Isaac Kohane

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Publications

Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. bioRxiv. 2024 Aug 13. View Abstract
Medical Artificial Intelligence and Human Values. N Engl J Med. 2024 May 30; 390(20):1895-1904. View Abstract
Polygenic risk scores for autoimmune related diseases are significantly different in cancer exceptional responders. NPJ Precis Oncol. 2024 May 25; 8(1):120. View Abstract
Large-scale mutational analysis identifies UNC93B1 variants that drive TLR-mediated autoimmunity in mice and humans. J Exp Med. 2024 Aug 05; 221(8). View Abstract
Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder. Genet Med. 2024 Sep; 26(9):101166. View Abstract
Causal machine learning for predicting treatment outcomes. Nat Med. 2024 Apr; 30(4):958-968. View Abstract
Leveraging Large Language Models to Analyze Continuous Glucose Monitoring Data: A Case Study. medRxiv. 2024 Apr 08. View Abstract
Mobilizing data during a crisis: Building rapid evidence pipelines using multi-institutional real world data. Healthc (Amst). 2024 Jun; 12(2):100738. View Abstract
Undiagnosed Disease Network collaborative approach in diagnosing rare disease in a patient with a mosaic CACNA1D variant. Am J Med Genet A. 2024 07; 194(7):e63597. View Abstract
Recurrent ATP1A1 variant Gly903Arg causes developmental delay, intellectual disability, and autism. Ann Clin Transl Neurol. 2024 Apr; 11(4):1075-1079. View Abstract
Disease progression strikingly differs in research and real-world Parkinson's populations. NPJ Parkinsons Dis. 2024 Mar 13; 10(1):58. View Abstract
To do no harm - and the most good - with AI in health care. Nat Med. 2024 Mar; 30(3):623-627. View Abstract
Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis. Genet Med. 2024 06; 26(6):101115. View Abstract
De novo variants in DENND5B cause a neurodevelopmental disorder. Am J Hum Genet. 2024 03 07; 111(3):529-543. View Abstract
The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities. Commun Biol. 2024 02 19; 7(1):174. View Abstract
Disease progression strikingly differs in research and real-world Parkinson's populations. medRxiv. 2024 Feb 18. View Abstract
EFEMP1 haploinsufficiency causes a Marfan-like hereditary connective tissue disorder. Am J Med Genet A. 2024 06; 194(6):e63556. View Abstract
Recurring homozygous ACTN2 variant (p.Arg506Gly) causes a recessive myopathy. Ann Clin Transl Neurol. 2024 Mar; 11(3):629-640. View Abstract
LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants. BMC Genomics. 2024 Jan 26; 25(1):115. View Abstract
A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3. Am J Hum Genet. 2024 01 04; 111(1):96-118. View Abstract
The digital-physical divide for pathology research. Lancet Digit Health. 2023 12; 5(12):e859-e861. View Abstract
Predicting seizure recurrence after an initial seizure-like episode from routine clinical notes using large language models: a retrospective cohort study. Lancet Digit Health. 2023 12; 5(12):e882-e894. View Abstract
Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections. Genet Med. 2024 02; 26(2):101023. View Abstract
Macrocephaly and developmental delay caused by missense variants in RAB5C. Hum Mol Genet. 2023 10 17; 32(21):3063-3077. View Abstract
Simulation of undiagnosed patients with novel genetic conditions. Nat Commun. 2023 10 12; 14(1):6403. View Abstract
De novo missense variants in ZBTB47 are associated with developmental delays, hypotonia, seizures, gait abnormalities, and variable movement abnormalities. Am J Med Genet A. 2024 01; 194(1):17-30. View Abstract
Clinical phenotypes and outcomes in children with multisystem inflammatory syndrome across SARS-CoV-2 variant eras: a multinational study from the 4CE consortium. EClinicalMedicine. 2023 Oct; 64:102212. View Abstract
Characterization of long COVID temporal sub-phenotypes by distributed representation learning from electronic health record data: a cohort study. EClinicalMedicine. 2023 Oct; 64:102210. View Abstract
HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder. Am J Hum Genet. 2023 08 03; 110(8):1414-1435. View Abstract
De novo missense variants in phosphatidylinositol kinase PIP5KI? underlie a neurodevelopmental syndrome associated with altered phosphoinositide signaling. Am J Hum Genet. 2023 08 03; 110(8):1377-1393. View Abstract
Polygenic risk prediction: why and when out-of-sample prediction R2 can exceed SNP-based heritability. Am J Hum Genet. 2023 07 06; 110(7):1207-1215. View Abstract
Unsupervised Anomaly Detection to Characterize Heterogeneity in Type 2 Diabetes. AMIA Jt Summits Transl Sci Proc. 2023; 2023:32-41. View Abstract
Dominant negative variants in IKZF2 cause ICHAD syndrome, a new disorder characterised by immunodysregulation, craniofacial anomalies, hearing impairment, athelia and developmental delay. J Med Genet. 2023 11; 60(11):1092-1104. View Abstract
Genomics Research with Undiagnosed Children: Ethical Challenges at the Boundaries of Research and Clinical Care. J Pediatr. 2023 10; 261:113537. View Abstract
Dominant-negative variant in SLC1A4 causes an autosomal dominant epilepsy syndrome. Ann Clin Transl Neurol. 2023 06; 10(6):1046-1053. View Abstract
Biallelic variants in ribonuclease inhibitor (RNH1), an inflammasome modulator, are associated with a distinctive subtype of acute, necrotizing encephalopathy. Genet Med. 2023 09; 25(9):100897. View Abstract
Trends in Medical Management of Moderately to Severely Active Ulcerative Colitis: A Nationwide Retrospective Analysis. Inflamm Bowel Dis. 2023 05 02; 29(5):695-704. View Abstract
Potential pitfalls in the use of real-world data for studying long COVID. Nat Med. 2023 05; 29(5):1040-1043. View Abstract
SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia. Brain. 2023 04 19; 146(4):1420-1435. View Abstract
Bi-allelic variants in INTS11 are associated with a complex neurological disorder. Am J Hum Genet. 2023 05 04; 110(5):774-789. View Abstract
Participation in a national diagnostic research study: assessing the patient experience. Orphanet J Rare Dis. 2023 04 10; 18(1):73. View Abstract
Unraveling non-participation in genomic research: A complex interplay of barriers, facilitators, and sociocultural factors. J Genet Couns. 2023 10; 32(5):993-1008. View Abstract
De novo variants in MRTFB have gain-of-function activity in Drosophila and are associated with a novel neurodevelopmental phenotype with dysmorphic features. Genet Med. 2023 06; 25(6):100833. View Abstract
Artificial Intelligence in Medicine. N Engl J Med. 2023 Mar 30; 388(13):1220-1221. View Abstract
H4C5 missense variant leads to a neurodevelopmental phenotype overlapping with Angelman syndrome. Am J Med Genet A. 2023 07; 191(7):1911-1916. View Abstract
An efficient landmark model for prediction of suicide attempts in multiple clinical settings. Psychiatry Res. 2023 05; 323:115175. View Abstract
Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med. 2023 Feb 10; 8(1):4. View Abstract
Continuing a search for a diagnosis: the impact of adolescence and family dynamics. Orphanet J Rare Dis. 2023 01 09; 18(1):6. View Abstract
Acute respiratory distress syndrome after SARS-CoV-2 infection on young adult population: International observational federated study based on electronic health records through the 4CE consortium. PLoS One. 2023; 18(1):e0266985. View Abstract
A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network. Genet Med. 2023 04; 25(4):100353. View Abstract
Hospitalizations Associated With Mental Health Conditions Among Adolescents in the US and France During the COVID-19 Pandemic. JAMA Netw Open. 2022 12 01; 5(12):e2246548. View Abstract
National Projections for Clinical Implications of Race-Free Creatinine-Based GFR Estimating Equations. J Am Soc Nephrol. 2023 02 01; 34(2):309-321. View Abstract
Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study. EClinicalMedicine. 2023 Jan; 55:101724. View Abstract
Endocannabinoid dysfunction in neurological disease: neuro-ocular DAGLA-related syndrome. Brain. 2022 10 21; 145(10):3383-3390. View Abstract
Analytics to monitor local impact of the Protecting Access to Medicare Act's imaging clinical decision support requirements. J Am Med Inform Assoc. 2022 10 07; 29(11):1870-1878. View Abstract
Association of Race and Socioeconomic Disadvantage With Missed Telemedicine Visits for Pediatric Patients During the COVID-19 Pandemic. JAMA Pediatr. 2022 09 01; 176(9):933-935. View Abstract
The microRNA processor DROSHA is a candidate gene for a severe progressive neurological disorder. Hum Mol Genet. 2022 08 25; 31(17):2934-2950. View Abstract
SurvMaximin: Robust federated approach to transporting survival risk prediction models. J Biomed Inform. 2022 10; 134:104176. View Abstract
Understanding Covid Vaccine Efficacy over Time - Bridging a Gap Between Public Health and Health Care. N Engl J Med. 2022 08 11; 387(6):483-485. View Abstract
Severity of Epilepsy and Response to Antiseizure Medications in Individuals With Multiple Sclerosis: Analysis of a Real-World Dataset. Neurol Clin Pract. 2022 Aug; 12(4):e49-e57. View Abstract
Gain-of-function mutations in ALPK1 cause an NF-?B-mediated autoinflammatory disease: functional assessment, clinical phenotyping and disease course of patients with ROSAH syndrome. Ann Rheum Dis. 2022 10; 81(10):1453-1464. View Abstract
A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis. Nat Commun. 2022 07 02; 13(1):3817. View Abstract
Association of Postsurgical Opioid Refills for Patients With Risk of Opioid Misuse and Chronic Opioid Use Among Family Members. JAMA Netw Open. 2022 07 01; 5(7):e2221316. View Abstract
International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. NPJ Digit Med. 2022 Jun 29; 5(1):81. View Abstract
Changes in laboratory value improvement and mortality rates over the course of the pandemic: an international retrospective cohort study of hospitalised patients infected with SARS-CoV-2. BMJ Open. 2022 06 23; 12(6):e057725. View Abstract
International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. NPJ Digit Med. 2022 Jun 13; 5(1):74. View Abstract
Building an i2b2-Based Population Repository for COVID-19 Research. Stud Health Technol Inform. 2022 May 25; 294:287-291. View Abstract
Distinguishing Admissions Specifically for COVID-19 From Incidental SARS-CoV-2 Admissions: National Retrospective Electronic Health Record Study. J Med Internet Res. 2022 05 18; 24(5):e37931. View Abstract
A novel DPH5-related diphthamide-deficiency syndrome causing embryonic lethality or profound neurodevelopmental disorder. Genet Med. 2022 07; 24(7):1567-1582. View Abstract
Large-scale real-world data analysis identifies comorbidity patterns in schizophrenia. Transl Psychiatry. 2022 04 11; 12(1):154. View Abstract
Identifying the Common Genetic Basis of Antidepressant Response. Biol Psychiatry Glob Open Sci. 2022 Apr; 2(2):115-126. View Abstract
Genome sequencing reveals novel noncoding variants in PLA2G6 and LMNB1 causing progressive neurologic disease. Mol Genet Genomic Med. 2022 04; 10(4):e1892. View Abstract
How NFTs could transform health information exchange. Science. 2022 02 04; 375(6580):500-502. View Abstract
Multi-PheWAS intersection approach to identify sex differences across comorbidities in 59 140 pediatric patients with autism spectrum disorder. J Am Med Inform Assoc. 2022 01 12; 29(2):230-238. View Abstract
Correction to: An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids. Genet Med. 2021 Dec; 23(12):2467. View Abstract
Authorship Correction: International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study. J Med Internet Res. 2021 Nov 30; 23(11):e34625. View Abstract
Integrative multiomics-histopathology analysis for breast cancer classification. NPJ Breast Cancer. 2021 Nov 29; 7(1):147. View Abstract
ATLAS: an automated association test using probabilistically linked health records with application to genetic studies. J Am Med Inform Assoc. 2021 11 25; 28(12):2582-2592. View Abstract
Longitudinal imaging history in early identification of intimate partner violence. Eur Radiol. 2022 Apr; 32(4):2824-2836. View Abstract
The Genetic Architecture of Depression in Individuals of East Asian Ancestry: A Genome-Wide Association Study. JAMA Psychiatry. 2021 11 01; 78(11):1258-1269. View Abstract
Effectiveness of a third dose of the BNT162b2 mRNA COVID-19 vaccine for preventing severe outcomes in Israel: an observational study. Lancet. 2021 12 04; 398(10316):2093-2100. View Abstract
Multinational characterization of neurological phenotypes in patients hospitalized with COVID-19. Sci Rep. 2021 10 12; 11(1):20238. View Abstract
International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study. J Med Internet Res. 2021 10 11; 23(10):e31400. View Abstract
Correction: Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genet Med. 2021 Oct; 23(10):2016. View Abstract
Evolving phenotypes of non-hospitalized patients that indicate long COVID. BMC Med. 2021 09 27; 19(1):249. View Abstract
Patient-led data sharing for clinical bioinformatics research: USCDI and beyond. J Am Med Inform Assoc. 2021 09 18; 28(10):2298-2300. View Abstract
Real-world data analyses unveiled the immune-related adverse effects of immune checkpoint inhibitors across cancer types. NPJ Precis Oncol. 2021 Sep 10; 5(1):82. View Abstract
Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors. Biol Psychiatry. 2022 02 01; 91(3):313-327. View Abstract
Fecal microbiota transplantation and Clostridioides difficile infection among privately insured patients in the United States. J Gastroenterol. 2022 01; 57(1):10-18. View Abstract
Effectiveness of the BNT162b2 mRNA COVID-19 vaccine in pregnancy. Nat Med. 2021 10; 27(10):1693-1695. View Abstract
Medication Use in the Management of Comorbidities Among Individuals With Autism Spectrum Disorder From a Large Nationwide Insurance Database. JAMA Pediatr. 2021 09 01; 175(9):957-965. View Abstract
Correction: Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank. Mol Psychiatry. 2021 Sep; 26(9):5465. View Abstract
Safety of the BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Setting. N Engl J Med. 2021 09 16; 385(12):1078-1090. View Abstract
Genetic counselor roles in the undiagnosed diseases network research study: Clinical care, collaboration, and curation. J Genet Couns. 2022 04; 31(2):326-337. View Abstract
Finding commonalities in rare diseases through the undiagnosed diseases network. J Am Med Inform Assoc. 2021 07 30; 28(8):1694-1702. View Abstract
Finding a new balance between a genetics-first or phenotype-first approach to the study of disease. Neuron. 2021 07 21; 109(14):2216-2219. View Abstract
COVID-19 infections following physical school reopening. Arch Dis Child. 2021 07 19; 106(8):e34. View Abstract
The Clinician and Dataset Shift in Artificial Intelligence. N Engl J Med. 2021 07 15; 385(3):283-286. View Abstract
Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data. J Am Med Inform Assoc. 2021 07 14; 28(7):1411-1420. View Abstract
One is the loneliest number: genotypic matchmaking using the electronic health record. Genet Med. 2021 10; 23(10):1830-1832. View Abstract
Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genet Med. 2021 10; 23(10):1922-1932. View Abstract
Illustrating potential effects of alternate control populations on real-world evidence-based statistical analyses. JAMIA Open. 2021 Apr; 4(2):ooab045. View Abstract
A description of novel variants and review of phenotypic spectrum in UBA5-related early epileptic encephalopathy. Cold Spring Harb Mol Case Stud. 2021 06; 7(3). View Abstract
Clinical application of a scale to assess genomic healthcare empowerment (GEmS): Process and illustrative case examples. J Genet Couns. 2022 02; 31(1):59-70. View Abstract
Heterozygous loss-of-function variants significantly expand the phenotypes associated with loss of GDF11. Genet Med. 2021 10; 23(10):1889-1900. View Abstract
International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries. JAMA Netw Open. 2021 06 01; 4(6):e2112596. View Abstract
Accelerating diagnosis of Parkinson's disease through risk prediction. BMC Neurol. 2021 May 18; 21(1):201. View Abstract
Progressive cerebellar atrophy in a patient with complex II and III deficiency and a novel deleterious variant in SDHA: A Counseling Conundrum. Mol Genet Genomic Med. 2021 06; 9(6):e1692. View Abstract
Model organisms contribute to diagnosis and discovery in the undiagnosed diseases network: current state and a future vision. Orphanet J Rare Dis. 2021 05 07; 16(1):206. View Abstract
Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Mol Genet Genomic Med. 2021 07; 9(7):e1665. View Abstract
A Comparison of Ten Polygenic Score Methods for Psychiatric Disorders Applied Across Multiple Cohorts. Biol Psychiatry. 2021 11 01; 90(9):611-620. View Abstract
A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases. Sci Data. 2021 04 21; 8(1):114. View Abstract
A fast divide-and-conquer sparse Cox regression. Biostatistics. 2021 04 10; 22(2):381-401. View Abstract
Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain. Genet Med. 2021 08; 23(8):1465-1473. View Abstract
Healthcare spending and utilization for pediatric Irritable Bowel Syndrome in a commercially insured population. Neurogastroenterol Motil. 2021 11; 33(11):e14147. View Abstract
Machine learning for patient risk stratification: standing on, or looking over, the shoulders of clinicians? NPJ Digit Med. 2021 Mar 30; 4(1):62. View Abstract
Measuring health-care delays among privately insured patients with tuberculosis in the USA: an observational cohort study. Lancet Infect Dis. 2021 08; 21(8):1175-1183. View Abstract
Sex-Dependent Shared and Nonshared Genetic Architecture Across Mood and Psychotic Disorders. Biol Psychiatry. 2022 01 01; 91(1):102-117. View Abstract
Development of a Histopathology Informatics Pipeline for Classification and Prediction of Clinical Outcomes in Subtypes of Renal Cell Carcinoma. Clin Cancer Res. 2021 05 15; 27(10):2868-2878. View Abstract
What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask. J Med Internet Res. 2021 03 02; 23(3):e22219. View Abstract
Temporal bias in case-control design: preventing reliable predictions of the future. Nat Commun. 2021 02 17; 12(1):1107. View Abstract
Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers. J Am Med Inform Assoc. 2021 02 15; 28(2):393-401. View Abstract
Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases. Genet Med. 2021 06; 23(6):1075-1085. View Abstract
International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe COVID-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study. medRxiv. 2021 Feb 05. View Abstract
Machine Learning of Patient Characteristics to Predict Admission Outcomes in the Undiagnosed Diseases Network. JAMA Netw Open. 2021 02 01; 4(2):e2036220. View Abstract
Multinational Prevalence of Neurological Phenotypes in Patients Hospitalized with COVID-19. medRxiv. 2021 Jan 29. View Abstract
Clinical Implications of Removing Race From Estimates of Kidney Function. JAMA. 2021 Jan 12; 325(2):184-186. View Abstract
Cross-modal representation alignment of molecular structure and perturbation-induced transcriptional profiles. Pac Symp Biocomput. 2021; 26:273-284. View Abstract
Deep Learning Benchmarks on L1000 Gene Expression Data. IEEE/ACM Trans Comput Biol Bioinform. 2020 Nov-Dec; 17(6):1846-1857. View Abstract
An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids. Genet Med. 2021 04; 23(4):740-750. View Abstract
DYRK1A pathogenic variants in two patients with syndromic intellectual disability and a review of the literature. Mol Genet Genomic Med. 2020 12; 8(12):e1544. View Abstract
Prolonged Auditory Brainstem Response in Universal Hearing Screening of Newborns with Autism Spectrum Disorder. Autism Res. 2021 01; 14(1):46-52. View Abstract
Family genetic result communication in rare and undiagnosed disease communities: Understanding the practice. J Genet Couns. 2021 04; 30(2):439-447. View Abstract
Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science. Genet Med. 2021 02; 23(2):259-271. View Abstract
Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist. Nat Med. 2020 09; 26(9):1320-1324. View Abstract
Scalability and cost-effectiveness analysis of whole genome-wide association studies on Google Cloud Platform and Amazon Web Services. J Am Med Inform Assoc. 2020 09 01; 27(9):1425-1430. View Abstract
International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium. NPJ Digit Med. 2020; 3:109. View Abstract
Deciphering serous ovarian carcinoma histopathology and platinum response by convolutional neural networks. BMC Med. 2020 08 18; 18(1):236. View Abstract
A multidimensional precision medicine approach identifies an autism subtype characterized by dyslipidemia. Nat Med. 2020 09; 26(9):1375-1379. View Abstract
Reproducible Machine Learning Methods for Lung Cancer Detection Using Computed Tomography Images: Algorithm Development and Validation. J Med Internet Res. 2020 08 05; 22(8):e16709. View Abstract
EHRtemporalVariability: delineating temporal data-set shifts in electronic health records. Gigascience. 2020 08 01; 9(8). View Abstract
Biallelic MADD variants cause a phenotypic spectrum ranging from developmental delay to a multisystem disorder. Brain. 2020 08 01; 143(8):2437-2453. View Abstract
Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation. Bioinformatics. 2020 07 01; 36(13):4047-4057. View Abstract
An interactive online dashboard for tracking COVID-19 in U.S. counties, cities, and states in real time. J Am Med Inform Assoc. 2020 07 01; 27(7):1121-1125. View Abstract
A phenome-wide association and Mendelian Randomisation study of polygenic risk for depression in UK Biobank. Nat Commun. 2020 05 08; 11(1):2301. View Abstract
Classifying non-small cell lung cancer types and transcriptomic subtypes using convolutional neural networks. J Am Med Inform Assoc. 2020 05 01; 27(5):757-769. View Abstract
AI for the Eye - Automated Assistance for Clinicians Screening for Papilledema. N Engl J Med. 2020 04 30; 382(18):1760-1761. View Abstract
De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. Am J Hum Genet. 2020 04 02; 106(4):570-583. View Abstract
Association of polygenic score for major depression with response to lithium in patients with bipolar disorder. Mol Psychiatry. 2021 06; 26(6):2457-2470. View Abstract
Data Citizenship under the 21st Century Cures Act. N Engl J Med. 2020 May 07; 382(19):1781-1783. View Abstract
Estimates of healthcare spending for preterm and low-birthweight infants in a commercially insured population: 2008-2016. J Perinatol. 2020 07; 40(7):1091-1099. View Abstract
Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank. Mol Psychiatry. 2020 07; 25(7):1430-1446. View Abstract
The phenotypical implications of immune dysregulation in fragile X syndrome. Eur J Neurol. 2020 03; 27(3):590-593. View Abstract
Big Data in the Assessment of Pediatric Medication Safety. Pediatrics. 2020 02; 145(2). View Abstract
Clinical Concept Embeddings Learned from Massive Sources of Multimodal Medical Data. Pac Symp Biocomput. 2020; 25:295-306. View Abstract
Making the 'invisible' visible: transforming the detection of intimate partner violence. BMJ Qual Saf. 2020 03; 29(3):241-244. View Abstract
High-throughput phenotyping with electronic medical record data using a common semi-supervised approach (PheCAP). Nat Protoc. 2019 12; 14(12):3426-3444. View Abstract
Examining the Use of Real-World Evidence in the Regulatory Process. Clin Pharmacol Ther. 2020 04; 107(4):843-852. View Abstract
Bipolar multiplex families have an increased burden of common risk variants for psychiatric disorders. Mol Psychiatry. 2021 04; 26(4):1286-1298. View Abstract
The Genetics of the Mood Disorder Spectrum: Genome-wide Association Analyses of More Than 185,000 Cases and 439,000 Controls. Biol Psychiatry. 2020 07 15; 88(2):169-184. View Abstract
High-throughput multimodal automated phenotyping (MAP) with application to PheWAS. J Am Med Inform Assoc. 2019 11 01; 26(11):1255-1262. View Abstract
Aberrant mitochondrial function in patient-derived neural cells from CDKL5 deficiency disorder and Rett syndrome. Hum Mol Genet. 2019 11 01; 28(21):3625-3636. View Abstract
Automated grouping of medical codes via multiview banded spectral clustering. J Biomed Inform. 2019 12; 100:103322. View Abstract
Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease. PLoS One. 2019; 14(10):e0222952. View Abstract
VarSight: prioritizing clinically reported variants with binary classification algorithms. BMC Bioinformatics. 2019 Oct 15; 20(1):496. View Abstract
Autoimmune Effects of Lung Cancer Immunotherapy Revealed by Data-Driven Analysis on a Nationwide Cohort. Clin Pharmacol Ther. 2020 02; 107(2):388-396. View Abstract
Donald A. B. Lindberg (1933-2019). Science. 2019 Oct 04; 366(6461):37. View Abstract
De Novo Pathogenic Variants in N-cadherin Cause a Syndromic Neurodevelopmental Disorder with Corpus Collosum, Axon, Cardiac, Ocular, and Genital Defects. Am J Hum Genet. 2019 10 03; 105(4):854-868. View Abstract
De Novo Variants in WDR37 Are Associated with Epilepsy, Colobomas, Dysmorphism, Developmental Delay, Intellectual Disability, and Cerebellar Hypoplasia. Am J Hum Genet. 2019 Sep 05; 105(3):672-674. View Abstract
Genomics in medicine: a novel elective rotation for internal medicine residents. Postgrad Med J. 2019 Oct; 95(1128):569-572. View Abstract
Use of Narrative Concepts in Electronic Health Records to Validate Associations Between Genetic Factors and Response to Treatment of Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2020 07; 18(8):1890-1892. View Abstract
Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression. Biol Psychiatry. 2020 03 01; 87(5):419-430. View Abstract
De Novo Variants in WDR37 Are Associated with Epilepsy, Colobomas, Dysmorphism, Developmental Delay, Intellectual Disability, and Cerebellar Hypoplasia. Am J Hum Genet. 2019 08 01; 105(2):413-424. View Abstract
Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor ß Signaling. Biol Psychiatry. 2020 01 15; 87(2):100-112. View Abstract
Machine Learning in Medicine. Reply. N Engl J Med. 2019 06 27; 380(26):2589-2590. View Abstract
Magnetic Resonance Imaging characteristics in case of TOR1AIP1 muscular dystrophy. Clin Imaging. 2019 Nov - Dec; 58:108-113. View Abstract
Suicide Rates Among Adolescents and Young Adults in the United States, 2000-2017. JAMA. 2019 06 18; 321(23):2362-2364. View Abstract
Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns. Nat Commun. 2019 06 11; 10(1):2548. View Abstract
Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. Nat Med. 2019 06; 25(6):911-919. View Abstract
Lysosomal Storage and Albinism Due to Effects of a De Novo CLCN7 Variant on Lysosomal Acidification. Am J Hum Genet. 2019 06 06; 104(6):1127-1138. View Abstract
Batch correction evaluation framework using a-priori gene-gene associations: applied to the GTEx dataset. BMC Bioinformatics. 2019 May 28; 20(1):268. View Abstract
Heterozygous variants in MYBPC1 are associated with an expanded neuromuscular phenotype beyond arthrogryposis. Hum Mutat. 2019 08; 40(8):1115-1126. View Abstract
Evaluation of the association of bariatric surgery with subsequent depression. Int J Obes (Lond). 2019 12; 43(12):2528-2535. View Abstract
Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction. EBioMedicine. 2019 May; 43:356-369. View Abstract
IgG4-related disease: Association with a rare gene variant expressed in cytotoxic T cells. Mol Genet Genomic Med. 2019 06; 7(6):e686. View Abstract
Machine Learning in Medicine. N Engl J Med. 2019 04 04; 380(14):1347-1358. View Abstract
A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing. J Genet Couns. 2019 04; 28(2):213-228. View Abstract
Adversarial attacks on medical machine learning. Science. 2019 03 22; 363(6433):1287-1289. View Abstract
Pre-existing autoimmune disease and the risk of immune-related adverse events among patients receiving checkpoint inhibitors for cancer. Cancer Immunol Immunother. 2019 Jun; 68(6):917-926. View Abstract
Systemic nature of spinal muscular atrophy revealed by studying insurance claims. PLoS One. 2019; 14(3):e0213680. View Abstract
Identification of common genetic risk variants for autism spectrum disorder. Nat Genet. 2019 03; 51(3):431-444. View Abstract
Bi-allelic Variants in TONSL Cause SPONASTRIME Dysplasia and a Spectrum of Skeletal Dysplasia Phenotypes. Am J Hum Genet. 2019 03 07; 104(3):422-438. View Abstract
Feature extraction for phenotyping from semantic and knowledge resources. J Biomed Inform. 2019 03; 91:103122. View Abstract
Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students. J Genet Couns. 2019 04; 28(2):466-476. View Abstract
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Learning Contextual Hierarchical Structure of Medical Concepts with Poincairé Embeddings to Clarify Phenotypes. Pac Symp Biocomput. 2019; 24:8-17. View Abstract
A whole genome approach for discovering the genetic basis of blood group antigens: independent confirmation for P1 and Xga. Transfusion. 2019 03; 59(3):908-915. View Abstract
Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet. 2019 01 03; 104(1):164-178. View Abstract
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Data-driven analyses revealed the comorbidity landscape of tuberous sclerosis complex. Neurology. 2018 11 20; 91(21):974-976. View Abstract
Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease. N Engl J Med. 2018 11 29; 379(22):2131-2139. View Abstract
Artificial intelligence in healthcare. Nat Biomed Eng. 2018 10; 2(10):719-731. View Abstract
Applying polygenic risk scoring for psychiatric disorders to a large family with bipolar disorder and major depressive disorder. Commun Biol. 2018; 1:163. View Abstract
Framing the challenges of artificial intelligence in medicine. BMJ Qual Saf. 2019 03; 28(3):238-241. View Abstract
Further evidence for the involvement of EFL1 in a Shwachman-Diamond-like syndrome and expansion of the phenotypic features. Cold Spring Harb Mol Case Stud. 2018 10; 4(5). View Abstract
PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. J Am Med Inform Assoc. 2018 10 01; 25(10):1359-1365. View Abstract
IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet. 2018 09 06; 103(3):456. View Abstract
Characteristics of undiagnosed diseases network applicants: implications for referring providers. BMC Health Serv Res. 2018 Aug 22; 18(1):652. View Abstract
A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project. J Proteome Res. 2018 12 07; 17(12):4345-4357. View Abstract
Association of Whole-Genome and NETRIN1 Signaling Pathway-Derived Polygenic Risk Scores for Major Depressive Disorder and White Matter Microstructure in the UK Biobank. Biol Psychiatry Cogn Neurosci Neuroimaging. 2019 01; 4(1):91-100. View Abstract
IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet. 2018 08 02; 103(2):245-260. View Abstract
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Development of an Algorithm to Identify Patients with Physician-Documented Insomnia. Sci Rep. 2018 05 18; 8(1):7862. View Abstract
Automated typing of red blood cell and platelet antigens: a whole-genome sequencing study. Lancet Haematol. 2018 Jun; 5(6):e241-e251. View Abstract
Biomedical informatics and machine learning for clinical genomics. Hum Mol Genet. 2018 05 01; 27(R1):R29-R34. View Abstract
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Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. Nat Genet. 2018 05; 50(5):668-681. View Abstract
Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API. Bioinformatics. 2018 04 15; 34(8):1431-1432. View Abstract
Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma. Sci Rep. 2018 04 03; 8(1):5437. View Abstract
Big Data and Machine Learning in Health Care. JAMA. 2018 Apr 03; 319(13):1317-1318. View Abstract
Systematic Protein Prioritization for Targeted Proteomics Studies through Literature Mining. J Proteome Res. 2018 04 06; 17(4):1383-1396. View Abstract
Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder. Am J Hum Genet. 2018 03 01; 102(3):494-504. View Abstract
Postsurgical prescriptions for opioid naive patients and association with overdose and misuse: retrospective cohort study. BMJ. 2018 01 17; 360:j5790. View Abstract
Enabling phenotypic big data with PheNorm. J Am Med Inform Assoc. 2018 01 01; 25(1):54-60. View Abstract
Challenges and recommendations for epigenomics in precision health. Nat Biotechnol. 2017 12 08; 35(12):1128-1132. View Abstract
Genetic Association of Major Depression With Atypical Features and Obesity-Related Immunometabolic Dysregulations. JAMA Psychiatry. 2017 12 01; 74(12):1214-1225. View Abstract
Association of Sex With Recurrence of Autism Spectrum Disorder Among Siblings. JAMA Pediatr. 2017 11 01; 171(11):1107-1112. View Abstract
Utilization, Cost, and Outcome of Branded vs Compounded 17-Alpha Hydroxyprogesterone Caproate in Prevention of Preterm Birth. JAMA Intern Med. 2017 11 01; 177(11):1689-1690. View Abstract
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Does Childhood Trauma Moderate Polygenic Risk for Depression? A Meta-analysis of 5765 Subjects From the Psychiatric Genomics Consortium. Biol Psychiatry. 2018 07 15; 84(2):138-147. View Abstract
Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases. Genet Med. 2018 04; 20(4):464-469. View Abstract
Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports. Am J Med Genet B Neuropsychiatr Genet. 2018 10; 177(7):613-624. View Abstract
Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders. Cell Syst. 2017 08 23; 5(2):140-148.e2. View Abstract
The Impact of Whole-Genome Sequencing on the Primary Care and Outcomes of Healthy Adult Patients: A Pilot Randomized Trial. Ann Intern Med. 2017 08 01; 167(3):159-169. View Abstract
A 21st-Century Health IT System - Creating a Real-World Information Economy. N Engl J Med. 2017 May 18; 376(20):1905-1907. View Abstract
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. Am J Hum Genet. 2017 Jun 01; 100(6):843-853. View Abstract
A window into living with an undiagnosed disease: illness narratives from the Undiagnosed Diseases Network. Orphanet J Rare Dis. 2017 04 17; 12(1):71. View Abstract
Combining clinical and genomics queries using i2b2 - Three methods. PLoS One. 2017; 12(4):e0172187. View Abstract
Surrogate-assisted feature extraction for high-throughput phenotyping. J Am Med Inform Assoc. 2017 Apr 01; 24(e1):e143-e149. View Abstract
Predictive Modeling of Physician-Patient Dynamics That Influence Sleep Medication Prescriptions and Clinical Decision-Making. Sci Rep. 2017 02 09; 7:42282. View Abstract
The Undiagnosed Diseases Network: Accelerating Discovery about Health and Disease. Am J Hum Genet. 2017 02 02; 100(2):185-192. View Abstract
Systematic correlation of environmental exposure and physiological and self-reported behaviour factors with leukocyte telomere length. Int J Epidemiol. 2017 02 01; 46(1):44-56. View Abstract
A Recurrent De Novo Variant in NACC1 Causes a Syndrome Characterized by Infantile Epilepsy, Cataracts, and Profound Developmental Delay. Am J Hum Genet. 2017 Feb 02; 100(2):343-351. View Abstract
A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Am J Hum Genet. 2017 Jan 05; 100(1):128-137. View Abstract
Translating Artificial Intelligence Into Clinical Care. JAMA. 2016 12 13; 316(22):2368-2369. View Abstract
Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. Genome Biol. 2016 11 14; 17(1):228. View Abstract
A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey. Sci Data. 2016 10 25; 3:160096. View Abstract
Suboptimal Clinical Documentation in Young Children with Severe Obesity at Tertiary Care Centers. Int J Pediatr. 2016; 2016:4068582. View Abstract
Genetic Misdiagnoses and the Potential for Health Disparities. N Engl J Med. 2016 Aug 18; 375(7):655-65. View Abstract
A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease. J Biomed Inform. 2016 10; 63:366-378. View Abstract
Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development. PeerJ. 2016; 4:e2318. View Abstract
Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder. PLoS One. 2016; 11(7):e0159621. View Abstract
Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers. Appl Clin Inform. 2016 07 20; 7(3):693-706. View Abstract
Treating the enigmatic "exceptional responders" as patients with undiagnosed diseases. Sci Transl Med. 2016 05 25; 8(340):340ed8. View Abstract
Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis. Inflamm Bowel Dis. 2016 Apr; 22(4):880-5. View Abstract
SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care. J Am Med Inform Assoc. 2016 07; 23(4):701-10. View Abstract
Clinical Genomics: From Pathogenicity Claims to Quantitative Risk Estimates. JAMA. 2016 Mar 22-29; 315(12):1233-4. View Abstract
Statin Use Is Associated With Reduced Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2016 07; 14(7):973-9. View Abstract
SMART on FHIR: a standards-based, interoperable apps platform for electronic health records. J Am Med Inform Assoc. 2016 09; 23(5):899-908. View Abstract
ksRepo: a generalized platform for computational drug repositioning. BMC Bioinformatics. 2016 Feb 09; 17:78. View Abstract
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Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study. Transl Psychiatry. 2016 Jan 05; 6:e708. View Abstract
Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort. Inflamm Bowel Dis. 2016 Jan; 22(1):151-8. View Abstract
METHODS TO ENHANCE THE REPRODUCIBILITY OF PRECISION MEDICINE. Pac Symp Biocomput. 2016; 21:180-182. View Abstract
Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures. Mol Autism. 2015; 6:66. View Abstract
Comprehensive red blood cell and platelet antigen prediction from whole genome sequencing: proof of principle. Transfusion. 2016 Mar; 56(3):743-54. View Abstract
Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases. Inflamm Bowel Dis. 2015 Nov; 21(11):2507-14. View Abstract
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Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts. PLoS One. 2015; 10(8):e0136651. View Abstract
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SMART on FHIR Genomics: facilitating standardized clinico-genomic apps. J Am Med Inform Assoc. 2015 Nov; 22(6):1173-8. View Abstract
HEALTH CARE POLICY. Ten things we have to do to achieve precision medicine. Science. 2015 Jul 03; 349(6243):37-8. View Abstract
Driving Innovation in Health Systems through an Apps-Based Information Economy. Cell Syst. 2015 Jul; 1(1):8-13. View Abstract
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Development of phenotype algorithms using electronic medical records and incorporating natural language processing. BMJ. 2015 Apr 24; 350:h1885. View Abstract
Increasing the efficiency of trial-patient matching: automated clinical trial eligibility pre-screening for pediatric oncology patients. BMC Med Inform Decis Mak. 2015 Apr 14; 15:28. View Abstract
Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases. Aliment Pharmacol Ther. 2015 Jun; 41(11):1141-8. View Abstract
TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. PLoS One. 2015; 10(4):e0122271. View Abstract
Federalist principles for healthcare data networks. Nat Biotechnol. 2015 Apr; 33(4):360-3. View Abstract
A clinical perspective on the relevance of research domain criteria in electronic health records. Am J Psychiatry. 2015 Apr; 172(4):316-20. View Abstract
Roger et al. respond to "future of population studies". Am J Epidemiol. 2015 Mar 15; 181(6):372-3. View Abstract
Strategic transformation of population studies: recommendations of the working group on epidemiology and population sciences from the National Heart, Lung, and Blood Advisory Council and Board of External Experts. Am J Epidemiol. 2015 Mar 15; 181(6):363-8. View Abstract
A microRNA-1280/JAG2 network comprises a novel biological target in high-risk medulloblastoma. Oncotarget. 2015 Feb 20; 6(5):2709-24. View Abstract
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A one-page summary report of genome sequencing for the healthy adult. Public Health Genomics. 2015; 18(2):123-9. View Abstract
A systematic approach to the reporting of medically relevant findings from whole genome sequencing. BMC Med Genet. 2014 Dec 14; 15:134. View Abstract
Validation of electronic health record phenotyping of bipolar disorder cases and controls. Am J Psychiatry. 2015 Apr; 172(4):363-72. View Abstract
Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis. Front Genet. 2014; 5:401. View Abstract
Stratification of risk for hospital admissions for injury related to fall: cohort study. BMJ. 2014 Oct 24; 349:g5863. View Abstract
Summarizing polygenic risks for complex diseases in a clinical whole-genome report. Genet Med. 2015 Jul; 17(7):536-44. View Abstract
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An electronic health records study of long-term weight gain following antidepressant use. JAMA Psychiatry. 2014 Aug; 71(8):889-96. View Abstract
Improving the power of genetic association tests with imperfect phenotype derived from electronic medical records. Hum Genet. 2014 Nov; 133(11):1369-82. View Abstract
Colonoscopy is associated with a reduced risk for colon cancer and mortality in patients with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2015 Feb; 13(2):322-329.e1. View Abstract
Are Meaningful Use Stage 2 certified EHRs ready for interoperability? Findings from the SMART C-CDA Collaborative. J Am Med Inform Assoc. 2014 Nov-Dec; 21(6):1060-8. View Abstract
Finding the missing link for big biomedical data. JAMA. 2014 Jun 25; 311(24):2479-80. View Abstract
Reducing false-positive incidental findings with ensemble genotyping and logistic regression based variant filtering methods. Hum Mutat. 2014 Aug; 35(8):936-44. View Abstract
An autism case history to review the systematic analysis of large-scale data to refine the diagnosis and treatment of neuropsychiatric disorders. Biol Psychiatry. 2015 Jan 01; 77(1):59-65. View Abstract
Medicine's uncomfortable relationship with math: calculating positive predictive value. JAMA Intern Med. 2014 Jun; 174(6):991-3. View Abstract
Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): architecture. J Am Med Inform Assoc. 2014 Jul-Aug; 21(4):615-20. View Abstract
Population-level evidence for an autoimmune etiology of epilepsy. JAMA Neurol. 2014 May; 71(5):569-74. View Abstract
HD CAGnome: a search tool for huntingtin CAG repeat length-correlated genes. PLoS One. 2014; 9(4):e95556. View Abstract
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol. 2014 Mar 25; 15(3):R53. View Abstract
The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine. Trials. 2014 Mar 20; 15:85. View Abstract
Higher plasma vitamin D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases. Aliment Pharmacol Ther. 2014 May; 39(10):1136-42. View Abstract
Thromboprophylaxis is associated with reduced post-hospitalization venous thromboembolic events in patients with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2014 Nov; 12(11):1905-10. View Abstract
Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline. Hum Mutat. 2014 May; 35(5):537-47. View Abstract
Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis. Mol Autism. 2014 Feb 24; 5(1):16. View Abstract
Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease. J Crohns Colitis. 2014 Sep; 8(9):956-63. View Abstract
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Serum inflammatory markers and risk of colorectal cancer in patients with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2014 Aug; 12(8):1342-8.e1. View Abstract
Deeper, longer phenotyping to accelerate the discovery of the genetic architectures of diseases. Genome Biol. 2014; 15(5):115. View Abstract
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS. 2014 Jan; 18(1):10-4. View Abstract
iPSC-derived neurons as a higher-throughput readout for autism: promises and pitfalls. Trends Mol Med. 2014 Feb; 20(2):91-104. View Abstract
Comorbidity clusters in autism spectrum disorders: an electronic health record time-series analysis. Pediatrics. 2014 Jan; 133(1):e54-63. View Abstract
EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children. Front Genet. 2013; 4:268. View Abstract
Lipid and lipoprotein levels and trend in rheumatoid arthritis compared to the general population. Arthritis Care Res (Hoboken). 2013 Dec; 65(12):2046-50. View Abstract
Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data. 2013 Dec; 1(4):196-201. View Abstract
Modeling disease severity in multiple sclerosis using electronic health records. PLoS One. 2013; 8(11):e78927. View Abstract
Urinary-cell mRNA and acute kidney-transplant rejection. N Engl J Med. 2013 11 07; 369(19):1859. View Abstract
Early detection of poor adherers to statins: applying individualized surveillance to pay for performance. PLoS One. 2013; 8(11):e79611. View Abstract
Can we measure autism? Sci Transl Med. 2013 Oct 30; 5(209):209ed18. View Abstract
Secondary use of health information: are we asking the right question? JAMA Intern Med. 2013 Oct 28; 173(19):1806-7. View Abstract
Association between reduced plasma 25-hydroxy vitamin D and increased risk of cancer in patients with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2014 May; 12(5):821-7. View Abstract
Improved de-identification of physician notes through integrative modeling of both public and private medical text. BMC Med Inform Decis Mak. 2013 Oct 02; 13:112. View Abstract
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Opportunities for genomic clinical decision support interventions. Genet Med. 2013 Oct; 15(10):817-23. View Abstract
Normalization of plasma 25-hydroxy vitamin D is associated with reduced risk of surgery in Crohn's disease. Inflamm Bowel Dis. 2013 Aug; 19(9):1921-7. View Abstract
Scalable decision support at the point of care: a substitutable electronic health record app for monitoring medication adherence. Interact J Med Res. 2013 Jul 22; 2(2):e13. View Abstract
The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genet Med. 2013 Oct; 15(10):761-71. View Abstract
Improving case definition of Crohn's disease and ulcerative colitis in electronic medical records using natural language processing: a novel informatics approach. Inflamm Bowel Dis. 2013 Jun; 19(7):1411-20. View Abstract
Extracting physician group intelligence from electronic health records to support evidence based medicine. PLoS One. 2013; 8(5):e64933. View Abstract
Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls. Ann Rheum Dis. 2014 Jun; 73(6):1170-5. View Abstract
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Dominant effects of the Huntington's disease HTT CAG repeat length are captured in gene-expression data sets by a continuous analysis mathematical modeling strategy. Hum Mol Genet. 2013 Aug 15; 22(16):3227-38. View Abstract
Genomic medicine, health information technology, and patient care. JAMA. 2013 Apr 10; 309(14):1467-8. View Abstract
SHRINE: enabling nationally scalable multi-site disease studies. PLoS One. 2013; 8(3):e55811. View Abstract
Automating the study of population variation of electrocardiographic features. Circulation. 2013 Apr 02; 127(13):1357-8. View Abstract
Data re-identification: societal safeguards. Science. 2013 Mar 01; 339(6123):1032-3. View Abstract
Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. Arthritis Rheum. 2013 Mar; 65(3):571-81. View Abstract
QT interval and antidepressant use: a cross sectional study of electronic health records. BMJ. 2013 Jan 29; 346:f288. View Abstract
Similar risk of depression and anxiety following surgery or hospitalization for Crohn's disease and ulcerative colitis. Am J Gastroenterol. 2013 Apr; 108(4):594-601. View Abstract
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A glimpse of the next 100 years in medicine. N Engl J Med. 2012 Dec 27; 367(26):2538-9. View Abstract
Characteristics and predictive value of blood transcriptome signature in males with autism spectrum disorders. PLoS One. 2012; 7(12):e49475. View Abstract
Structural, genetic, and functional signatures of disordered neuro-immunological development in autism spectrum disorder. PLoS One. 2012; 7(12):e48835. View Abstract
Feasibility of studying brain morphology in major depressive disorder with structural magnetic resonance imaging and clinical data from the electronic medical record: a pilot study. Psychiatry Res. 2013 Mar 30; 211(3):202-13. View Abstract
Apps to display patient data, making SMART available in the i2b2 platform. AMIA Annu Symp Proc. 2012; 2012:960-9. View Abstract
Next-generation sequencing in the clinic: are we ready? Nat Rev Genet. 2012 11; 13(11):818-24. View Abstract
A unified inference procedure for a class of measures to assess improvement in risk prediction systems with survival data. Stat Med. 2013 Jun 30; 32(14):2430-42. View Abstract
Antidepressant response in patients with major depression exposed to NSAIDs: a pharmacovigilance study. Am J Psychiatry. 2012 Oct; 169(10):1065-72. View Abstract
Designing a public square for research computing. Sci Transl Med. 2012 Aug 29; 4(149):149fs32. View Abstract
A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. Genome Biol. 2012 Aug 21; 13(8):R71. View Abstract
Comparative RNA editing in autistic and neurotypical cerebella. Mol Psychiatry. 2013 Sep; 18(9):1041-8. View Abstract
Escaping the EHR trap--the future of health IT. N Engl J Med. 2012 Jun 14; 366(24):2240-2. View Abstract
Meaningful use of electronic health records. Health Aff (Millwood). 2012 Jun; 31(6):1365; author reply 1366. View Abstract
What's a Genome Worth? Sci Transl Med. 2012 May 09; 4(133):133fs13. View Abstract
Limbic system white matter microstructure and long-term treatment outcome in major depressive disorder: a diffusion tensor imaging study using legacy data. World J Biol Psychiatry. 2014 Feb; 15(2):122-34. View Abstract
The co-morbidity burden of children and young adults with autism spectrum disorders. PLoS One. 2012; 7(4):e33224. View Abstract
A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry. 2013 Apr; 18(4):497-511. View Abstract
Managing incidental findings and research results in genomic research involving biobanks and archived data sets. Genet Med. 2012 Apr; 14(4):361-84. View Abstract
Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with major depressive disorder treated with antidepressants. BMJ Open. 2012; 2(2):e000544. View Abstract
Making sense out of massive data by going beyond differential expression. Proc Natl Acad Sci U S A. 2012 Apr 10; 109(15):5594-9. View Abstract
The SMART Platform: early experience enabling substitutable applications for electronic health records. J Am Med Inform Assoc. 2012 Jul-Aug; 19(4):597-603. View Abstract
Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease. Aliment Pharmacol Ther. 2012 Apr; 35(7):789-95. View Abstract
Taxonomizing, sizing, and overcoming the incidentalome. Genet Med. 2012 Apr; 14(4):399-404. View Abstract
(Mis)treating the pharmacogenetic incidentalome. Nat Rev Drug Discov. 2012 Feb 01; 11(2):89-90. View Abstract
Interview with Isaac S. Kohane conducted by Sarah Miller. Pharmacogenomics. 2012 Feb; 13(3):257-60. View Abstract
Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome. Bioinformatics. 2012 Feb 15; 28(4):538-45. View Abstract
Technical desiderata for the integration of genomic data into Electronic Health Records. J Biomed Inform. 2012 Jun; 45(3):419-22. View Abstract
Identification of autoimmune gene signatures in autism. Transl Psychiatry. 2011 Dec 13; 1:e63. View Abstract
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS One. 2011; 6(11):e27156. View Abstract
A translational engine at the national scale: informatics for integrating biology and the bedside. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):181-5. View Abstract
BioNØT: a searchable database of biomedical negated sentences. BMC Bioinformatics. 2011 Oct 27; 12:420. View Abstract
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DNA hypermethylation in lung cancer is targeted at differentiation-associated genes. Oncogene. 2012 Mar 01; 31(9):1181-8. View Abstract
Cambogin is preferentially cytotoxic to cells expressing PDGFR. PLoS One. 2011; 6(6):e21370. View Abstract
Using electronic medical records to enable large-scale studies in psychiatry: treatment resistant depression as a model. Psychol Med. 2012 Jan; 42(1):41-50. View Abstract
Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels. Clin Pharmacol Ther. 2011 Jul; 90(1):133-42. View Abstract
DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases. PLoS One. 2011; 6(5):e19800. View Abstract
Using electronic health records to drive discovery in disease genomics. Nat Rev Genet. 2011 Jun; 12(6):417-28. View Abstract
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Marco Ramoni: an appreciation of academic achievement. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):367-9. View Abstract
Counterpoint: Do not opine before it's time. Nat Biotechnol. 2011 Mar; 29(3):218-9. View Abstract
Inferring cell cycle feedback regulation from gene expression data. J Biomed Inform. 2011 Aug; 44(4):565-75. View Abstract
Assessing the reproducibility of asthma genome-wide association studies in a general clinical population. J Allergy Clin Immunol. 2011 Apr; 127(4):1067-9. View Abstract
Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations. Bioinformatics. 2011 Mar 15; 27(6):891-3. View Abstract
Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records. Am J Hum Genet. 2011 Jan 07; 88(1):57-69. View Abstract
Does collocation inform the impact of collaboration? PLoS One. 2010 Dec 15; 5(12):e14279. View Abstract
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Electronic medical records for discovery research in rheumatoid arthritis. Arthritis Care Res (Hoboken). 2010 Aug; 62(8):1120-7. View Abstract
Multidimensional results reporting to participants in genomic studies: getting it right. Sci Transl Med. 2010 Jun 23; 2(37):37cm19. View Abstract
A novel approach to investigate tissue-specific trinucleotide repeat instability. BMC Syst Biol. 2010 Mar 19; 4:29. View Abstract
Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med Inform Assoc. 2010 Mar-Apr; 17(2):124-30. View Abstract
Rapid identification of myocardial infarction risk associated with diabetes medications using electronic medical records. Diabetes Care. 2010 Mar; 33(3):526-31. View Abstract
High throughput single cell bioinformatics. Biotechnol Prog. 2009 Nov-Dec; 25(6):1772-9. View Abstract
Transcriptomic analysis of human lung development. Am J Respir Crit Care Med. 2010 Jan 01; 181(1):54-63. View Abstract
Longitudinal histories as predictors of future diagnoses of domestic abuse: modelling study. BMJ. 2009 Sep 29; 339:b3677. View Abstract
Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics. 2009 Dec 01; 25(23):3121-7. View Abstract
Expression differences by continent of origin point to the immortalization process. Hum Mol Genet. 2009 Oct 15; 18(20):3864-75. View Abstract
Instrumenting the health care enterprise for discovery research in the genomic era. Genome Res. 2009 Sep; 19(9):1675-81. View Abstract
The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc. 2009 Sep-Oct; 16(5):624-30. View Abstract
Calculating the return on investment of mobile healthcare. BMC Med. 2009 Jun 02; 7:27. View Abstract
Tissue and process specific microRNA-mRNA co-expression in mammalian development and malignancy. PLoS One. 2009; 4(5):e5436. View Abstract
A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood. PLoS One. 2009; 4(4):e5157. View Abstract
Comment on "Autistic-like phenotypes in Cadps2-knockout mice and aberrant CADPS2 splicing in autistic patients". J Clin Invest. 2009 Apr; 119(4):679-80; author reply 680-1. View Abstract
No small change for the health information economy. N Engl J Med. 2009 Mar 26; 360(13):1278-81. View Abstract
High-throughput single cell arrays as a novel tool in biopreservation. Cryobiology. 2009 Jun; 58(3):315-21. View Abstract
Prediction of chronic obstructive pulmonary disease (COPD) in asthma patients using electronic medical records. J Am Med Inform Assoc. 2009 May-Jun; 16(3):371-9. View Abstract
The twin questions of personalized medicine: who are you and whom do you most resemble? Genome Med. 2009 Jan 20; 1(1):4. View Abstract
Ten thousand views of bioinformatics: a bibliome perspective. Yearb Med Inform. 2009; 113-6. View Abstract
Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells. PLoS One. 2008; 3(11):e3794. View Abstract
Comparative analysis of neurological disorders focuses genome-wide search for autism genes. Genomics. 2009 Feb; 93(2):120-9. View Abstract
Integrating outside modules into the i2b2 architecture. AMIA Annu Symp Proc. 2008 Nov 06; 1054. View Abstract
Characterization of patients who suffer asthma exacerbations using data extracted from electronic medical records. AMIA Annu Symp Proc. 2008 Nov 06; 308-12. View Abstract
Cytotoxic diarylheptanoid induces cell cycle arrest and apoptosis via increasing ATF3 and stabilizing p53 in SH-SY5Y cells. Cancer Chemother Pharmacol. 2009 May; 63(6):1131-9. View Abstract
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23; 455(7216):1061-8. View Abstract
Expression profiles of the mouse lung identify a molecular signature of time-to-birth. Am J Respir Cell Mol Biol. 2009 Jan; 40(1):47-57. View Abstract
My sister's keeper?: genomic research and the identifiability of siblings. BMC Med Genomics. 2008 Jul 25; 1:32. View Abstract
Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biol. 2008; 9(7):R108. View Abstract
iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One. 2008 May 28; 3(5):e2265. View Abstract
Tectonic shifts in the health information economy. N Engl J Med. 2008 Apr 17; 358(16):1732-7. View Abstract
Dulxanthone A induces cell cycle arrest and apoptosis via up-regulation of p53 through mitochondrial pathway in HepG2 cells. Int J Cancer. 2008 Jan 01; 122(1):31-8. View Abstract
What are the benefits and risks of fitting patients with radiofrequency identification devices. PLoS Med. 2007 Nov 27; 4(11):e322. View Abstract
A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch. BMC Genomics. 2007 Nov 23; 8:430. View Abstract
Identifying patient smoking status from medical discharge records. J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):14-24. View Abstract
Distinctive patterns of microRNA expression in primary muscular disorders. Proc Natl Acad Sci U S A. 2007 Oct 23; 104(43):17016-21. View Abstract
Architecture of the open-source clinical research chart from Informatics for Integrating Biology and the Bedside. AMIA Annu Symp Proc. 2007 Oct 11; 548-52. View Abstract
Genomic expression pathways associated with brain injury after cardiopulmonary bypass. J Thorac Cardiovasc Surg. 2007 Oct; 134(4):996-1005. View Abstract
The tell-tale heart: population-based surveillance reveals an association of rofecoxib and celecoxib with myocardial infarction. PLoS One. 2007 Sep 05; 2(9):e840. View Abstract
Human disease classification in the postgenomic era: a complex systems approach to human pathobiology. Mol Syst Biol. 2007; 3:124. View Abstract
Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism. PLoS Genet. 2007 Aug; 3(8):e135. View Abstract
Computational analysis of non-adherence and non-attendance using the text of narrative physician notes in the electronic medical record. Med Inform Internet Med. 2007 Jun; 32(2):93-102. View Abstract
Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 2007 Jun; 3(6):e96. View Abstract
An epidemiological network model for disease outbreak detection. PLoS Med. 2007 Jun; 4(6):e210. View Abstract
Medicine. Reestablishing the researcher-patient compact. Science. 2007 May 11; 316(5826):836-7. View Abstract
A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network. Hum Pathol. 2007 Aug; 38(8):1212-25. View Abstract
A self-scaling, distributed information architecture for public health, research, and clinical care. J Am Med Inform Assoc. 2007 Jul-Aug; 14(4):527-33. View Abstract
Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location. Proc Natl Acad Sci U S A. 2007 Mar 20; 104(12):5020-5. View Abstract
Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms. BMC Genomics. 2007 Mar 10; 8:68. View Abstract
Availability and quality of paraffin blocks identified in pathology archives: a multi-institutional study by the Shared Pathology Informatics Network (SPIN). BMC Cancer. 2007 Feb 28; 7:37. View Abstract
Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia. Genome Biol. 2007; 8(10):R210. View Abstract
An unsupervised classification method for inferring original case locations from low-resolution disease maps. Int J Health Geogr. 2006 Dec 08; 5:56. View Abstract
Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Res. 2006; 34(22):e151. View Abstract
A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma. Cancer Res. 2006 Nov 15; 66(22):10815-23. View Abstract
Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin. J Cell Biol. 2006 Oct 09; 175(1):99-110. View Abstract
A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet. 2006 Sep; 38(9):1043-8. View Abstract
Mass spectrometry-based study of the plasma proteome in a mouse intestinal tumor model. J Proteome Res. 2006 Aug; 5(8):1866-78. View Abstract
The incidentalome: a threat to genomic medicine. JAMA. 2006 Jul 12; 296(2):212-5. View Abstract
Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development. PLoS Med. 2006 Jul; 3(7):e232. View Abstract
Induction of the plasminogen activator system by mechanical stimulation of human bronchial epithelial cells. Am J Respir Cell Mol Biol. 2006 Dec; 35(6):628-38. View Abstract
A Bayesian dynamic model for influenza surveillance. Stat Med. 2006 Jun 15; 25(11):1803-16; discussion 1817-25. View Abstract
Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemia. Stem Cells. 2006 Sep; 24(9):2034-44. View Abstract
GenePING: secure, scalable management of personal genomic data. BMC Genomics. 2006 Apr 26; 7:93. View Abstract
Effect of acute aldosterone administration on gene expression profile in the heart. Endocrinology. 2006 Jul; 147(7):3183-9. View Abstract
Transcriptome-scale similarities between mouse and human skeletal muscles with normal and myopathic phenotypes. BMC Musculoskelet Disord. 2006 Mar 07; 7:23. View Abstract
Lower expression of genes near microRNA in C. elegans germline. BMC Bioinformatics. 2006 Mar 06; 7:112. View Abstract
START: an automated tool for serial analysis of chromatin occupancy data. Bioinformatics. 2006 Apr 15; 22(8):999-1001. View Abstract
Creation and implications of a phenome-genome network. Nat Biotechnol. 2006 Jan; 24(1):55-62. View Abstract
Mapping tool for maintaining vocabulary relationships. AMIA Annu Symp Proc. 2006; 939. View Abstract
Integration of clinical and genetic data in the i2b2 architecture. AMIA Annu Symp Proc. 2006; 1040. View Abstract
Integration of the personally controlled electronic medical record into regional inter-regional data exchanges: a national demonstration. AMIA Annu Symp Proc. 2006; 1099. View Abstract
Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. BMC Genomics. 2005 Nov 27; 6:168. View Abstract
Health-information altruists--a potentially critical resource. N Engl J Med. 2005 Nov 10; 353(19):2074-7. View Abstract
The influence of muscle type and dystrophin deficiency on murine expression profiles. Mamm Genome. 2005 Oct; 16(10):739-48. View Abstract
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics. 2005 Sep 14; 6:227. View Abstract
Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13544-9. View Abstract
Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats. Pediatr Nephrol. 2005 Dec; 20(12):1717-23. View Abstract
Identification of patients with diabetes from the text of physician notes in the electronic medical record. Diabetes Care. 2005 Jul; 28(7):1794-5. View Abstract
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics. 2005 Apr 25; 6:107. View Abstract
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics. 2005 Mar 30; 6:79. View Abstract
Parents as partners in obtaining the medication history. J Am Med Inform Assoc. 2005 May-Jun; 12(3):299-305. View Abstract
Wireless technology infrastructures for authentication of patients: PKI that rings. J Am Med Inform Assoc. 2005 May-Jun; 12(3):263-8. View Abstract
CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays. Bioinformatics. 2005 May 01; 21(9):2116-7. View Abstract
DITTO - a tool for identification of patient cohorts from the text of physician notes in the electronic medical record. AMIA Annu Symp Proc. 2005; 744-8. View Abstract
Reverse geocoding: concerns about patient confidentiality in the display of geospatial health data. AMIA Annu Symp Proc. 2005; 905. View Abstract
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D91-7. View Abstract
Side population cells isolated from different tissues share transcriptome signatures and express tissue-specific markers. Exp Cell Res. 2005 Feb 15; 303(2):360-74. View Abstract
The PING personally controlled electronic medical record system: technical architecture. J Am Med Inform Assoc. 2005 Jan-Feb; 12(1):47-54. View Abstract
Mechanical stretch is a highly selective regulator of gene expression in human bladder smooth muscle cells. Physiol Genomics. 2004 Dec 15; 20(1):36-44. View Abstract
Differences in gene expression profiles of diabetic and nondiabetic patients undergoing cardiopulmonary bypass and cardioplegic arrest. Circulation. 2004 Sep 14; 110(11 Suppl 1):II280-6. View Abstract
Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics. 2004 Aug 11; 18(3):308-15. View Abstract
The asthma kiosk: a patient-centered technology for collaborative decision support in the emergency department. J Am Med Inform Assoc. 2004 Nov-Dec; 11(6):458-67. View Abstract
Bayesian approach to discovering pathogenic SNPs in conserved protein domains. Hum Mutat. 2004 Aug; 24(2):178-84. View Abstract
Identification of a transcriptional profile associated with in vitro invasion in non-small cell lung cancer cell lines. Cancer Biol Ther. 2004 Jul; 3(7):624-31. View Abstract
Gene regulation and DNA damage in the ageing human brain. Nature. 2004 Jun 24; 429(6994):883-91. View Abstract
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res. 2004 May 25; 32(9):e74. View Abstract
Molecular classification of nemaline myopathies: "nontyping" specimens exhibit unique patterns of gene expression. Neurobiol Dis. 2004 Apr; 15(3):590-600. View Abstract
A SNP-centric database for the investigation of the human genome. BMC Bioinformatics. 2004 Mar 26; 5:33. View Abstract
Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev. 2004 Mar 15; 18(6):629-40. View Abstract
Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. 2004 Feb 25; 5:18. View Abstract
Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics. J Am Med Inform Assoc. 2004 May-Jun; 11(3):167-72. View Abstract
Prediction of mortality in an Indian intensive care unit. Comparison between APACHE II and artificial neural networks. Intensive Care Med. 2004 Feb; 30(2):248-253. View Abstract
Inter-species differences of co-expression of neighboring genes in eukaryotic genomes. BMC Genomics. 2004 Jan 13; 5(1):4. View Abstract
A submission model for use in the indexing, searching, and retrieval of distributed pathology case and tissue specimens. Stud Health Technol Inform. 2004; 107(Pt 2):1264-7. View Abstract
Analysis and robot pipelined automation for SELDI-TOF mass spectrometry. Conf Proc IEEE Eng Med Biol Soc. 2004; 2004:3068-71. View Abstract
Expression profiling and identification of novel genes involved in myogenic differentiation. FASEB J. 2004 Feb; 18(2):403-5. View Abstract
Gene expression profile after cardiopulmonary bypass and cardioplegic arrest. J Thorac Cardiovasc Surg. 2003 Nov; 126(5):1521-30. View Abstract
Minimal haplotype tagging. Proc Natl Acad Sci U S A. 2003 Aug 19; 100(17):9900-5. View Abstract
Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A. 2003 Jul 08; 100(14):8466-71. View Abstract
Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics. 2003 Jun 25; 4:27. View Abstract
Gene expression profiling of Duchenne muscular dystrophy skeletal muscle. Neurogenetics. 2003 Aug; 4(4):163-71. View Abstract
PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Bioinformatics. 2003 Apr 12; 19(6):778-9. View Abstract
Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscle. Proc Natl Acad Sci U S A. 2003 Apr 15; 100(8):4666-71. View Abstract
The value of parental report for diagnosis and management of dehydration in the emergency department. Ann Emerg Med. 2003 Feb; 41(2):196-205. View Abstract
Localization and characterization of mouse-human alignments within the human genome. Does evolutionary conservation suggest functional importance? AMIA Annu Symp Proc. 2003; 994. View Abstract
Gene homology resources on the World Wide Web. Physiol Genomics. 2002 Dec 03; 11(3):165-77. View Abstract
Comparing expression profiles of genes with similar promoter regions. Bioinformatics. 2002 Dec; 18(12):1576-84. View Abstract
SNPper: retrieval and analysis of human SNPs. Bioinformatics. 2002 Dec; 18(12):1681-5. View Abstract
Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):15000-5. View Abstract
Molecular profiles of inflammatory myopathies. Neurology. 2002 Oct 22; 59(8):1170-82. View Abstract
Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A. 2002 Jul 09; 99(14):9121-6. View Abstract
Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5704-9. View Abstract
The contributions of biomedical informatics to the fight against bioterrorism. J Am Med Inform Assoc. 2002 Mar-Apr; 9(2):116-9. View Abstract
Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 2002 Mar; 18(3):405-12. View Abstract
Newborn screening program practices in the United States: notification, research, and consent. Pediatrics. 2002 Feb; 109(2):269-73. View Abstract
Visualization and evaluation of clusters for exploratory analysis of gene expression data. J Biomed Inform. 2002 Feb; 35(1):25-36. View Abstract
Computerized reminders to physicians in the emergency department: a web-based system to report late-arriving abnormal laboratory results. Proc AMIA Symp. 2002; 91-5. View Abstract
Accessing genomic data through XML-based remote procedure calls. Proc AMIA Symp. 2002; 662-6. View Abstract
An unsupervised self-optimizing gene clustering algorithm. Proc AMIA Symp. 2002; 682-6. View Abstract
CHIP TUNER: a web tool for evidence-based noise reduction in gene discovery. Proc AMIA Symp. 2002; 810-4. View Abstract
Linking gene expression data with patient survival times using partial least squares. Bioinformatics. 2002; 18 Suppl 1:S120-7. View Abstract
Comparing the similarity of time-series gene expression using signal processing metrics. J Biomed Inform. 2001 Dec; 34(6):396-405. View Abstract
Corticotropin releasing hormone increases apparent potency of adrenocorticotropic hormone stimulation of cortisol secretion. Med Hypotheses. 2001 Nov; 57(5):544-8. View Abstract
The personal internetworked notary and guardian. Int J Med Inform. 2001 Jun; 62(1):27-40. View Abstract
The ever imminent electronic medical record. J Med Pract Manage. 2001 Mar-Apr; 16(5):264-5. View Abstract
Public standards and patients' control: how to keep electronic medical records accessible but private. BMJ. 2001 Feb 03; 322(7281):283-7. View Abstract
Extracting knowledge from dynamics in gene expression. J Biomed Inform. 2001 Feb; 34(1):15-27. View Abstract
Optimal data entry by patients: effects of interface structure and design. Stud Health Technol Inform. 2001; 84(Pt 1):141-5. View Abstract
A web-based tool to retrieve human genome polymorphisms from public databases. Proc AMIA Symp. 2001; 558-62. View Abstract
Building ICU artifact detection models with more data in less time. Proc AMIA Symp. 2001; 706-10. View Abstract
Unsupervised learning from complex data: the matrix incision tree algorithm. Pac Symp Biocomput. 2001; 30-41. View Abstract
On reporting fold differences. Pac Symp Biocomput. 2001; 496-507. View Abstract
Determining significant fold differences in gene expression analysis. Pac Symp Biocomput. 2001; 6-17. View Abstract
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A. 2000 Oct 24; 97(22):12182-6. View Abstract
Potential impact of a computerized system to report late-arriving laboratory results in the emergency department. Pediatr Emerg Care. 2000 Oct; 16(5):313-5. View Abstract
Bioinformatics and clinical informatics: the imperative to collaborate. J Am Med Inform Assoc. 2000 Sep-Oct; 7(5):512-6. View Abstract
Multiple signal integration by decision tree induction to detect artifacts in the neonatal intensive care unit. Artif Intell Med. 2000 Jul; 19(3):189-202. View Abstract
Implementation of an electronic medical record system in a pediatric psychopharmacology program. Int J Med Inform. 2000 Jul; 57(2-3):109-16. View Abstract
Growth and determinants of access in patient e-mail and Internet use. Arch Pediatr Adolesc Med. 2000 May; 154(5):508-11. View Abstract
Parents as direct contributors to the medical record: validation of their electronic input. Ann Emerg Med. 2000 Apr; 35(4):346-52. View Abstract
Temporal expressiveness in querying a time-stamp--based clinical database. J Am Med Inform Assoc. 2000 Mar-Apr; 7(2):152-63. View Abstract
Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput. 2000; 418-29. View Abstract
Enrolling patients into clinical trials faster using RealTime Recuiting. Proc AMIA Symp. 2000; 111-5. View Abstract
The new peer review. Proc AMIA Symp. 2000; 433-7. View Abstract
Glucoweb: a case study of secure, remote biomonitoring and communication. Proc AMIA Symp. 2000; 610-4. View Abstract
Artifact detection in the PO2 and PCO2 time series monitoring data from preterm infants. J Clin Monit Comput. 1999 Aug; 15(6):369-78. View Abstract
Using 'off the shelf', computer programs to mine additional insights from published data: diurnal variation in potency of ACTH stimulation of cortisol secretion revealed. Comput Methods Programs Biomed. 1999 Mar; 58(3):227-38. View Abstract
The challenges of automating a real-time clinical practice guideline. Clin Perform Qual Health Care. 1999 Jan-Mar; 7(1):28-35. View Abstract
Artifact detection in cardiovascular time series monitoring data from preterm infants. Proc AMIA Symp. 1999; 207-11. View Abstract
Unsupervised knowledge discovery in medical databases using relevance networks. Proc AMIA Symp. 1999; 711-5. View Abstract
Healthconnect: clinical grade patient-physician communication. Proc AMIA Symp. 1999; 849-53. View Abstract
Scaling a data retrieval and mining application to the enterprise-wide level. Proc AMIA Symp. 1999; 901-5. View Abstract
Electronic patient-physician communication: problems and promise. Ann Intern Med. 1998 Sep 15; 129(6):495-500. View Abstract
Social equity and access to the World Wide Web and E-mail: implications for design and implementation of medical applications. Proc AMIA Symp. 1998; 215-9. View Abstract
Health information identification and de-identification toolkit. Proc AMIA Symp. 1998; 356-60. View Abstract
Linking multiple heterogeneous data sources to practice guidelines. Proc AMIA Symp. 1998; 391-5. View Abstract
Data mining by clinicians. Proc AMIA Symp. 1998; 957-61. View Abstract
Computer-based Patient Records. Yearb Med Inform. 1998; (1):227-229. View Abstract
Computer-assisted adjustment of inspired oxygen concentration improves control of oxygen saturation in newborn infants requiring mechanical ventilation. J Pediatr. 1997 Nov; 131(5):754-6. View Abstract
Maintaining the confidentiality of medical records shared over the Internet and the World Wide Web. Ann Intern Med. 1997 Jul 15; 127(2):138-41. View Abstract
Physician pushes for the use of technology. Interview by Tyler L. Chin. Health Data Manag. 1997 Jul; 5(7):30, 32, 34-6. View Abstract
Using the technology of the World Wide Web to manage clinical information. BMJ. 1997 May 31; 314(7094):1600-3. View Abstract
Patient assessment systems using the World Wide Web. Behav Healthc Tomorrow. 1997 Feb; 6(1):77-9. View Abstract
A Java-based multi-institutional medical information retrieval system. Proc AMIA Annu Fall Symp. 1997; 538-42. View Abstract
Exploring the functions of World Wide Web-based electronic medical record systems. MD Comput. 1996 Jul-Aug; 13(4):339-46. View Abstract
Managing temporal worlds for medical trend diagnosis. Artif Intell Med. 1996 Jul; 8(3):299-321. View Abstract
Building national electronic medical record systems via the World Wide Web. J Am Med Inform Assoc. 1996 May-Jun; 3(3):191-207. View Abstract
Follow-up study of adolescent girls with a history of premature pubarche. J Adolesc Health. 1996 Apr; 18(4):301-5. View Abstract
Sharing electronic medical records across multiple heterogeneous and competing institutions. Proc AMIA Annu Fall Symp. 1996; 608-12. View Abstract
Using HL7 and the World Wide Web for unifying patient data from remote databases. Proc AMIA Annu Fall Symp. 1996; 643-7. View Abstract
A real time patient monitoring system on the World Wide Web. Proc AMIA Annu Fall Symp. 1996; 729-32. View Abstract
Editorial. Artif Intell Med. 1995 Dec; 7(6):471-2. View Abstract
Clinical monitoring using regression-based trend templates. Artif Intell Med. 1995 Dec; 7(6):473-96. View Abstract
Topical iodine and neonatal hypothyroidism. Arch Pediatr Adolesc Med. 1995 Dec; 149(12):1336-9. View Abstract
WHAM!: a forms constructor for medical record access via the World Wide Web. Proc Annu Symp Comput Appl Med Care. 1995; 116-20. View Abstract
Using a pen-based computer to collect health-related quality of life and utilities information. Proc Annu Symp Comput Appl Med Care. 1995; 839-43. View Abstract
PEFIOS: an expert closed-loop oxygenation algorithm. Medinfo. 1995; 8 Pt 2:1132-6. View Abstract
Against simple universal health-care identifiers. J Am Med Inform Assoc. 1994 Jul-Aug; 1(4):316-9. View Abstract
Corticotrophin releasing hormone levels in human plasma and amniotic fluid during gestation. Clin Endocrinol (Oxf). 1994 Feb; 40(2):257-62. View Abstract
Getting the data in: three year experience with a pediatric electronic medical record system. Proc Annu Symp Comput Appl Med Care. 1994; 457-61. View Abstract
A computer simulation of the hypothalamic-pituitary-adrenal axis. Proc Annu Symp Comput Appl Med Care. 1994; 1010. View Abstract
Fuzzy logic assisted control of inspired oxygen in ventilated newborn infants. Proc Annu Symp Comput Appl Med Care. 1994; 757-61. View Abstract
Monitor-driven data visualization: SmartDisplay. Proc Annu Symp Comput Appl Med Care. 1994; 939-43. View Abstract
Hypothesis-driven data abstraction with trend templates. Proc Annu Symp Comput Appl Med Care. 1993; 444-8. View Abstract
Influences on the performance of hospital clinical event monitoring. Proc Annu Symp Comput Appl Med Care. 1991; 614-8. View Abstract
Effect of selection, mutation, and linkage on the equilibrium structure of selfing systems. J Hered. 1983 May-Jun; 74(3):175-80. View Abstract

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