Assoc. Prof. Vahap ELDEM

Publication Network

Articles 38

1. Long-Term Transcriptomic Reprogramming in Peripheral Blood Mononuclear Cells of Severe COVID-19 Survivors Reveals Pro-Oncogenic Signatures and Cancer-Associated Hub Genes

Duru Cetinkaya P., Kayalar O., Eldem V., Argun Baris S., Kokturk N., Kuralay S. C., et al.

VIRUSES , vol.17, no.12, pp.1-18, 2025 (Scopus)

2. Dietary phytase and xylanase improves growth performance, intestinal morphometric properties, and metabolic gene expression in rainbow trout (Oncorhynchus mykiss)

YILDIZ M., Ofori-Mensah S., Adabi S. G., METİN Ö., ELDEM V., Kaiza V. E., et al.

Aquaculture International , vol.33, no.5, 2025 (SCI-Expanded)

3. Phenotypic plasticity in Mediterranean gorgonians Eunicella singularis and Paramuricea clavata at high temperature and low pH

BELİVERMİŞ M., KILIÇ Ö., ÖZALP H. B., Demiralp S., OKTAYOĞLU S., ELDEM V., et al.

Science of the Total Environment , vol.990, 2025 (SCI-Expanded) Sustainable Development

4. Mortality event of the Mediterranean Invasive Sea Urchin Diadema setosum from Gokova Bay (Southern Aegean Sea)

Didem Demırcan M. D., Özlem Arslan-Aydogdu E., Dalyan C., Eldem V., Gönülal O., Tüney İ.

ESTUARINE COASTAL AND SHELF SCIENCE , vol.319, 2025 (SCI-Expanded) Sustainable Development

5. **De novo genome assembly and annotations of Bombus lapidarius and Bombus niveatus provide insights into the environmental adaptability**

Eldem V., Çınar Y. U., Çay S. B., Obut O., Kuralay S. C., Balcı M. A., et al.

APIDOLOGIE , vol.56, no.1, 2025 (SCI-Expanded)

6. Biosystematics studies of endemic Thlaspi violascens Boiss. and T. densiflorum Boiss. & Kotschy: Highlights on molecular and morphological identification

Karaismailoğlu M. C., Eldem V., İnal B., Balcı M. A.

FLORA , vol.322, 2025 (SCI-Expanded) Sustainable Development

7. The effects of using hydrolyzed feather meal, amino acids, and probiotics in the diet of juvenile rainbow trout on growth, digestibility, and expression of growth-related genes

Metin Ö., Yıldız M., Eldem V., Adabi S. G.

AQUACULTURE INTERNATIONAL , vol.32, no.7, pp.9671-9693, 2024 (SCI-Expanded)

8. Transcriptome-wide analysis uncovers regulatory elements of the antennal transcriptome repertoire of bumblebee at different life stages

Dikmen F., Dabak T., Özgişi B. D., Özenirler Ç., Kuralay S. C., Çay S. B., et al.

Insect Molecular Biology , vol.33, no.6, pp.571-588, 2024 (SCI-Expanded) Sustainable Development

9. Comparative Transcriptomic Analyses of Peripheral Blood Mononuclear Cells of COVID-19 Patients without Pneumonia and with Severe Pneumonia in the First Year of Follow-Up

Kayalar O., Cetinkaya P. D., Eldem V., Argun Baris S., Kokturk N., Kuralay S. C., et al.

VIRUSES , vol.16, no.8, pp.1-19, 2024 (SCI-Expanded)

10. Deciphering the host genetic factors conferring susceptibility to severe COVID-19 using exome sequencing

Uslu K., Ozcelik F., Zararsiz G., Eldem V., Cephe A., Sahin I. O., et al.

GENES AND IMMUNITY , vol.25, no.1, pp.14-42, 2024 (SCI-Expanded) Sustainable Development

11. Mining NCBI Sequence Read Archive Database: An Untapped Source of Organelle Genomes for Taxonomic and Comparative Genomics Research

Eldem V., Balcı M. A.

DIVERSITY-BASEL , vol.16, no.2, 2024 (SCI-Expanded)

12. The effects of dietary microbial 6-phytase on growth parameters, intestinal morphometric properties and selected intestinal genes expression in rainbow trout (Oncorhynchus mykiss, Walbaum 1876)

Kaiza V. E., YILDIZ M., ELDEM V., Golzaradabi S., Ofori-Mensah S.

Journal of Animal Physiology and Animal Nutrition , vol.107, no.6, pp.1517-1529, 2023 (SCI-Expanded) Sustainable Development

13. Global expression pattern of genes containing positively selected sites in European anchovy (Engraulis encrasicolus L.) may shed light on teleost reproduction

Eldem V., Zararsız G., Erkan M.

PLOS ONE , vol.18, no.8, 2023 (SCI-Expanded)

14. Comprehensive analysis of circulating viral DNA in maternal plasma at population-scale using low-pass whole-genome sequencing

Eldem V., Kuralay S. C., Ozdogan G., Ozcelik G. H., Aydin D., Cakmak G., et al.

Genomics , vol.115, no.2, 2023 (SCI-Expanded)

15. Genetic and morphometric comparisons of populations of Lacerta diplochondrodes Wettstein, 1952 (Squamata: Lacertidae) in Türkiye

Kaya N., ÖZULUĞ O., TOSUNOĞLU M., ELDEM V.

Zoology in the Middle East , vol.69, no.4, pp.355-363, 2023 (SCI-Expanded)

16. voomSOM: voom-based Self-Organizing Maps for Clustering RNA-Sequencing Data

Cephe A., Koçhan N., Zararsız G. E., Eldem V., Coşgun E., Karabulut E., et al.

CURRENT BIOINFORMATICS , vol.18, no.2, pp.154-169, 2023 (SCI-Expanded)

17. Effect of dietary inclusion of camelina or chia oil on fatty acid digestibility, histology, blood biochemistry and molecular biomarkers in juvenile gilthead sea bream (Sparus aurata, L.)

Ofori-Mensah S., Yildiz M., Eldem V., Urku C., Kaplan C.

TURKISH JOURNAL OF FISHERIES AND AQUATIC SCIENCES , vol.22, no.11, 2022 (SCI-Expanded) Sustainable Development

18. Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukans

Cay S. B., Cinar Y. U., Kuralay S. C., Inal B., Zararsiz G., Ciftci A., et al.

PLOS ONE , vol.17, no.6, 2022 (SCI-Expanded) Sustainable Development

19. Substitution of fish oil with camelina or chia oils in gilthead sea bream (Sparus aurata, L.) diets: Effect on growth performance, fatty acid composition, haematology and gene expression

Ofori-Mensah S., Yıldız M., Arslan M., Eldem V., Gelibolu S.

AQUACULTURE NUTRITION , vol.26, no.6, pp.1943-1957, 2020 (SCI-Expanded)

20. Fish oil replacement with different vegetable oils in gilthead seabream, Sparus aurata diets: Effects on fatty acid metabolism based on whole-body fatty acid balance method and genes expression

Ofori-Mensah S., Yıldız M., Arslan M., Eldem V.

AQUACULTURE , vol.529, 2020 (SCI-Expanded) Sustainable Development

21. Sodium Arsenic Alters the Gene Expression of some Steroidogenic Genes in TM3 Leydig Cell.

Taşçi T., ELDEM V., ERKAN M. B.

Celal Bayar University Journal of Science , vol.15, no.3, pp.265-270, 2019 (Peer-Reviewed Journal)

22. MLSeq: Machine learning interface for RNA-sequencing data

GÖKSÜLÜK D., ZARARSIZ G., KORKMAZ S., Eldem V., Zararsiz G. E., Ozcetin E., et al.

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE , vol.175, pp.223-231, 2019 (SCI-Expanded)

23. The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in Izmir province, Turkey

Bozcal E., Eldem V., Aydemir S., Skurnik M.

PEERJ , vol.6, 2018 (SCI-Expanded, Scopus)

24. The Relationship Between Blood Pressure and Sleep Duration in Turkish Children: A Cross-Sectional Study

BAL C., ÖZTÜRK A., ÇİÇEK B., Ozdemir A., ZARARSIZ G., ÜNALAN D., et al.

JOURNAL OF CLINICAL RESEARCH IN PEDIATRIC ENDOCRINOLOGY , vol.10, no.1, pp.51-58, 2018 (SCI-Expanded) Sustainable Development

25. Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826)

ELDEM V.

Celal Bayar University Journal of Science , vol.14, no.1, pp.135-140, 2018 (Peer-Reviewed Journal)

26. voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data

ZARARSIZ G., Goksuluk D., Klaus B., Korkmaz S., Eldem V., KARABULUT E., et al.

PEERJ , vol.5, 2017 (SCI-Expanded) Sustainable Development

27. A comprehensive simulation study on classification of RNA-Seq data

Zararsiz G., Goksuluk D., Korkmaz S., Eldem V., Zararsiz G. E., Duru I. P., et al.

PLOS ONE , vol.12, no.8, 2017 (SCI-Expanded) Sustainable Development

28. A Quick and Efficient Method for DNA Isolation from Freshwater Ostracods

KUBANÇ S. N., Taşcı T., KUBANÇ C., Özuluğ O., ELDEM V.

Genetics of Aquatic Organisms , vol.1, no.1, pp.1-7, 2017 (Scopus)

29. Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves

Bakir Y., Eldem V., ZARARSIZ G., Unver T.

PLANT GENOME , vol.9, no.2, 2016 (SCI-Expanded)

30. Theory of room temperature ferromagnetism in Cr modified DNA nanowire

Duru I. P., DEĞER C., Eldem V., Kalayci T., AKTAŞ Ş.

JOURNAL OF PHYSICS D-APPLIED PHYSICS , vol.49, no.13, 2016 (SCI-Expanded)

31. The complete mitochondrial genome of Alburnus tarichi (Teleostei, Cyprinidae)

Kubanc N., Eldem V., Kubanc C.

Mitochondrial DNA , vol.27, no.2, pp.1243-1244, 2016 (SCI-Expanded) Sustainable Development

32. Complete mitochondrial genome of Alburnus istanbulensis (Teleostei, Cyprinidae).

Eldem V., Kubanc C., Kubanc N.

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis , vol.27, no.2, pp.1241-2, 2016 (SCI-Expanded)

33. De novo assembly and comprehensive characterization of the skeletal muscle transcriptomes of the European anchovy (Engraulis encrasicolus)

Eldem V., ZARARSIZ G., Erkan M., Bakir Y.

MARINE GENOMICS , vol.20, pp.7-9, 2015 (SCI-Expanded)

34. Genome-Wide Analysis of the bZIP Transcription Factors in Cucumber

Baloglu M. C., Eldem V., Hajyzadeh M., Unver T.

PLOS ONE , vol.9, no.4, 2014 (SCI-Expanded) Sustainable Development

35. Boron Stress Responsive MicroRNAs and Their Targets in Barley

Ozhuner E., Eldem V., Ipek A., Okay S., Sakcali S., Zhang B., et al.

PLOS ONE , vol.8, no.3, 2013 (SCI-Expanded) Sustainable Development

36. Plant microRNAs: new players in functional genomics

Eldem V., Okay S., Unver T.

TURKISH JOURNAL OF AGRICULTURE AND FORESTRY , vol.37, no.1, pp.1-21, 2013 (SCI-Expanded)

37. Genome-Wide Identification of miRNAs Responsive to Drought in Peach (Prunus persica) by High-Throughput Deep Sequencing

Eldem V., Akcay U. C., Ozhuner E., Bakir Y., Uranbey S., Unver T.

PLOS ONE , vol.7, no.12, 2012 (SCI-Expanded) Sustainable Development

38. Micro-RNA Regulation for Boron Toxicity Tolerance in Barley

ÜNVER T., Erkilic E. G., Eldem V., Sakcali S., İPEK A., Uranbey S., et al.

IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL , vol.48, pp.40, 2012 (SCI-Expanded)

Papers Presented at Peer-Reviewed Scientific Conferences 15

1. Hidroliz Tüy Unu ve Probiyotik İçeren Diyetlerin Jüvenil Gökkuşağı Alabalığında Büyüme Performansı, Sindirilebilirlik, Et Kalitesi, Bağırsak H4stolojisi ve Gen Ekspresyonuna Etkisi

Metin Ö., Yıldız M., Eldem V., Adabi S. G.

23. Ulusal Su Ürünleri Sempozyumu, Elazığ, Turkey, 23 - 25 September 2025, pp.48, (Summary Text)

2. Yemlerde Kullanılan Mikrobiyal 6-Fitaz ve Ksilanazın Gökkuşağı Alabalığında Büyüme Performansına, Et Kalitesine, Yem Kullanımına, Bağırsak Morfometrik Özelliklerine ve Gen Ekspresyonuna Etkileri

Yıldız M., Kaıza V., Eldem V., Metin Ö., Ofori-Mensah S., Karataş Steınum S., et al.

23. Ulusal Su Ürünleri Sempozyumu, Elazığ, Turkey, 23 - 25 September 2025, pp.33, (Full Text)

3. ANTENNAL TRANSCRIPTOME ANALYSIS AND BEHAVIORAL STUDIES TO DECIPHER THE GENETIC BASIS OF OLFACTION IN BOMBUS TERRESTRIS L.

Dikmen F., Dabak T., Özenirler Ç., Daşer-Özgişi B., Eldem V.

Eurbee 10th Congress of Apidology, Tallinn, Estonia, 16 - 19 September 2024, pp.222, (Summary Text)

4. CHROMOSOME-SCALE GENOMIC ANALYSIS INSIGHTS INTO LOCAL ADAPTATION AND FUTURE CLIMATE-INDUCED VULNERABILITY OF TWO BUMBLEBEE SPECIES: BOMBUS LAPIDARIUS AND BOMBUS NIVEATUS

Eldem V., Çınar Y. U., Çay S. B., Kuralay S. C., Balcı M. A., Akbaba P., et al.

Eurbee 10th Apidology Congress, Tallinn, Estonia, 16 - 19 September 2024, pp.99, (Summary Text)

5. Effects of ocean acidification and warming on Mediterranean gorgonians: physiological, transcriptomic, and epigenetic responses

Belivermiş M., Kılıç Ö., Oktayoğlu S., Eldem V., Demiralp S., Şahin B., et al.

European Coral Reef Symposium , Naples, Italy, 2 - 05 July 2024, pp.1, (Full Text)

6. The multistressor effect of ocean acidification, microplastic and lanthanum on sea urchin Arbacia lixula.

Şahin B., Belivermiş M., Demiralp S., Sezer N., Bektaş S., Eldem V., et al.

PRIMO22, Nantes, France, 26 - 29 May 2024, pp.236, (Summary Text)

7. Mikrobiyal 6-Fitazın Gökkuşağı Alabalığında (Oncorhynchus mykiss) Büyüme Performansı, Bağırsak Histolojisi ve Gen Ekspresyonuna Etkileri

Yıldız M., Eldem V.

6. BALIK BESLEME VE YEM TEKNOLOJİSİ ÇALIŞTAYI, Antalya, Turkey, 27 - 28 September 2023, pp.22, (Summary Text)

8. The Comprehensive Characterization of Segmental Duplication in Zebrafish Genome

DİKMEN F., YILDIZBAYRAK N., ELDEM V., ERKAN M. B.

13th International Symposium on Fisheries and Aquatic Sciences (FABA), Ankara, Turkey, 21 - 23 November 2018, pp.81, (Summary Text)

9. Phylogenetic relationship and virulence properties of extraintestinal pathogenic Escherichia coli

Bozcal E., Eldem V., Aydemir S., Skurnik M.

10th Balkan Congress of Microbiology, Sofia, Bulgaria, 16 - 18 November 2017, pp.17, (Summary Text)

10. Genomic regions associated with virulence and antibiotic resistance in Extraintestinal Pathogenic Escherichia coli strains Phylogenetic group B2

Bozcal E., Eldem V., Aydemir S., Skurnik M.

7th European Conference on Prokaryotic and Fungal Genomics, Göttingen, Germany, 19 - 22 September 2017, pp.20, (Summary Text)

11. Whole-Genome Characterization and Composition of European Anchovy (Engraulis Encrasicolus L., 1758)

ELDEM V., Yüksel B., ERKAN M. B., Zararsız G., DİKMEN F., Saraç A., et al.

FABA 2016: International Symposium on Fisheries and Aquatic Sciences, Antalya, Turkey, 3 - 05 November 2016, pp.111-112, (Full Text)

12. Hamsi balığı (Engraulis Encrasicolus)’nın yumurta gelişiminde rol oynayan genlerin karşılaştırmalı transkriptomik yaklaşım ile belirlenmesi

ELDEM V., AYDIN Y., Yüksel B., ERKAN M. B.

II. Ulusal Su Ürünleri Yetiştiriciliğinde Gamet Biyolojisi Çalıştayı, Muğla, Turkey, 19 - 21 April 2016, pp.1, (Full Text)

13. Şeftali (Prunus persica L.)’ de kuraklık stresi ile ilişkili mikroRNA’ ların yeni nesil dizileme teknolojisiyle tanımlanması ve karekterizasyonu

ELDEM V., Bakır Y., Akçay U. Ç., ÜNVER T.

2. Ulusal Moleküler Biyoloji ve Biyoteknoloji Kongresi, Antalya, Turkey, 1 - 04 December 2012, pp.58-59, (Summary Text) Sustainable Development

14. İşlevsel Genomiğin Yeni Oyuncusu; Bitki MikroRNA’ları

ÜNVER T., Erkılıç E. G., Özhüner E., Yanık H., Böke H., Hajyzadeh M., et al.

2. Ulusal Moleküler Biyoloji ve Biyoteknoloji Kongresi, Antalya, Turkey, 1 - 04 December 2012, pp.18-19, (Summary Text)

15. Micro-RNA Regulation for Boron Toxicity Tolerance in Barley

Unver T., ELDEM V.

World Congress on In vitro biology, Washington, United States Of America, 3 - 07 June 2012, vol.48, pp.40, (Full Text)

Books 10

Other Publications 1

1. Machine learning interface for RNA-Seq data

Zararsiz G., Goksuluk D., Korkmaz S., ELDEM V., Duru I. P., Unver T., et al.

Other, pp.1-10, 2014 Sustainable Development

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