Publications by authors named "Stephen Piccolo"

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Translating short-form Python exercises to other programming languages using diverse prompting strategies.
Stephen R Piccolo, Harlan P Stevens

Gigascience· December 2025

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Opportunities and considerations for using artificial intelligence in bioinformatics education.
Stephen R Piccolo, Aparna Nathan, Michelle D Brazas, Manoj Kandpal, Aida T Miró-Herrans

Bioinform Adv· September 2025

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Using semantic search to find publicly available gene-expression datasets.
Grace S Brown, James Wengler, Aaron Joyce S Fabelico, Abigail Muir, Anna Tubbs, Stephen R Piccolo

bioRxiv· March 2025

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Comparison of Predictive Factors of Flu Vaccine Uptake Pre- and Post-COVID-19 Using the NIS-Teen Survey.
Ty J Skyles, Harlan P Stevens, Spencer C Davis, Acelan M Obray, Dashiell S Miner, Stephen R Piccolo

Vaccines (Basel)· October 2024

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Identifying images in the biology literature that are problematic for people with a color-vision deficiency.
Harlan P Stevens, Carly V Winegar, Arwen F Oakley, Stephen R Piccolo

Elife· September 2024

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Comparison of B-Cell Lupus and Lymphoma Using a Novel Immune Imbalance Transcriptomics Algorithm Reveals Potential Therapeutic Targets.
Naomi Rapier-Sharman, Sehi Kim, Madelyn Mudrow, Michael T Told, Lane Fischer, Stephen R Piccolo

Genes (Basel)· September 2024

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Predicting drug sensitivity of cancer cells based on DNA methylation levels.
Sofia P Miranda, Fernanda A Baião, Julia L Fleck, Stephen R Piccolo

PLoS One· July 2024

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Toward a methodology for evaluating DNA variants in nuclear families.
Dustin B Miller, Reid Robison, Stephen R Piccolo

PLoS One· July 2024

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Differential Serum Peptidomics Reveal Multi-Marker Models That Predict Breast Cancer Progression.
Adhari AlZaabi, Stephen Piccolo, Steven Graves, Marc Hansen

Cancers (Basel)· June 2024

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TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus.
Avery Mecham, Ashlie Stephenson, Badi I Quinteros, Grace S Brown, Stephen R Piccolo

J Integr Bioinform· March 2024

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Integrating Clinical Cancer and PTM Proteomics Data Identifies a Mechanism of ACK1 Kinase Activation.
Eranga R Balasooriya, Deshan Madhusanka, Tania P López-Palacios, Riley J Eastmond, Dasun Jayatunge, Stephen R Piccolo

Mol Cancer Res· February 2024

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Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course.
Stephen R Piccolo, Paul Denny, Andrew Luxton-Reilly, Samuel H Payne, Perry G Ridge

PLoS Comput Biol· September 2023

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition.
Davy Weissenbacher, Karen O'Connor, Siddharth Rawal, Yu Zhang, Richard Tzong-Han Tsai, Stephen Piccolo

Database (Oxford)· February 2023

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The DNA methylation landscape of five pediatric-tumor types.
Alyssa C Parker, Badí I Quinteros, Stephen R Piccolo

PeerJ· January 2023

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Gender differences contribute to variability of serum lipid biomarkers for Alzheimer's disease.
Jie Kawakami, Stephen R Piccolo, John Ks Kauwe, Steven W Graves

Biomark Med· October 2022

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The ability to classify patients based on gene-expression data varies by algorithm and performance metric.
Stephen R Piccolo, Avery Mecham, Nathan P Golightly, Jérémie L Johnson, Dustin B Miller

PLoS Comput Biol· March 2022

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SGK2, 14-3-3, and HUWE1 Cooperate to Control the Localization, Stability, and Function of the Oncoprotein PTOV1.
Katie L Pennington, Colten M McEwan, James Woods, Colin M Muir, A G Pramoda Sahankumari, Stephen R Piccolo

Mol Cancer Res· February 2022

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trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios.
Dustin B Miller, Stephen R Piccolo

BMC Bioinformatics· November 2021

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Simplifying the development of portable, scalable, and reproducible workflows.
Stephen R Piccolo, Zachary E Ence, Elizabeth C Anderson, Jeffrey T Chang, Andrea H Bild

Elife· October 2021

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A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer.
Ifeanyichukwu O Nwosu, Stephen R Piccolo

Cancer Biol Ther· September 2021

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CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline.
Dustin B Miller, Stephen R Piccolo

F1000Res· April 2021

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A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects.
Dustin B Miller, Stephen R Piccolo

Front Genet· March 2021

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Topsentinol L Trisulfate, a Marine Natural Product That Targets Basal-like and Claudin-Low Breast Cancers.
Nader N El-Chaar, Thomas E Smith, Gajendra Shrestha, Stephen R Piccolo, Mary Kay Harper

Mar Drugs· January 2021

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Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures.
Weston R Bodily, Brian H Shirts, Tom Walsh, Suleyman Gulsuner, Mary-Claire King, Stephen R Piccolo

PLoS One· November 2020

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Evaluation of the upregulation and surface expression of hypoxanthine guanine phosphoribosyltransferase in acute lymphoblastic leukemia and Burkitt's B cell lymphoma.
Michelle H Townsend, Zac E Ence, Taylor P Cox, John E Lattin, Weston Burrup, Stephen R Piccolo

Cancer Cell Int· August 2020

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