publications

publications and selected abstracts in reversed chronological order.

2024

  1. nSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
    Zhihan Zhang, Christiana Wang, Ziyin Zhao, and 4 more authors
    In PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024 , 2024
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  2. Human alveolar macrophages display marked hypo-responsiveness to IFN-γin both proteomic and gene expression analysis
    Bonnie A Thiel, Kathleen C Lundberg, Daniela Schlatzer, and 8 more authors
    Plos one, 2024
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  3. Inflammation and cytoskeleton pathway gene expression relates to rate of clinical progression in individuals with Alzheimers disease
    Gurkan Bebek, Hyun Jo Kim, Penelope Benchek, and 4 more authors
    In Alzheimerś Association International Conference , 2024
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  4. CSF immune cell phenotypes and their related pathway activation differ by Alzheimers disease stage compared to normal controls
    Gurkan Bebek, Ziyin Zhao, Mi-Hyun Hwang, and 2 more authors
    In Alzheimer’s Association International Conference , 2024
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  5. CADRE: Utilizing CAncer Drug Response nEtwork for Drug Synergy Prediction
    Chunguang Lai, Arda Durmaz, Doug Brubaker, and 1 more author
    In , 2024
    Presented at the RECOMB CCB 2024

2023

  1. Transcriptomic analysis of lung development in wildtype and CFTR-/- sheep suggests an early inflammatory signature in the CF distal lung
    Jenny L Kerschner, Alekh Paranjapye, Makayla Schacht, and 8 more authors
    Functional & Integrative Genomics, 2023
  2. Microbiome, socioeconomic status (SES), fiber intake, and response to checkpoint inhibitor therapy in patients with non-small cell lung cancer (NSCLC): A pilot study.
    Monaliben Patel, Gurkan Bebek, Brandon Vu, and 3 more authors
    2023
  3. CSF immune cell phenotypes and their related pathway activation differ in MCI stage of Alzheimer’s disease compared to controls
    Gurkan Bebek, Mi-Hyun Hwang, Ziyin Zhao, and 4 more authors
    In Alzheimer’s Association International Conference , 2023

2022

  1. Hypo-responsiveness of human alveolar macrophages to IFN-γis not due to attenuated STAT1 signaling
    Bonnie A Thiel, Kathleen C Lundberg, Daniela Schlatzer, and 8 more authors
    bioRxiv, 2022

2021

  1. Piwil1 regulates glioma stem cell maintenance and glioblastoma progression
    Haidong Huang, Xingjiang Yu, Xiangzi Han, and 8 more authors
    Cell reports, 2021
  2. TNFRSF1B gene variants and related soluble TNFR2 levels impact resilience in Alzheimer’s disease
    Jagan A Pillai, Gurkan Bebek, Maria Khrestian, and 5 more authors
    Frontiers in aging neuroscience, 2021
  3. Evaluation of microbiome alterations following consumption of BIOHM, a novel probiotic
    Mahmoud A Ghannoum, Thomas S McCormick, Mauricio Retuerto, and 5 more authors
    Current issues in molecular biology, 2021

2020

  1. Role for Specific Inflammatory Pathway Analytes Predicting Clinical Progression in MCI Stage of Alzheimer’s Disease (4466)
    Jagan Pillai, Gurkan Bebek, James Bena, and 4 more authors
    Neurology, 2020
  2. The transcriptional repressor BCL11A promotes breast cancer metastasis
    Darcie D Seachrist, Molly M Hannigan, Natasha N Ingles, and 8 more authors
    Journal of Biological Chemistry, 2020
  3. Inflammatory pathway analytes predicting rapid cognitive decline in MCI stage of Alzheimer’s disease
    Jagan A Pillai, James Bena, Gurkan Bebek, and 8 more authors
    Annals of Clinical and Translational Neurology, 2020
  4. A functional genomics approach to investigate the differentiation of iPSCs into lung epithelium at air-liquid interface
    Jenny L Kerschner, Alekh Paranjapye, Shiyi Yin, and 4 more authors
    Journal of cellular and molecular medicine, 2020
  5. Frequent subgraph mining of functional interaction patterns across multiple cancers
    Arda Durmaz, Tim AD Henderson, and Gurkan Bebek
    In BIOCOMPUTING 2021: Proceedings of the Pacific Symposium , 2020

2018

  1. Hypoxic induction of vasorin regulates Notch1 turnover to maintain glioma stem-like cells
    Jianghong Man, Xingjiang Yu, Haidong Huang, and 8 more authors
    Cell stem cell, 2018
  2. PARP1 is up-regulated in non-small cell lung cancer tissues in the presence of the cyanobacterial toxin microcystin
    Patrick L Apopa, Lisa Alley, Rosalind B Penney, and 8 more authors
    Frontiers in microbiology, 2018

2017

  1. Frequent subgraph mining of personalized signaling pathway networks groups patients with frequently dysregulated disease pathways and predicts prognosis
    Arda Durmaz, Tim AD Henderson, Douglas Brubaker, and 1 more author
    In PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017 , 2017
  2. Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas
    Hannah Wang, Pauline Funchain, Gurkan Bebek, and 7 more authors
    Genome medicine, 2017
  3. Mitotic vulnerability in triple-negative breast cancer associated with LIN9 is targetable with BET inhibitors
    Jennifer M Sahni, Sylvia S Gayle, Bryan M Webb, and 8 more authors
    Cancer research, 2017
  4. Network based model of social media big data predicts contagious disease diffusion
    Lauren S Elkin, Kamil Topal, and Gurkan Bebek
    Information discovery and delivery, 2017
  5. Identifying gene interaction networks
    Danica Wiredja, and Gurkan Bebek
    Statistical Human Genetics: Methods and Protocols, 2017
  6. LIN9 is a mitotic vulnerability in triple-negative breast cancer that is targetable with BET inhibitors.
    JM Sahni, SS Gayle, BM Webb, and 7 more authors
    In MOLECULAR BIOLOGY OF THE CELL , 2017
  7. Functional Characteristics of Cancer Driver Genes in Colorectal Cancer
    Gurkan Bebek
    Case Western Reserve University , 2017

2016

  1. Neural transcriptome of constitutional Pten dysfunction in mice and its relevance to human idiopathic autism spectrum disorder
    Amanda K Tilot, Gurkan Bebek, Farshad Niazi, and 4 more authors
    Molecular psychiatry, 2016
  2. Proteome dynamics reveals pro-inflammatory remodeling of plasma proteome in a mouse model of NAFLD
    Ling Li, Gurkan Bebek, Stephen F Previs, and 5 more authors
    Journal of proteome research, 2016
  3. BET protein inhibition blocks growth of triple-negative breast cancer by inducing mitotic and cytokinetic dysfunction
    Jennifer M Brancato, Sylvia Gayle, Kristen Weber-Bonk, and 3 more authors
    Cancer Research, 2016

2015

  1. Proteomic and bioinformatics profile of paired human alveolar macrophages and peripheral blood monocytes
    Sara E Tomechko, Kathleen C Lundberg, Jessica Jarvela, and 7 more authors
    Proteomics, 2015
  2. Abstract B1-43: Cancer drug response networks built for comparative cancer pharmacogenomics identifies combination therapies for repositioning
    Douglas Brubaker, Elena Svenson, Smith Kai, and 5 more authors
    Cancer Research, 2015
  3. Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response
    Xing-Huang Gao, Dawid Krokowski, Bo-Jhih Guan, and 8 more authors
    elife, 2015
  4. Cancer drug response networks built for comparative cancer pharmacogenomics identifies combination therapies for repositioning
    Douglas Brubaker, Elena Svenson, Smith Kai, and 5 more authors
    In CANCER RESEARCH , 2015

2014

  1. Drug intervention response predictions with PARADIGM (DIRPP) identifies drug resistant cancer cell lines and pathway mechanisms of resistance
    Douglas Brubaker, Analisa Difeo, Yanwen Chen, and 5 more authors
    In Biocomputing 2014 , 2014
  2. Germline alterations in RASAL1 in Cowden syndrome patients presenting with follicular thyroid cancer and in individuals with apparently sporadic epithelial thyroid cancer
    Joanne Ngeow, Ying Ni, Rita Tohme, and 3 more authors
    The Journal of Clinical Endocrinology & Metabolism, 2014
  3. Hypomethylation of the MMP7 promoter and increased expression of MMP7 distinguishes the basal-like breast cancer subtype from other triple-negative tumors
    Steven T Sizemore, Gina M Sizemore, Christine N Booth, and 6 more authors
    Breast cancer research and treatment, 2014
  4. Germline Alterations in RASAL1 in PTEN Wildtype Cowden Syndrome Patients Presenting with Follicular Thyroid Cancer and in Individuals with Apparently Sporadic Epithelial Thyroid Cancer
    Joanne Ngeow, Gurkan Bebek, Rita Tohme, and 3 more authors
    In ENDOCRINE REVIEWS , 2014
  5. Integrative pathway analysis of molecular profiles of glioblastoma multiforme for predicting patient survival
    Arda Durmaz, Douglas Brubaker, and Gurkan Bebek
    Cancer Research, 2014
  6. A125: immunomodulatory factors produced by mesenchymal stem cells after in vitro priming with danger signals
    Hulya Bukulmez, Asuman Bilgin, Gurkan Bebek, and 2 more authors
    Arthritis & Rheumatology, 2014

2013

  1. FOXA1 represses the molecular phenotype of basal breast cancer cells
    Gina M Bernardo, Gurkan Bebek, Charles L Ginther, and 8 more authors
    Oncogene, 2013
  2. Proteomic analysis of synovial fluid from the osteoarthritic knee: comparison with transcriptome analyses of joint tissues
    Susan Y Ritter, Roopashree Subbaiah, Gurkan Bebek, and 8 more authors
    Arthritis & Rheumatism, 2013
  3. Post-NGS: Interpretation and analysis of next generation sequencing data for basic and translational science
    Gurkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, and 2 more authors
    In Biocomputing 2013 , 2013
  4. Identification of mutated peptides/proteins driving cancer phenotype utilizing improved shotgun proteomics and data analysis approaches.
    Gurkan Bebek, Giridharan Gokulrangan, Hua Xu, and 1 more author
    Cancer Research, 2013

2012

  1. Specific kinesin expression profiles associated with taxane resistance in basal-like breast cancer
    Min Han Tan, Sarmishtha De, Gurkan Bebek, and 6 more authors
    Breast cancer research and treatment, 2012
  2. Chromosome 3 status in uveal melanoma: a comparison of fluorescence in situ hybridization and single-nucleotide polymorphism array
    Arun D Singh, Mary E Aronow, Yang Sun, and 7 more authors
    Investigative ophthalmology & visual science, 2012
  3. Integrative genomic analysis reveals extended germline homozygosity with lung cancer risk in the PLCO cohort
    Mohammed S Orloff, Li Zhang, Gurkan Bebek, and 1 more author
    PloS one, 2012
  4. Integrated analysis reveals critical genomic regions in prostate tumor microenvironment associated with clinicopathologic phenotypes
    Shingo Ashida, Mohammed S Orloff, Gurkan Bebek, and 4 more authors
    Clinical Cancer Research, 2012
  5. Network biology methods integrating biological data for translational science
    Gurkan Bebek, Mehmet Koyutürk, Nathan D Price, and 1 more author
    Briefings in bioinformatics, 2012
  6. Microbiomic subprofiles and MDR1 promoter methylation in head and neck squamous cell carcinoma
    Gurkan Bebek, Kristi L Bennett, Pauline Funchain, and 5 more authors
    Human molecular genetics, 2012
  7. Magnet: Microarray gene expression and network evaluation toolkit
    George C Linderman, Mark R Chance, and Gurkan Bebek
    Nucleic acids research, 2012
  8. Proteomic and bioinformatic profile of primary human oral epithelial cells
    Santosh K Ghosh, Elizabeth Yohannes, Gurkan Bebek, and 6 more authors
    Journal of proteome research, 2012
  9. Identifying gene interaction networks
    Gurkan Bebek
    Statistical human genetics: methods and protocols, 2012
  10. Correlation of microbiomic profiles with disease status and MDR1 methylation in head and neck squamous cell carcinoma (HNSCC).
    Pauline Funchain, Gurkan Bebek, Kristi L Bennett, and 2 more authors
    2012

2011

  1. Identification of a central role for complement in osteoarthritis
    Qian Wang, Andrew L Rozelle, Christin M Lepus, and 8 more authors
    Nature medicine, 2011
  2. DADA: degree-aware algorithms for network-based disease gene prioritization
    Sinan Erten, Gurkan Bebek, Rob M Ewing, and 1 more author
    BioData mining, 2011
  3. Disease gene prioritization based on topological similarity in protein-protein interaction networks
    Sinan Erten, Gurkan Bebek, and Mehmet Koyutürk
    In Research in Computational Molecular Biology: 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings 15 , 2011
  4. Germline mutations in MSR1, ASCC1, and CTHRC1 in patients with Barrett esophagus and esophageal adenocarcinoma
    Mohammed Orloff, Charissa Peterson, Xin He, and 8 more authors
    JAmA, 2011
  5. Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks
    Sinan Erten, Gurkan Bebek, and Mehmet Koyutürk
    Journal of computational biology, 2011
  6. Microenvironmental genomic alterations reveal signaling networks for head and neck squamous cell carcinoma
    Gurkan Bebek, Mohammed Orloff, and Charis Eng
    Journal of clinical bioinformatics, 2011
  7. INTEGRATIVE–OMICS FOR TRANSLATIONAL SCIENCE–Session Introduction
    Gurkan Bebek, Mehmet Koyutürk, Mark R Chance, and 1 more author
    In Biocomputing 2011 , 2011
  8. BiC: a web server for calculating bimodality of coexpression between gene and protein networks
    George C Linderman, Vishal N Patel, Mark R Chance, and 1 more author
    Bioinformatics, 2011
  9. Pacific symposium on biocomputing 2011
    Gurkan Bebek, Mark Chance, Mehmet Koyuturk, and 8 more authors
    In Pacific Symposium on Biocomputing 2011, PSB 2011 , 2011

2010

  1. Prediction and testing of biological networks underlying intestinal cancer
    Vishal N Patel, Gurkan Bebek, John M Mariadason, and 3 more authors
    PLoS One, 2010
  2. PETALS: Proteomic evaluation and topological analysis of a mutated locus’ signaling
    Gurkan Bebek, Vishal Patel, and Mark R Chance
    BMC bioinformatics, 2010

2009

  1. Phylogenetic analysis of modularity in protein interaction networks
    Sinan Erten, Xin Li, Gurkan Bebek, and 2 more authors
    BMC bioinformatics, 2009
  2. Comparative analysis of modularity in biological systems
    Xin Li, Sinan Erten, Gurkan Bebek, and 2 more authors
    In 2009 Ohio Collaborative Conference on Bioinformatics , 2009

2007

  1. PathFinder: mining signal transduction pathway segments from protein-protein interaction networks
    Gurkan Bebek, and Jiong Yang
    BMC bioinformatics, 2007
  2. Analyzing and modeling large biological networks: Inferring signal transduction pathways
    Gurkan Bebek
    Case Western Reserve University , 2007
  3. Accurate Elimination of False Protein-Protein Interactions
    Gurkan Bebek, and Keiji Takamoto
    RECOMB 2007, 2007

2006

  1. The degree distribution of the generalized duplication model
    Gürkan Bebek, Petra Berenbrink, Colin Cooper, and 3 more authors
    Theoretical Computer Science, 2006
  2. Improved duplication models for proteome network evolution
    Gürkan Bebek, Petra Berenbrink, Colin Cooper, and 3 more authors
    In Systems Biology and Regulatory Genomics: Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers , 2006

2005

  1. Topological properties of proteome networks
    G Bebek, P Berenbrink, C Cooper, and 3 more authors
    In Proceedings of RECOMB satellite meeting on System Biology. LNBI, Springer , 2005

2002

  1. Anti-Tamper Databases: Inference control techniques
    G Bebek
    unpublished paper, 2002