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  1. AU="Suner, Asli"
  2. AU="Charles Thickstun"
  3. AU="Tatar, Emel Cadalli"
  4. AU="Shcherbakova Tatyana"
  5. AU="Coats, Brittany"
  6. AU="Monte, Natasha"
  7. AU="Sarma, D.K."
  8. AU=Deng Lisi AU=Deng Lisi
  9. AU=Deshmukh V
  10. AU="Gutiérrez-García, Carmen"
  11. AU="Johnson, Sally"
  12. AU="Sousa, Amanda Freire Tamburini"
  13. AU="Cronin, Chunxia"
  14. AU=Weder W
  15. AU="Nirja Thakur"
  16. AU="Jiang, Shimin"
  17. AU="Wu, Xue-Ying"
  18. AU="Carlos Augusto de Mattos"
  19. AU="Procopio, Francesco A"
  20. AU="Nagata, Kosei"
  21. AU="Kevin Pottie"
  22. AU=Das Tandrila AU=Das Tandrila
  23. AU="Couto Souza, Paulo Henrique"
  24. AU="Morris, Zachary"

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  1. Artikel ; Online: Clustering methods for single-cell RNA-sequencing expression data: performance evaluation with varying sample sizes and cell compositions.

    Suner, Aslı

    Statistical applications in genetics and molecular biology

    2019  Band 18, Heft 5

    Abstract: A number of specialized clustering methods have been developed so far for the accurate analysis of single-cell RNA-sequencing (scRNA-seq) expression data, and several reports have been published documenting the performance measures of these clustering ... ...

    Abstract A number of specialized clustering methods have been developed so far for the accurate analysis of single-cell RNA-sequencing (scRNA-seq) expression data, and several reports have been published documenting the performance measures of these clustering methods under different conditions. However, to date, there are no available studies regarding the systematic evaluation of the performance measures of the clustering methods taking into consideration the sample size and cell composition of a given scRNA-seq dataset. Herein, a comprehensive performance evaluation study of 11 selected scRNA-seq clustering methods was performed using synthetic datasets with known sample sizes and number of subpopulations, as well as varying levels of transcriptome complexity. The results indicate that the overall performance of the clustering methods under study are highly dependent on the sample size and complexity of the scRNA-seq dataset. In most of the cases, better clustering performances were obtained as the number of cells in a given expression dataset was increased. The findings of this study also highlight the importance of sample size for the successful detection of rare cell subpopulations with an appropriate clustering tool.
    Mesh-Begriff(e) Algorithms ; Cluster Analysis ; RNA-Seq/methods ; Sample Size ; Single-Cell Analysis/methods ; Software ; Transcriptome
    Sprache Englisch
    Erscheinungsdatum 2019-08-14
    Erscheinungsland Germany
    Dokumenttyp Evaluation Study ; Journal Article
    ISSN 1544-6115
    ISSN (online) 1544-6115
    DOI 10.1515/sagmb-2019-0004
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  2. Artikel: Platelet-to-lymphocyte and neutrophil-to-lymphocyte ratios predict tumor size and survival in HCC patients: Retrospective study.

    Suner, Aslı / Carr, Brian I

    Annals of medicine and surgery (2012)

    2020  Band 58, Seite(n) 167–171

    Abstract: Background: Inflammation is a recognized concomitant of hepatocellular carcinoma (HCC) and its indices are prognostically useful.: Aims: To evaluate two commonly used inflammatory indices, neutrophil-to-lymphocyte ratio (NLR) and the platelet-to- ... ...

    Abstract Background: Inflammation is a recognized concomitant of hepatocellular carcinoma (HCC) and its indices are prognostically useful.
    Aims: To evaluate two commonly used inflammatory indices, neutrophil-to-lymphocyte ratio (NLR) and the platelet-to-lymphocyte ratio (PLR), to examine their relationship to maximum tumor diameter (MTD) and to survival.
    Methods: A database of 1024 prospectively-accrued HCC patients was examined, who had full baseline tumor parameter data, including CT scan information on HCC size and whose survival was known. Analyses of NLR and PLR were correlated to MDT and to survival. NLR and PLR cutoffs were calculated from receiver operator characteristic curves.
    Results: Every MTD pair had significantly different PLR values, for MTD groups of groups <2/≥2, <3/≥3, <4/≥4, <5/≥5 cm. However there were few significant differences in NLR values. Logistic regression models of different MTD groups likewise showed significance for PLR. Patients with both low NLR and low PLR had the longest overall survival compared to all the other 3 combinations of NLR and PLR. In a Cox regression analysis, univariate models on NLR (≤3.02/>3.02) and PLR (≤6.82/>6.82) groups, showed significance for PLR, p = 0.034 and approaching significance for NLR, p = 0.057.
    Conclusions: MTD pairs down to <2/≥2 cm showed significance for PLR, survival showed significance for PLR and almost for NLR.
    Sprache Englisch
    Erscheinungsdatum 2020-09-06
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2745440-X
    ISSN 2049-0801
    ISSN 2049-0801
    DOI 10.1016/j.amsu.2020.08.042
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  3. Artikel ; Online: An

    Özbek, Melih / Toy, Halil Ibrahim / Oktay, Yavuz / Karakülah, Gökhan / Suner, Aslı / Pavlopoulou, Athanasia

    PeerJ

    2023  Band 11, Seite(n) e15096

    Abstract: Low-grade gliomas (LGG) are central nervous system Grade I tumors, and as they progress they are becoming one of the deadliest brain tumors. There is still great need for timely and accurate diagnosis and prognosis of LGG. Herein, we aimed to identify ... ...

    Abstract Low-grade gliomas (LGG) are central nervous system Grade I tumors, and as they progress they are becoming one of the deadliest brain tumors. There is still great need for timely and accurate diagnosis and prognosis of LGG. Herein, we aimed to identify diagnostic and prognostic biomarkers associated with LGG, by employing diverse computational approaches. For this purpose, differential gene expression analysis on high-throughput transcriptomics data of LGG
    Mesh-Begriff(e) Humans ; Prognosis ; Neoplasm Grading ; Glioma/diagnosis ; Brain Neoplasms/diagnosis ; Gene Expression Profiling ; Membrane Proteins/genetics ; Amino Acid Transport System y+L/genetics
    Chemische Substanzen NCKAP1L protein, human (144351-15-5) ; Membrane Proteins ; SLC7A7 protein, human ; Amino Acid Transport System y+L
    Sprache Englisch
    Erscheinungsdatum 2023-03-16
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359 ; 2167-8359
    ISSN (online) 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.15096
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  4. Artikel ; Online: A prospective cohort study: can advanced ultrasonography replace magnetic resonance imaging in the diagnosis of placental adhesion disorders?

    Ari, Sabahattin Anil / Suner, Asli / Senkaya, Ayse Rabia / Okmen, Firat / Akdemir, Ali / Ergenoglu, Ahmet Mete

    Journal of perinatal medicine

    2023  Band 51, Heft 5, Seite(n) 675–681

    Abstract: Objectives: To define and compare the diagnostic accuracy of ultrasonography (USG) and magnetic resonance imaging (MRI) for the placental adhesive disorder (PAD).: Methods: A prospective study was conducted between January 2019 and February 2020 in a ...

    Abstract Objectives: To define and compare the diagnostic accuracy of ultrasonography (USG) and magnetic resonance imaging (MRI) for the placental adhesive disorder (PAD).
    Methods: A prospective study was conducted between January 2019 and February 2020 in a tertiary referral university hospital. A total of 115 placenta previa cases were included in the study during the third trimester of gestation. USG examination was performed, and the placenta was scanned in a systematic manner using gray-scale ultrasound, color Doppler flow mapping, and 3-D imaging for each participant. Thereafter, all participants underwent an MRI examination. USG and MRI findings were compared with histopathological findings.
    Results: Loss of the retroplacental sonolucent zone (71% [95% CI 47-88]) and an irregular retroplacental sonolucent zone (71% [95% CI 47-88]) were the most sensitive USG parameters. For MRI, the uterine bulging parameter was the most sensitive (60% [95% CI 36-80]) and specific (91% [95% CI 83-96]) findings, and it had the highest accuracy rate (85% [95% CI 77-91]). Overall, the USG sensitivity, specificity, and accuracy rates were 77% (95% CI 54-92), 87% (95% CI 79-93), and 85% (95% CI 77-91), respectively. The MRI sensitivity, specificity, and accuracy rates for all participants were 81% (95% CI 59-94), 85% (95% CI 76-92), and 84% (95% CI 76-90), respectively.
    Conclusions: In the diagnosis of PAD, the specificity and accuracy of USG are higher than that of MRI, whereas the sensitivity of MRI is better than that of USG.
    Mesh-Begriff(e) Pregnancy ; Female ; Humans ; Placenta/diagnostic imaging ; Placenta/pathology ; Prospective Studies ; Placenta Accreta/diagnosis ; Ultrasonography, Prenatal/methods ; Ultrasonography ; Magnetic Resonance Imaging/methods
    Sprache Englisch
    Erscheinungsdatum 2023-01-06
    Erscheinungsland Germany
    Dokumenttyp Journal Article
    ZDB-ID 123512-6
    ISSN 1619-3997 ; 0300-5577 ; 0936-174X
    ISSN (online) 1619-3997
    ISSN 0300-5577 ; 0936-174X
    DOI 10.1515/jpm-2022-0407
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  5. Artikel: 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.

    Eskier, Doğa / Suner, Aslı / Karakülah, Gökhan / Oktay, Yavuz

    PeerJ

    2020  Band 8, Seite(n) e9703

    Abstract: Since its emergence in Wuhan, China in late 2019, the origin and evolution of SARS-CoV-2 have been among the most debated issues related to COVID-19. Throughout its spread around the world, the viral genome continued acquiring new mutations and some of ... ...

    Abstract Since its emergence in Wuhan, China in late 2019, the origin and evolution of SARS-CoV-2 have been among the most debated issues related to COVID-19. Throughout its spread around the world, the viral genome continued acquiring new mutations and some of them became widespread. Among them, 14408 C>T and 23403 A>G mutations in RdRp and S, respectively, became dominant in Europe and the US, which led to debates regarding their effects on the mutability and transmissibility of the virus. In this study, we aimed to investigate possible differences between time-dependent variation of mutation densities (MDe) of viral strains that carry these two mutations and those that do not. Our analyses at the genome and gene level led to two important findings: First, time-dependent changes in the average MDe of circulating SARS-CoV-2 genomes showed different characteristics before and after the beginning of April, when daily new case numbers started levelling off. Second, this pattern was much delayed or even non-existent for the "mutant" (MT) strain that harbored both 14408 C>T and 23403 A>G mutations. Although these differences were not limited to a few hotspots, it is intriguing that the MDe increase is most evident in two critical genes, S and Orf1ab, which are also the genes that harbor the defining mutations of the MT genotype. The nature of these unexpected relationships warrants further research.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-08-19
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.9703
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  6. Artikel: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load.

    Eskier, Doğa / Suner, Aslı / Oktay, Yavuz / Karakülah, Gökhan

    PeerJ

    2020  Band 8, Seite(n) e10181

    Abstract: SARS-CoV-2 is a betacoronavirus responsible for COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic ... ...

    Abstract SARS-CoV-2 is a betacoronavirus responsible for COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load without selective pressure and across the genome, compared to nsp7, nsp8 and nsp12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates and nsp14 mutations as potential predictors for high mutability strains.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-10-12
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.10181
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  7. Artikel: RdRp mutations are associated with SARS-CoV-2 genome evolution.

    Eskier, Doğa / Karakülah, Gökhan / Suner, Aslı / Oktay, Yavuz

    PeerJ

    2020  Band 8, Seite(n) e9587

    Abstract: COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral ...

    Abstract COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral genome over time as it spread across the world. An important question that still needs to be answered is whether any of the common mutations affect the viral properties, and therefore the disease characteristics. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C>T mutation, on mutation rate and viral spread. By focusing on mutations in the slowly evolving M or E genes, we aimed to minimize the effects of selective pressure. Our results indicate that 14408C>T mutation increases the mutation rate, while the third-most common RdRp mutation, 15324C>T, has the opposite effect. It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-07-21
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.9587
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  8. Artikel ; Online: Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations.

    Koçhan, Necla / Eskier, Doğa / Suner, Aslı / Karakülah, Gökhan / Oktay, Yavuz

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

    2021  Band 91, Seite(n) 104796

    Abstract: SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic that has affected millions of people worldwide. Pharmaceutical research against COVID-19 and the most frequently used tests for SARS-CoV-2 both depend on the genomic and peptide ... ...

    Abstract SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic that has affected millions of people worldwide. Pharmaceutical research against COVID-19 and the most frequently used tests for SARS-CoV-2 both depend on the genomic and peptide sequences of the virus for their robustness. Therefore, understanding the mutation rates and content of the virus is critical. Two key proteins for SARS-CoV-2 infection and replication are the S protein, responsible for viral entry into the cells, and RdRp, the RNA polymerase responsible for replicating the viral genome. Due to their roles in the viral cycle, these proteins are crucial for the fitness and infectiousness of the virus. Our previous findings had shown that the two most frequently observed mutations in the SARS-CoV-2 genome, 14408C>T in the RdRp coding region, and 23403A>G in the S gene, are correlated with higher mutation density over time. In this study, we further detail the selection dynamics and the mutation rates of SARS-CoV-2 genes, comparing them between isolates carrying both mutations, and isolates carrying neither. We find that the S gene and the RdRp coding region show the highest variance between the genotypes, and their selection dynamics contrast each other over time. The S gene displays higher tolerance for positive selection in mutant isolates early during the appearance of the double mutant genotype, and undergoes increasing negative selection over time, whereas the RdRp region in the mutant isolates shows strong negative selection throughout the pandemic.
    Mesh-Begriff(e) COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Evolution, Molecular ; Gene Expression Regulation, Viral ; Genome, Viral ; Genotype ; Humans ; Mutation Rate ; Open Reading Frames ; Point Mutation ; RNA-Dependent RNA Polymerase/genetics ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; Selection, Genetic ; Spike Glycoprotein, Coronavirus/genetics ; United Kingdom/epidemiology ; United States/epidemiology
    Chemische Substanzen Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
    Sprache Englisch
    Erscheinungsdatum 2021-03-03
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2037068-4
    ISSN 1567-7257 ; 1567-1348
    ISSN (online) 1567-7257
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2021.104796
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  9. Artikel ; Online: A 10-year retrospective analysis of intimate partner violence patients in the emergency department.

    Kavak, Nezih / Kavak, Rasime Pelin / Özdemir, Meltem / Sever, Mustafa / Ertan, Nurcan / Suner, Aslı

    Ulusal travma ve acil cerrahi dergisi = Turkish journal of trauma & emergency surgery : TJTES

    2022  Band 28, Heft 6, Seite(n) 796–804

    Abstract: Background: Intimate partner violence (IPV) is an important human rights problem faced by one in three women worldwide. The aim of this study is to evaluate the demographic, trauma, and radiological characteristics of patients admitted to a tertiary ... ...

    Titelübersetzung Acil servise müracaat eden yakın arkadaş şiddeti hastalarının 10 yıllık geriye dönük analizi.
    Abstract Background: Intimate partner violence (IPV) is an important human rights problem faced by one in three women worldwide. The aim of this study is to evaluate the demographic, trauma, and radiological characteristics of patients admitted to a tertiary emer-gency department due to IPV.
    Methods: Sociodemographic characteristics (age, gender, education level, and marital status), trauma characteristics (severity, type, and location), radiological imaging findings (radiography, computed tomography, and magnetic resonance imaging) of patients diagnosed with IPV were evaluated.
    Results: In the study, 1225 patients were evaluated, and 98.7% of them were women (mean age 35 [IQR: 17] years). Of the pa-tients, 63.1% were high school and university graduates. The rate of married women was 74.6%. No relationship was found between gender, age, educational status, and marital status (p>0.05). Most of the traumas were minor (85.4%) and blunt (81.9%) trauma, and the most common types of trauma were kicking (49.9%) and punching (47.3%). It was found that the most frequently affected areas of the patients were the head and neck (76.7%), and the frequency of pelvic trauma was high in male patients (p<0.05). The most com-mon bone fracture was nasal (40.5%) followed by ulna fractures (14.5%). The left-sided diaphyseal fractures were the most common in patients exposed to IPV. In our study, the frequency of mortality was 12.9%, and it was found to be significantly higher in males (p<0.05).
    Conclusion: Female patients are more frequently exposed to IPV. Specific injury characteristics can be detected in patients diagnosed with IPV and old fractures detected in these patients should alert the clinician about IPV.
    Mesh-Begriff(e) Adult ; Emergency Service, Hospital ; Female ; Humans ; Intimate Partner Violence ; Male ; Retrospective Studies
    Sprache Englisch
    Erscheinungsdatum 2022-05-31
    Erscheinungsland Turkey
    Dokumenttyp Journal Article
    ZDB-ID 2253739-9
    ISSN 1307-7945 ; 1306-696X
    ISSN (online) 1307-7945
    ISSN 1306-696X
    DOI 10.14744/tjtes.2021.90453
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  10. Artikel ; Online: The expression of HDAC9 and P300 in papillary thyroid carcinoma cell line.

    Ozisik, Hatice / Ozdil, Berrin / Suner, Aslı / Sipahi, Murat / Erdogan, Mehmet / Cetinkalp, Sevki / Ozgen, Gokhan / Saygili, Fusun / Oktay, Gulgun / Aktug, Huseyin

    Pathology, research and practice

    2023  Band 243, Seite(n) 154385

    Abstract: Purpose: Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer and accounts for 85-90% of all thyroid cancers. Metastatic differentiated thyroid cancer, radioiodine-refractory thyroid cancer, and anaplastic thyroid cancer still ... ...

    Abstract Purpose: Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer and accounts for 85-90% of all thyroid cancers. Metastatic differentiated thyroid cancer, radioiodine-refractory thyroid cancer, and anaplastic thyroid cancer still lack effective therapeutic options. Here, we aimed to assess HDAC9 and P300 expression in the papillary thyroid carcinoma cell line and compare them with normal thyroid cells.
    Methods: Nthy-ori-3-1, a normal thyroid cell line, and BCPAP, a PTC cell line, were cultured for 24 and 48 h and immunofluorescence staining was used to determine the levels of HDAC9 and P300 protein expression. HDAC9 paracrine release was assessed using an ELISA assay.
    Results: HDAC9 protein expression was higher in both cell groups at the 48th hour than at the 24th hour; however, P300 protein expression was lower in BCPAP cells at the 48th hour than at the 24th hour. In comparison to Nthy-ori-3-1, BCPAP expressed more HDAC9 and P300 proteins. HDAC9 secretion slightly increased in Nthy-ori-3-1 cells from 24 to 48 h. Furthermore, HDAC9 secretion in BCPAP cells dramatically decreased from 24 to 48 h.
    Conclusion: Our findings revealed that the expression of HDAC9 and P300 was higher in the PTC cell line than in normal thyroid cells. This indicates that the acetylation mechanism in thyroid cancer cells is not the same as it is in healthy cells. Epigenetic studies may reveal the mechanisms underlying PTC with further analysis.
    Mesh-Begriff(e) Humans ; Thyroid Cancer, Papillary ; Iodine Radioisotopes ; Cell Line, Tumor ; Cell Proliferation ; Carcinoma, Papillary/pathology ; Thyroid Neoplasms/pathology ; Histone Deacetylases ; Repressor Proteins
    Chemische Substanzen Iodine Radioisotopes ; HDAC9 protein, human (EC 3.5.1.98) ; Histone Deacetylases (EC 3.5.1.98) ; Repressor Proteins
    Sprache Englisch
    Erscheinungsdatum 2023-02-24
    Erscheinungsland Germany
    Dokumenttyp Journal Article
    ZDB-ID 391889-0
    ISSN 1618-0631 ; 0344-0338
    ISSN (online) 1618-0631
    ISSN 0344-0338
    DOI 10.1016/j.prp.2023.154385
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