Joel S. Parker, Ph.D. - Publications

Affiliations: 
2010 Bioinformatics & Computational Biology University of North Carolina, Chapel Hill, Chapel Hill, NC 
Area:
Bioinformatics, Genetics, Oncology

145 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Feng W, Simpson DA, Carvajal-Garcia J, Price BA, Kumar RJ, Mose LE, Wood RD, Rashid N, Purvis JE, Parker JS, Ramsden DA, Gupta GP. Genetic determinants of cellular addiction to DNA polymerase theta. Nature Communications. 10: 4286. PMID 31537809 DOI: 10.1038/s41467-019-12234-1  0.68
2019 Smith CC, Chai S, Washington AR, Lee SJ, Landoni E, Field K, Garness J, Bixby LM, Selitsky SR, Parker JS, Savoldo B, Serody JS, Vincent BG. Machine-Learning Prediction of Tumor Antigen Immunogenicity in the Selection of Therapeutic Epitopes. Cancer Immunology Research. PMID 31515258 DOI: 10.1158/2326-6066.CIR-19-0155  0.44
2019 Barrow MA, Martin ME, Coffey A, Andrews PL, Jones GS, Reaves DK, Parker JS, Troester MA, Fleming JM. A functional role for the cancer disparity-linked genes, CRYβB2 and CRYβB2P1, in the promotion of breast cancer. Breast Cancer Research : Bcr. 21: 105. PMID 31511085 DOI: 10.1186/s13058-019-1191-3  0.4
2019 Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, ... ... Parker JS, et al. The Immune Landscape of Cancer. Immunity. 51: 411-412. PMID 31433971 DOI: 10.1016/j.immuni.2019.08.004  0.68
2019 Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, et al. Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data. Cell Systems. 9: 24-34.e10. PMID 31344359 DOI: 10.1016/j.cels.2019.06.006  0.44
2019 Selitsky SR, Mose LE, Smith CC, Chai S, Hoadley KA, Dittmer DP, Moschos SJ, Parker JS, Vincent BG. Prognostic value of B cells in cutaneous melanoma. Genome Medicine. 11: 36. PMID 31138334 DOI: 10.1186/s13073-019-0647-5  0.68
2019 Wong KY, Fan C, Tanioka M, Parker JS, Nobel AB, Zeng D, Lin DY, Perou CM. I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms. Genome Biology. 20: 52. PMID 30845957 DOI: 10.1186/s13059-019-1640-4  0.68
2019 Alzubi MA, Turner TH, Olex AL, Sohal SS, Tobin NP, Recio SG, Bergh J, Hatschek T, Parker JS, Sartorius CA, Perou CM, Dozmorov MG, Harrell JC. Separation of breast cancer and organ microenvironment transcriptomes in metastases. Breast Cancer Research : Bcr. 21: 36. PMID 30841919 DOI: 10.1186/s13058-019-1123-2  0.68
2019 Mose LE, Perou CM, Parker JS. Improved Indel Detection in DNA and RNA via Realignment with ABRA2. Bioinformatics (Oxford, England). PMID 30649250 DOI: 10.1093/bioinformatics/btz033  0.68
2018 Zhao X, Little P, Hoyle AP, Pegna GJ, Hayward MC, Ivanova A, Parker JS, Marron DL, Soloway MG, Jo H, Salazar AH, Papakonstantinou MP, Bouchard DM, Jefferys SR, Hoadley KA, et al. The Prognostic Significance of Low-Frequency Somatic Mutations in Metastatic Cutaneous Melanoma. Frontiers in Oncology. 8: 584. PMID 30662871 DOI: 10.3389/fonc.2018.00584  0.44
2018 Kensler KH, Sankar VN, Wang J, Zhang X, Rubadue CA, Baker GM, Parker JS, Hoadley KA, Stancu AL, Pyle ME, Collins LC, Hunter DJ, Elissen AH, Hankinson SE, Tamimi RM, et al. PAM50 Molecular Intrinsic Subtypes in the Nurses' Health Study Cohorts. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. PMID 30591591 DOI: 10.1158/1055-9965.EPI-18-0863  0.44
2018 Conway K, Edmiston SN, Parker JS, Kuan PF, Tsai YH, Groben PA, Zedek DC, Scott GA, Parrish EA, Hao H, Pearlstein MV, Frank JS, Carson CC, Wilkerson MD, Zhao X, et al. Identification of a robust methylation classifier for cutaneous melanoma diagnosis. The Journal of Investigative Dermatology. PMID 30529013 DOI: 10.1016/j.jid.2018.11.024  0.36
2018 Selitsky SR, Marron D, Mose LE, Parker JS, Dittmer DP. Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality. Msystems. 3. PMID 30271878 DOI: 10.1128/mSystems.00081-18  0.68
2018 Gucalp A, Traina TA, Eisner JR, Parker JS, Selitsky SR, Park BH, Elias AD, Baskin-Bey ES, Cardoso F. Male breast cancer: a disease distinct from female breast cancer. Breast Cancer Research and Treatment. PMID 30267249 DOI: 10.1007/s10549-018-4921-9  0.44
2018 Smith CC, Beckermann KE, Bortone DS, de Cubas AA, Bixby LM, Lee SJ, Panda A, Ganesan S, Bhanot G, Wallen EM, Milowsky MI, Kim WY, Rathmell WK, Swanstrom R, Parker JS, et al. Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma. The Journal of Clinical Investigation. PMID 30137025 DOI: 10.1172/JCI121476  0.44
2018 Tanioka M, Fan C, Parker JS, Hoadley KA, Hu Z, Li Y, Hyslop TM, Pitcher BN, Soloway MG, Spears PA, Henry NL, Tolaney S, Dang CT, Krop I, Harris LN, et al. Integrated analysis of RNA and DNA from a phase III trial of trastuzumab-based neoadjuvant chemotherapy identifies response predictors in HER2-positive breast cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 30037817 DOI: 10.1158/1078-0432.CCR-17-3431  0.68
2018 Zhang J, Wu T, Simon J, Takada M, Saito R, Fan C, Liu XD, Jonasch E, Xie L, Chen X, Yao X, Teh BT, Tan P, Zheng X, Li M, ... ... Parker JS, et al. VHL substrate transcription factor ZHX2 as an oncogenic driver in clear cell renal cell carcinoma. Science (New York, N.Y.). 361: 290-295. PMID 30026228 DOI: 10.1126/science.aap8411  0.68
2018 Dellon ES, Selitsky SR, Genta RM, Lash RH, Parker JS. Gene expression-phenotype associations in adults with eosinophilic esophagitis. Digestive and Liver Disease : Official Journal of the Italian Society of Gastroenterology and the Italian Association For the Study of the Liver. PMID 29628359 DOI: 10.1016/j.dld.2018.03.021  0.44
2018 Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, ... ... Parker JS, et al. The Immune Landscape of Cancer. Immunity. PMID 29628290 DOI: 10.1016/j.immuni.2018.03.023  0.68
2018 Siegel MB, He X, Hoadley KA, Hoyle A, Pearce JB, Garrett AL, Kumar S, Moylan VJ, Brady CM, Van Swearingen AE, Marron D, Gupta GP, Thorne LB, Kieran N, Livasy C, ... ... Parker JS, et al. Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer. The Journal of Clinical Investigation. PMID 29480819 DOI: 10.1172/JCI96153  0.68
2018 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, et al. Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes. Nature Communications. 9: 572. PMID 29402882 DOI: 10.1038/s41467-017-02383-6  0.44
2018 Montgomery ND, Selitsky SR, Patel NM, Hayes DN, Parker JS, Weck KE. Identification of Germline Variants in Tumor Genomic Sequencing Analysis. The Journal of Molecular Diagnostics : Jmd. 20: 123-125. PMID 29249243 DOI: 10.1016/j.jmoldx.2017.09.008  0.44
2017 Liu W, Snell JM, Jeck WR, Hoadley KA, Wilkerson MD, Parker JS, Patel N, Mlombe YB, Mulima G, Liomba NG, Wolf LL, Shores CG, Gopal S, Sharpless NE. Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis. Jci Insight. 2. PMID 29148985 DOI: 10.1172/jci.insight.98457  0.44
2017 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, et al. Combating subclonal evolution of resistant cancer phenotypes. Nature Communications. 8: 1231. PMID 29093439 DOI: 10.1038/s41467-017-01174-3  0.44
2017 Taylor NA, Vick SC, Iglesia MD, Brickey WJ, Midkiff BR, McKinnon KP, Reisdorf S, Anders CK, Carey LA, Parker JS, Perou CM, Vincent BG, Serody JS. Treg depletion potentiates checkpoint inhibition in claudin-low breast cancer. The Journal of Clinical Investigation. PMID 28825599 DOI: 10.1172/JCI90499  0.68
2017 O'Flanagan CH, Rossi EL, McDonell SB, Chen X, Tsai YH, Parker JS, Usary J, Perou CM, Hursting SD. Metabolic reprogramming underlies metastatic potential in an obesity-responsive murine model of metastatic triple negative breast cancer. Npj Breast Cancer. 3: 26. PMID 28748213 DOI: 10.1038/s41523-017-0027-5  0.68
2017 Silva GO, Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M. SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. Genome Biology. 18: 66. PMID 28390427 DOI: 10.1186/s13059-017-1193-3  0.68
2017 Dellon ES, Veerappan R, Selitsky SR, Parker JS, Higgins LL, Beitia R, Genta RM, Lash RH. A Gene Expression Panel is Accurate for Diagnosis and Monitoring Treatment of Eosinophilic Esophagitis in Adults. Clinical and Translational Gastroenterology. 8: e74. PMID 28181994 DOI: 10.1038/ctg.2017.2  0.44
2017 Mehta GA, Parker JS, Silva GO, Hoadley KA, Perou CM, Gatza ML. Amplification of SOX4 promotes PI3K/Akt signaling in human breast cancer. Breast Cancer Research and Treatment. PMID 28176176 DOI: 10.1007/s10549-017-4139-2  0.68
2017 Zawistowski JS, Bevill SM, Goulet DR, Stuhlmiller TJ, Beltran AS, Olivares-Quintero JF, Singh D, Sciaky N, Parker JS, Rashid NU, Chen X, Duncan JS, Whittle MC, Angus SP, Velarde SH, et al. Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex. Cancer Discovery. PMID 28108460 DOI: 10.1158/2159-8290.CD-16-0653  0.68
2017 Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER. Correction: Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. Plos Medicine. 14: e1002222. PMID 28068332 DOI: 10.1371/journal.pmed.1002222  0.68
2016 Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER. Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. Plos Medicine. 13: e1002174. PMID 27923045 DOI: 10.1371/journal.pmed.1002174  0.68
2016 Prat A, Lluch A, Turnbull AK, Dunbier AK, Calvo L, Albanell J, de la Haba-Rodríguez J, Arcusa A, Chacón I, Sánchez-Rovira P, Plazaola A, Muñoz M, Paré L, Parker JS, Ribelles N, et al. A PAM50-based Chemo-Endocrine Score for Hormone Receptor-Positive Breast Cancer with an Intermediate Risk of Relapse. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 27903675 DOI: 10.1158/1078-0432.CCR-16-2092  0.68
2016 Liu W, Snell JM, Jeck WR, Hoadley KA, Wilkerson MD, Parker JS, Patel N, Mlombe YB, Mulima G, Liomba NG, Wolf LL, Shores CG, Gopal S, Sharpless NE. Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis. Jci Insight. 1: e88755. PMID 27734031 DOI: 10.1172/jci.insight.88755  0.44
2016 Kardos J, Chai S, Mose LE, Selitsky SR, Krishnan B, Saito R, Iglesia MD, Milowsky MI, Parker JS, Kim WY, Vincent BG. Claudin-low bladder tumors are immune infiltrated and actively immune suppressed. Jci Insight. 1: e85902. PMID 27699256 DOI: 10.1172/jci.insight.85902  0.68
2016 Wood WA, Krishnamurthy J, Mitin N, Torrice C, Parker JS, Snavely AC, Shea TC, Serody JS, Sharpless NE. Chemotherapy and Stem Cell Transplantation Increase p16(INK4a) Expression, a Biomarker of T-cell Aging. Ebiomedicine. PMID 27591832 DOI: 10.1016/j.ebiom.2016.08.029  0.44
2016 Mose LE, Selitsky SR, Bixby LM, Marron DL, Iglesia MD, Serody JS, Perou CM, Vincent BG, Parker JS. Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer. Bioinformatics (Oxford, England). PMID 27559159 DOI: 10.1093/bioinformatics/btw526  0.68
2016 Iglesia MD, Parker JS, Hoadley KA, Serody JS, Perou CM, Vincent BG. Genomic Analysis of Immune Cell Infiltrates Across 11 Tumor Types. Journal of the National Cancer Institute. 108. PMID 27335052 DOI: 10.1093/jnci/djw144  0.68
2016 Souroullas GP, Jeck WR, Parker JS, Simon JM, Liu JY, Paulk J, Xiong J, Clark KS, Fedoriw Y, Qi J, Burd CE, Bradner JE, Sharpless NE. An oncogenic Ezh2 mutation induces tumors through global redistribution of histone 3 lysine 27 trimethylation. Nature Medicine. PMID 27135738 DOI: 10.1038/nm.4092  0.56
2016 Seifert BA, O'Daniel JM, Amin K, Marchuk DS, Patel NM, Parker JS, Hoyle AP, Mose LE, Marron A, Hayward MC, Bizon C, Wilhelmsen KC, Evans JP, Earp HS, Sharpless N, et al. Germline Analysis from Tumor-Germline Sequencing Dyads to identify clinically actionable secondary findings. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 27083775 DOI: 10.1158/1078-0432.CCR-16-0015  0.56
2016 Hu S, Divaris K, Parker J, Padilla R, Murrah V, Wright JT. Transcriptome Variability in Keratocystic Odontogenic Tumor Suggests Distinct Molecular Subtypes. Scientific Reports. 6: 24236. PMID 27066764 DOI: 10.1038/srep24236  0.56
2016 Billard MJ, Fitzhugh DJ, Parker JS, Brozowski JM, McGinnis MW, Timoshchenko RG, Serafin DS, Lininger R, Klauber-Demore N, Sahagian G, Truong YK, Sassano MF, Serody JS, Tarrant TK. G Protein Coupled Receptor Kinase 3 Regulates Breast Cancer Migration, Invasion, and Metastasis. Plos One. 11: e0152856. PMID 27049755 DOI: 10.1371/journal.pone.0152856  0.56
2016 Zhao W, Hoadley KA, Parker JS, Perou CM. Identification of mRNA isoform switching in breast cancer. Bmc Genomics. 17: 181. PMID 26939613 DOI: 10.1186/s12864-016-2521-9  0.68
2016 Brooks SA, Khandani A, Fielding J, Lin W, Sills T, Lee Y, Arreola A, Milowsky MI, Wallen EM, Woods ME, Smith AB, Nielsen ME, Parker JS, Lalush DS, Rathmell WK. Alternate metabolic programs define regional variation of relevant biological features in renal cell carcinoma progression. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 26787754 DOI: 10.1158/1078-0432.CCR-15-2115  0.56
2015 Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B. Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. Bioinformatics (Oxford, England). PMID 26607490 DOI: 10.1093/bioinformatics/btv693  0.56
2015 Linnstaedt SD, Walker MG, Parker JS, Yeh E, Sons RL, Zimny E, Lewandowski C, Hendry PL, Damiron K, Pearson C, Velilla MA, O'Neil BJ, Jones J, Swor R, Domeier R, et al. MicroRNA circulating in the early aftermath of motor vehicle collision predict persistent pain development and suggest a role for microRNA in sex-specific pain differences. Molecular Pain. 11: 66. PMID 26498117 DOI: 10.1186/s12990-015-0069-3  0.56
2015 Montgomery ND, Parker JS, Eberhard DA, Patel NM, Weck KE, Sharpless NE, Hu Z, Hayes DN, Gulley ML. Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next-generation Sequencing. Applied Immunohistochemistry & Molecular Morphology : Aimm / Official Publication of the Society For Applied Immunohistochemistry. PMID 26371432 DOI: 10.1097/PAI.0000000000000215  0.56
2015 Simon JM, Parker JS, Liu F, Rothbart SB, Ait-Si-Ali S, Strahl BD, Jin J, Davis IJ, Mosley AL, Pattenden SG. A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin. The Journal of Biological Chemistry. 290: 26088-102. PMID 26338712 DOI: 10.1074/jbc.M115.654459  0.56
2015 Wallden B, Storhoff J, Nielsen T, Dowidar N, Schaper C, Ferree S, Liu S, Leung S, Geiss G, Snider J, Vickery T, Davies SR, Mardis ER, Gnant M, Sestak I, ... ... Parker JS, et al. Development and verification of the PAM50-based Prosigna breast cancer gene signature assay. Bmc Medical Genomics. 8: 54. PMID 26297356 DOI: 10.1186/s12920-015-0129-6  0.56
2015 Parker JS, Perou CM. Tumor Heterogeneity: Focus on the Leaves, the Trees, or the Forest? Cancer Cell. 28: 149-50. PMID 26267531 DOI: 10.1016/j.ccell.2015.07.011  0.56
2015 Silva GO, He X, Parker JS, Gatza ML, Carey LA, Hou JP, Moulder SL, Marcom PK, Ma J, Rosen JM, Perou CM. Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. Breast Cancer Research and Treatment. PMID 26109346 DOI: 10.1007/s10549-015-3476-2  0.56
2015 Zhao X, Wang A, Walter V, Patel NM, Eberhard DA, Hayward MC, Salazar AH, Jo H, Soloway MG, Wilkerson MD, Parker JS, Yin X, Zhang G, Siegel MB, Rosson GB, et al. Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC. Plos One. 10: e0129280. PMID 26076459 DOI: 10.1371/journal.pone.0129280  0.56
2015 Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, ... ... Parker JS, et al. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. The New England Journal of Medicine. 372: 2481-98. PMID 26061751 DOI: 10.1056/NEJMoa1402121  0.56
2015 Karaca M, Liu Y, Zhang Z, De Silva D, Parker JS, Earp HS, Whang YE. Mutation of androgen receptor N-terminal phosphorylation site Tyr-267 leads to inhibition of nuclear translocation and DNA binding. Plos One. 10: e0126270. PMID 25950519 DOI: 10.1371/journal.pone.0126270  0.56
2015 Cheang MC, Martin M, Nielsen TO, Prat A, Voduc D, Rodriguez-Lescure A, Ruiz A, Chia S, Shepherd L, Ruiz-Borrego M, Calvo L, Alba E, Carrasco E, Caballero R, Tu D, ... ... Parker J, et al. Defining breast cancer intrinsic subtypes by quantitative receptor expression. The Oncologist. 20: 474-82. PMID 25908555 DOI: 10.1634/theoncologist.2014-0372  0.56
2015 Stuhlmiller TJ, Miller SM, Zawistowski JS, Nakamura K, Beltran AS, Duncan JS, Angus SP, Collins KA, Granger DA, Reuther RA, Graves LM, Gomez SM, Kuan PF, Parker JS, Chen X, et al. Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast Cancer by Targeting BET Family Bromodomains. Cell Reports. 11: 390-404. PMID 25865888 DOI: 10.1016/j.celrep.2015.03.037  0.56
2015 Hu S, Parker J, Wright JT. Towards unraveling the human tooth transcriptome: the dentome. Plos One. 10: e0124801. PMID 25849153 DOI: 10.1371/journal.pone.0124801  0.56
2015 Karginova O, Siegel MB, Van Swearingen AE, Deal AM, Adamo B, Sambade MJ, Bazyar S, Nikolaishvili-Feinberg N, Bash R, O'Neal S, Sandison K, Parker JS, Santos C, Darr D, Zamboni W, et al. Efficacy of Carboplatin Alone and in Combination with ABT888 in Intracranial Murine Models of BRCA-Mutated and BRCA-Wild-Type Triple-Negative Breast Cancer. Molecular Cancer Therapeutics. 14: 920-30. PMID 25824335 DOI: 10.1158/1535-7163.MCT-14-0474  0.56
2015 . Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 517: 576-82. PMID 25631445 DOI: 10.1038/nature14129  0.56
2015 Stasulli NM, Eichelberger KR, Price PA, Pechous RD, Montgomery SA, Parker JS, Goldman WE. Spatially distinct neutrophil responses within the inflammatory lesions of pneumonic plague Mbio. 6.  0.56
2014 Gatza ML, Silva GO, Parker JS, Fan C, Perou CM. An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer. Nature Genetics. 46: 1051-9. PMID 25151356 DOI: 10.1038/ng.3073  0.56
2014 Prat A, Carey LA, Adamo B, Vidal M, Tabernero J, Cortés J, Parker JS, Perou CM, Baselga J. Molecular features and survival outcomes of the intrinsic subtypes within HER2-positive breast cancer. Journal of the National Cancer Institute. 106. PMID 25139534 DOI: 10.1093/jnci/dju152  0.56
2014 Orvis T, Hepperla A, Walter V, Song S, Simon J, Parker J, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman B. BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. Cancer Research. 74: 6486-98. PMID 25115300 DOI: 10.1158/0008-5472.CAN-14-0061  0.56
2014 Prat A, Lluch A, Albanell J, Barry WT, Fan C, Chacón JI, Parker JS, Calvo L, Plazaola A, Arcusa A, Seguí-Palmer MA, Burgues O, Ribelles N, Rodriguez-Lescure A, Guerrero A, et al. Predicting response and survival in chemotherapy-treated triple-negative breast cancer. British Journal of Cancer. 111: 1532-41. PMID 25101563 DOI: 10.1038/bjc.2014.444  0.56
2014 Anders C, Deal AM, Abramson V, Liu MC, Storniolo AM, Carpenter JT, Puhalla S, Nanda R, Melhem-Bertrandt A, Lin NU, Kelly Marcom P, Van Poznak C, Stearns V, Melisko M, Smith JK, ... ... Parker J, et al. TBCRC 018: phase II study of iniparib in combination with irinotecan to treat progressive triple negative breast cancer brain metastases. Breast Cancer Research and Treatment. 146: 557-66. PMID 25001612 DOI: 10.1007/s10549-014-3039-y  0.56
2014 Wilkerson MD, Cabanski CR, Sun W, Hoadley KA, Walter V, Mose LE, Troester MA, Hammerman PS, Parker JS, Perou CM, Hayes DN. Integrated RNA and DNA sequencing improves mutation detection in low purity tumors. Nucleic Acids Research. 42: e107. PMID 24970867 DOI: 10.1093/nar/gku489  0.56
2014 Iglesia MD, Vincent BG, Parker JS, Hoadley KA, Carey LA, Perou CM, Serody JS. Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 3818-29. PMID 24916698 DOI: 10.1158/1078-0432.CCR-13-3368  0.56
2014 Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS. ABRA: improved coding indel detection via assembly-based realignment. Bioinformatics (Oxford, England). 30: 2813-5. PMID 24907369 DOI: 10.1093/bioinformatics/btu376  0.56
2014 Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM. Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. Bmc Genomics. 15: 419. PMID 24888378 DOI: 10.1186/1471-2164-15-419  0.56
2014 Jeck WR, Parker J, Carson CC, Shields JM, Sambade MJ, Peters EC, Burd CE, Thomas NE, Chiang DY, Liu W, Eberhard DA, Ollila D, Grilley-Olson J, Moschos S, Neil Hayes D, et al. Targeted next generation sequencing identifies clinically actionable mutations in patients with melanoma. Pigment Cell & Melanoma Research. 27: 653-63. PMID 24628946 DOI: 10.1111/pcmr.12238  0.56
2014 Brooks SA, Brannon AR, Parker JS, Fisher JC, Sen O, Kattan MW, Hakimi AA, Hsieh JJ, Choueiri TK, Tamboli P, Maranchie JK, Hinds P, Miller CR, Nielsen ME, Rathmell WK. ClearCode34: A prognostic risk predictor for localized clear cell renal cell carcinoma. European Urology. 66: 77-84. PMID 24613583 DOI: 10.1016/j.eururo.2014.02.035  0.56
2014 Damrauer JS, Hoadley KA, Chism DD, Fan C, Tiganelli CJ, Wobker SE, Yeh JJ, Milowsky MI, Iyer G, Parker JS, Kim WY. Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology. Proceedings of the National Academy of Sciences of the United States of America. 111: 3110-5. PMID 24520177 DOI: 10.1073/pnas.1318376111  0.56
2014 Rager JE, Bailey KA, Smeester L, Miller SK, Parker JS, Laine JE, Drobná Z, Currier J, Douillet C, Olshan AF, Rubio-Andrade M, Stýblo M, García-Vargas G, Fry RC. Prenatal arsenic exposure and the epigenome: altered microRNAs associated with innate and adaptive immune signaling in newborn cord blood. Environmental and Molecular Mutagenesis. 55: 196-208. PMID 24327377 DOI: 10.1002/em.21842  0.56
2014 Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ. Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Research. 24: 241-50. PMID 24158655 DOI: 10.1101/gr.158253.113  0.56
2014 Rathmell WK, Brooks SA, Parker JS, Nielsen ME. Reply to Alexander S. Parker, Brad C. Leibovich, Jeanette E. Eckel-Passow, John C. Cheville's Letter to the Editor re: Samira A. Brooks, A. Rose Brannon, Joel S. Parker, et al. ClearCode34: A Prognostic Risk Predictor for Localized Clear Cell Renal Cell Carcinoma. Eur Urol 2014;66:77-84 European Urology. DOI: 10.1016/j.eururo.2014.07.002  0.56
2013 Bardowell SA, Parker J, Fan C, Crandell J, Perou CM, Swift-Scanlan T. Differential methylation relative to breast cancer subtype and matched normal tissue reveals distinct patterns. Breast Cancer Research and Treatment. 142: 365-80. PMID 24212716 DOI: 10.1007/s10549-013-2738-0  0.56
2013 Prat A, Karginova O, Parker JS, Fan C, He X, Bixby L, Harrell JC, Roman E, Adamo B, Troester M, Perou CM. Characterization of cell lines derived from breast cancers and normal mammary tissues for the study of the intrinsic molecular subtypes. Breast Cancer Research and Treatment. 142: 237-55. PMID 24162158 DOI: 10.1007/s10549-013-2743-3  0.56
2013 Roll JD, Rivenbark AG, Sandhu R, Parker JS, Jones WD, Carey LA, Livasy CA, Coleman WB. Dysregulation of the epigenome in triple-negative breast cancers: basal-like and claudin-low breast cancers express aberrant DNA hypermethylation. Experimental and Molecular Pathology. 95: 276-87. PMID 24045095 DOI: 10.1016/j.yexmp.2013.09.001  0.56
2013 Polkinghorn WR, Parker JS, Lee MX, Kass EM, Spratt DE, Iaquinta PJ, Arora VK, Yen WF, Cai L, Zheng D, Carver BS, Chen Y, Watson PA, Shah NP, Fujisawa S, et al. Androgen receptor signaling regulates DNA repair in prostate cancers. Cancer Discovery. 3: 1245-53. PMID 24027196 DOI: 10.1158/2159-8290.CD-13-0172  0.56
2013 King IF, Yandava CN, Mabb AM, Hsiao JS, Huang HS, Pearson BL, Calabrese JM, Starmer J, Parker JS, Magnuson T, Chamberlain SJ, Philpot BD, Zylka MJ. Topoisomerases facilitate transcription of long genes linked to autism. Nature. 501: 58-62. PMID 23995680 DOI: 10.1038/nature12504  0.56
2013 Cabanski CR, Wilkerson MD, Soloway M, Parker JS, Liu J, Prins JF, Marron JS, Perou CM, Hayes DN. BlackOPs: increasing confidence in variant detection through mappability filtering. Nucleic Acids Research. 41: e178. PMID 23935067 DOI: 10.1093/nar/gkt692  0.56
2013 Cleary SP, Jeck WR, Zhao X, Chen K, Selitsky SR, Savich GL, Tan TX, Wu MC, Getz G, Lawrence MS, Parker JS, Li J, Powers S, Kim H, Fischer S, et al. Identification of driver genes in hepatocellular carcinoma by exome sequencing. Hepatology (Baltimore, Md.). 58: 1693-702. PMID 23728943 DOI: 10.1002/hep.26540  0.56
2013 Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, et al. Integrated genomic characterization of endometrial carcinoma. Nature. 497: 67-73. PMID 23636398 DOI: 10.1038/nature12113  0.56
2013 Zawistowski JS, Nakamura K, Parker JS, Granger DA, Golitz BT, Johnson GL. MicroRNA 9-3p targets β1 integrin to sensitize claudin-low breast cancer cells to MEK inhibition. Molecular and Cellular Biology. 33: 2260-74. PMID 23530058 DOI: 10.1128/MCB.00269-13  0.56
2013 Prat A, Cheang MC, Martín M, Parker JS, Carrasco E, Caballero R, Tyldesley S, Gelmon K, Bernard PS, Nielsen TO, Perou CM. Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 31: 203-9. PMID 23233704 DOI: 10.1200/JCO.2012.43.4134  0.56
2012 Chao HH, He X, Parker JS, Zhao W, Perou CM. Micro-scale genomic DNA copy number aberrations as another means of mutagenesis in breast cancer. Plos One. 7: e51719. PMID 23284754 DOI: 10.1371/journal.pone.0051719  0.56
2012 Cabanski CR, Cavin K, Bizon C, Wilkerson MD, Parker JS, Wilhelmsen KC, Perou CM, Marron JS, Hayes DN. ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. Bmc Bioinformatics. 13: 221. PMID 22946927 DOI: 10.1186/1471-2105-13-221  0.56
2012 Prat A, Parker JS, Fan C, Perou CM. PAM50 assay and the three-gene model for identifying the major and clinically relevant molecular subtypes of breast cancer. Breast Cancer Research and Treatment. 135: 301-6. PMID 22752290 DOI: 10.1007/s10549-012-2143-0  0.56
2012 Chia SK, Bramwell VH, Tu D, Shepherd LE, Jiang S, Vickery T, Mardis E, Leung S, Ung K, Pritchard KI, Parker JS, Bernard PS, Perou CM, Ellis MJ, Nielsen TO. A 50-gene intrinsic subtype classifier for prognosis and prediction of benefit from adjuvant tamoxifen. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 4465-72. PMID 22711706 DOI: 10.1158/1078-0432.CCR-12-0286  0.56
2012 Prat A, Parker JS, Fan C, Cheang MC, Miller LD, Bergh J, Chia SK, Bernard PS, Nielsen TO, Ellis MJ, Carey LA, Perou CM. Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen. Annals of Oncology : Official Journal of the European Society For Medical Oncology / Esmo. 23: 2866-73. PMID 22532584 DOI: 10.1093/annonc/mds080  0.56
2012 Dahlman KB, Parker JS, Shamu T, Hieronymus H, Chapinski C, Carver B, Chang K, Hannon GJ, Sawyers CL. Modulators of prostate cancer cell proliferation and viability identified by short-hairpin RNA library screening Plos One. 7. PMID 22509301 DOI: 10.1371/journal.pone.0034414  0.56
2012 Cheang MC, Voduc KD, Tu D, Jiang S, Leung S, Chia SK, Shepherd LE, Levine MN, Pritchard KI, Davies S, Stijleman IJ, Davis C, Ebbert MT, Parker JS, Ellis MJ, et al. Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 2402-12. PMID 22351696 DOI: 10.1158/1078-0432.CCR-11-2956  0.56
2012 Weigman VJ, Chao HH, Shabalin AA, He X, Parker JS, Nordgard SH, Grushko T, Huo D, Nwachukwu C, Nobel A, Kristensen VN, Børresen-Dale AL, Olopade OI, Perou CM. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Research and Treatment. 133: 865-80. PMID 22048815 DOI: 10.1007/s10549-011-1846-y  0.56
2012 Harrell JC, Prat A, Parker JS, Fan C, He X, Carey L, Anders C, Ewend M, Perou CM. Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse. Breast Cancer Research and Treatment. 132: 523-35. PMID 21671017 DOI: 10.1007/s10549-011-1619-7  0.56
2011 Holbrook JD, Parker JS, Gallagher KT, Halsey WS, Hughes AM, Weigman VJ, Lebowitz PF, Kumar R. Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine. Journal of Translational Medicine. 9: 119. PMID 21781349 DOI: 10.1186/1479-5876-9-119  0.56
2011 Elloumi F, Hu Z, Li Y, Parker JS, Gulley ML, Amos KD, Troester MA. Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples. Bmc Medical Genomics. 4: 54. PMID 21718502 DOI: 10.1186/1755-8794-4-54  0.56
2011 Ellis MJ, Suman VJ, Hoog J, Lin L, Snider J, Prat A, Parker JS, Luo J, DeSchryver K, Allred DC, Esserman LJ, Unzeitig GW, Margenthaler J, Babiera GV, Marcom PK, et al. Randomized phase II neoadjuvant comparison between letrozole, anastrozole, and exemestane for postmenopausal women with estrogen receptor-rich stage 2 to 3 breast cancer: clinical and biomarker outcomes and predictive value of the baseline PAM50-based intrinsic subtype--ACOSOG Z1031. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: 2342-9. PMID 21555689 DOI: 10.1200/JCO.2010.31.6950  0.56
2011 Dunbier AK, Anderson H, Ghazoui Z, Salter J, Parker JS, Perou CM, Smith IE, Dowsett M. Association between breast cancer subtypes and response to neoadjuvant anastrozole. Steroids. 76: 736-40. PMID 21447351 DOI: 10.1016/j.steroids.2011.02.025  0.56
2011 Bivona TG, Hieronymus H, Parker J, Chang K, Taron M, Rosell R, Moonsamy P, Dahlman K, Miller VA, Costa C, Hannon G, Sawyers CL. FAS and NF-κB signalling modulate dependence of lung cancers on mutant EGFR. Nature. 471: 523-6. PMID 21430781 DOI: 10.1038/nature09870  0.56
2011 Fan C, Prat A, Parker JS, Liu Y, Carey LA, Troester MA, Perou CM. Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures. Bmc Medical Genomics. 4: 3. PMID 21214954 DOI: 10.1186/1755-8794-4-3  0.56
2011 Anders CK, Fan C, Parker JS, Carey LA, Blackwell KL, Klauber-DeMore N, Perou CM. Breast carcinomas arising at a young age: unique biology or a surrogate for aggressive intrinsic subtypes? Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: e18-20. PMID 21115855 DOI: 10.1200/JCO.2010.28.9199  0.56
2011 Chung CH, Pohlmann PR, Rothenberg ML, Burkey BB, Parker J, Palka K, Aulino J, Puzanov I, Murphy B. Insulin-like growth factor-1 receptor inhibitor, AMG-479, in cetuximab-refractory head and neck squamous cell carcinoma Head and Neck. 33: 1804-1808. PMID 20652976 DOI: 10.1002/hed.21478  0.56
2011 Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM. Correction: An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer Breast Cancer Research. 13. DOI: 10.1186/bcr2909  0.56
2010 Thorner AR, Parker JS, Hoadley KA, Perou CM. Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer. Plos One. 5: e13073. PMID 20949095 DOI: 10.1371/journal.pone.0013073  0.56
2010 Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, Vickery T, Davies SR, Snider J, Stijleman IJ, Reed J, Cheang MC, Mardis ER, Perou CM, Bernard PS, Ellis MJ. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 16: 5222-32. PMID 20837693 DOI: 10.1158/1078-0432.CCR-10-1282  0.56
2010 Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM. Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Research : Bcr. 12: R68. PMID 20813035 DOI: 10.1186/bcr2635  0.56
2010 Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PS. Clinical implementation of the intrinsic subtypes of breast cancer. The Lancet. Oncology. 11: 718-9; author reply . PMID 20688274 DOI: 10.1016/S1470-2045(10)70176-5  0.56
2010 Tsuchiya M, Parker JS, Kono H, Matsuda M, Fujii H, Rusyn I. Gene expression in nontumoral liver tissue and recurrence-free survival in hepatitis C virus-positive hepatocellular carcinoma. Molecular Cancer. 9: 74. PMID 20380719 DOI: 10.1186/1476-4598-9-74  0.56
2010 Mavrakis KJ, Wolfe AL, Oricchio E, Palomero T, de Keersmaecker K, McJunkin K, Zuber J, James T, Khan AA, Leslie CS, Parker JS, Paddison PJ, Tam W, Ferrando A, Wendel HG. Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nature Cell Biology. 12: 372-9. PMID 20190740 DOI: 10.1038/ncb2037  0.56
2010 Dunbier AK, Anderson H, Ghazoui Z, Folkerd EJ, A'hern R, Crowder RJ, Hoog J, Smith IE, Osin P, Nerurkar A, Parker JS, Perou CM, Ellis MJ, Dowsett M. Relationship between plasma estradiol levels and estrogen-responsive gene expression in estrogen receptor-positive breast cancer in postmenopausal women. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 28: 1161-7. PMID 20124184 DOI: 10.1200/JCO.2009.23.9616  0.56
2010 Haugen AC, Di Prospero NA, Parker JS, Fannin RD, Chou J, Meyer JN, Halweg C, Collins JB, Durr A, Fischbeck K, Van Houten B. Altered gene expression and DNA damage in peripheral blood cells from Friedreich's ataxia patients: cellular model of pathology. Plos Genetics. 6: e1000812. PMID 20090835 DOI: 10.1371/journal.pgen.1000812  0.56
2010 Korde LA, Lusa L, McShane L, Lebowitz PF, Lukes L, Camphausen K, Parker JS, Swain SM, Hunter K, Zujewski JA. Gene expression pathway analysis to predict response to neoadjuvant docetaxel and capecitabine for breast cancer. Breast Cancer Research and Treatment. 119: 685-99. PMID 20012355 DOI: 10.1007/s10549-009-0651-3  0.56
2010 Fannin RD, Russo M, O'Connell TM, Gerrish K, Winnike JH, Macdonald J, Newton J, Malik S, Sieber SO, Parker J, Shah R, Zhou T, Watkins PB, Paules RS. Acetaminophen dosing of humans results in blood transcriptome and metabolome changes consistent with impaired oxidative phosphorylation. Hepatology (Baltimore, Md.). 51: 227-36. PMID 19918972 DOI: 10.1002/hep.23330  0.56
2010 Chung CH, Aulino J, Muldowney NJ, Hatakeyama H, Baumann J, Burkey B, Netterville J, Sinard R, Yarbrough WG, Cmelak AJ, Slebos RJ, Shyr Y, Parker J, Gilbert J, Murphy BA. Nuclear factor-kappa B pathway and response in a phase II trial of bortezomib and docetaxel in patients with recurrent and/or metastatic head and neck squamous cell carcinoma. Annals of Oncology : Official Journal of the European Society For Medical Oncology / Esmo. 21: 864-70. PMID 19850643 DOI: 10.1093/annonc/mdp390  0.56
2010 Connor EE, Kahl S, Elsasser TH, Parker JS, Li RW, Van Tassell CP, Baldwin RL, Barao SM. Enhanced mitochondrial complex gene function and reduced liver size may mediate improved feed efficiency of beef cattle during compensatory growth. Functional & Integrative Genomics. 10: 39-51. PMID 19777276 DOI: 10.1007/s10142-009-0138-7  0.56
2010 Sandhu R, Parker JS, Jones WD, Livasy CA, Coleman WB. Microarray-based gene expression profiling for molecular classification of breast cancer and identification of new targets for therapy Laboratory Medicine. 41: 364-372. DOI: 10.1309/LMLIK0VIE3CJK0WD  0.56
2009 Schisler JC, Charles PC, Parker JS, Hilliard EG, Mapara S, Meredith D, Lineberger RE, Wu SS, Alder BD, Stouffer GA, Patterson C. Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry. Plos One. 4: e8183. PMID 20016837 DOI: 10.1371/journal.pone.0008183  0.56
2009 Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM. An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. Breast Cancer Research : Bcr. 11: R55. PMID 19638211 DOI: 10.1186/bcr2344  0.56
2009 Jarinova O, Stewart AF, Roberts R, Wells G, Lau P, Naing T, Buerki C, McLean BW, Cook RC, Parker JS, McPherson R. Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus. Arteriosclerosis, Thrombosis, and Vascular Biology. 29: 1671-7. PMID 19592466 DOI: 10.1161/ATVBAHA.109.189522  0.56
2009 Hester SD, Reid L, Nowak N, Jones WD, Parker JS, Knudtson K, Ward W, Tiesman J, Denslow ND. Comparison of comparative genomic hybridization technologies across microarray platforms. Journal of Biomolecular Techniques : Jbt. 20: 135-51. PMID 19503625  0.56
2009 Bierie B, Chung CH, Parker JS, Stover DG, Cheng N, Chytil A, Aakre M, Shyr Y, Moses HL. Abrogation of TGF-beta signaling enhances chemokine production and correlates with prognosis in human breast cancer. The Journal of Clinical Investigation. 119: 1571-82. PMID 19451693 DOI: 10.1172/JCI37480  0.56
2009 Cheang MC, Chia SK, Voduc D, Gao D, Leung S, Snider J, Watson M, Davies S, Bernard PS, Parker JS, Perou CM, Ellis MJ, Nielsen TO. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. Journal of the National Cancer Institute. 101: 736-50. PMID 19436038 DOI: 10.1093/jnci/djp082  0.56
2009 Crowder RJ, Phommaly C, Tao Y, Hoog J, Luo J, Perou CM, Parker JS, Miller MA, Huntsman DG, Lin L, Snider J, Davies SR, Olson JA, Watson MA, Saporita A, et al. PIK3CA and PIK3CB inhibition produce synthetic lethality when combined with estrogen deprivation in estrogen receptor-positive breast cancer. Cancer Research. 69: 3955-62. PMID 19366795 DOI: 10.1158/0008-5472.CAN-08-4450  0.56
2009 Ezhkova E, Pasolli HA, Parker JS, Stokes N, Su IH, Hannon G, Tarakhovsky A, Fuchs E. Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells. Cell. 136: 1122-35. PMID 19303854 DOI: 10.1016/j.cell.2008.12.043  0.56
2009 Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 27: 1160-7. PMID 19204204 DOI: 10.1200/JCO.2008.18.1370  0.56
2009 Uziel T, Karginov FV, Xie S, Parker JS, Wang YD, Gajjar A, He L, Ellison D, Gilbertson RJ, Hannon G, Roussel MF. The miR-17~92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma. Proceedings of the National Academy of Sciences of the United States of America. 106: 2812-7. PMID 19196975 DOI: 10.1073/pnas.0809579106  0.56
2009 Cohen EE, Zhu H, Lingen MW, Martin LE, Kuo WL, Choi EA, Kocherginsky M, Parker JS, Chung CH, Rosner MR. A feed-forward loop involving protein kinase Calpha and microRNAs regulates tumor cell cycle. Cancer Research. 69: 65-74. PMID 19117988 DOI: 10.1158/0008-5472.CAN-08-0377  0.56
2009 Thorner AR, Hoadley KA, Parker JS, Winkel S, Millikan RC, Perou CM. In vitro and in vivo analysis of B-Myb in basal-like breast cancer. Oncogene. 28: 742-51. PMID 19043454 DOI: 10.1038/onc.2008.430  0.56
2009 Liu X, Parker J, Fan C, Perou CM, Marron JS. Visualization of Cross-Platform Microarray Normalization Batch Effects and Noise in Microarray Experiments: Sources and Solutions. 167-181. DOI: 10.1002/9780470685983.ch14  0.56
2008 Wakamatsu N, Collins JB, Parker JS, Tessema M, Clayton NP, Ton TV, Hong HH, Belinsky S, Devereux TR, Sills RC, Lahousse SA. Gene expression studies demonstrate that the K-ras/Erk MAP kinase signal transduction pathway and other novel pathways contribute to the pathogenesis of cumene-induced lung tumors. Toxicologic Pathology. 36: 743-52. PMID 18648096 DOI: 10.1177/0192623308320801  0.56
2008 Gohlke JM, Armant O, Parham FM, Smith MV, Zimmer C, Castro DS, Nguyen L, Parker JS, Gradwohl G, Portier CJ, Guillemot F. Characterization of the proneural gene regulatory network during mouse telencephalon development. Bmc Biology. 6: 15. PMID 18377642 DOI: 10.1186/1741-7007-6-15  0.56
2008 Silva JM, Marran K, Parker JS, Silva J, Golding M, Schlabach MR, Elledge SJ, Hannon GJ, Chang K. Profiling essential genes in human mammary cells by multiplex RNAi screening Science. 319: 617-620. PMID 18239125 DOI: 10.1126/science.1149185  0.56
2007 Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ. A biochemical approach to identifying microRNA targets. Proceedings of the National Academy of Sciences of the United States of America. 104: 19291-6. PMID 18042700 DOI: 10.1073/pnas.0709971104  0.56
2007 Thomson JM, Parker JS, Hammond SM. Microarray analysis of miRNA gene expression. Methods in Enzymology. 427: 107-22. PMID 17720481 DOI: 10.1016/S0076-6879(07)27006-5  0.56
2007 Mori K, Blackshear PE, Lobenhofer EK, Parker JS, Orzech DP, Roycroft JH, Walker KL, Johnson KA, Marsh TA, Irwin RD, Boorman GA. Hepatic transcript levels for genes coding for enzymes associated with xenobiotic metabolism are altered with age. Toxicologic Pathology. 35: 242-51. PMID 17366318 DOI: 10.1080/01926230601156286  0.56
2007 Perkins DO, Jeffries CD, Jarskog LF, Thomson JM, Woods K, Newman MA, Parker JS, Jin J, Hammond SM. microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder. Genome Biology. 8: R27. PMID 17326821 DOI: 10.1186/gb-2007-8-2-r27  0.56
2006 Lai WS, Parker JS, Grissom SF, Stumpo DJ, Blackshear PJ. Novel mRNA targets for tristetraprolin (TTP) identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts. Molecular and Cellular Biology. 26: 9196-208. PMID 17030620 DOI: 10.1128/MCB.00945-06  0.56
2006 Chung CH, Parker JS, Ely K, Carter J, Yi Y, Murphy BA, Ang KK, El-Naggar AK, Zanation AM, Cmelak AJ, Levy S, Slebos RJ, Yarbrough WG. Gene expression profiles identify epithelial-to-mesenchymal transition and activation of nuclear factor-kappaB signaling as characteristics of a high-risk head and neck squamous cell carcinoma. Cancer Research. 66: 8210-8. PMID 16912200 DOI: 10.1158/0008-5472.CAN-06-1213  0.56
2006 Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T, Hammond SM. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes & Development. 20: 2202-7. PMID 16882971 DOI: 10.1101/gad.1444406  0.56
2005 Powell CL, Kosyk O, Bradford BU, Parker JS, Lobenhofer EK, Denda A, Uematsu F, Nakae D, Rusyn I. Temporal correlation of pathology and DNA damage with gene expression in a choline-deficient model of rat liver injury. Hepatology (Baltimore, Md.). 42: 1137-47. PMID 16250055 DOI: 10.1002/hep.20910  0.56
2004 Troester MA, Hoadley KA, Parker JS, Perou CM. Prediction of toxicant-specific gene expression signatures after chemotherapeutic treatment of breast cell lines. Environmental Health Perspectives. 112: 1607-13. PMID 15598611 DOI: 10.1289/txg.7204  0.56
2004 Aune TM, Parker JS, Maas K, Liu Z, Olsen NJ, Moore JH. Co-localization of differentially expressed genes and shared susceptibility loci in human autoimmunity. Genetic Epidemiology. 27: 162-72. PMID 15305332 DOI: 10.1002/gepi.20013  0.56
2004 Chung CH, Parker JS, Karaca G, Wu J, Funkhouser WK, Moore D, Butterfoss D, Xiang D, Zanation A, Yin X, Shockley WW, Weissler MC, Dressler LG, Shores CG, Yarbrough WG, et al. Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell. 5: 489-500. PMID 15144956 DOI: 10.1016/S1535-6108(04)00112-6  0.56
2003 Ritchie MD, White BC, Parker JS, Hahn LW, Moore JH. Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases. Bmc Bioinformatics. 4: 28. PMID 12846935 DOI: 10.1186/1471-2105-4-28  0.56
2002 Moore JH, Parker JS, Olsen NJ, Aune TM. Symbolic discriminant analysis of microarray data in autoimmune disease. Genetic Epidemiology. 23: 57-69. PMID 12112248 DOI: 10.1002/gepi.1117  0.56
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