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Stephen R. Piccolo · SciRah

Researcher profile · Semantic Scholar

Stephen R. Piccolo

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Stephen R. Piccolo — researcher profile on SciRah

h-index: 22
Works: 92
Citations: 2,685

Most-cited papers

The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
H. Bolouri, J. Farrar, T. Triche, R. Ries +25 more
2017Nature Medicine629 citations Open access
Semantic Scholar
A single-sample microarray normalization method to facilitate personalized-medicine workflows
Stephen R. Piccolo, Ying Sun, Joshua D. Campbell, M. Lenburg +2 more
2012Genomics229 citations Open access
Semantic Scholar
Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results
Mumtahena Rahman, L. Jackson, W. E. Johnson, Dean Y. Li +2 more
2015Bioinform.207 citations Open access
Semantic Scholar
Tools and techniques for computational reproducibility
Stephen R. Piccolo, Adam B. Lee, Michael B. Frampton
2015bioRxiv170 citations Open access
Semantic Scholar
Combating subclonal evolution of resistant cancer phenotypes
Samuel W. Brady, Jasmine A. McQuerry, Yi Qiao, Stephen R. Piccolo +24 more
2017Nature Communications148 citations Open access
Semantic Scholar
Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data
J. Guinney, Tao Wang, T. D. Laajala, Kimberly R. Kanigel Winner +170 more
2016The Lancet Oncology147 citations Open access
Semantic Scholar
Multiplatform single-sample estimates of transcriptional activation
Stephen R. Piccolo, M. R. Withers, Owen E Francis, Andrea H. Bild +1 more
2013Proceedings of the National Academy of Sciences of the United States of America88 citations Open access
Semantic Scholar
Crowdsourced estimation of cognitive decline and resilience in Alzheimer’s disease
G. Allen, N. Amoroso, Catalina V. Anghel, V. Balagurusamy +97 more
2016Alzheimer's & Dementia85 citations Open access
Semantic Scholar
A cloud-based workflow to quantify transcript-expression levels in public cancer compendia
P. Tatlow, Stephen R. Piccolo
2016Scientific Reports78 citations Open access
Semantic Scholar
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 Payne +1 more
2023PLoS Comput. Biol.63 citations Open access
Semantic Scholar
DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics
B. Naylor, Michael T. Porter, Elise Wilson, A. Herring +5 more
2017Bioinform.55 citations Open access
Semantic Scholar
Potential new biomarkers for endometrial cancer
Michelle H. Townsend, Zachary E. Ence, Abigail M. Felsted, A. Parker +3 more
2019Cancer Cell International51 citations Open access
Semantic Scholar
Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers
Adam L. Cohen, Stephen R. Piccolo, Luis Cheng, Rafaella Soldi +3 more
2013BMC Medical Genomics37 citations Open access
Semantic Scholar
Membrane expression of thymidine kinase 1 and potential clinical relevance in lung, breast, and colorectal malignancies
Evita G. Weagel, Weston Burrup, Roman Kovtun, Edwin J. Velazquez +8 more
2018Cancer Cell International35 citations Open access
Semantic Scholar
ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways
Ying Shen, Mumtahena Rahman, Stephen R. Piccolo, D. Gusenleitner +5 more
2015Bioinform.35 citations Open access
Semantic Scholar
Menthol induces cell-cycle arrest in PC-3 cells by down-regulating G2/M genes, including polo-like kinase 1.
Su-Hwa Kim, Sanghoon Lee, Stephen R. Piccolo, K. Allen-Brady +7 more
2012Biochemical and Biophysical Research Communications - BBRC33 citations
Semantic Scholar
Predicting Phenotypic Severity of Uncertain Gene Variants in the RET Proto-Oncogene
David K. Crockett, Stephen R. Piccolo, P. Ridge, R. Margraf +3 more
2011PLoS ONE32 citations Open access
Semantic Scholar
Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study
Stephen R. Piccolo, R. Abo, K. Allen-Brady, N. Camp +3 more
2009BMC Proceedings29 citations Open access
Semantic Scholar
Histone Deacetylase 6 (HDAC6) Promotes the Pro-survival Activity of 14-3-3ζ via Deacetylation of Lysines within the 14-3-3ζ Binding Pocket*
J. Mortenson, Lisa N. Heppler, C. Banks, Vajira Kaushalya Weerasekara +5 more
2015Journal of Biological Chemistry27 citations Open access
Semantic Scholar
Clinical and molecular models of Glioblastoma multiforme survival
Stephen R. Piccolo, Lewis J. Frey
2013International Journal of Data Mining and Bioinformatics26 citations Open access
Semantic Scholar
Elevated Expression of Hypoxanthine Guanine Phosphoribosyltransferase within Malignant Tissue
Michelle H. Townsend, Abigail M. Felsted, Zachary E. Ence, Stephen R. Piccolo +2 more
201725 citations Open access
Semantic Scholar
Functional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line
T. Viscarra, K. Buchegger, I. Jofré, I. Riquelme +7 more
2019Biological Research22 citations Open access
Semantic Scholar
Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures
Weston R. Bodily, B. Shirts, T. Walsh, S. Gulsuner +4 more
2019bioRxiv22 citations Open access
Semantic Scholar
Systems Approaches to Cancer Biology
Tenley C. Archer, E. Fertig, Sara J. C. Gosline, M. Hafner +5 more
2016Cancer Research21 citations Open access
Semantic Scholar
Functional and transcriptomic characterization of cisplatin-resistant AGS and MKN-28 gastric cancer cell lines
Barbara Mora-Lagos, Irene Cartas-Espinel, I. Riquelme, A. Parker +7 more
2020PLoS ONE20 citations Open access
Semantic Scholar
The ability to classify patients based on gene-expression data varies by algorithm and performance metric
Stephen R. Piccolo, A. Mecham, Nathan P Golightly, Jérémie L. Johnson +1 more
2022PLoS Comput. Biol.17 citations Open access
Semantic Scholar
Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors
Babita Singh, J. Trincado, P. J. Tatlow, Stephen R. Piccolo +1 more
2018Molecular Cancer Research17 citations Open access
Semantic Scholar
Falling from grace: HPRT is not suitable as an endogenous control for cancer-related studies
Michelle H. Townsend, Abigail M. Felsted, Zachary E. Ence, Stephen R. Piccolo +2 more
2019Molecular & Cellular Oncology16 citations Open access
Semantic Scholar
Genomic classification of the RAS network identifies a personalized treatment strategy for lung cancer
N. El-Chaar, Stephen R. Piccolo, K. Boucher, Adam L. Cohen +3 more
2014Molecular Oncology16 citations Open access
Semantic Scholar
Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review
Dustin B. Miller, Stephen R. Piccolo
2020Frontiers in Genetics15 citations Open access
Semantic Scholar
Metastatic colon adenocarcinoma has a significantly elevated expression of IL-10 compared with primary colon adenocarcinoma tumors
Michelle H. Townsend, Abigail M. Felsted, Stephen R. Piccolo, R. Robison +1 more
2018Cancer Biology & Therapy15 citations Open access
Semantic Scholar
Inferring pathway dysregulation in cancers from multiple types of omic data
Shelley Macneil, W. E. Johnson, Dean Y. Li, Stephen R. Piccolo +1 more
2015Genome Medicine15 citations Open access
Semantic Scholar
ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data
Stephen R. Piccolo, Terry J Lee, Erica Suh, Kimball Hill
2019bioRxiv14 citations Open access
Semantic Scholar
A Field Guide to Genomics Research
Andrea H. Bild, Jeffrey T. Chang, W. E. Johnson, Stephen R. Piccolo
2014PLoS Biology14 citations Open access
Semantic Scholar
Hypoxanthine Guanine Phosphoribosyltransferase expression is negatively correlated with immune activity through its regulation of purine synthesis.
Michelle H. Townsend, Claudia M. Tellez Freitas, D. Larsen, Stephen R. Piccolo +3 more
2020Immunobiology13 citations
Semantic Scholar
Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility
Stephen R. Piccolo, I. Andrulis, Adam L. Cohen, Thomas A. Conner +5 more
2015BMC Medical Genomics13 citations Open access
Semantic Scholar
TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus
A. Mecham, Ashlie Stephenson, Badi I. Quinteros, Grace S. Brown +1 more
2023bioRxiv12 citations Open access
Semantic Scholar
A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects
Dustin B. Miller, Stephen R. Piccolo
2021Frontiers in Genetics12 citations Open access
Semantic Scholar
Curated compendium of human transcriptional biomarker data
Nathan P Golightly, A. Bell, Annabell Bischoff, P. Hollingsworth +1 more
2017Scientific Data12 citations Open access
Semantic Scholar
Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility
Stephen R. Piccolo, Laura M. Hoffman, Thomas A. Conner, G. Shrestha +11 more
2016Molecular Systems Biology12 citations Open access
Semantic Scholar
Simplifying the development of portable, scalable, and reproducible workflows
Stephen R. Piccolo, Zachary E. Ence, E. Anderson, Jeffrey T. Chang +1 more
2021bioRxiv11 citations Open access
Semantic Scholar
ML-Flex: A Flexible Toolbox for Performing Classification Analyses In Parallel
Stephen R. Piccolo, Lewis J. Frey
2012Journal of machine learning research11 citations
Semantic Scholar
The DNA methylation landscape of five pediatric-tumor types
A. Parker, Badi I. Quinteros, Stephen R. Piccolo
2021bioRxiv10 citations Open access
Semantic Scholar
Publisher Correction: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
H. Bolouri, J. Farrar, T. Triche, R. Ries +25 more
2019Nature Medicine10 citations Open access
Semantic Scholar
Evaluation of the upregulation and surface expression of hypoxanthine guanine phosphoribosyltransferase in acute lymphoblastic leukemia and Burkitt’s B cell lymphoma
Michelle H. Townsend, Zachary E. Ence, Taylor P. Cox, John Lattin +5 more
2020Cancer Cell International9 citations Open access
Semantic Scholar
Classifying cancer genome aberrations by their mutually exclusive effects on transcription
Jonathan B. Dayton, Stephen R. Piccolo
2017BMC Medical Genomics9 citations Open access
Semantic Scholar
Window-of-Opportunity Study of Valproic Acid in Breast Cancer Testing a Gene Expression Biomarker
Adam L. Cohen, L. Neumayer, K. Boucher, R. Factor +9 more
2017JCO Precision Oncology9 citations Open access
Semantic Scholar
Multiplicity: an organizing principle for cancers and somatic mutations
Lewis J. Frey, Stephen R. Piccolo, M. Edgerton
2011BMC Medical Genomics9 citations Open access
Semantic Scholar
trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios
Dustin B. Miller, Stephen R. Piccolo
2021BMC Bioinformatics7 citations Open access
Semantic Scholar
A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer
Fatemeh Seyednasrollah, D. Koestler, Tao Wang, Stephen R. Piccolo +23 more
2017JCO Clinical Cancer Informatics7 citations Open access
Semantic Scholar

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