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Yidong Chen

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Oligonucleotide Array Sequence Analysis

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Fei Gu; Tim H M Huang; Yi-Wen Huang; E Lynette Kizer; Juan C Roa; Mark S Doderer; Paul J Goodfellow; Yidong Chen
CMS: A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers.
Patricia Sanchez Diaz; Mimi C Tan; Gail Tomlinson; Dong Yue; Judy C Chang; Hung-I Harry Chen; Yidong Chen; Tzu-Hung Hsiao; Yufei Huang; Jaclyn Y Hung
De-Regulated MicroRNAs in Pediatric Cancer Stem Cells Target Pathways Involved in Cell Proliferation, Cell Cycle and Development.
Mario Flores; Tzu-Hung Hsiao; Yufei Huang; Yu-Chiao Chiu; Eric Y Chuang; Yidong Chen
Gene regulation, modulation, and their applications in gene expression data analysis.

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2013: Fei Gu; Tim H M Huang; Yi-Wen Huang; E Lynette Kizer; Juan C Roa; Mark S Doderer; Paul J Goodfellow; Yidong Chen
CMS: A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers.
PloS one 2013;8(4):e60980.
2013: Patricia Sanchez Diaz; Mimi C Tan; Gail Tomlinson; Dong Yue; Judy C Chang; Hung-I Harry Chen; Yidong Chen; Tzu-Hung Hsiao; Yufei Huang; Jaclyn Y Hung
De-Regulated MicroRNAs in Pediatric Cancer Stem Cells Target Pathways Involved in Cell Proliferation, Cell Cycle and Development.
PloS one 2013;8(4):e61622.
2013: Mario Flores; Tzu-Hung Hsiao; Yufei Huang; Yu-Chiao Chiu; Eric Y Chuang; Yidong Chen
Gene regulation, modulation, and their applications in gene expression data analysis.
Advances in bioinformatics 2013;2013():360678.
2012: Fang-Han Hsu; Erchin Serpedin; Yidong Chen; Edward R Dougherty
Evaluating dynamic effects of copy number alterations on gene expression using a single transcription model.
IEEE transactions on bio-medical engineering 2012;59(10):2726-36.
2012: C A Derosa; Albert Dobi; Bungo Furusato; David G McLeod; Martin E Nau; Yidong Chen; Lakshmi Ravindranath; Isabell A Sesterhenn; Syed Shaheduzzaman; M Siefert; Vasantha Srikantan; Shiv Srivastava; Maryanne Vahey; Z Wang; T Werner; D Young; M Seifert; Gyorgy Petrovics
Elevated osteonectin/SPARC expression in primary prostate cancer predicts metastatic progression.
Prostate cancer and prostatic diseases 2012;15(2):150-6.
2012: Stephanie Roessler; Zhao-You Tang; Snorri S Thorgeirsson; Robert Walker; Qing-Hai Ye; Xuelian Zhao; Anuradha Budhu; Yidong Chen; Ping He; Kent W Hunter; Junfang Ji; Hu-Liang Jia; Ezhou Lori Long; Paul S Meltzer; Lun-Xiu Qin; Xin Wei Wang
Integrative genomic identification of genes on 8p associated with hepatocellular carcinoma progression and patient survival.
Gastroenterology 2012;142(4):957-966.e12.
2012: Stephanie N Zimmer; Uthra Suresh; Qing Zhou; Ting Zhou; Alexander bishop; Yidong Chen; Claudia Day; Bijal P Karia; Marsha C Kinney; Andrew L Kung; Madeleine E Lemieux; Vivienne Rebel
Mice heterozygous for CREB binding protein are hypersensitive to γ-radiation and invariably develop myelodysplastic/myeloproliferative neoplasm.
Experimental hematology 2012;40(4):295-306.e5.
2012: J Saadi Imam; Subbarayalu Panneerdoss; Alexander Pertsemlidis; Jason R Plyler; Suresh Prajapati; Jennifer Rebeles; Gail Tomlinson; Ratna K Vadlamudi; Behyar Zoghi; Hima Bansal; Sanjay Bansal; Russell Broaddus; Kalyan C Buddavarapu; Yao-Fu Chang; Hung-I Harry Chen; Yidong Chen; Jeffrey Dome; Peter Hornsby; Manjeet K Rao
Genomic loss of tumor suppressor miRNA-204 promotes cancer cell migration and invasion by activating AKT/mTOR/Rac1 signaling and actin reorganization.
PloS one 2012;7(12):e52397.
2012: Dong Yue; Yidong Chen; Maozu Guo; Yufei Huang
A Bayesian decision fusion approach for microRNA target prediction.
BMC genomics 2012;13 Suppl 8():S13.
2012: Fang-Han Hsu; Erchin Serpedin; Alexander J R Bishop; Edward R Dougherty; Tzu-Hung Hsiao; Yidong Chen
Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer.
BMC genomics 2012;13 Suppl 6():S13.
2012: Ranadip Pal; Yufei Huang; Yidong Chen
Selected articles from the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'2011).
BMC genomics 2012;13 Suppl 6():S1.
2012: Mark S Doderer; Uthra Suresh; Zachry Anguiano; Alexander J R Bishop; Ravi Dashnamoorthy; Yidong Chen
Pathway Distiller - multisource biological pathway consolidation.
BMC genomics 2012;13 Suppl 6():S18.
2012: Subbarayalu Panneerdoss; Gunapala Shetty; Huizhen Wang; Kalyan C Buddavarapu; Yao-Fu Chang; Hung-I Harry Chen; Yidong Chen; T Rajendra Kumar; Manjeet K Rao
Androgen-responsive microRNAs in mouse Sertoli cells.
PloS one 2012;7(7):e41146.
2012: J Keith Killian; William Smith; Robert L Walker; Sven Bilke; Yidong Chen; Robert Cornelison; Sean Davis; Paul S Meltzer
Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples.
Methods in molecular biology (Clifton, N.J.) 2012;823():107-18.
2012: Fang-Han Hsu; Erchin Serpedin; Yidong Chen; Edward R Dougherty
Stochastic modeling of the relationship between copy number and gene expression based on transcriptional logic.
IEEE transactions on bio-medical engineering 2012;59(1):272-80.
2011: S Sharad; A Srivastava; S Ravulapalli; P Parker; Yidong Chen; H Li; Gyorgy Petrovics; Albert Dobi
Prostate cancer gene expression signature of patients with high body mass index.
Prostate cancer and prostatic diseases 2011;14(1):22-9.
2011: Brian P Rubin; Koichi Nishijo; Hung-I Harry Chen; Xiaolan Yi; David P Schuetze; Ranadip Pal; Suresh Prajapati; Jinu Abraham; Benjamin R Arenkiel; Qing-Rong Chen; Sean Davis; Amanda T McCleish; Mario R Capecchi; Joel Michalek; Lee Ann Zarzabal; Javed Khan; Zhongxin Yu; David M Parham; Frederic G Barr; Paul S Meltzer; Yidong Chen; Charles Keller
Evidence for an unanticipated relationship between undifferentiated pleomorphic sarcoma and embryonal rhabdomyosarcoma.
Cancer cell 2011;19(2):177-91.
2011: Jia Meng; Jianqiu Michelle Zhang; Yidong Chen; Yufei Huang
Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks.
Proteome science 2011;9 Suppl 1():S9.
2011: Fang-Han Hsu; Chi-Cheng Huang; Liang-Chuan Lai; Mong-Hsun Tsai; Shih-Hsin Tu; Hung-I H Chen; Eric Y Chuang; Yidong Chen
A model-based circular binary segmentation algorithm for the analysis of array CGH data.
BMC research notes 2011;4():394.
2011: Manuel S Valenzuela; Yidong Chen; Sean Davis; Fan Yang; Robert L Walker; Sven Bilke; John Lueders; Melvenia M Martin; Mirit I Aladjem; Pierre P Massion; Paul S Meltzer
Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences.
PloS one 2011;6(5):e17308.
2011: Ravi Dashnamoorthy; Yidong Chen; Bijal Karia; Adam Brown; Ting Ting Gu; Jie Li; Mark S Carey; Bryan T Hennessy; Alexander bishop
14-3-3 σ expression effects G2/M response to oxygen and correlates with ovarian cancer metastasis.
PloS one 2011;6(1):e15864.
2010: D Hawksworth; Lakshmi Ravindranath; Yidong Chen; Bungo Furusato; Isabell A Sesterhenn; David G McLeod; Shiv Srivastava; Gyorgy Petrovics
Overexpression of C-MYC oncogene in prostate cancer predicts biochemical recurrence.
Prostate cancer and prostatic diseases 2010;13(4):311-5.
2010: Bungo Furusato; Shyh-Han Tan; D Young; Albert Dobi; Chen Sun; A A Mohamed; R Thangapazham; Yidong Chen; G McMaster; T Sreenath; Gyorgy Petrovics; David G McLeod; Shiv Srivastava; Isabell A Sesterhenn
ERG oncoprotein expression in prostate cancer: clonal progression of ERG-positive tumor cells and potential for ERG-based stratification.
Prostate cancer and prostatic diseases 2010;13(3):228-37.
2010: Hui Liu; Dong Yue; Lin Zhang; Yidong Chen; Shou-Jiang Gao; Yufei Huang
A Bayesian approach for identifying miRNA targets by combining sequence prediction and gene expression profiling.
BMC genomics 2010;11 Suppl 3():S12.
2010: Jia Meng; Mingzhu Lu; Yidong Chen; Shou-Jiang Gao; Yufei Huang
Robust inference of the context specific structure and temporal dynamics of gene regulatory network.
BMC genomics 2010;11 Suppl 3():S11.
2010: Hui Liu; Dong Yue; Yidong Chen; Shou-Jiang Gao; Yufei Huang
Improving performance of mammalian microRNA target prediction.
BMC bioinformatics 2010;11():476.
2009: Junfang Ji; Jiong Shi; Anuradha Budhu; Zhipeng Yu; Marshonna Forgues; Stephanie Roessler; Stefan Ambs; Yidong Chen; Paul S Meltzer; Carlo M Croce; Lun-Xiu Qin; Kwan Man; Chung-Mau Lo; Joyce Lee; Irene O L Ng; Jia Fan; Zhao-You Tang; Hui-Chuan Sun; Xin Wei Wang
MicroRNA expression, survival, and response to interferon in liver cancer.
The New England journal of medicine 2009;361(15):1437-47.
2009: J Keith Killian; Sven Bilke; Sean Davis; Robert L Walker; Michael Scott Killian; Erich B Jaeger; Yidong Chen; Jason Hipp; Stefania Pittaluga; Mark Raffeld; Robert Cornelison; William Smith; Marina Bibikova; Jian-Bing Fan; Michael R Emmert-Buck; Elaine S Jaffe; Paul S Meltzer
Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome.
Cancer research 2009;69(3):758-64.
2009: Stacie K Loftus; Anthony Antonellis; Ivana Matera; Gabriel Renaud; Laura L Baxter; Duncan Reid; Tyra G Wolfsberg; Yidong Chen; Chenwei Wang; Megana K Prasad; Seneca L Bessling; Andy McCallion; Eric Green; Dorothy C Bennett; William J Pavan
Gpnmb is a melanoblast-expressed, MITF-dependent gene.
Pigment cell & melanoma research 2009;22(1):99-110.
2008: Yuelin Zhu; Sean Davis; Robert Stephens; Paul S Meltzer; Yidong Chen
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.
Bioinformatics (Oxford, England) 2008;24(23):2798-800.
2008: Hung-I Harry Chen; Fang-Han Hsu; Yuan Jiang; Mong-Hsun Tsai; Pan-Chyr Yang; Paul S Meltzer; Eric Y Chuang; Yidong Chen
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.
Bioinformatics (Oxford, England) 2008;24(16):1749-56.
2008: Taro Yamashita; Marshonna Forgues; Wei Wang; Jin Woo Kim; Qinghai Ye; Huliang Jia; Anuradha Budhu; Krista A Zanetti; Yidong Chen; Lun-Xiu Qin; Zhao-You Tang; Xin Wei Wang
EpCAM and alpha-fetoprotein expression defines novel prognostic subtypes of hepatocellular carcinoma.
Cancer research 2008;68(5):1451-61.
2008: Jordi Camps; Marian Grade; Quang Tri Nguyen; Patrick Hörmann; Sandra Becker; Amanda B Hummon; Virginia Rodriguez; Settara C Chandrasekharappa; Yidong Chen; Michael J Difilippantonio; Heinz Becker; B Michael Ghadimi; Thomas Ried
Chromosomal breakpoints in primary colon cancer cluster at sites of structural variants in the genome.
Cancer research 2008;68(5):1284-95.
2008: Shixia Huang; Yidong Chen; Katrina Podsypanina; Yi Li
Comparison of expression profiles of metastatic versus primary mammary tumors in MMTV-Wnt-1 and MMTV-Neu transgenic mice.
Neoplasia (New York, N.Y.) 2008;10(2):118-24.
2008: Sally A Amundson; Khanh T Do; Lisa C Vinikoor; R Anthony Lee; Christine A Koch-Paiz; Jaeyong Ahn; Mark Reimers; Yidong Chen; Dominic A Scudiero; John N Weinstein; Jeffrey M. Trent; Michael Bittner; Paul S Meltzer; Albert J Fornace
Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen.
Cancer research 2008;68(2):415-24.
2007: Youngmi Ji; Nijaguna B Prasad; Elizabeth A Novotny; Sukhbir Kaur; Abdel G Elkahloun; Yidong Chen; Rui-Zhu Zhang; Mon-Li Chu; Sunita K Agarwal; Stephen J Marx; Francis S Collins; Settara C Chandrasekharappa
Mouse embryo fibroblasts lacking the tumor suppressor menin show altered expression of extracellular matrix protein genes.
Molecular cancer research : MCR 2007;5(10):1041-51.
2007: Syed Shaheduzzaman; Anu Vishwanath; Bungo Furusato; Jennifer Cullen; Yidong Chen; Lionel Bañez; Martin E Nau; Lakshmi Ravindranath; Kee-Hong Kim; Ahmed Mohammed; Yidong Chen; Mathias Ehrich; Vasantha Srikantan; Isabell A Sesterhenn; David McLeod; Maryanne Vahey; Gyorgy Petrovics; Albert Dobi; Shiv Srivastava
Silencing of Lactotransferrin expression by methylation in prostate cancer progression.
Cancer biology & therapy 2007;6(7):1088-95.
2007: Virginia Rodriguez; Yidong Chen; Abdel G Elkahloun; Amalia Dutra; Evgenia Pak; Settara C Chandrasekharappa
Chromosome 8 BAC array comparative genomic hybridization and expression analysis identify amplification and overexpression of TRMT12 in breast cancer.
Genes, chromosomes & cancer 2007;46(7):694-707.
2007: Anuradha Budhu; Yidong Chen; Jin Woo Kim; Marshonna Forgues; Kristoffer Valerie; Curtis C Harris; Xin Wei Wang
Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins.
Carcinogenesis 2007;28(7):1552-60.
2007: Hu-Liang Jia; Qing-Hai Ye; Lun-Xiu Qin; Anuradha Budhu; Marshonna Forgues; Yidong Chen; Yin-Kun Liu; Hui-Chuan Sun; Lu Wang; Hua-zhong Lu; Fang Shen; Zhao-You Tang; Xin Wei Wang
Gene expression profiling reveals potential biomarkers of human hepatocellular carcinoma.
Clinical cancer research : an official journal of the American Association for Cancer Research 2007;13(4):1133-9.
2007: Arne Hansen; Yidong Chen; Jason M Inman; Quang N Phan; Zhi-Qing Qi; Charlie C Xiang; Miklós Palkovits; Natasha Cherman; Sergei A Kuznetsov; Pamela Robey; Eva Mezey; Michael J Brownstein
Sensitive and specific method for detecting G protein-coupled receptor mRNAs.
Nature methods 2007;4(1):35-7.
2006: Shixia Huang; Katrina Podsypanina; Yidong Chen; Weiyan Cai; Anna Tsimelzon; Susan G Hilsenbeck; Yi Li
Wnt-1 is dominant over neu in specifying mammary tumor expression profiles.
Technology in cancer research & treatment 2006;5(6):565-71.
2006: Thomas A Dunn; Shenglin Chen; Dennis A Faith; Jessica L Hicks; Elizabeth A Platz; Yidong Chen; Charles M Ewing; Jurga Sauvageot; William B Isaacs; Angelo M DeMarzo; Jun Luo
A novel role of myosin VI in human prostate cancer.
The American journal of pathology 2006;169(5):1843-54.
2006: Anuradha Budhu; Marshonna Forgues; Qing-Hai Ye; Hu-Liang Jia; Ping He; Krista A Zanetti; Udai S Kammula; Yidong Chen; Lun-Xiu Qin; Zhao-You Tang; Xin Wei Wang
Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment.
Cancer cell 2006;10(2):99-111.
2006: Idhaliz Flores; Elizabeth Rivera; Spyro Mousses; Yidong Chen; Ester Rozenblum
Identification of molecular markers for endometriosis in blood lymphocytes by using deoxyribonucleic acid microarrays.
Fertility and sterility 2006;85(6):1676-83.
2006: Stefan R Hansson; Yidong Chen; Jana Brodszki; M Chen; Edgar Hernandez-Andrade; J M Inman; Olga A Kozhich; Irene Larsson; Karel Marsál; P Medstrand; C C Xiang; M J Brownstein
Gene expression profiling of human placentas from preeclamptic and normotensive pregnancies.
Molecular human reproduction 2006;12(3):169-79.
2006: Mong-Hsun Tsai; Xinbin Chen; Gadisetti V R Chandramouli; Yidong Chen; H Yan; S Zhao; P Keng; H L Liber; C Norman Coleman; James B Mitchell; Eric Y Chuang
Transcriptional responses to ionizing radiation reveal that p53R2 protects against radiation-induced mutagenesis in human lymphoblastoid cells.
Oncogene 2006;25(4):622-32.
2006: Jianping Hua; yoganand balagurunathan; Yidong Chen; James Lowey; Michael Bittner; Zixiang Xiong; Edward Suh; Edward R Dougherty
Normalization benefits microarray-based classification.
EURASIP journal on bioinformatics & systems biology 2006;():43056.
2006: Gregory E Crawford; Ingeborg E Holt; James Whittle; Bryn D Webb; Denise Tai; Sean Davis; Elliott H Margulies; Yidong Chen; John A Bernat; David Ginsburg; Daixing Zhou; Shujun Luo; thomas vasicek; Mark J Daly; Tyra G Wolfsberg; Francis S Collins
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).
Genome research 2006;16(1):123-31.
2005: Kristin Baird; Sean Davis; Cristina R Antonescu; Ursula L Harper; Robert L Walker; Yidong Chen; Arthur A Glatfelter; Paul H Duray; Paul S Meltzer
Gene expression profiling of human sarcomas: insights into sarcoma biology.
Cancer research 2005;65(20):9226-35.
2005: Yidong Chen; Paul S Meltzer
Gene expression analysis via multidimensional scaling.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2005;Chapter 7():Unit 7.11.
2005: Gyorgy Petrovics; Aijun Liu; Syed Shaheduzzaman; Bungo Furusato; Bungo Furasato; Chen Sun; Yidong Chen; Martin E Nau; Lakshmi Ravindranath; Yidong Chen; Albert Dobi; Vasantha Srikantan; Isabell A Sesterhenn; David G McLeod; Maryanne Vahey; Judd W Moul; Shiv Srivastava
Frequent overexpression of ETS-related gene-1 (ERG1) in prostate cancer transcriptome.
Oncogene 2005;24(23):3847-52.
2005: Shixia Huang; Yi Li; Yidong Chen; Katrina Podsypanina; Mario Chamorro; Adam B Olshen; Kartiki V Desai; Anne Tann; David Petersen; Jeffrey E Green; Harold Varmus
Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice.
Genome biology 2005;6(10):R84.
2004: Sanju Attoor; Edward R Dougherty; Yidong Chen; Michael Bittner; Jeffrey M. Trent
Which is better for cDNA-microarray-based classification: ratios or direct intensities.
Bioinformatics (Oxford, England) 2004;20(16):2513-20.
2004: Pia Huusko; Damaris Ponciano-Jackson; Maija Wolf; Jeff Kiefer; David Azorsa; Sukru Tuzmen; Don Weaver; Christiane Robbins; Tracy Y Moses; Minna Allinen; Sampsa Hautaniemi; Yidong Chen; Abdel G Elkahloun; Mark Basik; G Steven Bova; Lukas Bubendorf; Alessandro Lugli; Guido Sauter; Johanna Schleutker; Hilmi Ozcelik; Sabine Elowe; Tony Pawson; Jeffrey M. Trent; John D Carpten; Olli Kallioniemi; Spyro Mousses
Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer.
Nature genetics 2004;36(9):979-83.
2004: yoganand balagurunathan; Naisyin Wang; Edward R Dougherty; Danh V Nguyen; Yidong Chen; Michael Bittner; Jeffrey M. Trent; Raymond Carroll
Noise factor analysis for cDNA microarrays.
Journal of biomedical optics 2004;9(4):663-78.
2004: Todd J Suscovich; Mini Paulose-Murphy; Jason Harlow; Yidong Chen; Seddon Y Thomas; Tiffany Mellott; Bruce D Walker; David T Scadden; Steven L Zeichner; Christian Brander
Defective immune function of primary effusion lymphoma cells is associated with distinct KSHV gene expression profiles.
Leukemia & lymphoma 2004;45(6):1223-38.
2004: Maija Wolf; Spyro Mousses; Sampsa Hautaniemi; Ritva Karhu; Pia Huusko; Minna Allinen; Abdel G Elkahloun; Outi Monni; Yidong Chen; Anne Kallioniemi; Olli Kallioniemi
High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression.
Neoplasia (New York, N.Y.) 2004;6(3):240-7.
2004: Ashani T Weeraratna; Dorothea Becker; Kristen M Carr; Paul H Duray; Kevin P Rosenblatt; Sherry Yang; Yidong Chen; Michael Bittner; Robert L Strausberg; Gregory J Riggins; Urs Wagner; Olli Kallioniemi; Jeffrey M. Trent; Patrice J Morin; Paul S Meltzer
Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome.
Oncogene 2004;23(12):2264-74.
2004: Jin Woo Kim; Qinghai Ye; Marshonna Forgues; Yidong Chen; Anuradha Budhu; Jessica Sime; Lorne J Hofseth; Rashmi Kaul; Xin Wei Wang
Cancer-associated molecular signature in the tissue samples of patients with cirrhosis.
Hepatology (Baltimore, Md.) 2004;39(2):518-27.
2003: Heather Cunliffe; Markus Ringnér; Sven Bilke; Robert L Walker; Jennifer M Cheung; Yidong Chen; Paul S Meltzer
The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles.
Cancer research 2003;63(21):7158-66.
2003: Roberto Bomprezzi; Markus Ringnér; Seungchan Kim; Michael Bittner; Javed Khan; Yidong Chen; Abdel G Elkahloun; Aimee Yu; Bibiana Bielekova; Paul S Meltzer; Roland Martin; Henry McFarland; Jeffrey M. Trent
Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease.
Human molecular genetics 2003;12(17):2191-9.
2003: Paul M Yen; Xu Feng; Frédéric Flamant; Yidong Chen; Robert L Walker; Roy E Weiss; Olivier Chassande; Jacques Samarut; Samuel Refetoff; Paul S Meltzer
Effects of ligand and thyroid hormone receptor isoforms on hepatic gene expression profiles of thyroid hormone receptor knockout mice.
EMBO reports 2003;4(6):581-7.
2003: Qing-Hai Ye; Lun-Xiu Qin; Marshonna Forgues; Ping He; Jin Woo Kim; Amy C Peng; Richard Simon; Yan Li; Ana I Robles; Yidong Chen; Zeng-Chen Ma; Zhi-Quan Wu; Sheng-Long Ye; Yin-Kun Liu; Zhao-You Tang; Xin Wei Wang
Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning.
Nature medicine 2003;9(4):416-23.
2003: Ingrid Hedenfalk; Markus Ringner; Amir Ben-Dor; Zohar Yakhini; Yidong Chen; Gunilla Chebil; Robert Ach; Niklas Loman; Håkan Olsson; Paul Meltzer; Ake Borg; Jeffrey M. Trent
Molecular classification of familial non-BRCA1/BRCA2 breast cancer.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(5):2532-7.
2003: Charlie C Xiang; Mei Chen; Olga A Kozhich; Quang N Phan; Jason M Inman; Yidong Chen; Michael J Brownstein
Probe generation directly from small numbers of cells for DNA microarray studies.
BioTechniques 2003;34(2):386-8, 390, 392-3.
2002: Yao-Yu Eric Chuang; Yidong Chen; V R Chandramouli; John A Cook; Deborah Coffin; Mong-Hsun Tsai; William DeGraff; Hailing Yan; Shuping Zhao; Angelo Russo; Edison Liu; James B Mitchell
Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells.
Cancer research 2002;62(21):6246-54.
2002: Susanne V Allander; PETER ILLEI; Yidong Chen; Cristina R Antonescu; Mike Bittner; Marc Ladanyi; Paul S Meltzer
Expression profiling of synovial sarcoma by cDNA microarrays: association of ERBB2, IGFBP2, and ELF3 with epithelial differentiation.
The American journal of pathology 2002;161(5):1587-95.
2002: Yidong Chen; Vishnu Kamat; Edward R Dougherty; Michael Bittner; Paul S Meltzer; Jeffrey M. Trent
Ratio statistics of gene expression levels and applications to microarray data analysis.
Bioinformatics (Oxford, England) 2002;18(9):1207-15.
2002: yoganand balagurunathan; Edward R Dougherty; Yidong Chen; Michael Bittner; Jeffrey M. Trent
Simulation of cDNA microarrays via a parameterized random signal model.
Journal of biomedical optics 2002;7(3):507-23.
2002: Charlie C Xiang; Olga A Kozhich; Mei Chen; Jason M Inman; Quang N Phan; Yidong Chen; Michael J Brownstein
Amine-modified random primers to label probes for DNA microarrays.
Nature biotechnology 2002;20(7):738-42.
2002: Jun Luo; Thomas Dunn; Charles M Ewing; Jurga Sauvageot; Yidong Chen; Jeffrey M. Trent; William B Isaacs
Gene expression signature of benign prostatic hyperplasia revealed by cDNA microarray analysis.
The Prostate 2002;51(3):189-200.
2002: Stacie K Loftus; Denise M Larson; Laura L Baxter; Anthony Antonellis; Yidong Chen; Xufeng Wu; Yuan Jiang; Michael Bittner; John A Hammer; William J Pavan
Mutation of melanosome protein RAB38 in chocolate mice.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(7):4471-6.
2002: Mattias Wahde; Gregory T Klus; Michael Bittner; Yidong Chen; Zoltan Szallasi
Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices.
Bioinformatics (Oxford, England) 2002;18(3):389-94.
2002: Seungchan Kim; Edward R Dougherty; Junior Barrera; Yidong Chen; Michael Bittner; Jeffrey M. Trent
Strong feature sets from small samples.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(1):127-46.
2002: Edward R Dougherty; Junior Barrera; Marcel Brun; Seungchan Kim; Roberto M Cesar; Yidong Chen; Michael Bittner; Jeffrey M. Trent
Inference from clustering with application to gene-expression microarrays.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(1):105-26.
2001: Susanne V Allander; Nina N Nupponen; Markus Ringnér; Galen Hostetter; G W Maher; N Goldberger; Yidong Chen; John D Carpten; Abdel G Elkahloun; Paul S Meltzer
Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile.
Cancer research 2001;61(24):8624-8.
2001: Spyro Mousses; Urs Wagner; Yidong Chen; J W Kim; Lukas Bubendorf; Michael Bittner; T Pretlow; Abdel G Elkahloun; Jane Trepel; Olli Kallioniemi
Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling.
Oncogene 2001;20(46):6718-23.
2001: Tobey J MacDonald; Kevin Brown; Bonnie LaFleur; K Peterson; Christopher Lawlor; Yidong Chen; Roger J Packer; Philip H Cogen; Dietrich A Stephan
Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease.
Nature genetics 2001;29(2):143-52.
2001: S Gruvberger; Markus Ringnér; Yidong Chen; S Panavally; Lao H Saal; M Fernö; C Peterson; Paul S Meltzer
Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns.
Cancer research 2001;61(16):5979-84.
2001: P W Ng; H Iha; Y Iwanaga; Michael Bittner; Yidong Chen; Yuan Jiang; Gerald C Gooden; Jeffrey M. Trent; Paul Meltzer; Kuan-Teh Jeang; Steven L Zeichner
Genome-wide expression changes induced by HTLV-1 Tax: evidence for MLK-3 mixed lineage kinase involvement in Tax-mediated NF-kappaB activation.
Oncogene 2001;20(33):4484-96.
2001: Gregory T Klus; N Rokaeus; Michael Bittner; Yidong Chen; Dorian Korz; Saraswati Sukumar; A Schick; Zoltan Szallasi
Down-regulation of the desmosomal cadherin desmocollin 3 in human breast cancer.
International journal of oncology 2001;19(1):169-74.
2001: Jun Luo; David Duggan; Yidong Chen; Jurga Sauvageot; Charles M Ewing; Michael Bittner; Jeffrey M. Trent; William B Isaacs
Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling.
Cancer research 2001;61(12):4683-8.
2001: Outi Monni; M Barlund; Spyro Mousses; Juha Kononen; Guido Sauter; Mervi Heiskanen; P Paavola; Kristiina Avela; Yidong Chen; Michael Bittner; Anne Kallioniemi
Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(10):5711-6.
2001: Mini Paulose-Murphy; N K Ha; C Xiang; Yidong Chen; L Gillim; Robert Yarchoan; Paul Meltzer; Michael Bittner; Jeffrey M. Trent; Steven L Zeichner
Transcription program of human herpesvirus 8 (kaposi's sarcoma-associated herpesvirus).
Journal of virology 2001;75(10):4843-53.
2001: Ingrid Hedenfalk; DJ Duggan; Yidong Chen; Michael D Radmacher; Michael Bittner; R Simon; Paul Meltzer; B Gusterson; M Esteller; Olli Kallioniemi; Benjamin S Wilfond; Ake Borg; Jeffrey M. Trent; Mark Raffeld; Zohar Yakhini; Amir Ben-Dor; Edward R Dougherty; Juha Kononen; Lukas Bubendorf; W Fehrle; S Pittaluga; S Gruvberger; Niklas Loman; Oskar T Johannsson; Håkan Olsson; Guido Sauter
Gene-expression profiles in hereditary breast cancer.
The New England journal of medicine 2001;344(8):539-48.
2001: Yidong Chen; Zohar Yakhini; Amir Ben-Dor; Edward R Dougherty; Jeffrey M. Trent; Michael Bittner
Analysis of expression patterns: the scope of the problem, the problem of scope.
Disease markers 2001;17(2):59-65.
2000: Seungchan Kim; Edward R Dougherty; Michael Bittner; Yidong Chen; K Sivakumar; Paul Meltzer; Jeffrey M. Trent
General nonlinear framework for the analysis of gene interaction via multivariate expression arrays.
Journal of biomedical optics 2000;5(4):411-24.
2000: F Forozan; Eija H Mahlamäki; Outi Monni; Yidong Chen; R Veldman; Yuan Jiang; Gerald C Gooden; Stephen Ethier; Anne Kallioniemi; Olli Kallioniemi
Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data.
Cancer research 2000;60(16):4519-25.
2000: Michael Bittner; Paul Meltzer; Yidong Chen; Yuan Jiang; E Seftor; M Hendrix; Michael D Radmacher; R Simon; Zohar Yakhini; Amir Ben-Dor; Nick Sampas; Edward R Dougherty; E Wang; F Marincola; C Gooden; J Lueders; Arthur A Glatfelter; Pam Pollock; John D Carpten; Elizabeth M Gillanders; D Leja; K Dietrich; Christian Beaudry; Michael Berens; D Alberts; V Sondak
Molecular classification of cutaneous malignant melanoma by gene expression profiling.
Nature 2000;406(6795):536-40.
2000: Maarit Bärlund; F Forozan; Juha Kononen; Lukas Bubendorf; Yidong Chen; Michael Bittner; Joachim Torhorst; Philippe Haas; christoph bucher; Guido Sauter; Olli Kallioniemi; Anne Kallioniemi
Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis.
Journal of the National Cancer Institute 2000;92(15):1252-9.
2000: Seungchan Kim; E R Dougherty; Yidong Chen; K Sivakumar; Paul Meltzer; Jeffrey M. Trent; Michael Bittner
Multivariate measurement of gene expression relationships.
Genomics 2000;67(2):201-9.
2000: Yan Su; Michael Bittner; Yidong Chen; L Tao; Y Jiang; Y Zhang; Dietrich A Stephan; Jeffrey M. Trent
Identification of tumor-suppressor genes using human melanoma cell lines UACC903, UACC903(+6), and SRS3 by comparison of expression profiles.
Molecular carcinogenesis 2000;28(2):119-27.
2000: Dietrich A Stephan; Yidong Chen; Y Jiang; L Malechek; J Z Gu; Christiane M Robbins; Michael Bittner; JA Morris; ED Carstea; Paul S Meltzer; K Adler; R Garlick; Jeffrey M. Trent; MA Ashlock
Positional cloning utilizing genomic DNA microarrays: the Niemann-Pick type C gene as a model system.
Molecular genetics and metabolism 2000;70(1):10-8.
2000: Mervi Heiskanen; Michael Bittner; Yidong Chen; Javed Khan; K E Adler; Jeffrey M. Trent; Paul S Meltzer
Detection of gene amplification by genomic hybridization to cDNA microarrays.
Cancer research 2000;60(4):799-802.
1999: Lukas Bubendorf; M Kolmer; Juha Kononen; Pasi A Koivisto; Spyro Mousses; Yidong Chen; Eija H Mahlamäki; Peter Schraml; Holger Moch; Niels Willi; Abdel G Elkahloun; T G Pretlow; Thomas C Gasser; Michael J Mihatsch; Guido Sauter; Olli Kallioniemi
Hormone therapy failure in human prostate cancer: analysis by complementary DNA and tissue microarrays.
Journal of the National Cancer Institute 1999;91(20):1758-64.
1999: Stacie K Loftus; Yidong Chen; Gerald C Gooden; Joseph F Ryan; G Birznieks; M Hilliard; Andreas D Baxevanis; Michael Bittner; Paul Meltzer; Jeffrey M. Trent; William J Pavan
Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(16):9277-80.
1999: Sally A Amundson; Michael Bittner; Yidong Chen; Jeffrey M. Trent; Paul Meltzer; Albert J Fornace
Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses.
Oncogene 1999;18(24):3666-72.
1999: Javed Khan; Michael Bittner; Yidong Chen; Paul S Meltzer; Jeffrey M. Trent
DNA microarray technology: the anticipated impact on the study of human disease.
Biochimica et biophysica acta 1999;1423(2):M17-28.
1999: Javed Khan; Lao H Saal; Michael Bittner; Yidong Chen; Jeffrey M. Trent; Paul S Meltzer
Expression profiling in cancer using cDNA microarrays.
Electrophoresis 1999;20(2):223-9.
1999: DJ Duggan; Michael Bittner; Yidong Chen; Paul Meltzer; Jeffrey M. Trent
Expression profiling using cDNA microarrays.
Nature genetics 1999;21(1 Suppl):10-4.
1998: Javed Khan; R Simon; Michael Bittner; Yidong Chen; S B Leighton; Thomas J Pohida; Paul D Smith; Yuan Jiang; Gerald C Gooden; Jeffrey M. Trent; Paul S Meltzer
Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays.
Cancer research 1998;58(22):5009-13.
1998: O Ermolaeva; M Rastogi; Kim D Pruitt; G D Schuler; Michael Bittner; Yidong Chen; R Simon; Paul Meltzer; Jeffrey M. Trent; Mark S Boguski
Data management and analysis for gene expression arrays.
Nature genetics 1998;20(1):19-23.
1996: Joe L DeRisi; L Penland; Patrick O Brown; Michael Bittner; Paul S Meltzer; M Ray; Yidong Chen; Yan A Su; Jeffrey M. Trent
Use of a cDNA microarray to analyse gene expression patterns in human cancer.
Nature genetics 1996;14(4):457-60.
1993: Yidong Chen; E R Dougherty; Saara Totterman; Joseph Hornak
Classification of trabecular structure in magnetic resonance images based on morphological granulometries.
Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine 1993;29(3):358-70.
1992: Shiv Srivastava; Y A Tong; K Devadas; Z Q Zou; Yidong Chen; Kathleen F Pirollo; Esther H Chang
The status of the p53 gene in human papilloma virus positive or negative cervical carcinoma cell lines.
Carcinogenesis 1992;13(7):1273-5.
1992: Shiv Srivastava; Y A Tong; K Devadas; Z Q Zou; V W Sykes; Yidong Chen; William A Blattner; Kathleen F Pirollo; Esther H Chang
Detection of both mutant and wild-type p53 protein in normal skin fibroblasts and demonstration of a shared 'second hit' on p53 in diverse tumors from a cancer-prone family with Li-Fraumeni syndrome.
Oncogene 1992;7(5):987-91.