Browsing Det medisinske fakultet by Author "Quackenbush, John"

Now showing items 1-10 of 10

  • Clustering Sparse Data with Feature Correlation with Application to Discover Subtypes in Cancer 
    Qiang, Jipeng; Ding, Wei; Kuijjer, Marieke Lydia; Quackenbush, John; Chen, Ping (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    In this paper, given data with high-dimensional features, we study this problem of how to calculate the similarity between two samples by considering feature interaction network, where a feature interaction network represents ...
  • Estimating Sample-Specific Regulatory Networks 
    Kuijjer, Marieke Lydia; Tung, Matthew George; Yuan, GuoCheng; Quackenbush, John; Glass, Kimberly (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2019)
    Biological systems are driven by intricate interactions among molecules. Many methods have been developed that draw on large numbers of expression samples to infer connections between genes (or their products). The result ...
  • gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit 
    Guebila, Marouen Ben; Morgan, Daniel C.; Glass, Kimberly; Kuijjer, Marieke; Demeo, Dawn L.; Quackenbush, John (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Abstract Gene regulatory network inference allows for the modeling of genome-scale regulatory processes that are altered during development, in disease, and in response to perturbations. Our group has developed ...
  • GRAND: a database of gene regulatory network models across human conditions 
    Ben Guebila, Marouen; Lopes-Ramos, Camila; Weighill, Deborah; Sonawane, Abhijeet; Burkholz, Rebekka; Shamsaei, Behrouz; Platig, John; Glass, Kimberly; Kuijjer, Marieke; Quackenbush, John (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Abstract Gene regulation plays a fundamental role in shaping tissue identity, function, and response to perturbation. Regulatory processes are controlled by complex networks of interacting elements, including ...
  • lionessR: single sample network inference in R 
    Kuijjer, Marieke L; Hsieh, Ping-Han; Quackenbush, John; Glass, Kimberly (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2019)
    Background In biomedical research, network inference algorithms are typically used to infer complex association patterns between biological entities, such as between genes or proteins, using data from a ...
  • Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function 
    Fagny, Maud; Platig, John; Kuijjer, Marieke Lydia; Lin, Xihong; Quackenbush, John (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    Background Genome-wide association studies (GWASes) have identified many noncoding germline single-nucleotide polymorphisms (SNPs) that are associated with an increased risk of developing cancer. However, how these SNPs ...
  • PUMA: PANDA Using MicroRNA Associations 
    Kuijjer, Marieke Lydia; Fagny, Maud; Marin, Alessandro; Quackenbush, John; Glass, Kimberly (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    Abstract Motivation Conventional methods to analyze genomic data do not make use of the interplay between multiple factors, such as between microRNAs (miRNAs) and the messenger RNA (mRNA) ...
  • Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme 
    Lopes-Ramos, Camila; Belova, Tatiana; Brunner, Tess; Ben Guebila, Marouen; Osorio, Daniel; Quackenbush, John; Kuijjer, Marieke (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2021)
    Glioblastoma is an aggressive cancer of the brain and spine. While analysis of glioblastoma ‘omics data has somewhat improved our understanding of the disease, it has not led to direct improvement in patient survival. ...
  • Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues 
    Lopes-ramos, Camila; Chen, Cho-Yi; Kuijjer, Marieke Lydia; Paulson, Joseph N.; Sonawane, Abhijeet; Fagny, Maud; Platig, John; Glass, Kimberly; Quackenbush, John; DeMeo, Dawn L. (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    Sex differences manifest in many diseases and may drive sex-specific therapeutic responses. To understand the molecular basis of sex differences, we evaluated sex-biased gene regulation by constructing sample-specific gene ...
  • The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks 
    Ben Guebila, Marouen; Wang, Tian; Lopes-Ramos, Camila M.; Fanfani, Viola; Weighill, Des; Burkholz, Rebekka; Schlauch, Daniel; Paulson, Joseph N.; Altenbuchinger, Michael; Shutta, Katherine H.; Sonawane, Abhijeet R.; Lim, James; Calderer, Genis; van IJzendoorn, David G.; Morgan, Daniel; Marin, Alessandro; Chen, Cho-Yi; Song, Qi; Saha, Enakshi; DeMeo, Dawn L.; Padi, Megha; Platig, John; Kuijjer, Marieke L.; Glass, Kimberly; Quackenbush, John (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2023)
    Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer ...