User profiles for S. R. Piccolo

Stephen Piccolo

Brigham Young University, Department of Biology
Verified email at byu.edu
Cited by 2880

Tools and techniques for computational reproducibility

SR Piccolo, MB Frampton - Gigascience, 2016 - academic.oup.com
When reporting research findings, scientists document the steps they followed so that others
can verify and build upon the research. When those steps have been described in sufficient …

The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions

…, G Ramsingh, CM Zwaan, S Noort, SR Piccolo… - Nature medicine, 2018 - nature.com
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and
characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG–…

[HTML][HTML] A single-sample microarray normalization method to facilitate personalized-medicine workflows

SR Piccolo, Y Sun, JD Campbell, ME Lenburg, AH Bild… - Genomics, 2012 - Elsevier
Gene-expression microarrays allow researchers to characterize biological phenomena in a
high-throughput fashion but are subject to technological biases and inevitable variabilities …

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results

…, WE Johnson, DY Li, AH Bild, SR Piccolo - …, 2015 - academic.oup.com
Motivation: The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for
research. TCGA provides ‘Level 3’ data, which have been processed using a pipeline specific …

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge …

…, J Peng, AH Petersen, R Philip, SR Piccolo… - The Lancet …, 2017 - thelancet.com
Background Improvements to prognostic models in metastatic castration-resistant prostate
cancer have the potential to augment clinical trial design and guide treatment strategies. In …

[HTML][HTML] Combating subclonal evolution of resistant cancer phenotypes

SW Brady, JA McQuerry, Y Qiao, SR Piccolo… - Nature …, 2017 - nature.com
Metastatic breast cancer remains challenging to treat, and most patients ultimately progress
on therapy. This acquired drug resistance is largely due to drug-refractory sub-populations (…

Multiplatform single-sample estimates of transcriptional activation

SR Piccolo, MR Withers, OE Francis… - Proceedings of the …, 2013 - National Acad Sciences
Over the past two decades, many biotechnology platforms have been developed for high-throughput
gene expression profiling. However, because each platform is subject to technology…

Many bioinformatics programming tasks can be automated with ChatGPT

SR Piccolo, P Denny, A Luxton-Reilly, S Payne… - arXiv preprint arXiv …, 2023 - arxiv.org
Computer programming is a fundamental tool for life scientists, allowing them to carry out
many essential research tasks. However, despite a variety of educational efforts, learning to …

[HTML][HTML] A cloud-based workflow to quantify transcript-expression levels in public cancer compendia

PJ Tatlow, SR Piccolo - Scientific reports, 2016 - nature.com
Public compendia of sequencing data are now measured in petabytes. Accordingly, it is
infeasible for researchers to transfer these data to local computers. Recently, the National …

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

…, S Peng, MA Peters, SR Piccolo… - Alzheimer's & …, 2016 - Wiley Online Library
Identifying accurate biomarkers of cognitive decline is essential for advancing early
diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM …