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  1. Book ; Online: Recent Developments in Cancer Systems Biology

    Sinha, Raghu / Arga, Kazim Yalcin

    2021  

    Keywords Medicine ; Sestrin2 ; lung cancer ; knockdown ; cancer progression ; bioinformatics ; patient survival ; lung adenocarcinoma ; circulating miR-1246 ; glycosaminoglycan binding ; prognosis ; PI3K-Akt signaling pathways ; TargetScan ; UBE2C ; cancer systems biology ; experimental model systems ; next-generation sequencing ; single-cell sequencing ; patient-derived xenografts ; patient-derived organoids ; triple-negative breast cancer ; personalized medicine ; computational methods ; drug repurposing ; clinical trials ; cancer stem cells ; ETS ; Elk-1 ; stem cell ; microarray ; brain-tumor-initiating cell (BTIC) ; pancreatic cancer ; systems biology ; omics ; biomarker ; genomics ; transcriptomics ; proteomics ; metabolomics ; glycomics ; metagenomics ; Ets ; PEA3 ; Ets-1 ; glioma ; optical genome mapping ; solid tumors ; cancer genomics ; breast ; ovarian ; cancer ; TCGA ; non-small-cell lung cancer ; lung adenocarcinoma (LUAD) ; lung squamous cell carcinoma (LUSC) ; differential expression ; SNV ; CNV ; risk group ; signature ; survival ; renal cancers ; protein interactome ; diagnostic biomarker ; prognostic biomarker ; virtual screening ; docking ; acute myeloid leukemia ; Boolean model ; drug resistance ; network ; n/a
    Size 1 electronic resource (272 pages)
    Publisher MDPI - Multidisciplinary Digital Publishing Institute
    Publishing place Basel, Switzerland
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021291572
    ISBN 9783036514710 ; 3036514716
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Tumor Mutation Burden as a Cornerstone in Precision Oncology Landscapes: Effect of Panel Size and Uncertainty in Cutoffs.

    Budak, Betul / Arga, Kazim Yalcin

    Omics : a journal of integrative biology

    2024  Volume 28, Issue 4, Page(s) 193–203

    Abstract: Tumor mutation burden (TMB) has profound implications for personalized cancer therapy, particularly immunotherapy. However, the size of the panel and the cutoff values for an accurate determination of TMB are still controversial. In this study, a pan- ... ...

    Abstract Tumor mutation burden (TMB) has profound implications for personalized cancer therapy, particularly immunotherapy. However, the size of the panel and the cutoff values for an accurate determination of TMB are still controversial. In this study, a pan-cancer analysis was performed on 22 cancer types from The Cancer Genome Atlas. The efficiency of gene panels of different sizes and the effect of cutoff values in accurate TMB determination was assessed on a large cohort using Whole Exome Sequencing data (
    MeSH term(s) Humans ; Neoplasms/genetics ; Neoplasms/therapy ; Precision Medicine/methods ; Mutation ; Biomarkers, Tumor/genetics ; Exome Sequencing/methods
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2024-04-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2024.0015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A Differential Transcriptional Regulome Approach to Unpack Cancer Biology: Insights on Renal Cell Carcinoma Subtypes.

    Caliskan, Aysegul / Arga, Kazim Yalcin

    Omics : a journal of integrative biology

    2023  Volume 27, Issue 11, Page(s) 536–545

    Abstract: Cancer research calls for new approaches that account for the regulatory complexities of biology. We present, in this study, the differential transcriptional regulome (DIFFREG) approach for the identification and prioritization of key transcriptional ... ...

    Abstract Cancer research calls for new approaches that account for the regulatory complexities of biology. We present, in this study, the differential transcriptional regulome (DIFFREG) approach for the identification and prioritization of key transcriptional regulators and apply it to the case of renal cell carcinoma (RCC) biology. Of note, RCC has a poor prognosis and the biomarker and drug discovery studies to date have tended to focus on gene expression independent from mutations and/or post-translational modifications. DIFFREG focuses on the differential regulation between transcription factors (TFs) and their target genes rather than differential gene expression and integrates transcriptome profiling with the human transcriptional regulatory network to analyze differential gene regulation between healthy and RCC cases. In this study, RNA-seq tissue samples (
    MeSH term(s) Humans ; Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/metabolism ; Carcinoma, Renal Cell/pathology ; Kidney Neoplasms/genetics ; Kidney Neoplasms/diagnosis ; Kidney Neoplasms/pathology ; Gene Expression Profiling ; Biomarkers ; Biology
    Chemical Substances Biomarkers
    Language English
    Publishing date 2023-11-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2023.0167
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: HPV16 status predicts potential protein biomarkers and therapeutics in head and neck squamous cell carcinoma.

    Kori, Medi / Arga, Kazim Yalcin

    Virology

    2023  Volume 582, Page(s) 90–99

    Abstract: Human papillomavirus (HPV) infection, especially HPV16, is one of the causative factors for the development of head and neck squamous cell (HNSC) carcinoma. HPV-positive and HPV-negative HNSC patients differ significantly in their molecular profiles and ... ...

    Abstract Human papillomavirus (HPV) infection, especially HPV16, is one of the causative factors for the development of head and neck squamous cell (HNSC) carcinoma. HPV-positive and HPV-negative HNSC patients differ significantly in their molecular profiles and clinical features, so they should be evaluated differently depending on their HPV status. Given the tremendous variation in HNSC cancers depending on HPV, our goal in this study was to present biomarkers and treatment options tailored to the patient's HPV status. Gene expression levels of HPV16-positive and -negative patients were used as proxies, and the differential interactome algorithm was employed to identify the differential interacting proteins (DIPs). By assessing the prognostic capabilities and druggabilities of DIPs and their interacting partners (DIP-centered modules), we introduce eight modules as potential biomarkers specialized for either positive or negative phenotype. Finally, raloxifene was repositioned for the first time as a drug candidate for the treatment of HPV16-positive HNSC patients.
    MeSH term(s) Human papillomavirus 16/genetics ; Head and Neck Neoplasms/drug therapy ; Head and Neck Neoplasms/pathology ; Head and Neck Neoplasms/virology ; Prognosis ; Biomarkers, Tumor/analysis ; Protein Interaction Maps ; Humans ; Gene Expression Profiling
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2023-04-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2023.03.013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.172: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Pharmacomicrobiomics-Guided Precision Oncology: A New Frontier of P4 (Predictive, Personalized, Preventive, and Participatory) Medicine and Microbiome-Based Therapeutics.

    Arga, Kazim Yalcin / Attia, Heba / Aziz, Ramy K

    Omics : a journal of integrative biology

    2024  Volume 28, Issue 1, Page(s) 5–7

    Abstract: Pharmacomicrobiomics is a rapidly developing field that promises to make significant contributions to predictive, personalized, preventive, and participatory (P4) medicine. This is becoming evident particularly in the field of precision (P4) oncology by ... ...

    Abstract Pharmacomicrobiomics is a rapidly developing field that promises to make significant contributions to predictive, personalized, preventive, and participatory (P4) medicine. This is becoming evident particularly in the field of precision (P4) oncology by taking seriously the crucial role microbiome plays in health and disease. Several studies have already shown that clinicians can harness insights from the microbiome to better predict treatment response, reduce side effects, and improve overall outcomes for cancer patients. Furthermore, pharmacomicrobiomics will undoubtedly play a crucial role in shaping the future of cancer treatment in the era of P4 oncology as we continue to unravel the intricate relationships between the microbiome and cancer. This perspective and innovation analysis discusses the emerging intersection of P4 medicine and P4 oncology, as seen through a lens of pharmacomicrobiomics. A key promise of pharmacomicrobiomics is the development of personalized microbiome-based therapeutics. In all, we suggest that optimizing cancer treatment and prevention by harnessing pharmacomicrobiomics has vast potentials for precision oncology, and personalized medicine using the right drug, at the right dose, for the right patient, and at the right time.
    MeSH term(s) Humans ; Precision Medicine ; Neoplasms/drug therapy ; Neoplasms/prevention & control ; Microbiota
    Language English
    Publishing date 2024-01-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2023.0254
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The Versatility of Plectin in Cancer: A Pan-Cancer Analysis on Potential Diagnostic and Prognostic Impacts of Plectin Isoforms.

    Gundesli, Hulya / Kori, Medi / Arga, Kazim Yalcin

    Omics : a journal of integrative biology

    2023  Volume 27, Issue 6, Page(s) 281–296

    Abstract: Plectin, encoded ... ...

    Abstract Plectin, encoded by
    MeSH term(s) Humans ; Plectin/genetics ; Plectin/metabolism ; Prognosis ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Neoplasms/diagnosis ; Neoplasms/genetics
    Chemical Substances Plectin ; Protein Isoforms
    Language English
    Publishing date 2023-06-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2023.0053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Editorial: Omics integration and network medicine to decipher human complex diseases.

    Zanfardino, Mario / Babbi, Giulia / Arga, Kazim Yalcin / Pane, Katia

    Frontiers in genetics

    2023  Volume 14, Page(s) 1119967

    Language English
    Publishing date 2023-03-31
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1119967
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Human oncogenic viruses: an overview of protein biomarkers in viral cancers and their potential use in clinics.

    Kori, Medi / Arga, Kazim Yalcin

    Expert review of anticancer therapy

    2022  Volume 22, Issue 11, Page(s) 1211–1224

    Abstract: Introduction: Although the idea that carcinogenesis might be caused by viruses was first voiced about 100 years ago, today's data disappointingly show that we have not made much progress in preventing and/or treating viral cancers in a century. ... ...

    Abstract Introduction: Although the idea that carcinogenesis might be caused by viruses was first voiced about 100 years ago, today's data disappointingly show that we have not made much progress in preventing and/or treating viral cancers in a century. According to recent studies, infections are responsible for approximately 13% of cancer development in the world. Today, it is accepted and proven by many authorities that Epstein-Barr virus (EBV), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Human Herpesvirus 8 (HHV8), Human T-cell Lymphotropic virus 1 (HTLV1) and highly oncogenic Human Papillomaviruses (HPVs) cause or/and contribute to cancer development in humans.
    Areas covered: Considering the insufficient prevention and/or treatment strategies for viral cancers, in this review we present the current knowledge on protein biomarkers of oncogenic viruses. In addition, we aimed to decipher their potential for clinical use by evaluating whether the proposed biomarkers are expressed in body fluids, are druggable, and act as tumor suppressors or oncoproteins.
    Expert opinion: Consequently, we believe that this review will shed light on researchers and provide a guide to find remarkable solutions for the prevention and/or treatment of viral cancers.
    MeSH term(s) Humans ; Oncogenic Viruses ; Epstein-Barr Virus Infections/complications ; Herpesvirus 4, Human ; Neoplasms/pathology ; Carcinogenesis ; Biomarkers
    Chemical Substances Biomarkers
    Language English
    Publishing date 2022-11-05
    Publishing country England
    Document type Review ; Journal Article
    ZDB-ID 2112544-2
    ISSN 1744-8328 ; 1473-7140
    ISSN (online) 1744-8328
    ISSN 1473-7140
    DOI 10.1080/14737140.2022.2139681
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5907: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: HPV16 status predicts potential protein biomarkers and therapeutics in head and neck squamous cell carcinoma

    Kori, Medi / Arga, Kazim Yalcin

    Virology. 2023 May, v. 582 p.90-99

    2023  

    Abstract: Human papillomavirus (HPV) infection, especially HPV16, is one of the causative factors for the development of head and neck squamous cell (HNSC) carcinoma. HPV-positive and HPV-negative HNSC patients differ significantly in their molecular profiles and ... ...

    Abstract Human papillomavirus (HPV) infection, especially HPV16, is one of the causative factors for the development of head and neck squamous cell (HNSC) carcinoma. HPV-positive and HPV-negative HNSC patients differ significantly in their molecular profiles and clinical features, so they should be evaluated differently depending on their HPV status. Given the tremendous variation in HNSC cancers depending on HPV, our goal in this study was to present biomarkers and treatment options tailored to the patient's HPV status. Gene expression levels of HPV16-positive and -negative patients were used as proxies, and the differential interactome algorithm was employed to identify the differential interacting proteins (DIPs). By assessing the prognostic capabilities and druggabilities of DIPs and their interacting partners (DIP-centered modules), we introduce eight modules as potential biomarkers specialized for either positive or negative phenotype. Finally, raloxifene was repositioned for the first time as a drug candidate for the treatment of HPV16-positive HNSC patients.
    Keywords Papillomaviridae ; algorithms ; biomarkers ; carcinoma ; drugs ; gene expression ; head ; head and neck squamous cell carcinoma ; humans ; patients ; phenotype ; therapeutics ; virology ; HPV16 ; Differential interactome ; System biomarkers ; Raloxifene
    Language English
    Dates of publication 2023-05
    Size p. 90-99.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2023.03.013
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 3686: Show issues

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  10. Article: Drug repositioning

    Kori, Medi / Turanli, Beste / Arga, Kazim Yalcin

    Frontiers in oncology

    2023  Volume 13, Page(s) 1096081

    Abstract: Introduction: Integrating interaction data with biological knowledge can be a critical approach for drug development or drug repurposing. In this context, host-pathogen-protein-protein interaction (HP-PPI) networks are useful instrument to uncover the ... ...

    Abstract Introduction: Integrating interaction data with biological knowledge can be a critical approach for drug development or drug repurposing. In this context, host-pathogen-protein-protein interaction (HP-PPI) networks are useful instrument to uncover the phenomena underlying therapeutic effects in infectious diseases, including cervical cancer, which is almost exclusively due to human papillomavirus (HPV) infections. Cervical cancer is one of the second leading causes of death, and HPV16 and HPV18 are the most common subtypes worldwide. Given the limitations of traditionally used virus-directed drug therapies for infectious diseases and, at the same time, recent cancer statistics for cervical cancer cases, the need for innovative treatments becomes clear.
    Methods: Accordingly, in this study, we emphasize the potential of host proteins as drug targets and identify promising host protein candidates for cervical cancer by considering potential differences between HPV subtypes (i.e., HPV16 and HPV18) within a novel bioinformatics framework that we have developed. Subsequently, subtype-specific HP-PPI networks were constructed to obtain host proteins. Using this framework, we next selected biologically significant host proteins. Using these prominent host proteins, we performed drug repurposing analysis. Finally, by following our framework we identify the most promising host-oriented drug candidates for cervical cancer.
    Results: As a result of this framework, we discovered both previously associated and novel drug candidates, including interferon alfacon-1, pimecrolimus, and hyaluronan specifically for HPV16 and HPV18 subtypes, respectively.
    Discussion: Consequently, with this study, we have provided valuable data for further experimental and clinical efforts and presented a novel bioinformatics framework that can be applied to any infectious disease.
    Language English
    Publishing date 2023-01-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2023.1096081
    Database MEDical Literature Analysis and Retrieval System OnLINE

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