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RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes

Genomics (San Diego, Calif.), 2018-09, Vol.110 (5), p.257-262

Karakülah, Gökhan

2018

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Repeat expression is linked to patient survival and exhibits single nucleotide variation in pancreatic cancer revealing LTR70:r.879A>G

Gene, 2022-05, Vol.822, p.146344-146344, Article 146344

2022

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Expression dynamics of repetitive DNA in early human embryonic development

BMC genomics, 2019-05, Vol.20 (1), p.439-439, Article 439

2019

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PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants

Genomics (San Diego, Calif.), 2017-10, Vol.109 (5-6), p.336-340

2017

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Dysregulated expression of repetitive DNA in ER+/HER2- breast cancer

Cancer genetics, 2019-11, Vol.239, p.36-45

2019

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PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs)

PloS one, 2016-12, Vol.11 (12), p.e0167698-e0167698

2016

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Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival

Turkish journal of biology, 2021-01, Vol.45 (5), p.599-612

2021

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Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence

Turkish journal of biology, 2020-01, Vol.44 (6), p.356-370

2020

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Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations

Infection, genetics and evolution, 2021-07, Vol.91, p.104796-104796, Article 104796

2021

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StemnesScoRe: an R package to estimate the stemness of glioma cancer cells at single-cell resolution

Turkish journal of biology, 2023-01, Vol.47 (6), p.383-392

2023

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"In the light of evolution:" keratins as exceptional tumor biomarkers

PeerJ (San Francisco, CA), 2023-03, Vol.11, p.e15099-e15099, Article e15099

2023

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Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load

PeerJ (San Francisco, CA), 2020-10, Vol.8, p.e10181-e10181, Article e10181

2020

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Alteration of miRNAs in Small Neuron-Derived Extracellular Vesicles of Alzheimer's Disease Patients and the Effect of Extracellular Vesicles on Microglial Immune Responses

Journal of molecular neuroscience, 2022-06, Vol.72 (6), p.1182-1194

2022

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Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research

Progress in retinal and eye research, 2016-11, Vol.55, p.1-31

2016

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Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment

Journal of autism and developmental disorders, 2023-03, Vol.53 (3), p.1091-1106

2023

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In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

Genes, 2018-06, Vol.9 (6), p.284

2018

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NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors

Cell reports (Cambridge), 2016-11, Vol.17 (9), p.2460-2473

2016

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Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp

PeerJ (San Francisco, CA), 2020-08, Vol.8, p.e9703-e9703, Article e9703

2020

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TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model

PeerJ (San Francisco, CA), 2019-12, Vol.7, p.e8192-e8192, Article e8192

2019

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Retinoids and EZH2 inhibitors cooperate to orchestrate anti-oncogenic effects on bladder cancer cells

Cancer gene therapy, 2024-04, Vol.31 (4), p.537-551

2024

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TRAIL promotes the polarization of human macrophages toward a proinflammatory M1 phenotype and is associated with increased survival in cancer patients with high tumor macrophage content

Frontiers in immunology, 2023-09, Vol.14, p.1209249-1209249

2023

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Current mutatome of SARS-CoV-2 in Turkey reveals mutations of interest

Turkish journal of biology, 2021-01, Vol.45 (1), p.104-113

2021

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Alternative splicing and gene co-expression network-based analysis of dizygotic twins with autism-spectrum disorder and their parents

Genomics (San Diego, Calif.), 2021-07, Vol.113 (4), p.2561-2571

2021

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In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia

International journal of molecular sciences, 2021-09, Vol.22 (17), p.9601

2021

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Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach

PeerJ (San Francisco, CA), 2022-10, Vol.10, p.e14149-e14149, Article e14149

2022

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RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes

Repeat expression is linked to patient survival and exhibits single nucleotide variation in pancreatic cancer revealing LTR70:r.879A>G

Expression dynamics of repetitive DNA in early human embryonic development

PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants

Dysregulated expression of repetitive DNA in ER+/HER2- breast cancer

PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs)

Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival

Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence

Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations

StemnesScoRe: an R package to estimate the stemness of glioma cancer cells at single-cell resolution

"In the light of evolution:" keratins as exceptional tumor biomarkers

Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load

Alteration of miRNAs in Small Neuron-Derived Extracellular Vesicles of Alzheimer's Disease Patients and the Effect of Extracellular Vesicles on Microglial Immune Responses

Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research

Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment

In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors

Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp

TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model

Retinoids and EZH2 inhibitors cooperate to orchestrate anti-oncogenic effects on bladder cancer cells

TRAIL promotes the polarization of human macrophages toward a proinflammatory M1 phenotype and is associated with increased survival in cancer patients with high tumor macrophage content

Current mutatome of SARS-CoV-2 in Turkey reveals mutations of interest

Alternative splicing and gene co-expression network-based analysis of dizygotic twins with autism-spectrum disorder and their parents

In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia

Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach

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