Ronglai Shen

Summary

Affiliation: Memorial Sloan-Kettering Cancer Center
Country: USA

Publications

  1. pmc Integrative subtype discovery in glioblastoma using iCluster
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS ONE 7:e35236. 2012
  2. ncbi request reprint Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Bioinformatics 24:2880-6. 2008
  3. pmc Modeling intra-tumor protein expression heterogeneity in tissue microarray experiments
    Ronglai 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
  4. pmc Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Bioinformatics 25:2906-12. 2009
  5. doi request reprint Distinct clinical course of EGFR-mutant resected lung cancers: results of testing of 1118 surgical specimens and effects of adjuvant gefitinib and erlotinib
    Sandra P D'Angelo
    Department of Medicine, Division of Solid Tumor Oncology, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    J Thorac Oncol 7:1815-22. 2012
  6. doi request reprint A phase 1 study of everolimus + weekly cisplatin + intensity modulated radiation therapy in head-and-neck cancer
    Matthew G Fury
    Department of Medicine, Head and Neck Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York Department of Medicine, Weill Cornell Medical College, New York, New York
    Int J Radiat Oncol Biol Phys 87:479-86. 2013
  7. doi request reprint A phase 2 study of bevacizumab with cisplatin plus intensity-modulated radiation therapy for stage III/IVB head and neck squamous cell cancer
    Matthew G Fury
    Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Cancer 118:5008-14. 2012
  8. pmc EGFR-mutant lung adenocarcinomas treated first-line with the novel EGFR inhibitor, XL647, can subsequently retain moderate sensitivity to erlotinib
    Juliann Chmielecki
    Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
    J Thorac Oncol 7:434-42. 2012
  9. pmc Dual targeting of EGFR can overcome a major drug resistance mutation in mouse models of EGFR mutant lung cancer
    Lucia Regales
    Pao Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    J Clin Invest 119:3000-10. 2009
  10. pmc Pattern discovery and cancer gene identification in integrated cancer genomic data
    Qianxing 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

Detail Information

Publications48

  1. pmc Integrative subtype discovery in glioblastoma using iCluster
    Ronglai 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...
  2. ncbi request reprint Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model
    Ronglai 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...
  3. pmc Modeling intra-tumor protein expression heterogeneity in tissue microarray experiments
    Ronglai 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...
  4. pmc Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
    Ronglai 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...
  5. doi request reprint Distinct clinical course of EGFR-mutant resected lung cancers: results of testing of 1118 surgical specimens and effects of adjuvant gefitinib and erlotinib
    Sandra P D'Angelo
    Department of Medicine, Division of Solid Tumor Oncology, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    J Thorac Oncol 7:1815-22. 2012
    ..The clinical significance of these mutations in patients with resected stage I-III lung cancers is unclear...
  6. doi request reprint A phase 1 study of everolimus + weekly cisplatin + intensity modulated radiation therapy in head-and-neck cancer
    Matthew G Fury
    Department of Medicine, Head and Neck Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York Department of Medicine, Weill Cornell Medical College, New York, New York
    Int J Radiat Oncol Biol Phys 87:479-86. 2013
    ..Preclinically, inhibition of mTORC1 with everolimus sensitizes cancer cells to cisplatin and radiation...
  7. doi request reprint A phase 2 study of bevacizumab with cisplatin plus intensity-modulated radiation therapy for stage III/IVB head and neck squamous cell cancer
    Matthew 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...
  8. pmc EGFR-mutant lung adenocarcinomas treated first-line with the novel EGFR inhibitor, XL647, can subsequently retain moderate sensitivity to erlotinib
    Juliann 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...
  9. pmc Dual targeting of EGFR can overcome a major drug resistance mutation in mouse models of EGFR mutant lung cancer
    Lucia 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...
  10. pmc Pattern discovery and cancer gene identification in integrated cancer genomic data
    Qianxing 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...
  11. pmc Impact on disease-free survival of adjuvant erlotinib or gefitinib in patients with resected lung adenocarcinomas that harbor EGFR mutations
    Yelena 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...
  12. pmc Molecular epidemiology of EGFR and KRAS mutations in 3,026 lung adenocarcinomas: higher susceptibility of women to smoking-related KRAS-mutant cancers
    Snjezana 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...
  13. pmc Breast cancer methylomes establish an epigenomic foundation for metastasis
    Fang 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...
  14. pmc 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 gene
    Naiyer 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)...
  15. doi request reprint IDH mutation and neuroglial developmental features define clinically distinct subclasses of lower grade diffuse astrocytic glioma
    Daniel 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...
  16. ncbi request reprint Contemporary results of surgical resection of non-small cell lung cancer after induction therapy: a review of 549 consecutive cases
    Stephen 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...
  17. pmc The BMP inhibitor Coco reactivates breast cancer cells at lung metastatic sites
    Hua 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...
  18. pmc Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles
    Parminder K Mankoo
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS ONE 6:e24709. 2011
    ....
  19. doi request reprint A phase I study of daily everolimus plus low-dose weekly cisplatin for patients with advanced solid tumors
    Matthew 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...
  20. doi request reprint A phase 2 study of pemetrexed plus gemcitabine every 2 weeks for patients with recurrent or metastatic head and neck squamous cell cancer
    Matthew 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)...
  21. pmc 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 meningococci
    Lee 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...
  22. pmc 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...
  23. pmc Pack-years of cigarette smoking as a prognostic factor in patients with stage IIIB/IV nonsmall cell lung cancer
    Yelena 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
    ....
  24. pmc Selumetinib-enhanced radioiodine uptake in advanced thyroid cancer
    Alan 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...
  25. pmc Comparative genomic analysis of primary versus metastatic colorectal carcinomas
    Efsevia 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...
  26. ncbi request reprint Prognostic immune markers in non-small cell lung cancer
    Kei 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...
  27. pmc Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas
    Nicolas 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...
  28. pmc 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)...
  29. pmc Erlotinib resistance in mouse models of epidermal growth factor receptor-induced lung adenocarcinoma
    Katerina 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...
  30. doi request reprint The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma
    Matthew 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...
  31. pmc Expression of the platelet-derived growth factor receptor in prostate cancer and treatment implications with tyrosine kinase inhibitors
    Matthias 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...
  32. pmc Internet-based Profiler system as integrative framework to support translational research
    Robert 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...
  33. ncbi request reprint Eigengene-based linear discriminant model for tumor classification using gene expression microarray data
    Ronglai Shen
    Department of Biostatistics, University of Michigan Ann Arbor, MI 48109 0602, USA
    Bioinformatics 22:2635-42. 2006
    ..The univariate statistics summarize gene expression profiles outside of the gene co-regulation network context, leading to redundant information being included in the selection procedure...
  34. pmc Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens
    Atreya Dash
    Department of Urology, University of Michigan, Ann Arbor, USA
    Am J Pathol 161:1743-8. 2002
    ....
  35. ncbi request reprint Usefulness of basal cell cocktail (34betaE12 + p63) in the diagnosis of atypical prostate glandular proliferations
    Rajal 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...
  36. ncbi request reprint Basal cell cocktail (34betaE12 + p63) improves the detection of prostate basal cells
    Ming 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...
  37. ncbi request reprint Heterogeneity of TMPRSS2 gene rearrangements in multifocal prostate adenocarcinoma: molecular evidence for an independent group of diseases
    Rohit 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...
  38. pmc A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments
    Hyungwon 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...
  39. pmc Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data
    Ronglai 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...
  40. ncbi request reprint Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program
    Rajal 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...
  41. ncbi request reprint Decreased alpha-methylacyl CoA racemase expression in localized prostate cancer is associated with an increased rate of biochemical recurrence and cancer-specific death
    Mark 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...
  42. ncbi request reprint Metastasis suppressor gene Raf kinase inhibitor protein (RKIP) is a novel prognostic marker in prostate cancer
    Zheng Fu
    Department of Urology, University of Michigan, Ann Arbor, Michigan 48109 0940, USA
    Prostate 66:248-56. 2006
    ..However, the prognostic significance of RKIP expression and its association with metastasis in PCa patients is unknown...
  43. ncbi request reprint Autoantibody signatures in prostate cancer
    Xiaoju Wang
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    N Engl J Med 353:1224-35. 2005
    ..New biomarkers, such as autoantibody signatures, may improve the early detection of prostate cancer...
  44. ncbi request reprint Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis
    Rohit 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...
  45. ncbi request reprint Alpha-methylacyl-CoA racemase protein expression is associated with the degree of differentiation in breast cancer using quantitative image analysis
    Agnieszka 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...
  46. ncbi request reprint Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer
    Rohit Mehra
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Mod Pathol 20:538-44. 2007
    ....
  47. ncbi request reprint Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer
    Jindan 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...