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Author Details

Stephen R Piccolo
Brigham Young University
2008
59
18
Timothy Clark (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37769024Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course.PLoS Comput Biol2023
38047898TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus.J Integr Bioinform2023
34654719SGK2, 14-3-3, and HUWE1 Cooperate to Control the Localization, Stability, and Function of the Oncoprotein PTOV1.Mol Cancer Res2022
35707123The DNA methylation landscape of five pediatric-tumor types.PeerJ2022
36625236Gender differences contribute to variability of serum lipid biomarkers for Alzheimer's disease.Biomark Med2022
35275931The ability to classify patients based on gene-expression data varies by algorithm and performance metric.PLoS Comput Biol2022
34624066Toward a methodology for evaluating DNA variants in nuclear families.PLoS One2021
33828584A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects.Front Genet2021
34412551A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer.Cancer Biol Ther2021
34643507Simplifying the development of portable, scalable, and reproducible workflows.Elife2021
34809557trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios.BMC Bioinformatics2021
32508881Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review.Front Genet2020
31990955Functional and transcriptomic characterization of cisplatin-resistant AGS and MKN-28 gastric cancer cell lines.PLoS One2020
31941542Diverse approaches to predicting drug-induced liver injury using gene-expression profiles.Biol Direct2020
32997669Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures.PLoS One2020
32782434Evaluation of the upregulation and surface expression of hypoxanthine guanine phosphoribosyltransferase in acute lymphoblastic leukemia and Burkitt's B cell lymphoma.Cancer Cell Int2020
32249316ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data.Gigascience2020
30679932Potential new biomarkers for endometrial cancer.Cancer Cell Int2019
30894224Functional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line.Biol Res2019
30705421Publisher Correction: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.Nat Med2019
31131300Falling from grace: HPRT is not suitable as an endogenous control for cancer-related studies.Mol Cell Oncol2019
30842894Remote sensing tree classification with a multilayer perceptron.PeerJ2019
28812429Metastatic colon adenocarcinoma has a significantly elevated expression of IL-10 compared with primary colon adenocarcinoma tumors.Cancer Biol Ther2018
30214377Membrane expression of thymidine kinase 1 and potential clinical relevance in lung, breast, and colorectal malignancies.Cancer Cell Int2018
29634680Erratum: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.Nat Med2018
29664470Curated compendium of human transcriptional biomarker data.Sci Data2018
29402882Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.Nat Commun2018
29592900Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors.Mol Cancer Res2018
29227476The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.Nat Med2018
29093439Combating subclonal evolution of resistant cancer phenotypes.Nat Commun2017
32913974Window-of-Opportunity Study of Valproic Acid in Breast Cancer Testing a Gene Expression Biomarker.JCO Precis Oncol2017
30657384A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.JCO Clin Cancer Inform2017
28446242Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.Genome Med2017
28093409DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics.Bioinformatics2017
29322935Classifying cancer genome aberrations by their mutually exclusive effects on transcription.BMC Med Genomics2017
26969729Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.Mol Syst Biol2016
27982081A cloud-based workflow to quantify transcript-expression levels in public cancer compendia.Sci Rep2016
27864348Systems Approaches to Cancer Biology.Cancer Res2016
27147563Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types.Oncotarget2016
27401684Tools and techniques for computational reproducibility.Gigascience2016
27079753Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.Alzheimers Dement2016
25770209Histone deacetylase 6 (HDAC6) promotes the pro-survival activity of 14-3-3ζ via deacetylation of lysines within the 14-3-3ζ binding pocket.J Biol Chem2015
26538066Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.BMC Med Genomics2015
26209429Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results.Bioinformatics2015
26170901Inferring pathway dysregulation in cancers from multiple types of omic data.Genome Med2015
25617415ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.Bioinformatics2015
24409093A field guide to genomics research.PLoS Biol2014
25142794Robust meta-analysis shows that glioma transcriptional subtyping complements traditional approaches.Cell Oncol (Dordr)2014
24908424Genomic classification of the RAS network identifies a personalized treatment strategy for lung cancer.Mol Oncol2014
23819258Clinical and molecular models of glioblastoma multiforme survival.Int J Data Min Bioinform2013
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Collaborators

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Clinical Research Division, Fred Hutchinson Cancer Research Center
Co-authored papers 3
Oregon Health and Science University
Co-authored papers 3
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Keck School of Medicine, University of Southern California
Co-authored papers 3
Virginia Tech Carilion Clinic
Co-authored papers 3
Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital
Co-authored papers 3
St. Jude Children's Research Hospital
Co-authored papers 3
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National Cancer Institute
Co-authored papers 3
National Cancer Institute
Co-authored papers 3
University of British Columbia
Co-authored papers 3
Fred Hutchinson Cancer Research Centre
Co-authored papers 3
Center for Epigenetics, Van Andel Research Institute
Co-authored papers 3
National Cancer Institute
Co-authored papers 3
Oregon Health Sciences University
Co-authored papers 3
University of Pittsburgh
Co-authored papers 3
Changhai Hospital, Second Military Medical University
Co-authored papers 3
University of Utah
Co-authored papers 2
University of Toronto
Co-authored papers 2
University of Wisconsin-Madison.
Co-authored papers 2
Center for Molecular Medicine, University Medical Center Utrecht
Co-authored papers 2
Bill & Melinda Gates Foundation
Co-authored papers 2
Institute for Systems Biology
Co-authored papers 2
Lineberger Cancer Center, University of North Carolina
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Boston University School of Medicine
Co-authored papers 2
Boulder and BioFrontiers Institute, University of Colorado Boulder
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