publications

2025

1. bioRxiv

   GenVarLoader: An accelerated dataloader for applying deep learning to personalized genomics

   David Laub, Aaron Ho, Jeremy Jaureguy, and 4 more authors

   bioRxiv, 2025

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2. bioRxiv

   GAME: Genomic API for Model Evaluation

   Ishika Luthra, Saksham Priyadarshi, Ruochi Guo, and 4 more authors

   bioRxiv, 2025

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2024

1. Nat Commun

   Pre-operative stereotactic radiosurgery and peri-operative dexamethasone for resectable brain metastases

   Caroline S. Jansen, Meghana S. Pagadala, Maria A. Cardenas, and 1 more author

   Nature Communications, 2024

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2. Sci Rep

   In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells

   Juan C. Jado, Michelle Dow, Krypton Carolino, and 5 more authors

   Scientific Reports, 2024

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3. Bioinformatics

   GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies

   James V. Talwar, Adam Klie, Meghana S. Pagadala, and 1 more author

   Bioinformatics, 2024

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2023

1. Nat Comput Sci

   Predictive analyses of regulatory sequences with EUGENe

   Adam Klie, David Laub, James V. Talwar, and 5 more authors

   Nature Computational Science, 2023

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   EUGENe is an open-source Python toolkit for end-to-end deep learning analyses of regulatory sequences — streamlining data loading, model training, interpretation, and benchmarking across DNA, RNA, and protein tasks.

2. Dev Cell

   Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development

   Granton A. Jindal, Alexis T. Bantle, Joe J. Solvason, and 8 more authors

   Developmental Cell, 2023

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2022

1. bioRxiv

   Affinity-optimizing variants within cardiac enhancers disrupt heart development

   Granton A. Jindal, Alexis T. Bantle, Joe J. Solvason, and 3 more authors

   bioRxiv, 2022

   Preprint of Jindal et al. 2023 (Dev Cell).

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2. bioRxiv

   EUGENe: A Python toolkit for predictive analyses of regulatory sequences

   Adam Klie, Hayden Stites, Tobias Jores, and 3 more authors

   bioRxiv, 2022

   Preprint of Klie et al. 2023 (Nat Comput Sci).

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2021

1. Database

   Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition

   Adam Klie, Brian Y. Tsui, Shamim Mollah, and 4 more authors

   Database, 2021

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2020

1. JMIR

   Text processing for detection of fungal ocular involvement in critical care patients

   Sally L. Baxter, Adam R. Klie, Bharanidharan Radha Saseendrakumar, and 2 more authors

   Journal of Medical Internet Research, 2020

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2. EMBC

   Predicting mortality in critical care patients with fungemia using structured and unstructured data

   Sally L. Baxter, Adam R. Klie, Bharanidharan Radha Saseendrakumar, and 3 more authors

   In 42nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2020

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2018

1. bioRxiv

   Increasing metadata coverage of SRA BioSample entries using deep learning based Named Entity Recognition

   Adam Klie, Brian Y. Tsui, Shamim Mollah, and 4 more authors

   bioRxiv, 2018

   Preprint of Klie et al. 2021 (Database).

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