Research Topics
Genomes and Genes | Ronglai ShenSummaryAffiliation: Memorial Sloan-Kettering Cancer Center Country: USA Publications
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Publications
Integrative subtype discovery in glioblastoma using iClusterRonglai Shen
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
PLoS ONE 7:e35236. 2012..The data analysis workflow we propose provides a unified and computationally scalable framework to harness the full potential of large-scale integrated cancer genomic data for integrative subtype discovery...- Modeling intra-tumor protein expression heterogeneity in tissue microarray experimentsRonglai Shen
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 307 East 63rd Street, New York, NY 10065, U S A
Stat Med 27:1944-59. 2008..A general advice is to use the joint model inference whenever results differ between the two-stage methods and the joint analysis... 
Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture modelRonglai Shen
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
Bioinformatics 24:2880-6. 2008..Standard analysis approach estimates a sample mean expression in the tumor, ignoring the complex tissue-specific staining patterns observed on tissue arrays...- Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysisRonglai Shen
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
Bioinformatics 25:2906-12. 2009..A more statistically powerful approach would incorporate all data types simultaneously and generate a single integrated cluster assignment... - A phase 2 study of bevacizumab with cisplatin plus intensity-modulated radiation therapy for stage III/IVB head and neck squamous cell cancerMatthew G Fury
Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Cancer 118:5008-14. 2012..HNSCC tumors that express high levels of vascular endothelial growth factor have been associated with a worse prognosis, and bevacizumab may sensitize tumors to cisplatin and radiation... - EGFR-mutant lung adenocarcinomas treated first-line with the novel EGFR inhibitor, XL647, can subsequently retain moderate sensitivity to erlotinibJuliann Chmielecki
Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
J Thorac Oncol 7:434-42. 2012..We explored whether all EGFR TKIs similarly select for the T790M mutation using data from early clinical trials and established in vitro models of acquired resistance... - Dual targeting of EGFR can overcome a major drug resistance mutation in mouse models of EGFR mutant lung cancerLucia Regales
Pao Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
J Clin Invest 119:3000-10. 2009..Moreover, this approach could serve as an important model for targeting other receptor tyrosine kinases activated in human cancers... - Impact on disease-free survival of adjuvant erlotinib or gefitinib in patients with resected lung adenocarcinomas that harbor EGFR mutationsYelena Y Janjigian
Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Medical College of Cornell University, New York City, New York, USA
J Thorac Oncol 6:569-75. 2011..Whether treatment with TKI improves outcomes in patients with resected lung adenocarcinoma and EGFR mutation is unknown... - Breast cancer methylomes establish an epigenomic foundation for metastasisFang Fang
Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
Sci Transl Med 3:75ra25. 2011..These findings significantly enhance our understanding of breast cancer oncogenesis and aid the development of new prognostic biomarkers for this common malignancy... - Molecular characteristics predict clinical outcomes: prospective trial correlating response to the EGFR tyrosine kinase inhibitor gefitinib with the presence of sensitizing mutations in the tyrosine binding domain of the EGFR geneNaiyer A Rizvi
Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, New York 10021, USA
Clin Cancer Res 17:3500-6. 2011..To determine if tumor regression following treatment with gefitinib correlates with the presence of sensitizing mutations in epidermal growth factor receptor (EGFR)... - Distinct Clinical Course of EGFR-Mutant Resected Lung Cancers: Results of Testing of 1118 Surgical Specimens and Effects of Adjuvant Gefitinib and ErlotinibSandra P D'Angelo
Department of Medicine, Division of Solid Tumor Oncology, Thoracic Oncology Service and Departments of Epidemiology and Biostatistics, Surgery, and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
J Thorac Oncol 7:1815-22. 2012..The clinical significance of these mutations in patients with resected stage I-III lung cancers is unclear... - IDH mutation and neuroglial developmental features define clinically distinct subclasses of lower grade diffuse astrocytic gliomaDaniel Gorovets
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Clin Cancer Res 18:2490-501. 2012..Accordingly, we sought to identify and characterize clinically relevant molecular subclasses of lower grade diffuse astrocytic gliomas... - Contemporary results of surgical resection of non-small cell lung cancer after induction therapy: a review of 549 consecutive casesStephen A Barnett
Thoracic Service, Department of Surgery, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, USA
J Thorac Oncol 6:1530-6. 2011..Recent reports suggest that operative mortality in these patients is declining. We analyzed our contemporary results to define operative mortality and factors determining surgical risk... - Pattern discovery and cancer gene identification in integrated cancer genomic dataQianxing Mo
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Proc Natl Acad Sci U S A 110:4245-50. 2013..Application of the cancer genome atlas colorectal cancer data reveals distinct integrated tumor subtypes, suggesting different genetic pathways in colon cancer progression... - The BMP inhibitor Coco reactivates breast cancer cells at lung metastatic sitesHua Gao
Cell Biology Program, Sloan Kettering Institute for Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Cell 150:764-79. 2012..These findings reveal that metastasis-initiating cells need to overcome organ-specific antimetastatic signals in order to undergo reactivation... - Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profilesParminder K Mankoo
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
PLoS ONE 6:e24709. 2011.... - A phase I study of daily everolimus plus low-dose weekly cisplatin for patients with advanced solid tumorsMatthew G Fury
Department of Medicine, Head and Neck Medical Oncology Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 532, New York, NY, 10021, USA
Cancer Chemother Pharmacol 69:591-8. 2012..We conducted a phase I study to establish the recommended phase II of oral everolimus to be given with low-dose weekly intravenous cisplatin... - A phase 2 study of pemetrexed plus gemcitabine every 2 weeks for patients with recurrent or metastatic head and neck squamous cell cancerMatthew G Fury
Head and Neck Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
Cancer 117:795-801. 2011..A phase 1 study of pemetrexed plus gemcitabine given every 2 weeks demonstrated encouraging preliminary efficacy against head and neck squamous cell cancer (HNSCC)... - Molecular epidemiology of EGFR and KRAS mutations in 3,026 lung adenocarcinomas: higher susceptibility of women to smoking-related KRAS-mutant cancersSnjezana Dogan
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
Clin Cancer Res 18:6169-77. 2012..The molecular epidemiology of most EGFR and KRAS mutations in lung cancer remains unclear... - Immunization with N-propionyl polysialic acid-KLH conjugate in patients with small cell lung cancer is safe and induces IgM antibodies reactive with SCLC cells and bactericidal against group B meningococciLee M Krug
Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, Weill Medical College of Cornell University, 1275 York Ave, New York, NY 10065, USA
Cancer Immunol Immunother 61:9-18. 2012..The objectives of the current trial were to establish the lowest optimal dose and to confirm the safety of the induction of antibodies against polySA with the NP-polySA vaccine... - High expression levels of total IGF-1R and sensitivity of NSCLC cells in vitro to an anti-IGF-1R antibody (R1507)Yixuan Gong
Pao Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
PLoS ONE 4:e7273. 2009..The IGF receptor type 1 (IGF-1R) pathway is frequently deregulated in human tumors and has become a target of interest for anti-cancer therapy... - Pack-years of cigarette smoking as a prognostic factor in patients with stage IIIB/IV nonsmall cell lung cancerYelena Y Janjigian
Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Medical College of Cornell University, New York, New York 10021, USA
Cancer 116:670-5. 2010.... - Selumetinib-enhanced radioiodine uptake in advanced thyroid cancerAlan L Ho
Head and Neck Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY 10065, USA
N Engl J Med 368:623-32. 2013..In mouse models of thyroid cancer, selective mitogen-activated protein kinase (MAPK) pathway antagonists increase the expression of the sodium-iodide symporter and uptake of iodine. Their effects in humans are not known... - Comparative genomic analysis of primary versus metastatic colorectal carcinomasEfsevia Vakiani
Memorial Sloan Kettering Cancer Center, New York, NY, USA
J Clin Oncol 30:2956-62. 2012..To compare the mutational and copy number profiles of primary and metastatic colorectal carcinomas (CRCs) using both unpaired and paired samples derived from primary and metastatic disease sites... - Prognostic immune markers in non-small cell lung cancerKei Suzuki
Division of Thoracic Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
Clin Cancer Res 17:5247-56. 2011..This first comprehensive review of prognostic immune markers provides a foundation for further investigating immune responses in NSCLC... - Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomasNicolas Girard
Human Oncology and Pathogenesis Program HOPP, Weill Medical College of Cornell University, New York, New York, USA
Clin Cancer Res 15:6790-9. 2009..However, whether the underlying biology of these tumors warrants such clustering is unclear, and the optimum treatment of either entity is unknown... 
Phase II study of saracatinib (AZD0530) for patients with recurrent or metastatic head and neck squamous cell carcinoma (HNSCC)Matthew G Fury
Head and Neck Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Anticancer Res 31:249-53. 2011..Saracatinib (AZD0530) is an orally available Src kinase inhibitor. A phase II study was conducted to evaluate saracatinib in patients with recurrent or metastatic head and neck squamous cell cancer (HNSCC)...- Erlotinib resistance in mouse models of epidermal growth factor receptor-induced lung adenocarcinomaKaterina Politi
Program in Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Dis Model Mech 3:111-9. 2010..This preclinical mouse model, therefore, recapitulates the molecular changes responsible for resistance to TKIs in human tumors and holds promise for the discovery of additional mechanisms of drug resistance in lung cancer... - The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesotheliomaMatthew Bott
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
Nat Genet 43:668-72. 2011..These findings implicate transcriptional deregulation in the pathogenesis of MPM... - Eigengene-based linear discriminant model for tumor classification using gene expression microarray dataRonglai Shen
Department of Biostatistics, University of Michigan Ann Arbor, MI 48109-0602, USA
Bioinformatics 22:2635-42. 2006..In the breast cancer data, we show false negative prognosis can be controlled via a cost-adjusted discriminant function. AVAILABILITY: R code for the ELDA algorithm is available from author upon request... - Internet-based Profiler system as integrative framework to support translational researchRobert Kim
Department of Pathology, Brigham and Women s Hospital, Boston, USA
BMC Bioinformatics 6:304. 2005..The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions... - Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimensAtreya Dash
Department of Urology, University of Michigan, Ann Arbor, USA
Am J Pathol 161:1743-8. 2002.... - Expression of the platelet-derived growth factor receptor in prostate cancer and treatment implications with tyrosine kinase inhibitorsMatthias D Hofer
Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
Neoplasia 6:503-12. 2004..2-fold downregulation). Taken together, this study suggests that only a small subset of PCas may be amenable to tyrosine kinase inhibitors specific for PDGFR... - Heterogeneity of TMPRSS2 gene rearrangements in multifocal prostate adenocarcinoma: molecular evidence for an independent group of diseasesRohit Mehra
Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Cancer Res 67:7991-5. 2007..Understanding this molecular heterogeneity is critical to the future development and utility of diagnostic and prognostic PCA biomarkers... - A latent variable approach for meta-analysis of gene expression data from multiple microarray experimentsHyungwon Choi
Department of Statistics and Huck Institute for Life Sciences, Penn State University, University Park, PA, USA
BMC Bioinformatics 8:364. 2007..With the explosion in data generated using microarray technology by different investigators working on similar experiments, it is of interest to combine results across multiple studies... - Basal cell cocktail (34betaE12 + p63) improves the detection of prostate basal cellsMing Zhou
Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
Am J Surg Pathol 27:365-71. 2003..We recommend this basal cell cocktail for routine Pca diagnostic work-up... - Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy programRajal B Shah
Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
Cancer Res 64:9209-16. 2004..An appreciation of this heterogeneity is critical to evaluating diagnostic and prognostic biomarkers as well as to designing therapeutic targets for advanced disease... - Usefulness of basal cell cocktail (34betaE12 + p63) in the diagnosis of atypical prostate glandular proliferationsRajal B Shah
Department of Pathology, University of Michigan School of Medicine, Ann Arbor 48109, USA
Am J Clin Pathol 122:517-23. 2004..The cocktail provides a simple, cost-effective improvement in basal cell immunohistochemical analysis of difficult prostate lesions... - Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray dataRonglai Shen
Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
BMC Genomics 5:94. 2004..With the accumulating amount of microarray data, one of the most intriguing yet challenging tasks is to develop robust statistical models to integrate the findings... - Alpha-methylacyl-CoA racemase protein expression is associated with the degree of differentiation in breast cancer using quantitative image analysisAgnieszka K Witkiewicz
Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
Cancer Epidemiol Biomarkers Prev 14:1418-23. 2005..Quantitative image analysis is a novel way to accurately and reproducibly evaluate immunohistochemistry in breast tissue samples using high-density tissue microarrays... - Decreased alpha-methylacyl CoA racemase expression in localized prostate cancer is associated with an increased rate of biochemical recurrence and cancer-specific deathMark A Rubin
Department of Pathology Amory 3 195, Brigham and Women s Hospital, Harvard Medical School, 75 Francis Street, Boston, Massachusetts 02115, USA
Cancer Epidemiol Biomarkers Prev 14:1424-32. 2005..This is the first study to show that AMACR expression is significantly associated with prostate cancer progression and suggests that not all surrogate end points may be optimal to define biomarkers of aggressive prostate cancer... - Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancerRohit Mehra
Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Mod Pathol 20:538-44. 2007.... - Metastasis suppressor gene Raf kinase inhibitor protein (RKIP) is a novel prognostic marker in prostate cancerZheng Fu
Department of Urology, University of Michigan, Ann Arbor, Michigan 48109-0940, USA
Prostate 66:248-56. 2006..001). CONCLUSION: In contrast to increased expression of pro-tumorigenic genes, these results demonstrate decreased protein expression of a gene, for example, RKIP, can serve as a prognostic marker in PCa patients... - Autoantibody signatures in prostate cancerXiaoju Wang
Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
N Engl J Med 353:1224-35. 2005..The remaining phage peptides were generated from untranslated sequences. CONCLUSIONS: Autoantibodies against peptides derived from prostate-cancer tissue could be used as the basis for a screening test for prostate cancer... - Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysisRohit Mehra
Department of Pathology, University of Michigan Medical School, Ann Arbor, 48109, USA
Cancer Res 65:11259-64. 2005..Our data suggest that immunohistochemical analysis of GATA3 may be the basis for a new clinically applicable test to predict tumor recurrence early in the progression of breast cancer... - Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancerJindan Yu
Department of Pathology, Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Cancer Cell 12:419-31. 2007..Taken together, we demonstrate the power of integrating multiple diverse genomic data to decipher targets of disease-related genes...