Now showing items 1-20 of 49

    • Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD 

      Chu, Jen-hwa; Hersh, Craig P; Castaldi, Peter J; Cho, Michael H; Raby, Benjamin A; Laird, Nan; Bowler, Russell; Rennard, Stephen; Loscalzo, Joseph; Quackenbush, John; Silverman, Edwin K (BioMed Central, 2014)
      Background: The investigation of complex disease heterogeneity has been challenging. Here, we introduce a network-based approach, using partial correlations, that analyzes the relationships among multiple disease-related ...
    • Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer 

      Risch, Thomas; Fan, Jian-Bing; Holton, Kristina; Rubio, Renee; April, Craig; Wickham-Garcia, Eliza; Bentink, Stefan; Haibe-Kains, Benjamin; Hirsch, Michelle S.; Chen, Jing; Liu, Joyce; Culhane, Aedin; Drapkin, Ronny I.; Quackenbush, John; Matulonis, Ursula Anne (Public Library of Science, 2012)
      Ovarian cancer is the fifth leading cause of cancer death for women in the U.S. and the seventh most fatal worldwide. Although ovarian cancer is notable for its initial sensitivity to platinum-based therapies, the vast ...
    • BatchQC: interactive software for evaluating sample and batch effects in genomic data 

      Manimaran, Solaiappan; Selby, Heather Marie; Okrah, Kwame; Ruberman, Claire; Leek, Jeffrey T.; Quackenbush, John; Haibe-Kains, Benjamin; Bravo, Hector Corrada; Johnson, W. Evan (Oxford University Press, 2016)
      Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. There are ...
    • Bipartite Community Structure of eQTLs 

      Platig, John; Castaldi, Peter J.; DeMeo, Dawn; Quackenbush, John (Public Library of Science, 2016)
      Genome Wide Association Studies (GWAS) and expression quantitative trait locus (eQTL) analyses have identified genetic associations with a wide range of human phenotypes. However, many of these variants have weak effects ...
    • Characterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencing 

      Campbell, Joshua D; Luo, Lingqi; Liu, Gang; Xiao, Ji; Gerrein, Joseph; Guardela, Brenda J; Tedrow, John; Aleksyev, Yuriy O; Yang, Ivana V; Correll, Mick; Geraci, Mark; Quackenbush, John; Sciurba, Frank; Schwartz, David A; Kaminski, Naftali; Lenburg, Marc E; Beane, Jennifer; Spira, Avrum (BioMed Central, 2012)
    • Comprehensive Genomic Profiling of the Lung Transcriptome in Emphysema and Idiopathic Pulmonary Fibrosis Using RNA-Seq 

      Kusko, Rebecca L; Brothers, John; Luo, Lingqi; Guardela, Brenda Juan; Tedrow, John; Aleksyev, Yuriy; Yang, Ivana V; Correll, Mick; Geraci, Mark; Sciurba, Frank; Lenburg, Marc; Beane, Jennifer; Kaminski, Naftali; Spira, Avrum; Liu, Gang; Quackenbush, John; Schwartz, David A (BioMed Central, 2012)
    • Confounding Effects in "A Six-Gene Signature Predicting Breast Cancer Lung Metastasis" 

      Culhane, Aedin; Quackenbush, John (American Association for Cancer Research (AACR), 2009)
      The majority of breast cancer deaths result from metastases rather than from direct effects of the primary tumor itself. Recently, Landemaine and colleagues described a six-gene signature purported to predict lung metastasis ...
    • A Cricket Gene Index: A Genomic Resource for Studying Neurobiology, Speciation, and Molecular Evolution 

      Danley, Patrick D; Mullen, Sean P; Liu, Fenglong; Nene, Vishvanath; Quackenbush, John; Shaw, Kerry L (BioMed Central, 2007)
      Background: As the developmental costs of genomic tools decline, genomic approaches to nonmodel systems are becoming more feasible. Many of these systems may lack advanced genetic tools but are extremely valuable models ...
    • CRX is a Diagnostic Marker of Retinal and Pineal Lineage Tumors 

      Santagata, Sandro; Maire, Cecile; Idbaih, Ahmed; Geffers, Lars; Correll, Mick; Holton, Kristina; Quackenbush, John; Ligon, Keith Lloyd (Public Library of Science, 2009)
      Background: CRX is a homeobox transcription factor whose expression and function is critical to maintain retinal and pineal lineage cells and their progenitors. To determine the biologic and diagnostic potential of CRX in ...
    • Data-Driven Normalization Strategies for High-Throughput Quantitative RT-PCR 

      Mar, Jessica Cara; Kimura, Yasumasa; Schroder, Kate; Irvine, Katharine M; Hayashizaki, Yoshihide; Suzuki, Harukazu; Hume, David; Quackenbush, John (BioMed Central, 2009)
      Background: High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to be profiled. Current stage ...
    • Deciphering the Biological Mechanisms Driving the Phenotype of Interest 

      Quiroz, Alejandro (2013-03-15)
      The two key concepts of Neo-Darwinian evolution theory are genotype and phenotype. Genotype is defined as the genetic constitution of an organism and phenotype refers to the observable characteristics of that organism. ...
    • Decomposition of Gene Expression State Space Trajectories 

      Mar, Jessica Cara; Quackenbush, John (Public Library of Science, 2009)
      Representing and analyzing complex networks remains a roadblock to creating dynamic network models of biological processes and pathways. The study of cell fate transitions can reveal much about the transcriptional regulatory ...
    • Defining an Informativeness Metric for Clustering Gene Expression Data 

      Mar, Jessica; Wells, Christine A.; Quackenbush, John (Oxford University Press, 2011)
      Motivation: Unsupervised ‘cluster’ analysis is an invaluable tool for exploratory microarray data analysis, as it organizes the data into groups of genes or samples in which the elements share common patterns. Once the ...
    • Epithelial Progeny of Estrogen-Exposed Breast Progenitor Cells Display a Cancer-like Methylome 

      Cheng, A. S.L.; Culhane, Aedin; Chan, M. W.Y.; Venkataramu, C. R.; Ehrich, M.; Nasir, A.; Rodriguez, B. A.T.; Liu, J.; Yan, P. S.; Quackenbush, John; Nephew, K. P.; Yeatman, T. J.; Huang, T. H-M. (American Association for Cancer Research (AACR), 2008)
      Estrogen imprinting is used to describe a phenomenon in which early developmental exposure to endocrine disruptors increases breast cancer risk later in adult life. We propose that long-lived, self-regenerating stem and ...
    • Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology 

      Wu, Weimiao; Parmar, Chintan; Grossmann, Patrick; Quackenbush, John; Lambin, Philippe; Bussink, Johan; Mak, Raymond; Aerts, Hugo J. W. L. (Frontiers Media S.A., 2016)
      Background: Radiomics can quantify tumor phenotypic characteristics non-invasively by applying feature algorithms to medical imaging data. In this study of lung cancer patients, we investigated the association between ...
    • Functional classification analysis of somatically mutated genes in human breast and colorectal cancers 

      Chittenden, Thomas W; Howe, Eleanor A.; Culhane, Aedin; Sultana, Razvan; Taylor, Jennifer M.; Holmes, Chris; Quackenbush, John (Elsevier BV, 2008)
      A recent study published by Sjoblom and colleagues performed comprehensive sequencing of 13,023 human genes and identified mutations in genes specific to breast and colorectal tumors, providing insight into organ-specific ...
    • Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells 

      Zhou, Xiaobo; Qiu, Weiliang; Sathirapongsasuti, J. Fah; Cho, Michael Hyosang; Mancini, John D.; Lao, Taotao; Thibault, Derek M.; Litonjua, Augusto Ampil; Bakke, Per S.; Gulsvik, Amund; Lomas, David A.; Beaty, Terri H.; Hersh, Craig Palmer; Anderson, Christopher David; Geigenmuller, Ute; Raby, Benjamin Alexander; Rennard, Stephen I.; Perrella, Mark A.; Choi, Augustine M.K.; Quackenbush, John; Silverman, Edwin Kepner (Elsevier BV, 2013)
      Hedgehog Interacting Protein (HHIP) was implicated in chronic obstructive pulmonary disease (COPD) by genome-wide association studies (GWAS). However, it remains unclear how HHIP contributes to COPD pathogenesis. To identify ...
    • GeneSigDB: A Manually Curated Database and Resource for Analysis of Gene Expression Signatures 

      Culhane, Aedín C.; Schröder, Markus S.; Sultana, Razvan; Picard, Shaita C.; Martinelli, Enzo N.; Kelly, Caroline; Kapushesky, Misha; St Pierre, Anne-Alyssa; Flahive, William; Gusenleitner, Daniel; Papenhausen, Gerald; O'Connor, Niall; Correll, Mick; Haibe-Kains, Benjamin; Picard, Kermshlise Cathchusca; Quackenbush, John (Oxford University Press, 2012)
      GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized ...
    • GeneSigDB—A Curated Database of Gene Expression Signatures 

      Culhane, Aedín C.; Schwarzl, Thomas; Sultana, Razvan; Picard, Shaita C.; Lu, Tim H.; Franklin, Katherine R.; French, Simon J.; Papenhausen, Gerald; Correll, Mick; Picard, Kermshlise; Quackenbush, John (Oxford University Press, 2009)
      The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are uniquely associated with a specific biological phenotype. Whilst ...
    • Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring 

      Lao, Taotao; Glass, Kimberly; Qiu, Weiliang; Polverino, Francesca; Gupta, Kushagra; Morrow, Jarrett; Mancini, John Dominic; Vuong, Linh; Perrella, Mark A; Hersh, Craig P; Owen, Caroline A; Quackenbush, John; Yuan, Guo-Cheng; Silverman, Edwin K; Zhou, Xiaobo (BioMed Central, 2015)
      Background: The HHIP gene, encoding Hedgehog interacting protein, has been implicated in chronic obstructive pulmonary disease (COPD) by genome-wide association studies (GWAS), and our subsequent studies identified a ...