Zachary B. Abrams

26 papers Misc 4Journal 17Unranked 5

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	PRISM: Differentially Private Synthetic Data with Structure-Aware Budget Allocation for Prediction. CoRR Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin
2026	J	`jnl`	Risk-Equalized Differentially Private Synthetic Data: Protecting Outliers by Controlling Record-Level Influence. CoRR Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin
2025	J	`jnl`	CeRTS: certainty retrieval token search in large language model clinical information extraction. J. Biomed. Informatics Lars E. Schimmelpfennig, Kriti Bhattarai, Inez Y. Oh, Jake Lever, Obi L. Griffith, Malachi Griffith, Albert M. Lai, Zachary B. Abrams
2024	J	`jnl`	Document-level Clinical Entity and Relation Extraction via Knowledge Base-Guided Generation. CoRR Kriti Bhattarai, Inez Y. Oh, Zachary B. Abrams, Albert M. Lai
2024	—	`conf`	Document-level Clinical Entity and Relation extraction via Knowledge Base-Guided Generation. BioNLP@ACL Kriti Bhattarai, Inez Y. Oh, Zachary B. Abrams, Albert M. Lai
2023	J	`jnl`	Electronic health record data quality assessment and tools: a systematic review. J. Am. Medical Informatics Assoc. Abigail E. Lewis, Nicole Gray Weiskopf, Zachary B. Abrams, Randi E. Foraker, Albert M. Lai, Philip R. O. Payne, Aditi Gupta
2022	—	`conf`	Self-explaining neural network with concept-based explanations for ICU mortality prediction. BCB Sayantan Kumar, Sean C. Yu, Thomas George Kannampallil, Zachary B. Abrams, Andrew P. Michelson, Philip R. O. Payne
2021	J	`jnl`	Mercator: a pipeline for multi-method, unsupervised visualization and distance generation. Bioinform. Zachary B. Abrams, Caitlin E. Coombes, Suli Li, Kevin R. Coombes
2021	J	`jnl`	Pattern recognition in lymphoid malignancies using CytoGPS and Mercator. BMC Bioinform. Zachary B. Abrams, Dwayne G. Tally, Lin Zhang, Caitlin E. Coombes, Philip R. O. Payne, Lynne V. Abruzzo, Kevin R. Coombes
2021	J	`jnl`	RCytoGPS: an R package for reading and visualizing cytogenetics data. Bioinform. Zachary B. Abrams, Dwayne G. Tally, Lynne V. Abruzzo, Kevin R. Coombes
2021	J	`jnl`	Simulation-derived best practices for clustering clinical data. J. Biomed. Informatics Caitlin E. Coombes, Xin Liu, Zachary B. Abrams, Kevin R. Coombes, Guy N. Brock
2020	Misc	`conf`	CytoGPS: A Web-Enabled Karyotype Analysis Tool for Cytogeneticists and Biomedical Data Scientists. AMIA Zachary B. Abrams, Lin Zhang, Ricky Rodriguez, Lynne V. Abruzzo, Kevin R. Coombes, Philip R. P. Payne
2020	J	`jnl`	Explaining Gene Expression Using Twenty-One MicroRNAs. J. Comput. Biol. Amir Asiaee T., Zachary B. Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes
2020	J	`jnl`	Umpire 2.0: Simulating realistic, mixed-type, clinical data for machine learning. F1000Research Caitlin E. Coombes, Zachary B. Abrams, Samantha Nakayiza, Guy N. Brock, Kevin R. Coombes
2020	J	`jnl`	Unsupervised machine learning and prognostic factors of survival in chronic lymphocytic leukemia. J. Am. Medical Informatics Assoc. Caitlin E. Coombes, Zachary B. Abrams, Suli Li, Lynne V. Abruzzo, Kevin R. Coombes
2019	J	`jnl`	A protocol to evaluate RNA sequencing normalization methods. BMC Bioinform. Zachary B. Abrams, Travis S. Johnson, Kun Huang, Philip R. O. Payne, Kevin R. Coombes
2019	J	`jnl`	CytoGPS: a web-enabled karyotype analysis tool for cytogenetics. Bioinform. Zachary B. Abrams, Lin Zhang, Lynne V. Abruzzo, Nyla A. Heerema, Suli Li, Tom Dillon, Ricky Rodriguez, Kevin R. Coombes, Philip R. O. Payne
2019	J	`jnl`	Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing. Bioinform. Mark R. Zucker, Lynne V. Abruzzo, Carmen D. Herling, Lynn L. Barron, Michael J. Keating, Zachary B. Abrams, Nyla A. Heerema, Kevin R. Coombes
2019	J	`jnl`	Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing. Bioinform. Mark R. Zucker, Lynne V. Abruzzo, Carmen D. Herling, Lynn L. Barron, Michael J. Keating, Zachary B. Abrams, Nyla A. Heerema, Kevin R. Coombes
2018	J	`jnl`	Thresher: determining the number of clusters while removing outliers. BMC Bioinform. Min Wang, Zachary B. Abrams, Steven M. Kornblau, Kevin R. Coombes
2017	Misc	`conf`	Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA Sequencing. PSB Travis S. Johnson, Zachary B. Abrams, Yan Zhang, Kun Huang
2016	Misc	`conf`	Session Introduction. PSB Kelly Regan, Zachary B. Abrams, Michael F. Sharpnack, Arunima Srivastava, Kun Huang, Nigam Shah, Philip R. O. Payne
2016	—	`conf`	Use of Administrative Data to Predict Risk of Liver Disease. CRI Tasneem Motiwala, Zachary B. Abrams, Kelly Regan, Bobbie Kite, Gregg M. Gascon, Philip R. O. Payne
2016	—	`conf`	Using Karyotype Data for Automated Disease Classification: A Proof of Concept Demonstration. CRI Satyajeet Raje, Zachary B. Abrams, Kevin R. Coombes, Philip R. O. Payne
2015	Misc	`conf`	KaryoViz: Designing A Karyotype Visualization Platform for Clinical Decision Support. AMIA Zachary B. Abrams, Satyajeet Raje
2015	—	`conf`	Text Mining and Data Modeling of Karyotypes to aid in Drug Repurposing Efforts. MedInfo Zachary B. Abrams, Andrea L. Peabody, Nyla A. Heerema, Philip R. O. Payne