Browsing HMS Scholarly Articles by Harvard-affiliated Author "Quackenbush, John"

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Browsing HMS Scholarly Articles by Harvard-affiliated Author "Quackenbush, John"

Now showing items 1-20 of 24

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 et al. (BMC Systems Biology, 2014) Link to Published Version
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 et al. (PLoS ONE, 2012) Link to Published Version
Biomarker correlation network in colorectal carcinoma by tumor anatomic location

Nishihara, Reiko; Glass, Kimberly; Mima, Kosuke; Hamada, Tsuyoshi; Nowak, Jonathan A.; Qian, Zhi Rong; Kraft, Peter et al. (BMC Bioinformatics, 2017) Link to Published Version
Bipartite Community Structure of eQTLs

Platig, John; Castaldi, Peter J.; DeMeo, Dawn; Quackenbush, John (PLoS Computational Biology, 2016) Link to Published Version
Challenges and emerging directions in single-cell analysis

Yuan, Guo-Cheng; Cai, Long; Elowitz, Michael; Enver, Tariq; Fan, Guoping; Guo, Guoji; Irizarry, Rafael et al. (Genome Biology, 2017) Link to Published Version
CRX is a Diagnostic Marker of Retinal and Pineal Lineage Tumors

Idbaih, Ahmed; Geffers, Lars; Correll, Mick; Holton, Kristina; Santagata, Sandro; Maire, Cecile; Quackenbush, John et al. (PLoS ONE, 2009) Link to Published Version
Estimating drivers of cell state transitions using gene regulatory network models

Schlauch, Daniel; Glass, Kimberly; Hersh, Craig P.; Silverman, Edwin K.; Quackenbush, John (BMC Systems Biology, 2017) Link to Published Version
Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology

Wu, Weimiao; Parmar, Chintan; Grossmann, Patrick; Quackenbush, John; Lambin, Philippe; Bussink, Johan; Mak, Raymond et al. (Frontiers in Oncology, 2016) Link to Published Version
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. et al. (Genomics, 2013) Link to Published Version
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 et al. (Genome Medicine, 2015) Link to Published Version
Integrated Analysis of Multiple Microarray Datasets Identifies a Reproducible Survival Predictor in Ovarian Cancer

Konstantinopoulos, Panagiotis; Cannistra, Stephen Anthony; Fountzilas, Helen; Culhane, Aedin; Pillay, Kamana; Rueda, Bo Ruben; Cramer, Daniel William et al. (PLoS ONE, 2011) Link to Published Version
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators

Padi, Megha; Quackenbush, John (BMC Systems Biology, 2015) Link to Published Version
Interpreting Cancer Genomes Using Systematic Host Perturbations by Tumour Virus Proteins

Rozenblatt-Rosen, Orit; Deo, Rahul C.; Dricot, Amélie; Askenazi, Manor; Tavares, Maria; Abderazzaq, Fieda; Byrdsong, Danielle et al. (Nature, 2012) Link to Published Version
Merkel Cell Polyomavirus Small T Antigen Promotes Pro-Glycolytic Metabolic Perturbations Required for Transformation

Berrios, Christian; Padi, Megha; Keibler, Mark A.; Park, Donglim Esther; Molla, Vadim; Cheng, Jingwei; Lee, Soo Mi et al. (PLoS Pathogens, 2016) Link to Published Version
A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study

Fountzilas, Elena; Kelly, Andrew D; Francoeur, Nancy; Correll, Mick; Rubio, Renee; Hu, Lan; Perez-Atayde, Antonio Rafael et al. (BMC Genomics, 2012) Link to Published Version
Mitochondrial iron chelation ameliorates cigarette-smoke induced bronchitis and emphysema in mice

Cloonan, Suzanne M.; Glass, Kimberly; Laucho-Contreras, Maria E.; Bhashyam, Abhiram R.; Cervo, Morgan; Pabón, Maria A.; Konrad, Csaba et al. (Nature medicine, 2015) Link to Published Version
Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface

Carette, Xavier; Platig, John; Young, David C.; Helmel, Michaela; Young, Albert T.; Wang, Zhe; Potluri, Lakshmi-Prasad et al. (mBio, 2018) Link to Published Version
A network model for angiogenesis in ovarian cancer

Glass, Kimberly; Quackenbush, John; Spentzos, Dimitrios; Haibe-Kains, Benjamin; Yuan, Guo-Cheng (BMC Bioinformatics, 2015) Link to Published Version
PyPanda: a Python package for gene regulatory network reconstruction

van IJzendoorn, David G.P.; Glass, Kimberly; Quackenbush, John; Kuijjer, Marieke L. (Bioinformatics, 2016) Link to Published Version
Regulatory network changes between cell lines and their tissues of origin

Lopes-Ramos, Camila M.; Paulson, Joseph N.; Chen, Cho-Yi; Kuijjer, Marieke L.; Fagny, Maud; Platig, John; Sonawane, Abhijeet R. et al. (BMC Genomics, 2017) Link to Published Version

Now showing items 1-20 of 24

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