Ishan Paranjpe's research while affiliated with Stanford Medicine and other places

Publications (92)

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A bstract Kidney disease affects 50% of all diabetic patients; however, prediction of disease progression has been challenging due to inherent disease heterogeneity. We use deep learning to identify novel genetic signatures prognostically associated with outcomes. Using autoencoders and unsupervised clustering of electronic health record data on 1,...
Article
Background and Aims Diabetic kidney disease (DKD) is a leading cause of end-stage kidney disease (ESKD), however therapies targeting causal pathways have been limited by disease heterogeneity. Integrating electronic health record (EHR) data and genomics may uncover hidden subphenotypes in DKD. In this study, we use deep learning to identify a novel...
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Background Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Methods Using measurements of ~4000 plasma proteins in two cohorts of patient...
Article
6652 Background: Following the 2021 Hospital Price Transparency Final Rule, US hospitals were mandated to publish their insurer-negotiated prices. We identified factors contributing to price variability of colorectal cancer (CRC) screening procedures across the US. Methods: We compared prices of colonoscopy, flexible sigmoidoscopy, CT colonography,...
Preprint
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Background Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Methods Using measurements of ~4000 plasma proteins in two cohorts of patients...
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Rationale & Objective The association between cannabis use and chronic kidney disease (CKD) is controversial. We aimed to assess association of CKD with cannabis use in a large cohort study and then assess causality using Mendelian Randomization with genome wide association study (GWAS). Study Design Retrospective cohort study and genome wide asso...
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Heart failure is a leading cause of cardiovascular morbidity and mortality. However, the contribution of common genetic variation to heart failure risk has not been fully elucidated, particularly in comparison to other common cardiometabolic traits. We report a multi-ancestry genome-wide association study meta-analysis of all-cause heart failure in...
Preprint
Full-text available
Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using longitudinally collected biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Using longitudinal measurements of ∼4000 plasma proteins in two...
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PurposeTo investigate the relationship between metabolic syndrome (MS) and urinary abnormalities in stone-forming patients. Additionally, to delineate whether severity of urinary derangements is impacted by the number of co-occurring MS components.Methods Stone-forming patients who underwent initial metabolic workup prior to medical intervention at...
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Background Despite advances in cardiovascular disease and risk factor management, mortality from ischemic heart failure (HF) in patients with coronary artery disease (CAD) remains high. Given the partial role of genetics in HF and lack of reliable risk stratification tools, we developed and validated a polygenic risk score for HF in patients with C...
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PurposeLimited mechanical ventilators (MV) during the Coronavirus disease (COVID-19) pandemic have led to the use of non-invasive ventilation (NIV) in hypoxemic patients, which has not been studied well. We aimed to assess the association of NIV versus MV with mortality and morbidity during respiratory intervention among hypoxemic patients admitted...
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Deep Learning (DL) models typically require large-scale, balanced training data to be robust, generalizable, and effective in the context of healthcare. This has been a major issue for developing DL models for the coronavirus-disease 2019 (COVID-19) pandemic where data are highly class imbalanced. Conventional approaches in DL use cross-entropy los...
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The evident genetic, pathological and clinical heterogeneity of Alzheimer’s disease (AD) poses challenges for traditional drug development. We conducted a computational drug-repurposing screen for drugs to treat apolipoprotein E4 (APOE4)-related AD. We first established APOE genotype-dependent transcriptomic signatures of AD by analyzing publicly a...
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Background: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the United States. In spite of evidence of females having a greater lifetime risk of developing Alzheimer’s Disease (AD) and greater apolipoprotein E4-related (APOE ε4) AD risk compared to males, molecular signatures underlying...
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Ca2+ entry into mitochondria is through the mitochondrial calcium uniporter complex (MCUcx), a Ca2+-selective channel composed of five subunit types. Two MCUcx subunits (MCU and EMRE) span the inner mitochondrial membrane, while three Ca2+-regulatory subunits (MICU1, MICU2 and MICU3) reside in the intermembrane space. Here we provide rigorous analy...
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Federated learning is a technique for training predictive models without sharing patient-level data, thus maintaining data security while allowing inter-institutional collaboration. We used federated learning to predict acute kidney injury within three and seven days of admission, using demographics, comorbidities, vital signs, and laboratory value...
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Introduction: Diabetes mellitus (DM) is associated with an increased risk of nephrolithiasis and is often treated with metformin. The relationship between metformin and nephrolithiasis formation remains unclear as studies have demonstrated conflicting results. Methods: We conducted a cross-sectional analysis of stone-forming patients at our ston...
Article
Background: Acute Kidney Injury treated with dialysis initiation is a common complication of COVID-19 infection among hospitalized patients. However, dialysis supplies and personnel are often limited. Methods: Using data from adult hospitalized COVID-19 patients from five hospitals from the Mount Sinai Health System who were admitted from March 10t...
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Systemic lupus erythematosus (SLE) is an autoimmune disease in which outcomes vary among different racial groups. We leverage cell-sorted RNA-seq data (CD14+ monocytes, B cells, CD4+ T cells, and NK cells) from 120 SLE patients (63 Asian and 57 White individuals) and apply a four-tier approach including unsupervised clustering, differential express...
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Diabetic retinopathy (DR) is a common consequence in type 2 diabetes (T2D) and a leading cause of blindness in working-age adults. Yet, its genetic predisposition is largely unknown. Here, we examined the polygenic architecture underlying DR by deriving and assessing a genome-wide polygenic risk score (PRS) for DR. We evaluated the PRS in 6079 indi...
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Background/aims: Acute kidney injury (AKI) in critically ill patients is common, and continuous renal replacement therapy (CRRT) is a preferred mode of renal replacement therapy (RRT) in hemodynamically unstable patients. Prediction of clinical outcomes in patients on CRRT is challenging. We utilized several approaches to predict RRT-free survival...
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Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the associated Coronavirus Disease 2019 (COVID-19) is a public health emergency. Acute kidney injury (AKI) is a common complication in hospitalized patients with COVID-19 although mechanisms underlying AKI are yet unclear. There may be a direct effect of SARS-CoV-2 virus on...
Preprint
Acute Kidney Injury (AKI) is among the most common complications of Coronavirus Disease 2019 (COVID-19). Throughout 2020 pandemic, the clinical approach to COVID-19 has progressively improved, but it is unknown how these changes have affected AKI incidence and severity. In this retrospective analysis, we report the trend over time of COVID-19 assoc...
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More than 800 million people in the world suffer from chronic kidney disease (CKD). Genome-wide association studies (GWAS) have identified hundreds of loci where genetic variants are associated with kidney function; however, causal genes and pathways for CKD remain unknown. Here, we performed integration of kidney function GWAS and human kidney–spe...
Preprint
Machine Learning (ML) models typically require large-scale, balanced training data to be robust, generalizable, and effective in the context of healthcare. This has been a major issue for developing ML models for the coronavirus-disease 2019 (COVID-19) pandemic where data is highly imbalanced, particularly within electronic health records (EHR) res...
Article
Full-text available
Machine Learning (ML) models typically require large-scale, balanced training data to be robust, generalizable, and effective in the context of healthcare. This has been a major issue for developing ML models for the coronavirus-disease 2019 (COVID-19) pandemic where data is highly imbalanced, particularly within electronic health records (EHR) res...
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Full-text available
Objective The COVID-19 pandemic is a global public health crisis, with over 33 million cases and 999 000 deaths worldwide. Data are needed regarding the clinical course of hospitalised patients, particularly in the USA. We aimed to compare clinical characteristic of patients with COVID-19 who had in-hospital mortality with those who were discharged...
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Background and objectives Sepsis-associated AKI is a heterogeneous clinical entity. We aimed to agnostically identify sepsis-associated AKI subphenotypes using deep learning on routinely collected data in electronic health records. Design, setting, participants, & measurements We used the Medical Information Mart for Intensive Care III database, w...
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Background COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The COVID-19 pandemic has necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods to meet these needs are lacking. Objective The aims of this study were to analyze...
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Objective Multiple clinical trials fail to identify clinically measurable health benefits of daily multivitamin and multimineral (MVM) consumption in the general adult population. Understanding the determinants of widespread use of MVMs may guide efforts to better educate the public about effective nutritional practices. The objective of this study...
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Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease in which outcomes vary among different racial groups. The aim of this study is to leverage large-scale transcriptomic data from diverse populations to better sub-classify SLE patients into more clinically actionable groups. We leverage cell sorted RNA-seq data (CD14 ⁺ monocyte...
Preprint
Full-text available
Systemic lupus erythematosus (SLE) is an autoimmune disease in which outcomes vary among different racial groups. We leverage cell-sorted RNA-seq data (CD14 + monocytes, B cells, CD4 + T cells, and NK cells) from 120 SLE patients (63 Asian and 57 White individuals) and apply a four-tier approach to identify SLE subgroups within this multiethnic coh...
Preprint
Full-text available
Background: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the United States. In spite of evidence of females having a greater lifetime risk of developing Alzheimer’s Disease (AD) and greater apolipoprotein E4-related (apoE4) AD risk compared to males, molecular signatures underlying th...
Article
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Background Abdominal aortic aneurysm (AAA) is an important cause of cardiovascular mortality; however, its genetic determinants remain incompletely defined. In total, 10 previously identified risk loci explain a small fraction of AAA heritability. Methods We performed a genome-wide association study in the Million Veteran Program testing ≈18 milli...
Preprint
BACKGROUND Machine learning models require large datasets that may be siloed across different health care institutions. Machine learning studies that focus on COVID-19 have been limited to single-hospital data, which limits model generalizability. OBJECTIVE We aimed to use federated learning, a machine learning technique that avoids locally aggreg...
Article
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Background: Machine learning (ML) models require large datasets which may be siloed across different healthcare institutions. Current ML studies focusing on coronavirus disease 2019 (COVID-19) are limited to single hospital data which limits model generalizability. Objective: Using federated learning, a ML technique that avoids locally aggregati...
Preprint
BACKGROUND COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The COVID-19 pandemic has necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods to meet these needs are lacking. OBJECTIVE The aims of this study were to analyze...
Article
Introduction and objective: Patients presenting with a urinary tract infection (UTI) with kidney or ureteral stones is a urological emergency often achieve early clinical stability but remain hospitalized while awaiting results from urine antibiotic sensitivity analyses. We aimed to identify clinical predictors of antibiotic resistance in patients...
Preprint
Full-text available
Machine learning (ML) models require large datasets which may be siloed across different healthcare institutions. Using federated learning, a ML technique that avoids locally aggregating raw clinical data across multiple institutions, we predict mortality within seven days in hospitalized COVID-19 patients. Patient data was collected from Electroni...
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Background: There have been limited data regarding the clinical impact of COVID-19 disease on people with HIV (PWH). In this study we compared outcomes for PWH with COVID-19 disease to a matched comparison group. Design: We identified 88 PWH hospitalized with laboratory confirmed COVID-19 in our hospital system in New York between March 12 and A...
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PURPOSE: Data have indicated that residual disease after neoadjuvant chemotherapy (NAC) for muscle-invasive bladder cancer (MIBC) may be associated with poor outcomes. OBJECTIVE: Analyze differences in overall survival (OS) of patients with residual MIBC treated with NAC + Radical cystectomy (RC), RC alone, or RC + Adjuvant Chemotherapy(AC). MATERI...
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Despite substantial advances in the study, treatment, and prevention of cardiovascular disease, numerous challenges relating to optimally screening, diagnosing, and managing patients remain. Simultaneous improvements in computing power, data storage, and data analytics have led to the development of new techniques to address these challenges. One p...
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Background The degree of myocardial injury, as reflected by troponin elevation, and associated outcomes among US hospitalized patients with Coronavirus Disease 2019 (COVID-19) are unknown. Objectives To describe the degree of myocardial injury and associated outcomes in a large hospitalized cohort with laboratory-confirmed COVID-19. Methods Patie...
Article
Urinary tract stones have high heritability indicating a strong genetic component. However, genome wide association studies (GWAS) have uncovered only a few genome wide significant single nucleotide polymorphisms (SNPs). Polygenic risk scores (PRS) sum cumulative effect of many SNPs and shed light on underlying genetic architecture. Using GWAS summ...
Preprint
Full-text available
Background: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the United States. In spite of evidence of females having a greater lifetime risk of developing Alzheimer’s Disease (AD) and greater apolipoprotein E4-related (apoE4) AD risk compared to males, molecular signatures underlying th...
Article
Electrophysiology (EP) procedures carry the risk of kidney injury due to contrast/hemodynamic fluctuations. We aim to evaluate the national epidemiology of acute kidney injury requiring dialysis (AKI-D) in patients undergoing EP procedures. Using the National Inpatient Sample, we included 2,747,605 adult hospitalizations undergoing invasive diagnos...
Preprint
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Importance: Preliminary reports indicate that acute kidney injury (AKI) is common in coronavirus disease (COVID)-19 patients and is associated with worse outcomes. AKI in hospitalized COVID-19 patients in the United States is not well-described. Objective: To provide information about frequency, outcomes and recovery associated with AKI and dialysi...
Preprint
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Coronavirus 2019 (COVID-19), caused by the SARS-CoV-2 virus, has become the deadliest pandemic in modern history, reaching nearly every country worldwide and overwhelming healthcare institutions. As of April 20, there have been more than 2.4 million confirmed cases with over 160,000 deaths. Extreme case surges coupled with challenges in forecasting...
Preprint
Full-text available
In spite of evidence of females having a greater lifetime risk of developing Alzheimer's Disease (AD) and greater apolipoprotein E4-related (apoE4) AD risk compared to males, molecular signatures underlying these findings remain elusive. We took a meta-analysis approach to study gene expression in the brains of 1,084 AD patients and age-matched con...
Preprint
Full-text available
Background: The degree of myocardial injury, reflected by troponin elevation, and associated outcomes among hospitalized patients with Coronavirus Disease (COVID-19) in the US are unknown. Objectives: To describe the degree of myocardial injury and associated outcomes in a large hospitalized cohort with laboratory-confirmed COVID-19. Methods:...
Preprint
Full-text available
Background: The coronavirus 2019 (Covid-19) pandemic is a global public health crisis, with over 1.6 million cases and 95,000 deaths worldwide. Data are needed regarding the clinical course of hospitalized patients, particularly in the United States. Methods Demographic, clinical, and outcomes data for patients admitted to five Mount Sinai Health S...
Preprint
Mitochondrial Ca ²⁺ uniporter (MCU) mediates mitochondrial Ca ²⁺ uptake, regulating ATP production and cell death. According to the existing paradigm, MCU is occluded at the resting cytosolic [Ca ²⁺ ] and only opens above an ∼400 nM threshold. This Ca ²⁺ -dependent gating is putatively conferred by MICUs, EF hand-containing auxiliary subunits that...
Article
Full-text available
Sleep quality has been directly linked to cognitive function, quality of life, and a variety of serious diseases across many clinical domains. Standard methods for assessing sleep involve overnight studies in hospital settings, which are uncomfortable, expensive, not representative of real sleep, and difficult to conduct on a large scale. Recently,...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Sleep quality has been directly linked to cognitive function, quality of life, and a variety of serious diseases across many clinical domains such as psychiatry and cardiology. Standard methods for assessing sleep involve overnight studies in hospital settings, which are uncomfortable, expensive, not representative of real sleep, and difficult to c...
Article
Background: Research experience is believed to be an important component of the neurosurgery residency application process. One measure of research productivity is publication volume. The pre-residency publication volume of US neurosurgery interns and any potential association between applicant publication volume and the match results of top ranke...
Article
Hypertension (HTN) is a major cause of morbidity and mortality and a subset may be caused by monogenic mutations. We identified the prevalence of these mutations in a multiethnic cohort and determined their association with blood pressure, appropriate diagnosis, and adverse cardiovascular outcomes. In 27,972 individuals from the Bio Me Biobank (830...
Article
Full-text available
Systemic lupus erythematous (SLE) is a heterogeneous autoimmune disease in which outcomes vary among different racial groups. Here, we aim to identify SLE subgroups within a multiethnic cohort using an unsupervised clustering approach based on the American College of Rheumatology (ACR) classification criteria. We identify three patient clusters tha...
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Timely dissemination of results from clinical studies is crucial for the advancement of knowledge and clinical decision making. A large body of research has shown that up to half of clinical trials do not publish their findings. In this study, we sought to determine whether clinical trial publication rates within neurology have increased over time....
Article
Calcium uptake by mitochondria plays an important role in sequestering cytosolic calcium, regulating ATP production and maintaining the redox homeostasis. Mitochondrial calcium uniporter (MCU), a macromolecular channel complex that resides in the inner mitochondrial membrane, is the primary electrogenic pathway for calcium influx into the matrix. B...
Conference Paper
Background Systemic lupus erythematosus (SLE) is a multifactorial disease with genetic and environmental risk factors that encompass a wide range of disease severity and heterogeneous manifestations. Long-term outcomes for individual patients are difficult to predict and little is known about why an affected individual might develop a particular SL...