Stephen Piccolo | Profiles RNS

Stephen Piccolo, PhD

Assistant professor

Brigham Young University

Websites

	Computational Biomedicine Faculty
	Brigham Young University

ORCID : 0000-0003-2001-5640

Stephen R. Piccolo is an assistant professor in the Department of Biology at Brigham Young University (BYU). He earned a B.S. degree in Management Information Systems from BYU in 2001 and then worked as a software engineer for five years at Intel Corporation in Chandler, Arizona. In 2011, he received a PhD in Biomedical Informatics from the University of Utah (advised by Dr. Lewis J. Frey). From 2011-2014, he was postdoctoral researcher jointly at the University of Utah (Department of Pharmacology and Toxicology, advised by Dr. Andrea H. Bild) and Chobanian and Avedisian School of Medicine (Division of Computational Biomedicine, advised by Dr. W. Evan Johnson).

Postdoctoral Fellow (Previously held)
Boston University Chobanian & Avedisian School of Medicine

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Brown GS, Wengler J, Fabelico AJS, Muir A, Tubbs A, Warren A, Millett AN, Yu XX, Pavlidis P, Rogic S, Piccolo SR. Using semantic search to find publicly available gene-expression datasets. bioRxiv. 2025 Mar 15. PMID: 40161731; PMCID: PMC11952526; DOI: 10.1101/2025.03.13.643153;

Skyles TJ, Stevens HP, Davis SC, Obray AM, Miner DS, East MJ, Davis T, Hoelzer H, Piccolo SR, Jensen JL, Poole BD. Comparison of Predictive Factors of Flu Vaccine Uptake Pre- and Post-COVID-19 Using the NIS-Teen Survey. Vaccines (Basel). 2024 Oct 12; 12(10). PMID: 39460330; PMCID: PMC11511354; DOI: 10.3390/vaccines12101164;

Rapier-Sharman N, Kim S, Mudrow M, Told MT, Fischer L, Fawson L, Parry J, Poole BD, O'Neill KL, Piccolo SR, Pickett BE. Comparison of B-Cell Lupus and Lymphoma Using a Novel Immune Imbalance Transcriptomics Algorithm Reveals Potential Therapeutic Targets. Genes (Basel). 2024 Sep 17; 15(9). PMID: 39336806; PMCID: PMC11431704; DOI: 10.3390/genes15091215;

Stevens HP, Winegar CV, Oakley AF, Piccolo SR. Identifying images in the biology literature that are problematic for people with a color-vision deficiency. Elife. 2024 Sep 11; 13. PMID: 39259199; PMCID: PMC11390107; DOI: 10.7554/eLife.95524;

AlZaabi A, Piccolo S, Graves S, Hansen M. Differential Serum Peptidomics Reveal Multi-Marker Models That Predict Breast Cancer Progression. Cancers (Basel). 2024 Jun 27; 16(13). PMID: 39001426; PMCID: PMC11240466; DOI: 10.3390/cancers16132365;

Balasooriya ER, Madhusanka D, López-Palacios TP, Eastmond RJ, Jayatunge D, Owen JJ, Gashler JS, Egbert CM, Bulathsinghalage C, Liu L, Piccolo SR, Andersen JL. Integrating Clinical Cancer and PTM Proteomics Data Identifies a Mechanism of ACK1 Kinase Activation. Mol Cancer Res. 2024 Feb 01; 22(2):137-151. PMID: 37847650; PMCID: PMC10831333; DOI: 10.1158/1541-7786.MCR-23-0153;

Mecham A, Stephenson A, Quinteros BI, Brown GS, Piccolo SR. TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus. J Integr Bioinform. 2024 Mar 01; 21(1). PMID: 38047898; PMCID: PMC11294518; DOI: 10.1515/jib-2023-0021;

Piccolo SR, Denny P, Luxton-Reilly A, Payne SH, Ridge PG. Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course. PLoS Comput Biol. 2023 Sep; 19(9):e1011511. PMID: 37769024; PMCID: PMC10564134; DOI: 10.1371/journal.pcbi.1011511;

Weissenbacher D, O'Connor K, Rawal S, Zhang Y, Tsai RT, Miller T, Xu D, Anderson C, Liu B, Han Q, Zhang J, Kulev I, Köprü B, Rodriguez-Esteban R, Ozkirimli E, Ayach A, Roller R, Piccolo S, Han P, Vydiswaran VGV, Tekumalla R, Banda JM, Bagherzadeh P, Bergler S, Silva JF, Almeida T, Martinez P, Rivera-Zavala R, Wang CK, Dai HJ, Alberto Robles Hernandez L, Gonzalez-Hernandez G. Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition. Database (Oxford). 2023 Feb 03; 2023. PMID: 36734300; PMCID: PMC9896308; DOI: 10.1093/database/baac108;

Kawakami J, Piccolo SR, Kauwe JK, Graves SW. Gender differences contribute to variability of serum lipid biomarkers for Alzheimer's disease. Biomark Med. 2022 Oct; 16(15):1089-1100. PMID: 36625236

Showing 10 of 71 results. Show More

Parker AC, Quinteros BI, Piccolo SR. The DNA methylation landscape of five pediatric-tumor types. PeerJ. 2022; 10:e13516. PMID: 35707123; PMCID: PMC9190670; DOI: 10.7717/peerj.13516;

Piccolo SR, Mecham A, Golightly NP, Johnson JL, Miller DB. The ability to classify patients based on gene-expression data varies by algorithm and performance metric. PLoS Comput Biol. 2022 03; 18(3):e1009926. PMID: 35275931; PMCID: PMC8942277; DOI: 10.1371/journal.pcbi.1009926;

Miller DB, Piccolo SR. trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios. BMC Bioinformatics. 2021 Nov 22; 22(1):559. PMID: 34809557; PMCID: PMC8607709; DOI: 10.1186/s12859-021-04470-4;

Pennington KL, McEwan CM, Woods J, Muir CM, Pramoda Sahankumari AG, Eastmond R, Balasooriya ER, Egbert CM, Kaur S, Heaton T, McCormack KK, Piccolo SR, Kurokawa M, Andersen JL. SGK2, 14-3-3, and HUWE1 Cooperate to Control the Localization, Stability, and Function of the Oncoprotein PTOV1. Mol Cancer Res. 2022 02; 20(2):231-243. PMID: 34654719; PMCID: PMC8816884; DOI: 10.1158/1541-7786.MCR-20-1076;

Piccolo SR, Ence ZE, Anderson EC, Chang JT, Bild AH. Simplifying the development of portable, scalable, and reproducible workflows. Elife. 2021 10 13; 10. PMID: 34643507; PMCID: PMC8514239; DOI: 10.7554/eLife.71069;

Miller DB, Robison R, Piccolo SR. Toward a methodology for evaluating DNA variants in nuclear families. PLoS One. 2021; 16(10):e0258375. PMID: 34624066; PMCID: PMC8500447; DOI: 10.1371/journal.pone.0258375;

Miranda SP, Baião FA, Fleck JL, Piccolo SR. Predicting drug sensitivity of cancer cells based on DNA methylation levels. PLoS One. 2021; 16(9):e0238757. PMID: 34506489; PMCID: PMC8432830; DOI: 10.1371/journal.pone.0238757;

Nwosu IO, Piccolo SR. A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer. Cancer Biol Ther. 2021 09 02; 22(7-9):417-429. PMID: 34412551; PMCID: PMC8489952; DOI: 10.1080/15384047.2021.1953902;

Miller DB, Piccolo SR. A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects. Front Genet. 2021; 12:640242. PMID: 33828584; PMCID: PMC8019969; DOI: 10.3389/fgene.2021.640242;

El-Chaar NN, Smith TE, Shrestha G, Piccolo SR, Harper MK, Van Wagoner RM, Lu Z, Venancio AR, Ireland CM, Bild AH, Moos PJ. Topsentinol L Trisulfate, a Marine Natural Product That Targets Basal-like and Claudin-Low Breast Cancers. Mar Drugs. 2021 Jan 18; 19(1). PMID: 33477536; PMCID: PMC7831112; DOI: 10.3390/md19010041;

Miller DB, Piccolo SR. CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline. F1000Res. 2020; 9:1211. PMID: 33680433; PMCID: PMC7905494; DOI: 10.12688/f1000research.26848.2;

Bodily WR, Shirts BH, Walsh T, Gulsuner S, King MC, Parker A, Roosan M, Piccolo SR. Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures. PLoS One. 2020; 15(9):e0239197. PMID: 32997669; PMCID: PMC7526916; DOI: 10.1371/journal.pone.0239197;

Townsend MH, Ence ZE, Cox TP, Lattin JE, Burrup W, Boyer MK, Piccolo SR, Robison RA, O'Neill KL. Evaluation of the upregulation and surface expression of hypoxanthine guanine phosphoribosyltransferase in acute lymphoblastic leukemia and Burkitt's B cell lymphoma. Cancer Cell Int. 2020; 20:375. PMID: 32782434; PMCID: PMC7409661; DOI: 10.1186/s12935-020-01457-8;

Miller DB, Piccolo SR. Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review. Front Genet. 2020; 11:493. PMID: 32508881; PMCID: PMC7249936; DOI: 10.3389/fgene.2020.00493;

Piccolo SR, Lee TJ, Suh E, Hill K. ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data. Gigascience. 2020 04 01; 9(4). PMID: 32249316; PMCID: PMC7131989; DOI: 10.1093/gigascience/giaa026;

Townsend MH, Tellez Freitas CM, Larsen D, Piccolo SR, Weber KS, Robison RA, O'Neill KL. Hypoxanthine Guanine Phosphoribosyltransferase expression is negatively correlated with immune activity through its regulation of purine synthesis. Immunobiology. 2020 05; 225(3):151931. PMID: 32291109

Mora-Lagos B, Cartas-Espinel I, Riquelme I, Parker AC, Piccolo SR, Viscarra T, Reyes ME, Zanella L, Buchegger K, Ili C, Brebi P. Functional and transcriptomic characterization of cisplatin-resistant AGS and MKN-28 gastric cancer cell lines. PLoS One. 2020; 15(1):e0228331. PMID: 31990955; PMCID: PMC6986722; DOI: 10.1371/journal.pone.0228331;

Sumsion GR, Bradshaw MS, Beales JT, Ford E, Caryotakis GRG, Garrett DJ, LeBaron ED, Nwosu IO, Piccolo SR. Diverse approaches to predicting drug-induced liver injury using gene-expression profiles. Biol Direct. 2020 01 15; 15(1):1. PMID: 31941542; PMCID: PMC6961287; DOI: 10.1186/s13062-019-0257-6;

Viscarra T, Buchegger K, Jofre I, Riquelme I, Zanella L, Abanto M, Parker AC, Piccolo SR, Roa JC, Ili C, Brebi P. Functional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line. Biol Res. 2019 Mar 21; 52(1):13. PMID: 30894224; PMCID: PMC6427839; DOI: 10.1186/s40659-019-0220-0;

Bolouri H, Farrar JE, Triche T, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. Publisher Correction: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med. 2019 Mar; 25(3):530. PMID: 30705421; PMCID: PMC7747938; DOI: 10.1038/s41591-019-0369-7;

Sumsion GR, Bradshaw MS, Hill KT, Pinto LDG, Piccolo SR. Remote sensing tree classification with a multilayer perceptron. PeerJ. 2019; 7:e6101. PMID: 30842894; PMCID: PMC6397751; DOI: 10.7717/peerj.6101;

Townsend MH, Felsted AM, Ence ZE, Piccolo SR, Robison RA, O'Neill KL. Falling from grace: HPRT is not suitable as an endogenous control for cancer-related studies. Mol Cell Oncol. 2019; 6(2):1575691. PMID: 31131300; PMCID: PMC6512905; DOI: 10.1080/23723556.2019.1575691;

Weagel EG, Burrup W, Kovtun R, Velazquez EJ, Felsted AM, Townsend MH, Ence ZE, Suh E, Piccolo SR, Weber KS, Robison RA, O'Neill KL. Correction to: Membrane expression of thymidine kinase 1 and potential clinical relevance in lung, breast, and colorectal malignancies. Cancer Cell Int. 2019; 19:29. PMID: 30792612; PMCID: PMC6369547; DOI: 10.1186/s12935-019-0749-6;

Townsend MH, Ence ZE, Felsted AM, Parker AC, Piccolo SR, Robison RA, O'Neill KL. Potential new biomarkers for endometrial cancer. Cancer Cell Int. 2019; 19:19. PMID: 30679932; PMCID: PMC6341571; DOI: 10.1186/s12935-019-0731-3;

Weagel EG, Burrup W, Kovtun R, Velazquez EJ, Felsted AM, Townsend MH, Ence ZE, Suh E, Piccolo SR, Weber KS, Robison RA, O'Neill KL. Membrane expression of thymidine kinase 1 and potential clinical relevance in lung, breast, and colorectal malignancies. Cancer Cell Int. 2018; 18:135. PMID: 30214377; PMCID: PMC6131957; DOI: 10.1186/s12935-018-0633-9;

Townsend MH, Felsted AM, Piccolo SR, Robison RA, O'Neill KL. Metastatic colon adenocarcinoma has a significantly elevated expression of IL-10 compared with primary colon adenocarcinoma tumors. Cancer Biol Ther. 2018; 19(10):913-920. PMID: 28812429; PMCID: PMC6300346; DOI: 10.1080/15384047.2017.1360453;

Golightly NP, Bell A, Bischoff AI, Hollingsworth PD, Piccolo SR. Curated compendium of human transcriptional biomarker data. Sci Data. 2018 04 17; 5:180066. PMID: 29664470; PMCID: PMC5903354; DOI: 10.1038/sdata.2018.66;

Bolouri H, Farrar JE, Triche T, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. Erratum: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med. 2018 Apr 10; 24(4):526. PMID: 29634680

Singh B, Trincado JL, Tatlow PJ, Piccolo SR, Eyras E. Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors. Mol Cancer Res. 2018 07; 16(7):1112-1124. PMID: 29592900

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH. Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes. Nat Commun. 2018 02 05; 9(1):572.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 29402882; PMCID: PMC5799176; DOI: 10.1038/s41467-017-02383-6;

Dayton JB, Piccolo SR. Classifying cancer genome aberrations by their mutually exclusive effects on transcription. BMC Med Genomics. 2017 12 21; 10(Suppl 4):66. PMID: 29322935; PMCID: PMC5763295; DOI: 10.1186/s12920-017-0303-0;

Bolouri H, Farrar JE, Triche T, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med. 2018 01; 24(1):103-112. PMID: 29227476; PMCID: PMC5907936; DOI: 10.1038/nm.4439;

Seyednasrollah F, Koestler DC, Wang T, Piccolo SR, Vega R, Greiner R, Fuchs C, Gofer E, Kumar L, Wolfinger RD, Kanigel Winner K, Bare C, Neto EC, Yu T, Shen L, Abdallah K, Norman T, Stolovitzky G, Soule HR, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Elo LL, Zhou FL, Guinney J, Costello JC. A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer. JCO Clin Cancer Inform. 2017 11; 1:1-15. PMID: 30657384; PMCID: PMC6874023; DOI: 10.1200/CCI.17.00018;

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH. Combating subclonal evolution of resistant cancer phenotypes. Nat Commun. 2017 11 01; 8(1):1231.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 29093439; PMCID: PMC5666005; DOI: 10.1038/s41467-017-01174-3;

Naylor BC, Porter MT, Wilson E, Herring A, Lofthouse S, Hannemann A, Piccolo SR, Rockwood AL, Price JC. DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics. Bioinformatics. 2017 May 15; 33(10):1514-1520. PMID: 28093409; DOI: 10.1093/bioinformatics/btx009;

Rahman M, MacNeil SM, Jenkins DF, Shrestha G, Wyatt SR, McQuerry JA, Piccolo SR, Heiser LM, Gray JW, Johnson WE, Bild AH. Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes. Genome Med. 2017 Apr 26; 9(1):40.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 28446242; PMCID: PMC5406893; DOI: 10.1186/s13073-017-0429-x;

Cohen AL, Neumayer L, Boucher K, Factor RE, Shrestha G, Wade M, Lamb JG, Arbogast K, Piccolo SR, Riegert J, Schabel M, Bild AH, Werner TL. Window-of-Opportunity Study of Valproic Acid in Breast Cancer Testing a Gene Expression Biomarker. JCO Precis Oncol. 2017; 1. PMID: 32913974; PMCID: PMC7446454; DOI: 10.1200/PO.16.00011;

Tatlow PJ, Piccolo SR. A cloud-based workflow to quantify transcript-expression levels in public cancer compendia. Sci Rep. 2016 12 16; 6:39259. PMID: 27982081; PMCID: PMC5159871; DOI: 10.1038/srep39259;

Archer TC, Fertig EJ, Gosline SJ, Hafner M, Hughes SK, Joughin BA, Meyer AS, Piccolo SR, Shajahan-Haq AN. Systems Approaches to Cancer Biology. Cancer Res. 2016 Dec 01; 76(23):6774-6777. PMID: 27864348; PMCID: PMC5135591; DOI: 10.1158/0008-5472.CAN-16-1580;

Piccolo SR, Frampton MB. Tools and techniques for computational reproducibility. Gigascience. 2016 Jul 11; 5(1):30. PMID: 27401684; PMCID: PMC4940747; DOI: 10.1186/s13742-016-0135-4;

Wang ZL, Li B, Piccolo SR, Zhang XQ, Li JH, Zhou H, Yang JH, Qu LH. Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types. Oncotarget. 2016 Jun 07; 7(23):35044-55. PMID: 27147563; PMCID: PMC5085208; DOI: 10.18632/oncotarget.9037;

Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJ, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JS, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease. Alzheimers Dement. 2016 Jun; 12(6):645-53. PMID: 27079753; PMCID: PMC5474755; DOI: 10.1016/j.jalz.2016.02.006;

Piccolo SR, Hoffman LM, Conner T, Shrestha G, Cohen AL, Marks JR, Neumayer LA, Agarwal CA, Beckerle MC, Andrulis IL, Spira AE, Moos PJ, Buys SS, Johnson WE, Bild AH. Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility. Mol Syst Biol. 2016 Mar 10; 12(3):860.View Related Profiles.

Spira, Avrum
Piccolo, Stephen
Johnson, William

PMID: 26969729; PMCID: PMC4812528; DOI: 10.15252/msb.20156506;

Piccolo SR, Andrulis IL, Cohen AL, Conner T, Moos PJ, Spira AE, Buys SS, Johnson WE, Bild AH. Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility. BMC Med Genomics. 2015; 8:72.View Related Profiles.

Spira, Avrum
Piccolo, Stephen
Johnson, William

PMID: 26538066; PMCID: PMC4634735; DOI: 10.1186/s12920-015-0145-6;

Rahman M, Jackson LK, Johnson WE, Li DY, Bild AH, Piccolo SR. Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results. Bioinformatics. 2015 Nov 15; 31(22):3666-72.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 26209429; PMCID: PMC4804769; DOI: 10.1093/bioinformatics/btv377;

MacNeil SM, Johnson WE, Li DY, Piccolo SR, Bild AH. Inferring pathway dysregulation in cancers from multiple types of omic data. Genome Med. 2015; 7(1):61.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 26170901; PMCID: PMC4499940; DOI: 10.1186/s13073-015-0189-4;

Mortenson JB, Heppler LN, Banks CJ, Weerasekara VK, Whited MD, Piccolo SR, Johnson WE, Thompson JW, Andersen JL. Histone deacetylase 6 (HDAC6) promotes the pro-survival activity of 14-3-3? via deacetylation of lysines within the 14-3-3? binding pocket. J Biol Chem. 2015 May 15; 290(20):12487-96.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 25770209; PMCID: PMC4432270; DOI: 10.1074/jbc.M114.607580;

Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE. ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. Bioinformatics. 2015 Jun 1; 31(11):1745-53.View Related Profiles.

Monti, Stefano
Piccolo, Stephen
Johnson, William

PMID: 25617415; PMCID: PMC4443674; DOI: 10.1093/bioinformatics/btv031;

Lee S, Piccolo SR, Allen-Brady K. Robust meta-analysis shows that glioma transcriptional subtyping complements traditional approaches. Cell Oncol (Dordr). 2014 Oct; 37(5):317-29. PMID: 25142794; DOI: 10.1007/s13402-014-0190-8;

El-Chaar NN, Piccolo SR, Boucher KM, Cohen AL, Chang JT, Moos PJ, Bild AH. Genomic classification of the RAS network identifies a personalized treatment strategy for lung cancer. Mol Oncol. 2014 Oct; 8(7):1339-54.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 24908424; PMCID: PMC4450766; DOI: 10.1016/j.molonc.2014.05.005;

Bild AH, Chang JT, Johnson WE, Piccolo SR. A field guide to genomics research. PLoS Biol. 2014 Jan; 12(1):e1001744.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 24409093; PMCID: PMC3883637; DOI: 10.1371/journal.pbio.1001744;

Piccolo SR, Withers MR, Francis OE, Bild AH, Johnson WE. Multiplatform single-sample estimates of transcriptional activation. Proc Natl Acad Sci U S A. 2013 Oct 29; 110(44):17778-83.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 24128763; PMCID: PMC3816418; DOI: 10.1073/pnas.1305823110;

Cohen AL, Piccolo SR, Cheng L, Soldi R, Han B, Johnson WE, Bild AH. Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers. BMC Med Genomics. 2013; 6:35.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 24079712; PMCID: PMC3850967; DOI: 10.1186/1755-8794-6-35;

Piccolo SR, Frey LJ. Clinical and molecular models of glioblastoma multiforme survival. Int J Data Min Bioinform. 2013; 7(3):245-65. PMID: 23819258; PMCID: PMC4018825

Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, Johnson WE. A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics. 2012 Dec; 100(6):337-44.View Related Profiles.

Campbell, Joshua
Lenburg, Marc
Piccolo, Stephen
Johnson, William

PMID: 22959562; PMCID: PMC3508193; DOI: 10.1016/j.ygeno.2012.08.003;

Kim SH, Lee S, Piccolo SR, Allen-Brady K, Park EJ, Chun JN, Kim TW, Cho NH, Kim IG, So I, Jeon JH. Menthol induces cell-cycle arrest in PC-3 cells by down-regulating G2/M genes, including polo-like kinase 1. Biochem Biophys Res Commun. 2012 Jun 8; 422(3):436-41. PMID: 22580005

Frey LJ, Piccolo SR, Edgerton ME. Multiplicity: an organizing principle for cancers and somatic mutations. BMC Med Genomics. 2011; 4:52. PMID: 21714919; PMCID: PMC3150236; DOI: 10.1186/1755-8794-4-52;

Crockett DK, Piccolo SR, Ridge PG, Margraf RL, Lyon E, Williams MS, Mitchell JA. Predicting phenotypic severity of uncertain gene variants in the RET proto-oncogene. PLoS One. 2011; 6(3):e18380. PMID: 21479187; PMCID: PMC3068179; DOI: 10.1371/journal.pone.0018380;

Piccolo SR, Abo RP, Allen-Brady K, Camp NJ, Knight S, Anderson JL, Horne BD. Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study. BMC Proc. 2009; 3 Suppl 7:S46. PMID: 20018038; PMCID: PMC2795945; DOI: 10.1186/1753-6561-3-s7-s46;

Piccolo SR, Frey LJ. Somatic mutation signatures of cancer. AMIA Annu Symp Proc. 2008; 202-6. PMID: 18999255; PMCID: PMC2655983

Piccolo SR, Camp N, Frey LJ. Polygenic model for predicting breast cancer risk via genome-wide polymorphisms. AMIA Annu Symp Proc. 2008; 1094. PMID: 18999159

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 71 publications over 17 distinct years, with a maximum of 8 publications in 2020 and 2021

Bar chart showing 71 publications over 17 distinct years, with a maximum of 8 publications in 2020 and 2021

Year	Publications
2008	2
2009	1
2011	2
2012	2
2013	3
2014	3
2015	5
2016	6
2017	7
2018	6
2019	6
2020	8
2021	8
2022	2
2023	4
2024	5
2025	1

Contact for Mentoring:

75 E. Newton St Evans Building
Boston MA 02118
Google Map

617.414.6960

Download vCard

Piccolo's Networks

Click the "See All" links for more information and interactive visualizations

Concepts

See all (221) concept(s)

Co-Authors

See all (5) people

Similar People

See all (60) people