Research Topics
Genomes and Genes | Li Xuan QinSummaryAffiliation: Memorial Sloan-Kettering Cancer Center Country: USA Publications
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Publications
Evaluation of methods for oligonucleotide array data via quantitative real-time PCRLi Xuan Qin
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
BMC Bioinformatics 7:23. 2006..An advantage of our approach over spike-in studies is that methods are validated on a real dataset that was collected to address a scientific question...
The clustering of regression models method with applications in gene expression dataLi Xuan Qin
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
Biometrics 62:526-33. 2006..The proposed methodology was applied to two microarray data sets, one from a breast cancer study and the other from a yeast cell cycle study...- Normalization method for transcriptional studies of heterogeneous samples--simultaneous array normalization and identification of equivalent expressionLi Xuan Qin
Memorial Sloan Kettering Cancer Center
Stat Appl Genet Mol Biol 8:Article 10. 2009..Empirical illustration of the proposed method is provided using a liposarcoma study from MSKCC to identify genes differentially expressed between normal fat tissue versus liposarcoma tissue samples... - Predicting outcome by growth rate of locally recurrent retroperitoneal liposarcoma: the one centimeter per month ruleJames O Park
Soft Tissue Sarcoma Program, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Ann Surg 250:977-82. 2009..To identify the prognostic variables that predict disease-specific survival and second local recurrence-free survival in patients with recurrent retroperitoneal liposarcoma so as to guide clinical management... 
Differentially expressed genes in window trials are influenced by the wound-healing process: lessons learned from a pilot study with anastrozoleMary Morrogh
Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
J Surg Res 176:121-32. 2012....- A postoperative nomogram for local recurrence risk in extremity soft tissue sarcomas after limb-sparing surgery without adjuvant radiationOren Cahlon
Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Ann Surg 255:343-7. 2012..To develop a nomogram based on clinicopathologic factors to quantify the risk of local recurrence (LR) after limb-sparing surgery without adjuvant radiation (RT)... - CD133 and CD44 are universally overexpressed in GIST and do not represent cancer stem cell markersJunwei Chen
Department of Pathology, Memorial Sloan Kettering Cancer Center, NY, USA
Genes Chromosomes Cancer 51:186-95. 2012..Our results show that CD133 and CD44 are universally expressed in GIST, and may represent a lineage rather than a cancer stem cell marker... - Do radiation-associated soft tissue sarcomas have the same prognosis as sporadic soft tissue sarcomas?Rebecca A Gladdy
Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Howard 1209, New York, NY 10065, USA
J Clin Oncol 28:2064-9. 2010..DSS in patients with primary RAS is significantly worse compared with sporadic STS independent of sarcoma histologic type... - Dermatofibrosarcoma protuberans (DFSP): predictors of recurrence and the use of systemic therapyRyan C Fields
Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
Ann Surg Oncol 18:328-36. 2011..We examine clinicopathologic factors associated with disease-free survival (DFS) in patients with primary and recurrent DFSP and evaluate responses to multimodality therapy... - Improved testing for microsatellite instability in colorectal cancer using a simplified 3-marker assayIyare Esemuede
Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
Ann Surg Oncol 17:3370-8. 2010..However, the optimal assay for MSI status is unknown. We have evaluated a simplified 3-marker assay for MSI and compared it with the 5-marker (NCI) assay to see if technical variations in MSI testing are important... - Oncologic outcomes of sporadic, neurofibromatosis-associated, and radiation-induced malignant peripheral nerve sheath tumorsJennifer LaFemina
Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
Ann Surg Oncol 20:66-72. 2013..It is controversial whether patients with NF1-associated MPNST have worse outcomes. We investigated the prognostic significance of sporadic, NF1-associated, and RT-induced MPNST... - Identification of unique MEK-dependent genes in GNAQ mutant uveal melanoma involved in cell growth, tumor cell invasion, and MEK resistanceGrazia Ambrosini
Laboratory of New Drug Development and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York 10065, USA
Clin Cancer Res 18:3552-61. 2012.... - Perioperative chemotherapy in patients undergoing pulmonary resection for metastatic soft-tissue sarcoma of the extremity : a retrospective analysisRobert J Canter
Division of Surgical Oncology, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
Cancer 110:2050-60. 2007..To the authors' knowledge, few studies to date have examined the effect of chemotherapy in patients undergoing pulmonary resection for metastatic STS of the extremity... - Expression profiling of liposarcoma yields a multigene predictor of patient outcome and identifies genes that contribute to liposarcomagenesisRyan M Gobble
Department of Surgery, Sarcoma Disease Management Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
Cancer Res 71:2697-705. 2011.... - Copy number losses define subgroups of dedifferentiated liposarcoma with poor prognosis and genomic instabilityAimee M Crago
Sarcoma Disease Management Program, Department of Surgery, Bioinformatics Core, Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
Clin Cancer Res 18:1334-40. 2012..This study sought to identify copy number alterations (CNA) associated with dedifferentiation of WDLS, with DDLS morphology, and with patient outcomes... - A synovial sarcoma-specific preoperative nomogram supports a survival benefit to ifosfamide-based chemotherapy and improves risk stratification for patientsRobert J Canter
Sarcoma Disease Management Program, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10022, USA
Clin Cancer Res 14:8191-7. 2008..To identify prognostic factors related to outcome in 255 patients with synovial sarcoma and to construct a preoperative nomogram to predict the risk of disease-specific death... - Why do patients with low-grade soft tissue sarcoma die?Robert J Canter
Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Ann Surg Oncol 15:3550-60. 2008..The patterns of failure and mechanisms of sarcoma-specific death are poorly characterized among the minority of patients with low-grade soft tissue sarcoma (STS) who succumb to disease... - Phase II study of sorafenib in patients with metastatic or recurrent sarcomasRobert G Maki
Melanoma Sarcoma Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Howard 909, New York, NY 10065, USA
J Clin Oncol 27:3133-40. 2009..Further evaluation of sorafenib in these and possibly other sarcoma subtypes appears warranted, presumably in combination with cytotoxic or kinase-specific agents... - Identification and validation of a gene expression signature that predicts outcome in adult men with germ cell tumorsJames E Korkola
Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, USA
J Clin Oncol 27:5240-7. 2009..Currently, patients are risk-stratified on the basis of clinical presentation and serum tumor markers. The introduction of molecular markers could improve outcome prediction... - Reduced risk of secondary leukemia with fewer cycles of dose-intensive induction chemotherapy in patients with neuroblastomaBrian H Kushner
Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
Pediatr Blood Cancer 53:17-22. 2009..We report a prospective study of secondary leukemia (SL)/myelodysplastic syndrome (MDS) in neuroblastoma (NB) patients treated with > or =5 cycles of dose-intensive chemotherapy... - A novel survival-based tissue microarray of pancreatic cancer validates MUC1 and mesothelin as biomarkersJordan M Winter
Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America corrected
PLoS ONE 7:e40157. 2012..To help researchers sort through the maze of biomarker data, a compendium of ∼2500 published candidate biomarkers in PDA was compiled (PLoS Med, 2009. 6(4) p. e1000046)... - A microRNA survival signature (MiSS) for advanced ovarian cancerKarin K Shih
Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
Gynecol Oncol 121:444-50. 2011..We tested the hypothesis that miRNA expression is associated with overall survival in advanced ovarian cancer... - The cyclin-dependent kinase inhibitor flavopiridol potentiates the effects of topoisomerase I poisons by suppressing Rad51 expression in a p53-dependent mannerGrazia Ambrosini
Laboratory of New Drug Development, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Cancer Res 68:2312-20. 2008..In conclusion, after DNA damage by Topo I poisons, flavopiridol targets homologous recombination through a p53-dependent down-regulation of Rad51, resulting in enhancement of apoptosis... - Cadherin-catenin complex dissociation in lobular neoplasia of the breastMary Morrogh
Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, 300 E 66th St, New York, NY 10065, USA
Breast Cancer Res Treat 132:641-52. 2012..Decreasing membranous catenin expression in tandem with increasing levels of TWIST across the spectrum of lobular lesions suggests that CCC dissociation is a progressive process... - Differential impact of high-dose cyclophosphamide, topotecan, and vincristine in clinical subsets of patients with chemoresistant neuroblastomaBrian H Kushner
Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Cancer 116:3054-60. 2010.... - Pancreatic cyst fluid protein expression profiling for discriminating between serous cystadenoma and intraductal papillary mucinous neoplasmPeter J Allen
Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10021, USA
Ann Surg 250:754-60. 2009.... - An Empirical Evaluation of Normalization Methods for MicroRNA Arrays in a Liposarcoma StudyLi Xuan Qin
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
Cancer Inform 12:83-101. 2013..However, these assumptions are not necessarily appropriate for microRNA expression arrays because they consist of only a few hundred genes and a reasonable fraction of them are anticipated to have disease relevance... - Cixutumumab and temsirolimus for patients with bone and soft-tissue sarcoma: a multicentre, open-label, phase 2 trialGary K Schwartz
Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA Electronic address
Lancet Oncol 14:371-82. 2013.... - Enteric neural crest differentiation in ganglioneuromas implicates Hedgehog signaling in peripheral neuroblastic tumor pathogenesisTimothy R Gershon
Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
PLoS ONE 4:e7491. 2009.... - KDR activating mutations in human angiosarcomas are sensitive to specific kinase inhibitorsCristina R Antonescu
Department of Pathology, Memorial Sloan Kettering Cancer, New York, New York 10065, USA
Cancer Res 69:7175-9. 2009..These data provide a basis for the activity of vascular endothelial growth factor receptor-directed therapy in the treatment of primary and radiation-induced AS... - MDM2 gene amplification is correlated to tumor progression but not to the presence of SNP309 or TP53 mutational status in primary colorectal cancersAnn Forslund
Memorial Sloan Kettering Cancer Center, Department of Surgery, Colorectal Surgery Service, New York, NY 10021, USA
Mol Cancer Res 6:205-11. 2008..Our results suggest that MDM2 is a promising target for this type of cancer therapy in a substantial subgroup of colorectal cancers... - Carbonic anhydrase IX expression in clear cell renal cell carcinoma: an immunohistochemical study comparing 2 antibodiesHikmat A Al-Ahmadie
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Am J Surg Pathol 32:377-82. 2008..Therefore, similar to the clone M75, NB100-417 can be used as a diagnostic and potentially a prognostic marker in CRCC, with the advantage of its commercial availability... - gamma-Secretase inhibitors abrogate oxaliplatin-induced activation of the Notch-1 signaling pathway in colon cancer cells resulting in enhanced chemosensitivityRaymond D Meng
Department of Medicine, Division of Solid Tumor Oncology, Laboratory of New Drug Development, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
Cancer Res 69:573-82. 2009..Therefore, combining GSIs with chemotherapy may represent a novel approach for treating metastatic colon cancers by mitigating the development of chemoresistance... - Empirical evaluation of data transformations and ranking statistics for microarray analysisLi-Xuan Qin
Department of Biostatistics, University of Washington, F-600 Health Sciences Building 1705 NE Pacific Street, Box 357232, Seattle, WA 98195, USA
Nucleic Acids Res 32:5471-9. 2004..Finally, we find that choice of image analysis software can also substantially influence experimental conclusions... - Standardizing global gene expression analysis between laboratories and across platformsTheodore Bammler
Nat Methods 2:351-6. 2005..These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used...