Paul Avillach
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View article: VarPPUD: Pinpointing diagnostic variants from sets of prioritized, strong candidate variants
VarPPUD: Pinpointing diagnostic variants from sets of prioritized, strong candidate variants Open
Rare and ultra-rare genetic conditions are estimated to impact nearly 1 in 17 people worldwide, yet accurately pinpointing the diagnostic variants underlying each of these conditions remains a formidable challenge. Because comprehensive, i…
View article: Correction: Neurological diagnoses in hospitalized COVID-19 patients associated with adverse outcomes: A multinational cohort study
Correction: Neurological diagnoses in hospitalized COVID-19 patients associated with adverse outcomes: A multinational cohort study Open
[This corrects the article DOI: 10.1371/journal.pdig.0000484.].
View article: Use of Computational Phenotypes for Predicting Genetic Subgroups of Cerebral Palsy
Use of Computational Phenotypes for Predicting Genetic Subgroups of Cerebral Palsy Open
Introduction Emerging evidence suggests that 20–30% of cases of cerebral palsy (CP) may have a genetic cause. Our group previously identified subsets of patients with CP or CP-masquerading conditions who warrant genetic testing, including …
View article: The potential of Generative Pre-trained Transformer 4 (GPT-4) to analyse medical notes in three different languages: a retrospective model-evaluation study
The potential of Generative Pre-trained Transformer 4 (GPT-4) to analyse medical notes in three different languages: a retrospective model-evaluation study Open
View article: Robust Automated Harmonization of Heterogeneous Data Through Ensemble Machine Learning: Algorithm Development and Validation Study
Robust Automated Harmonization of Heterogeneous Data Through Ensemble Machine Learning: Algorithm Development and Validation Study Open
Background Cohort studies contain rich clinical data across large and diverse patient populations and are a common source of observational data for clinical research. Because large scale cohort studies are both time and resource intensive,…
View article: Phenome-wide profiling identifies genotype-phenotype associations in Phelan-McDermid syndrome using family-sourced data from an international registry
Phenome-wide profiling identifies genotype-phenotype associations in Phelan-McDermid syndrome using family-sourced data from an international registry Open
View article: Development and validation of an open-source pipeline for automatic population of case report forms from electronic health records: a pediatric multi-center prospective study
Development and validation of an open-source pipeline for automatic population of case report forms from electronic health records: a pediatric multi-center prospective study Open
NIH Grant 1OT3HL147154-01, U24HL135691, UG1HL135685.
View article: VarPPUD: Variant post prioritization developed for undiagnosed genetic disorders
VarPPUD: Variant post prioritization developed for undiagnosed genetic disorders Open
Rare and ultra-rare genetic conditions are estimated to impact nearly 1 in 17 people worldwide, yet accurately pinpointing the diagnostic variants underlying each of these conditions remains a formidable challenge. Because comprehensive, i…
View article: Neurological diagnoses in hospitalized COVID-19 patients associated with adverse outcomes: A multinational cohort study
Neurological diagnoses in hospitalized COVID-19 patients associated with adverse outcomes: A multinational cohort study Open
Few studies examining the patient outcomes of concurrent neurological manifestations during acute COVID-19 leveraged multinational cohorts of adults and children or distinguished between central and peripheral nervous system (CNS vs. PNS) …
View article: Assessing the Potential of GPT-4 to Annotate Medical Notes Across Different Languages and Countries: A Model Evaluation Study
Assessing the Potential of GPT-4 to Annotate Medical Notes Across Different Languages and Countries: A Model Evaluation Study Open
View article: The Human Phenotype Ontology in 2024: phenotypes around the world
The Human Phenotype Ontology in 2024: phenotypes around the world Open
The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through seman…
View article: SONAR: Enabling Robust Automated Harmonization of Heterogeneous Data through Ensemble Machine Learning (Preprint)
SONAR: Enabling Robust Automated Harmonization of Heterogeneous Data through Ensemble Machine Learning (Preprint) Open
BACKGROUND Cohort studies contain rich clinical data across large and diverse patient populations that are a common source of observational data for clinical research. Because large scale cohort studies are both time and resource intensiv…
View article: Characterization of long COVID temporal sub-phenotypes by distributed representation learning from electronic health record data: a cohort study
Characterization of long COVID temporal sub-phenotypes by distributed representation learning from electronic health record data: a cohort study Open
View article: Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research
Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research Open
Research increasingly relies on interrogating large-scale data resources. The NIH National Heart, Lung, and Blood Institute developed the NHLBI BioData CatalystⓇ (BDC), a community-driven ecosystem where researchers, including bench and cl…
View article: Potential pitfalls in the use of real-world data for studying long COVID
Potential pitfalls in the use of real-world data for studying long COVID Open
View article: Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record? Open
View article: 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
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 Open
Purpose In young adults (18 to 49 years old), investigation of the acute respiratory distress syndrome (ARDS) after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been limited. We evaluated the risk factors and …
View article: Clinical Phenotypes and Outcomes in Children with Multisystem Inflammatory Syndrome Across Sars-CoV-2 Variant Eras: A Multinational Study from the 4CE Consortium
Clinical Phenotypes and Outcomes in Children with Multisystem Inflammatory Syndrome Across Sars-CoV-2 Variant Eras: A Multinational Study from the 4CE Consortium Open
View article: Hospitalizations Associated With Mental Health Conditions Among Adolescents in the US and France During the COVID-19 Pandemic
Hospitalizations Associated With Mental Health Conditions Among Adolescents in the US and France During the COVID-19 Pandemic Open
Importance The COVID-19 pandemic has been associated with an increase in mental health diagnoses among adolescents, though the extent of the increase, particularly for severe cases requiring hospitalization, has not been well characterized…
View article: Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: an international multi-centre observational cohort study
Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: an international multi-centre observational cohort study Open
View article: SurvMaximin: Robust federated approach to transporting survival risk prediction models
SurvMaximin: Robust federated approach to transporting survival risk prediction models Open
View article: Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization
Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization Open
The proposed MIKGI algorithm can effectively integrate incomplete summary data from biomedical text and EHR data to generate harmonized embeddings for EHR codes for knowledge graph modeling and cross-institutional translation of EHR codes.
View article: International electronic health record-derived post-acute sequelae profiles of COVID-19 patients
International electronic health record-derived post-acute sequelae profiles of COVID-19 patients Open
The risk profiles of post-acute sequelae of COVID-19 (PASC) have not been well characterized in multi-national settings with appropriate controls. We leveraged electronic health record (EHR) data from 277 international hospitals representi…
View article: International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality
International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality Open
View article: 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
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 Open
Objective To assess changes in international mortality rates and laboratory recovery rates during hospitalisation for patients hospitalised with SARS-CoV-2 between the first wave (1 March to 30 June 2020) and the second wave (1 July 2020 t…
View article: Distinguishing Admissions Specifically for COVID-19 From Incidental SARS-CoV-2 Admissions: National Retrospective Electronic Health Record Study
Distinguishing Admissions Specifically for COVID-19 From Incidental SARS-CoV-2 Admissions: National Retrospective Electronic Health Record Study Open
Background Admissions are generally classified as COVID-19 hospitalizations if the patient has a positive SARS-CoV-2 polymerase chain reaction (PCR) test. However, because 35% of SARS-CoV-2 infections are asymptomatic, patients admitted fo…
View article: 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
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 Open
Purpose In young adults (18 to 49 years old), investigation of the acute respiratory distress syndrome (ARDS) after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been limited. We evaluated the risk factors and …
View article: Validation of a computational phenotype for finding patients eligible for genetic testing for pathogenic PTEN variants across three centers
Validation of a computational phenotype for finding patients eligible for genetic testing for pathogenic PTEN variants across three centers Open
Background Computational phenotypes are most often combinations of patient billing codes that are highly predictive of disease using electronic health records (EHR). In the case of rare diseases that can only be diagnosed by genetic testin…
View article: Distinguishing Admissions Specifically for COVID-19 From Incidental SARS-CoV-2 Admissions: National Retrospective Electronic Health Record Study (Preprint)
Distinguishing Admissions Specifically for COVID-19 From Incidental SARS-CoV-2 Admissions: National Retrospective Electronic Health Record Study (Preprint) Open
BACKGROUND Admissions are generally classified as COVID-19 hospitalizations if the patient has a positive SARS-CoV-2 polymerase chain reaction (PCR) test. However, because 35% of SARS-CoV-2 infections are asymptomatic, patients admitted f…
View article: Long-term Survival after Hematopoietic Cell Transplant for Sickle Cell Disease Compared to the United States Population
Long-term Survival after Hematopoietic Cell Transplant for Sickle Cell Disease Compared to the United States Population Open