on patients in Maine. (2015, pdf)
• Risk prediction for future 6-month healthcare resource utilization in Maine. (2015, pdf)
• Risk prediction of emergency department revisit 30 days post discharge: a prospective study. (2014, pdf)
• A data-driven algorithm integrating clinical and laboratory features for the diagnosis and prognosis of necrotizing enterocolitis (2014, pdf)
• A novel severity index for the congenital heart disease, associated computational algorithm and software implementation 6/10/2014. Attorney docket: S13-204.
• AKI in hospitalized children: epidemiology and clinical associations in a national cohort (2013 pdf)

• Disturbance Propagation in Power System Based on an Epidemic Model (2017, pdf)