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Research | 8 January 2021 | Open
Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma
- Silvia Pomella
- , Prethish Sreenivas
- , Berkley E. Gryder
- , Long Wang
- , David Milewski
- , Matteo Cassandri
- , Kunal Baxi
- , Nicole R. Hensch
- , Elena Carcarino
- , Young Song
- , Hsien-Chao Chou
- , Marielle E. Yohe
- , Benjamin Z. Stanton
- , Bruno Amadio
- , Ignazio Caruana
- , Cristiano De Stefanis
- , Rita De Vito
- , Franco Locatelli
- , Yidong Chen
- , Eleanor Y. Chen
- , Peter Houghton
- , Javed Khan
- , Rossella Rota
- & Myron S. Ignatius
Nature Communications 12 , 1–15

Rights & permissionsfor article Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma . Opens in a new window.
Research | 19 November 2020
Campylobacter infection promotes IFNγ-dependent intestinal pathology via ILC3 to ILC1 conversion
- Wayne T. Muraoka
- , Anna A. Korchagina
- , Qingqing Xia
- , Sergey A. Shein
- , Xi Jing
- , Zhao Lai
- , Korri S. Weldon
- , Li-Ju Wang
- , Yidong Chen
- , Lawrence W. Kummer
- , Markus Mohrs
- , Eric Vivier
- , Ekaterina P. Koroleva
- & Alexei V. Tumanov
Mucosal Immunology , 1–14

Rights & permissionsfor article Campylobacter infection promotes IFNγ-dependent intestinal pathology via ILC3 to ILC1 conversion . Opens in a new window.
Research | 12 June 2020
Knock-out of Hopx disrupts stemness and quiescence of hematopoietic stem cells in mice
- Chien-Chin Lin
- , Chi-Yuan Yao
- , Yueh-Chwen Hsu
- , Hsin-An Hou
- , Chang-Tsu Yuan
- , Yi-Hung Li
- , Chein-Jun Kao
- , Po-Han Chuang
- , Yu-Chiao Chiu
- , Yidong Chen
- , Wen-Chien Chou
- & Hwei-Fang Tien
Oncogene 39 , 5112–5123

Rights & permissionsfor article Knock-out of <i>Hopx</i> disrupts stemness and quiescence of hematopoietic stem cells in mice . Opens in a new window.
1 November 1999
Gene expression profiling of human bone marrow stromal cells with FGFR-3 mutation (K650M) using cDNA microarrays
- Libin Jia
- , Michael Bittner
- , Yidong Chen
- , Kris Gooden
- , Yuan Jiang
- , Jeffery Trent
- , Erica Keen
- , Anna R. DeRubeis
- , Sergei Kuznetsov
- , Pamela Robey
- , Marian Young
- , John Powell
- , Liming Yang
- , Robert Hotchkiss
- & Claire Francomano
Nature Genetics 23 , 53–53

Rights & permissionsfor article Gene expression profiling of human bone marrow stromal cells with FGFR-3 mutation (K650M) using cDNA microarrays . Opens in a new window.
1 November 1999
Microarray analysis discriminates BRCA2 mutation-positive from BRCA1 and sporadic breast cancer patient tumour biopsies
- David J. Duggan
- , Ingrid A. Hedenfalk
- , Yidong Chen
- , Mike Bittner
- , Åke Borg
- & Jeffrey Trent
Nature Genetics 23 , 43–43

Rights & permissionsfor article Microarray analysis discriminates BRCA2 mutation-positive from BRCA1 and sporadic breast cancer patient tumour biopsies . Opens in a new window.
1 November 1999
Profiling expression patterns of 2,214 unigenes in mouse craniofacial development by cDNA microarray analysis
- Haochuan Li
- , Yidong Chen
- , Yuan Jiang
- , Michael L. Bittner
- , Paul S. Meltzer
- , Jeffery M. Trent
- , Kenneth M. Yamada
- & Yoshihiko Yamada
Nature Genetics 23 , 57–58

Rights & permissionsfor article Profiling expression patterns of 2,214 unigenes in mouse craniofacial development by cDNA microarray analysis . Opens in a new window.
1 November 1999
Evaluating altered levels of gene expression in cancer cells
- Yuan Jiang
- , Yidong Chen
- , Yan Su
- , Ena Wang
- , Francesco M. Marincola
- , Edward R. Dougherty
- , Paul S. Meltzer
- , Michael Bittner
- & Jeffery M. Trent
Nature Genetics 23 , 54–54

Rights & permissionsfor article Evaluating altered levels of gene expression in cancer cells . Opens in a new window.
1 April 2001
cDNA microarray analysis using both gene expression ratios and intensities
- Yidong Chen
- , Hongen Zhang
- , Sujatha Panavally
- , Edward Dougherty
- , Michael Bittner
- , Paul Meltzer
- & Jeffery Trent
Nature Genetics 27 , 46–47

Rights & permissionsfor article cDNA microarray analysis using both gene expression ratios and intensities . Opens in a new window.
1 November 1999
Identification of suppressor genes associated with the chromosome 6-mediated suppressed melanoma cell UACC903(+6) by cDNA microarray
- Yan A. Su
- , Michael L. Bittner
- , Yidong Chen
- , Lian Tao
- , Yuan Jiang
- & Jeffrey M. Trent
Nature Genetics 23 , 76–77

Rights & permissionsfor article Identification of suppressor genes associated with the chromosome 6-mediated suppressed melanoma cell UACC903(+6) by cDNA microarray . Opens in a new window.
1 April 2001
Classification of hereditary breast cancers based on gene expression
- Ingrid Hedenfalk
- , Yidong Chen
- , David Duggan
- , Åke Borg
- & Jeffrey Trent
Nature Genetics 27 , 58–58

Rights & permissionsfor article Classification of hereditary breast cancers based on gene expression . Opens in a new window.
1 April 1999
Elucidation of the Downstream Targets of the PAX3-FKHR Fusion Oncogene Found in Aveolar Rhabdomyosarcoma Using cDNA Microarrays
- Javed Khan
- , Michael L Bittner
- , Yidong Chen
- , Alicia J Faller
- , Lao H Saal
- , David A Azorsa
- , Uli Teichman
- , William Pavan
- , Jeffrey M Trent
- & Paul S Meltzer
Pediatric Research 45 , 148–148

Rights & permissionsfor article Elucidation of the Downstream Targets of the PAX3-FKHR Fusion Oncogene Found in Aveolar Rhabdomyosarcoma Using cDNA Microarrays . Opens in a new window.
1 April 2001
Relationship between gene expression profile and clinical outcome in malignant melanoma
- Kristen Carr
- , Mike Bittner
- , Yidong Chen
- , Paul Meltzer
- , Paul Duray
- , Vern Sondak
- & Jeffrey Trent
Nature Genetics 27 , 46–46

Rights & permissionsfor article Relationship between gene expression profile and clinical outcome in malignant melanoma . Opens in a new window.
1 April 2001
Development of a molecular taxonomy of small blue round-cell tumors using cDNA microarrays
- Javed Khan
- , Jun Wei
- , Lao Saal
- , Ladanyi Marc
- , Ringnér Markus
- , Carsten Peterson
- , Yidong Chen
- & Paul Meltzer
Nature Genetics 27 , 64–64

Rights & permissionsfor article Development of a molecular taxonomy of small blue round-cell tumors using cDNA microarrays . Opens in a new window.
1 April 2001
A layered perceptron approach to categorizing cDNA microarray measurements
- Markus Ringner
- , Carsten Peterson
- , Sofia Gruvberger
- , Mårten Fernö
- , Åke Borg
- , Javed Khan
- , Jun Wei
- , Lao Saal
- , Yidong Chen
- , Marc Ladanyi
- , Paul S. Meltzer
- & Jeff M. Trent
Nature Genetics 27 , 83–83

Rights & permissionsfor article A layered perceptron approach to categorizing cDNA microarray measurements . Opens in a new window.
1 November 1999
Determining the quantitative accuracy of cDNA microarrays
- Gerald Gooden
- , David Morse
- , Arthur Glatfelter
- , Yidong Chen
- , Jeffrey M. Trent
- , Paul S. Meltzer
- & Michael Bittner
Nature Genetics 23 , 48–48

Rights & permissionsfor article Determining the quantitative accuracy of cDNA microarrays . Opens in a new window.
1 April 2001
Clustering algorithms: can anything be concluded?
- Edward Dougherty
- , Junior Barrera
- , Marcel Brun
- , Seungchan Kim
- , Roberto Marcondes
- , Yidong Chen
- , Michael Bittner
- & Jeffrey Trent
Nature Genetics 27 , 51–51

Rights & permissionsfor article Clustering algorithms: can anything be concluded? . Opens in a new window.
1 November 1999
Microarray ratio analysis under noisy background
Nature Genetics 23 , 37–38

Rights & permissionsfor article Microarray ratio analysis under noisy background . Opens in a new window.
1 April 2001
Molecular profiling of prostate cancer progression
- David J. Duggan
- , Jun Luo
- , Jurga Sauvageot
- , Michael Bittner
- , Yidong Chen
- , Jeff Trent
- & William B. Isaacs
Nature Genetics 27 , 51–52

Rights & permissionsfor article Molecular profiling of prostate cancer progression . Opens in a new window.
1 November 1999
Isolation of chromosome 6-encoded differentially expressed genes associated with breast cancer cell lines MDA-MB-231 and MDA/H6 by cDNA microarray
- Lian Tao
- , Abdel G. Elkahloun
- , Hein T. Nguyen
- , Yidong Chen
- , Marc E. Lippman
- & Yan A. Su
Nature Genetics 23 , 77–77

Rights & permissionsfor article Isolation of chromosome 6-encoded differentially expressed genes associated with breast cancer cell lines MDA-MB-231 and MDA/H6 by cDNA microarray . Opens in a new window.
1 April 2001
High-resolution CGH analysis on cDNA microarrays for direct identification of amplification target genes
- Elizabeth Hyman
- , Outi Monni
- , Ester Rozenblum
- , Spyro Mousses
- , Michael Bittner
- , Yidong Chen
- , Olli Kallioniemi
- & Anne Kallioniemi
Nature Genetics 27 , 63–63

Rights & permissionsfor article High-resolution CGH analysis on cDNA microarrays for direct identification of amplification target genes . Opens in a new window.
1 April 2001
Microarray-based genetic analysis of synovial sarcomas
- Susanne Allander
- , Yidong Chen
- , Marc Ladanyi
- & Paul Meltzer
Nature Genetics 27 , 38–38

Rights & permissionsfor article Microarray-based genetic analysis of synovial sarcomas . Opens in a new window.
1 April 2001
An integrated approach to the extraction, storage, processing and analysis of microarray gene expression data
- Andreas D. Baxevanis
- , Izabela Makalowska
- , Kenneth Trout
- , Qien Zhou
- , Zheng-Zheng Zhou
- , Jaime Stein
- , Edward R. Dougherty
- , Paul S. Meltzer
- , Yidong Chen
- , Michael L. Bittner
- & Jeffrey M. Trent
Nature Genetics 27 , 42–42

Rights & permissionsfor article An integrated approach to the extraction, storage, processing and analysis of microarray gene expression data . Opens in a new window.
Amendments and Corrections | 27 June 2018
Author Correction: EWS–FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma
Nature 559 , E11–E11

Rights & permissionsfor article Author Correction: EWS–FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma . Opens in a new window.
Research | 22 August 2016 | Open
Liver Gene Expression Profiles Correlate with Virus Infection and Response to Interferon Therapy in Chronic Hepatitis B Patients
- Hui-Lin Wu
- , Tzu-Hung Hsiao
- , Pei-Jer Chen
- , Siao-Han Wong
- , Jia-Horng Kao
- , Ding-Shinn Chen
- , Jo-Yang Lu
- , Tzu-Pin Lu
- , Yidong Chen
- , Eric Y. Chuang
- , Hui-Chu Tu
- & Chun-Jen Liu
Scientific Reports 6 , 1–10

Rights & permissionsfor article Liver Gene Expression Profiles Correlate with Virus Infection and Response to Interferon Therapy in Chronic Hepatitis B Patients . Opens in a new window.
Research | 24 February 2020 | Open
Meningeal lymphatic vessels regulate brain tumor drainage and immunity
- Xueting Hu
- , Qiuping Deng
- , Lu Ma
- , Qingqing Li
- , Yidong Chen
- , Yuhan Liao
- , Fan Zhou
- , Chen Zhang
- , Linlin Shao
- , Jun Feng
- , Tubao He
- , Weihai Ning
- , Yan Kong
- , Yingqing Huo
- , Aibin He
- , Bing Liu
- , Jingjing Zhang
- , Ralf Adams
- , Yulong He
- , Fuchou Tang
- , Xiuwu Bian
- & Jincai Luo
Cell Research 30 , 229–243

Rights & permissionsfor article Meningeal lymphatic vessels regulate brain tumor drainage and immunity . Opens in a new window.
Research | 19 November 2006
Sensitive and specific method for detecting G protein–coupled receptor mRNAs
- Arne Hansen
- , Yidong Chen
- , Jason M Inman
- , Quang N Phan
- , Zhi-Qing Qi
- , Charlie C Xiang
- , Miklos Palkovits
- , Natasha Cherman
- , Sergei A Kuznetsov
- , Pamela G Robey
- , Eva Mezey
- & Michael J Brownstein
Nature Methods 4 , 35–37

Rights & permissionsfor article Sensitive and specific method for detecting G protein–coupled receptor mRNAs . Opens in a new window.
2 February 2004
Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome
- 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 P Kallioniemi
- , Jeffrey M Trent
- , Patrice J Morin
- & Paul S Meltzer
Oncogene 23 , 2264–2274

Rights & permissionsfor article Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome . Opens in a new window.
1 April 2001
Gene expression changes during hormonal therapy for prostate cancer reveal candidate diagnostic and drug targets
- Spyro Mousses
- , Lukas Bubendorf
- , Juha Kononen
- , Yidong Chen
- , Micheal Bittner
- , Pasi Koivisto
- , Jane Trepel
- , Jin Woo Kim
- , Mark Raffeld
- , Thomas Pretlow
- , Natalie Goldberger
- , Robert Cornelison
- , Urs Wagner
- , Galen Hostetter
- , Guido Sauter
- & Olli Kallioniemi
Nature Genetics 27 , 75–75

Rights & permissionsfor article Gene expression changes during hormonal therapy for prostate cancer reveal candidate diagnostic and drug targets . Opens in a new window.
Research | 1 July 2002
Amine-modified random primers to label probes for DNA microarrays
- Charlie C. Xiang
- , Olga A. Kozhich
- , Mei Chen
- , Jason M. Inman
- , Quang N. Phan
- , Yidong Chen
- & Michael J. Brownstein
Nature Biotechnology 20 , 738–742

Rights & permissionsfor article Amine-modified random primers to label probes for DNA microarrays . Opens in a new window.
1 September 1998
Data management and analysis for gene expression arrays
- Olga Ermolaeva
- , Mohit Rastogi
- , Kim D. Pruitt
- , Gregory D. Schuler
- , Michael L. Bittner
- , Yidong Chen
- , Richard Simon
- , Paul Meltzer
- , Jeffrey M. Trent
- & Mark S. Boguski
Nature Genetics 20 , 19–23

Rights & permissionsfor article Data management and analysis for gene expression arrays . Opens in a new window.
Reviews | 1 January 1999
Expression profiling using cDNA microarrays
- David J Duggan
- , Michael Bittner
- , Yidong Chen
- , Paul Meltzer
- & Jeffrey M. Trent
Nature Genetics 21 , 10–14

Rights & permissionsfor article Expression profiling using cDNA microarrays . Opens in a new window.
Research | 17 March 2003
Predicting hepatitis B virus–positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning
- 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
Nature Medicine 9 , 416–423

Rights & permissionsfor article Predicting hepatitis B virus–positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning . Opens in a new window.
7 March 2005
Frequent overexpression of ETS-related gene-1 (ERG1) in prostate cancer transcriptome
- Gyorgy Petrovics
- , Aijun Liu
- , Syed Shaheduzzaman
- , Bungo Furasato
- , Chen Sun
- , Yongmei Chen
- , Martin Nau
- , Lakshmi Ravindranath
- , Yidong Chen
- , Albert Dobi
- , Vasantha Srikantan
- , Isabell A Sesterhenn
- , David G McLeod
- , Maryanne Vahey
- , Judd W Moul
- & Shiv Srivastava
Oncogene 24 , 3847–3852

Rights & permissionsfor article Frequent overexpression of <i>ETS</i>-related gene-1 <i>(ERG1)</i> in prostate cancer transcriptome . Opens in a new window.
19 October 2001
Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling
- Spyro Mousses
- , Urs Wagner
- , Yidong Chen
- , J W Kim
- , Lukas Bubendorf
- , Michael Bittner
- , Thomas Pretlow
- , Abdel G Elkahloun
- , Jane B Trepel
- & Olli-P Kallioniemi
Oncogene 20 , 6718–6723

Rights & permissionsfor article Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling . Opens in a new window.
14 July 1999
Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses
- Sally A Amundson
- , Mike Bittner
- , Yidong Chen
- , Jeffrey Trent
- , Paul Meltzer
- & Albert J Fornace Jr
Oncogene 18 , 3666–3672

Rights & permissionsfor article Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses . Opens in a new window.
6 August 2001
Genome-wide expression changes induced by HTLV-1 Tax: evidence for MLK-3 mixed lineage kinase involvement in Tax-mediated NF-κB activation
- Patrick W P Ng
- , Hidekatsu Iha
- , Yoichi Iwanaga
- , Michael Bittner
- , Yidong Chen
- , Yuan Jiang
- , Gerald Gooden
- , Jeffrey M Trent
- , Paul Meltzer
- , Kuan-Teh Jeang
- & Steven L Zeichner
Oncogene 20 , 4484–4496

Rights & permissionsfor article Genome-wide expression changes induced by HTLV-1 Tax: evidence for MLK-3 mixed lineage kinase involvement in Tax-mediated NF-κB activation . Opens in a new window.
1 November 1999
Nonlinear stochastic determination for gene expressions via cDNA microarrays
Nature Genetics 23 , 41–41

Rights & permissionsfor article Nonlinear stochastic determination for gene expressions via cDNA microarrays . Opens in a new window.
Research | 8 August 2004
Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer
- Pia Huusko
- , Damaris Ponciano-Jackson
- , Maija Wolf
- , Jeff A Kiefer
- , David O Azorsa
- , Sukru Tuzmen
- , Don Weaver
- , Christiane Robbins
- , Tracy Moses
- , Minna Allinen
- , Sampsa Hautaniemi
- , Yidong Chen
- , Abdel 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-P Kallioniemi
- & Spyro Mousses
Nature Genetics 36 , 979–983

Rights & permissionsfor article Nonsense-mediated decay microarray analysis identifies mutations of <i>EPHB2</i> in human prostate cancer . Opens in a new window.
Research | 31 October 2018 | Open
MiR-584-5p potentiates vincristine and radiation response by inducing spindle defects and DNA damage in medulloblastoma
Nature Communications 9 , 1–19

Rights & permissionsfor article <i>MiR-584-5p</i> potentiates vincristine and radiation response by inducing spindle defects and DNA damage in medulloblastoma . Opens in a new window.
Research | 7 March 2018
EWS–FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma
Nature 555 , 387–391

Rights & permissionsfor article EWS–FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma . Opens in a new window.
Research | 19 September 2017 | Open
Cross-talk between miR-471-5p and autophagy component proteins regulates LC3-associated phagocytosis (LAP) of apoptotic germ cells
Nature Communications 8 , 1–14

Rights & permissionsfor article Cross-talk between miR-471-5p and autophagy component proteins regulates LC3-associated phagocytosis (LAP) of apoptotic germ cells . Opens in a new window.
Research | 29 February 2016 | Open
Roles of Distal and Genic Methylation in the Development of Prostate Tumorigenesis Revealed by Genome-wide DNA Methylation Analysis
- Yao Wang
- , Rohit Ramakant Jadhav
- , Joseph Liu
- , Desiree Wilson
- , Yidong Chen
- , Ian M. Thompson
- , Dean A. Troyer
- , Javier Hernandez
- , Huidong Shi
- , Robin J. Leach
- , Tim H.-M. Huang
- & Victor X. Jin
Scientific Reports 6 , 1–10

Rights & permissionsfor article Roles of Distal and Genic Methylation in the Development of Prostate Tumorigenesis Revealed by Genome-wide DNA Methylation Analysis . Opens in a new window.
Research | 14 March 2016 | Open
Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers
- Tzu-Hung Hsiao
- , Yu-Chiao Chiu
- , Pei-Yin Hsu
- , Tzu-Pin Lu
- , Liang-Chuan Lai
- , Mong-Hsun Tsai
- , Tim H.-M. Huang
- , Eric Y. Chuang
- & Yidong Chen
Scientific Reports 6 , 1–16

Rights & permissionsfor article Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers . Opens in a new window.
Research | 4 September 2001
Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease
- Tobey J. MacDonald
- , Kevin M. Brown
- , Bonnie LaFleur
- , Katia Peterson
- , Christopher Lawlor
- , Yidong Chen
- , Roger J. Packer
- , Philip Cogen
- & Dietrich A. Stephan
Nature Genetics 29 , 143–152

Rights & permissionsfor article Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease . Opens in a new window.

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