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51

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Tim F Rayner, Philippe Rocca-Serra, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, Junmin Liu, Donald S Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin S

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.37 MB

english, 2006

52

A robust method for the amplification of RNA in the sense orientation

Nicholas F Marko, Bryan Frank, John Quackenbush, Norman H Lee

Journal:

Year:

2005

Language:

english

File:

PDF, 1.74 MB

english, 2005

53

Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes

Valerie W Hu, Bryan C Frank, Shannon Heine, Norman H Lee, John Quackenbush

Journal:

Year:

2006

Language:

english

File:

PDF, 1.35 MB

english, 2006

54

A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution

Patrick D Danley, Sean P Mullen, Fenglong Liu, Vishvanath Nene, John Quackenbush, Kerry L Shaw

Journal:

Year:

2007

Language:

english

File:

PDF, 1021 KB

english, 2007

55

Seeded Bayesian Networks: Constructing genetic networks from microarray data

Amira Djebbari, John Quackenbush

Journal:

BMC Systems Biology

Year:

2008

Language:

english

File:

PDF, 371 KB

english, 2008

56

Biomarker-driven trial in metastatic pancreas cancer: feasibility in a multicenter study of saracatinib, an oral Src inhibitor, in previously treated pancreatic cancer

John Arcaroli, Kevin Quackenbush, Arvind Dasari, Rebecca Powell, Martine McManus, Aik-Choon Tan, Nathan R. Foster, Joel Picus, John Wright, Sujatha Nallapareddy, Charles Erlichman, Manuel Hidalgo, Wel

Journal:

Cancer Medicine

Year:

2012

Language:

english

File:

PDF, 1.13 MB

english, 2012

57

Yeast Artificial Chromosome Cloning of 3.2 Megabases within Chromosomal Band 11q24 Closely Linking c-ets 1 and Fli-1 and Encompassing the Ewing Sarcoma Breakpoint

Licia Selleri, Marco Giovannini, Gary G. Hermanson, Anthony Romo, John Quackenbush, Laura Penny, Jason V. Khristich, Glen A. Evans

Journal:

Year:

1994

File:

PDF, 826 KB

1994

58

Physical Mapping of Complex Genomes by Sampled Sequencing: A Theoretical Analysis

Kenneth Kupfer, Michael W. Smith, John Quackenbush, Glen A. Evans

Journal:

Year:

1995

File:

PDF, 758 KB

1995

59

An STS Content Map of Human Chromosome 11: Localization of 910 YAC Clones and 109 Islands

JOHN QUACKENBUSH, CHRISTOPHER DAVIES, JULIE M. BAILIS, JASON V. KHRISTICH, KARIN DIGGLE, YELENA MARCHUCK, JOSHUA TOBIN, STEPHEN P. CLARK, ANNIE RODKINS, STEWART MARCANO, ALLAN C. CHURUKIAN, JANE S. HU

Journal:

Year:

1995

Language:

english

File:

PDF, 179 KB

english, 1995

60

Characterization of a Vibrio vulnificus LysR homologue, HupR, which regulates expression of the haem uptake outer membrane protein, HupA

Christine M. Litwin, John Quackenbush

Journal:

Microbial Pathogenesis

Year:

2001

Language:

english

File:

PDF, 210 KB

english, 2001

61

Osteopontin identified as colon cancer tumor progression marker

Deepak Agrawal, Tingan Chen, Rosalyn Irby, John Quackenbush, Ann F Chambers, Marianna Szabo, Alan Cantor, Domenico Coppola, Timothy J Yeatman

Journal:

Comptes Rendus Biologies

Year:

2003

Language:

english

File:

PDF, 62 KB

english, 2003

62

Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva

Vishvanath Nene, Dan Lee, Simon Kang’a, Robert Skilton, Trushar Shah, Etienne de Villiers, Stephen Mwaura, David Taylor, John Quackenbush, Richard Bishop

Journal:

Insect Biochemistry and Molecular Biology

Year:

2004

Language:

english

File:

PDF, 540 KB

english, 2004

63

Genetic regulation of endotoxin-induced airway disease

Donald N. Cook, Shuibang Wang, Yonghong Wang, Gabriel P. Howles, Gregory S. Whitehead, Katherine G. Berman, Tony D. Church, Bryan C. Frank, Renee M. Gaspard, Yan Yu, John Quackenbush, David A. Schwart

Journal:

Year:

2004

Language:

english

File:

PDF, 379 KB

english, 2004

64

Functional classification analysis of somatically mutated genes in human breast and colorectal cancers

Thomas W. Chittenden, Eleanor A. Howe, Aedin C. Culhane, Razvan Sultana, Jennifer M. Taylor, Chris Holmes, John Quackenbush

Journal:

Year:

2008

Language:

english

File:

PDF, 934 KB

english, 2008

65

Left ventricular global transcriptional profiling in human end-stage dilated cardiomyopathy

Dilek Colak, Namik Kaya, Jawaher Al-Zahrani, Albandary Al Bakheet, Paul Muiya, Editha Andres, John Quackenbush, Nduna Dzimiri

Journal:

Year:

2009

Language:

english

File:

PDF, 1.13 MB

english, 2009

66

Comparative gene expression analysis in mouse models for multiple sclerosis, Alzheimer's disease and stroke for identifying commonly regulated and disease-specific gene changes

Vivian Tseveleki, Renee Rubio, Sotiris-Spyros Vamvakas, Joseph White, Era Taoufik, Edwige Petit, John Quackenbush, Lesley Probert

Journal:

Year:

2010

Language:

english

File:

PDF, 347 KB

english, 2010

67

Multi-Platform, Multi-Site, Microarray-Based Human Tumor Classification

Greg Bloom, Ivana V. Yang, David Boulware, Ka Yin Kwong, Domenico Coppola, Steven Eschrich, John Quackenbush, Timothy J. Yeatman

Journal:

The American Journal of Pathology

Year:

2004

Language:

english

File:

PDF, 1.08 MB

english, 2004

68

Specialized Contributions by α(1,3)-Fucosyltransferase-IV and FucT-VII during Leukocyte Rolling in Dermal Microvessels

Wolfgang Weninger, Laurien H Ulfman, Guiying Cheng, Natalia Souchkova, Elizabeth J Quackenbush, John B Lowe, Ulrich H von Andrian

Journal:

Year:

2000

Language:

english

File:

PDF, 397 KB

english, 2000

69

Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies

Christian J Stoeckert Jr., John Quackenbush, Alvis Brazma, Catherine A Ball

Journal:

Drug Discovery Today: TARGETS

Year:

2004

Language:

english

File:

PDF, 418 KB

english, 2004

70

Novel Application of Structural Equation Modeling to Correlation Structure Analysis of CpG Island Methylation in Colorectal Cancer

Noriko Tanaka, Curtis Huttenhower, Katsuhiko Nosho, Yoshifumi Baba, Kaori Shima, John Quackenbush, Kevin M. Haigis, Edward Giovannucci, Charles S. Fuchs, Shuji Ogino

Journal:

The American Journal of Pathology

Year:

2010

Language:

english

File:

PDF, 916 KB

english, 2010

71

ALDH+ tumor-initiating cells exhibiting gain in NOTCH1 gene copy number have enhanced regrowth sensitivity to a γ-secretase inhibitor and irinotecan in colorectal cancer

John J. Arcaroli, Rebecca W. Powell, Marileila Varella-Garcia, Martine McManus, Aik Choon Tan, Kevin S. Quackenbush, Todd M. Pitts, Dexiang Gao, Anna Spreafico, Arvind Dasari, Basel M. Touban, Wells A

Journal:

Molecular Oncology

Year:

2012

Language:

english

File:

PDF, 2.14 MB

english, 2012

72

Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old

Dilek Colak, Muhammad A Chishti, Al-Bandary Al-Bakheet, Ahmed Al-Qahtani, Mohamed M Shoukri, Malcolm H Goyns, Pinar T Ozand, John Quackenbush, Ben H Park, Namik Kaya

Journal:

Molecular Cancer

Year:

2010

Language:

english

File:

PDF, 3.45 MB

english, 2010

73

Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis

Elodie Ghedin, Anne Pumfery, Cynthia de la Fuente, Karen Yao, Naomi Miller, Vincent Lacoste, John Quackenbush, Steven Jacobson, Fatah Kashanchi

Journal:

Year:

2004

Language:

english

File:

PDF, 1.89 MB

english, 2004

74

Mutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting

Correll, Mick, Johnson, Christopher K., Ferrari, Giovanni, Brizzio, Mariano, Mak, Andrew W.C., Quackenbush, John, Shaw, Richard E., Zapolanski, Alex, Grau, Juan B.

Journal:

Year:

2013

Language:

english

File:

PDF, 392 KB

english, 2013

75

Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay

Laurent Perreard, Cheng Fan, John F Quackenbush, Michael Mullins…

Journal:

Breast Cancer Research

Year:

2006

Language:

english

File:

PDF, 1.37 MB

english, 2006

76

Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples

Jessica C Mar, Renee Rubio, John Quackenbush

Journal:

Year:

2006

Language:

english

File:

PDF, 821 KB

english, 2006

77

Open-source software accelerates bioinformatics

John Quackenbush

Journal:

Year:

2003

Language:

english

File:

PDF, 59 KB

english, 2003

78

Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: Applying RNA-sequencing analysis on archived specimens

Sharron Lin, Xuanhui, Hu, Lan, Sandy, Kirley, Correll, Mick, Quackenbush, John, Wu, Chin-Lee, Scott McDougal, William

Journal:

Urologic Oncology: Seminars and Original Investigations

Year:

2014

Language:

english

File:

PDF, 858 KB

english, 2014

79

Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: Preliminary assessment of cross-platform concordance

Kelly, Andrew D., Hill, Katherine E., Correll, Mick, Hu, Lan, Wang, Yaoyu E., Rubio, Renee, Duan, Shenghua, Quackenbush, John, Spentzos, Dimitrios

Journal:

Year:

2013

Language:

english

File:

PDF, 185 KB

english, 2013

80

CXCR4 pathway associated with family history of melanoma

Li, Wen-Qing, Han, Jiali, Widlund, Hans R., Correll, Mick, Wang, Yaoyu E., Quackenbush, John, Mihm, Martin C., Canales, Alvaro Laga, Wu, Shaowei, Golub, Todd, Hoshida, Yujin, Hunter, David J., Murphy,

Journal:

Cancer Causes & Control

Year:

2014

Language:

english

File:

PDF, 443 KB

english, 2014

81

Accelerating genomic data publishing and sharing

Fan, Jian-Bing, Quackenbush, John, Wacek, Bart

Journal:

Year:

2013

Language:

english

File:

PDF, 96 KB

english, 2013

82

A tiered hidden Markov model characterizes multi-scale chromatin states

Larson, Jessica L., Huttenhower, Curtis, Quackenbush, John, Yuan, Guo-Cheng

Journal:

Year:

2013

Language:

english

File:

PDF, 617 KB

english, 2013

83

Inference and validation of predictive gene networks from biomedical literature and gene expression data

Olsen, Catharina, Fleming, Kathleen, Prendergast, Niall, Rubio, Renee, Emmert-Streib, Frank, Bontempi, Gianluca, Haibe-Kains, Benjamin, Quackenbush, John

Journal:

Year:

2014

Language:

english

File:

PDF, 526 KB

english, 2014

84

Toxicogenomics || Microarray Data Standards: An Open Letter

Catherine Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C. Matese, Helen Parkinson, John Quackenbush, Martin Ringwald, Susanna-Assunta Sansone, Gavin Sherlock, Pau

Journal:

Environmental Health Perspectives

Year:

2004

Language:

english

File:

PDF, 1.11 MB

english, 2004

85

A phase II study of the gamma secretase inhibitor RO4929097 in patients with previously treated metastatic pancreatic adenocarcinoma

De Jesus-Acosta, Ana, Laheru, Daniel, Maitra, Anirban, Arcaroli, John, Rudek, Michelle A., Dasari, Arvind, Blatchford, Patrick J., Quackenbush, Kevin, Messersmith, Wells

Journal:

Investigational New Drugs

Year:

2014

Language:

english

File:

PDF, 199 KB

english, 2014

86

Microarray Analysis and Tumor Classification

Quackenbush, John

Journal:

Boston Medical and Surgical Journal

Year:

2006

Language:

english

File:

PDF, 766 KB

english, 2006

87

Personal report: Richard Mural

Quackenbush, John

Journal:

Year:

2014

Language:

english

File:

PDF, 88 KB

english, 2014

88

An Optimized Predictive Strategy for Interactome Mapping †

Aryee, Martin J. A., Quackenbush, John

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 763 KB

english, 2008

89

Gene Expression Variability as a Unifying Element of the Pluripotency Network

Mason, Elizabeth A., Mar, Jessica C., Laslett, Andrew L., Pera, Martin F., Quackenbush, John, Wolvetang, Ernst, Wells, Christine A.

Journal:

Stem Cell Reports

Year:

2014

Language:

english

File:

PDF, 1.78 MB

english, 2014

90

[IEEE 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering - Boston, MA, USA (2007.10.14-2007.10.17)] 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering - IEEE 7th BIBE Invited Plenary Keynote: Stochasticity and Networks in Genomic Data

Quackenbush, John

Year:

2007

Language:

english

File:

PDF, 129 KB

english, 2007

91

Data reporting standards: making the things we use better

John Quackenbush

Journal:

Genome Medicine

Year:

2009

Language:

english

File:

PDF, 62 KB

english, 2009

92

[IEEE 2014 Systems and Information Engineering Design Symposium (SIEDS) - Charlottesville, VA, USA (2014.4.25-2014.4.25)] 2014 Systems and Information Engineering Design Symposium (SIEDS) - Robotic platform for photography applications

Bojarski, Brian, Brown, Evan, Lumpkin, Jerald Blake, Nagel, Jacquelyn, Nagel, Robert, Quackenbush, John, Robinson, Margaret Farrell

Year:

2014

Language:

english

File:

PDF, 1.84 MB

english, 2014

93

Data Standards: A Call to Action

Brooksbank, Cath, Quackenbush, John

Journal:

Omics A Journal of Integrative Biology

Year:

2006

Language:

english

File:

PDF, 67 KB

english, 2006

94

Symposium on Genomic Medicine, University of Maryland, Shady Grove Campus, Rockville, Maryland, March 17-18, 1997

DOYLE, DARRELL J., QUACKENBUSH, JOHN

Journal:

Microbial & Comparative Genomics

Year:

1997

Language:

english

File:

PDF, 638 KB

english, 1997

95

Chiral anomalies in two-dimensional quantum field theory

Quackenbush, John

Journal:

Physical Review D

Year:

1989

Language:

english

File:

PDF, 312 KB

english, 1989

96

[American Thoracic Society American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California - ()] C67. TRANSLATIONAL 'OMICS' DISCOVERIES IN LUNG DISEASE - Identification Of Lung Disease-Associated Novel Transcripts And Alternative Splicing By RNA-Sequencing

Brothers, John F., Kusko, Rebecca L., Liu, Gang, Luo, Lingqi, Juan Guardela, Brenda, Tedrow, John, Alekseyev, Yuriy, Yang, Ivana V., Correll, Mick, Geraci, Mark, Quackenbush, John, Sciurba, Frank C.,

Year:

2012

Language:

english

File:

PDF, 20 KB

english, 2012

97

Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA

Frith, Martin C., Bailey, Timothy L., Kasukawa, Takeya, Mignone, Flavio, Kummerfeld, Sarah K., Madera, Martin, Sunkara, Sirisha, Furuno, Masaaki, Bult, Carol J., Quackenbush, John, Kai, Chikatoshi, Ka

Journal:

Year:

2006

Language:

english

File:

PDF, 816 KB

english, 2006

98

The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis

Jirawatnotai, Siwanon, Sharma, Samanta, Michowski, Wojciech, Suktitipat, Bhoom, Geng, Yan, Quackenbush, John, Elias, Joshua E, Gygi, Steven P, Wang, Yaoyu E, Sicinski, Piotr

Journal:

Year:

2014

Language:

english

File:

PDF, 920 KB

english, 2014

99

Perspective: Learning to share

Quackenbush, John

Journal:

Year:

2014

Language:

english

File:

PDF, 704 KB

english, 2014

100

Epstein—Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines

Bo Zhao, Jessica C. Mar, Seiji Maruo, Sungwook Lee, Benjamin E. Gewurz, Eric Johannsen, Kristina Holton, Renee Rubio, Kenzo Takada, John Quackenbush and Elliott Kieff

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.40 MB

english, 2011

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