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COBA paper on ImageJ and CellProfiler rated #1

News: February 10, 2022

COBA paper on ImageJ and CellProfiler rated #1 in Altmetrics for Best of Current Protocols 2021! ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis ImageJ and CellProfiler have long been leading open-source platforms in the field of bioimage analysis. ImageJ's traditional strength...

Katherine Stalnaker

Person: Research Associate II

Kate graduated from American University in 2016 with a BA in Psychology. In 2020 she graduated from Rutgers University with her MS in Biomedical Science with a concentration in Neuroscience. Her thesis was on glucose sensing in the brain and the relationship to feeding behavior. Kate has worked in...

How to Normalize Cell Painting Data

Blog: March 22, 2022

Rebecca Senft Workflow update June 2024 update Our recommended normalization workflow is evolving. Please see https://github.com/broadinstitute/jump-profiling-recipe/ for our latest developments on the normalization strategy in specific and aprofiling workflow in general. How to Normalize Cell...

Genetics of Myocardial Interstitial Fibrosis in the Human Heart and Association with Disease

Publication: Miscellaneous

Nauffal, Victor, Paolo Di Achille, Marcus. D. R. Klarqvist, Jonathan W. Cunningham, James P. Pirruccello, Lu-Chen Weng, Valerie N. Morrill, et al. 2021. “Genetics of Myocardial Interstitial Fibrosis in the Human Heart and Association With Disease.”

Cohort Design and Natural Language Processing to Reduce Bias in Electronic Health Records Research: The Community Care Cohort Project

Publication: Journal Article

Khurshid, Shaan, Christopher Reeder, Lia X. Harrington, Pulkit Singh, Gopal Sarma, Samuel F. Friedman, Paolo Di Achille, et al. 2021. “Cohort Design and Natural Language Processing to Reduce Bias in Electronic Health Records Research: The Community Care Cohort Project”. MedRxiv, 2021.05.26.21257872.

Estimating body fat distribution - a driver of cardiometabolic health - from silhouette images

Publication: Miscellaneous

Klarqvist, Marcus D.R., Saaket Agrawal, Nathaniel Diamant, Patrick T. Ellinor, Anthony Philippakis, Kenney Ng, Puneet Batra, and Amit V. Khera. 2022. “Estimating Body Fat Distribution - a Driver of Cardiometabolic Health - from Silhouette Images.”

Deep learning enables genetic analysis of the human thoracic aorta

Publication: Journal Article

Pirruccello, James P., Mark D. Chaffin, Elizabeth L. Chou, Stephen J. Fleming, Honghuang Lin, Mahan Nekoui, Shaan Khurshid, et al. 2022. “Deep Learning Enables Genetic Analysis of the Human Thoracic Aorta”. Nature Genetics 54 (1): 40-51.

Characterizing and Quantifying Performance Heterogeneity in Cardiovascular Risk Prediction Models — A Step Towards Improved Disease Risk Assessment

Publication: Miscellaneous

Kartoun, Uri, Shaan Khurshid, Bum Chul Kwon, Aniruddh Patel, Puneet Batra, Anthony Philippakis, Amit Khera, Patrick Ellinor, Steve Lubitz, and Kenney Ng. 2021. “Characterizing and Quantifying Performance Heterogeneity in Cardiovascular Risk Prediction Models — A Step Towards Improved Disease Risk Assessment.”

Deep learning to estimate cardiac magnetic resonance–derived left ventricular mass

Publication: Journal Article

Khurshid, Shaan, Samuel Freesun Friedman, James P. Pirruccello, Paolo Di Achille, Nathaniel Diamant, Christopher D. Anderson, Patrick T. Ellinor, et al. 2021. “Deep Learning to Estimate Cardiac Magnetic Resonance–derived Left Ventricular Mass”. Cardiovascular Digital Health Journal 2 (2): 109-17.

Abstract 10587: Frequency and Outcomes of Bradyarrhythmias in the Community

Publication: Journal Article

Haimovich, Julian, Shaan Khurshid, Paolo Di Achille, Victor Nauffal, Pulkit Singh, Christopher Reeder, Lia Harrington, et al. 2021. “Abstract 10587: Frequency and Outcomes of Bradyarrhythmias in the Community”. Circulation 144 (Suppl\_1): A10587—A10587.