Yayınlar & Eserler

Yayın Ağı
SCI, SSCI ve AHCI İndekslerine Giren Dergilerde Yayınlanan Makaleler 23

1. Efficient Storage and Analysis of Genomic Data: A k-mer Frequency Mapping and Image Representation Method

Luleci H. B., Yuka S., YILMAZ A.
Interdisciplinary Sciences - Computational Life Sciences , cilt.17, sa.3, ss.691-697, 2025 (SCI-Expanded) identifier identifier

2. The role of ceRNAs in breast cancer microenvironmental regulation and therapeutic implications

YILMAZ A., Ari Yuka S.
Journal of Molecular Medicine , cilt.103, sa.1, ss.33-49, 2025 (SCI-Expanded) identifier identifier

3. Decoding dynamic miRNA:ceRNA interactions unveils therapeutic insights and targets across predominant cancer landscapes.

Arı Yuka S., Yilmaz A.
BIODATA MINING , cilt.17, sa.1, ss.11, 2024 (SCI-Expanded) Sürdürülebilir Kalkınma identifier identifier

4. Comparative analysis of retrosynthesis applications for predicting of pathways for plant Secondary metabolite production

Yonet N., Ari Yuka S., Türker M., Yilmaz A.
Biotechnology and Biotechnological Equipment , cilt.38, sa.1, 2024 (SCI-Expanded) identifier

5. Biofabrication of Acer palmatum-Mediated Multifunctional CuO Nanoparticles for Dye Removal, Antibacterial-Antifungal Activity, and Molecular Docking

Sazak C., ATTAR A., YILMAZ A., ALTIKATOĞLU YAPAÖZ M.
ACS Omega , cilt.8, sa.40, ss.36835-36844, 2023 (SCI-Expanded) identifier identifier

6. PGT for structural chromosomal rearrangements in 300 couples reveals specific risk factors but an interchromosomal effect is unlikely

Ogur C., Kahraman S., Griffin D. K., Cinar Yapan C., Tufekci M. A., Cetinkaya M., et al.
Reproductive BioMedicine Online , cilt.46, sa.4, ss.713-727, 2023 (SCI-Expanded) identifier identifier

7. Robust and rigorous identification of tissue-specific genes by statistically extending tau score

Lüleci H. B., YILMAZ A.
BioData Mining , cilt.15, sa.1, 2022 (SCI-Expanded) identifier identifier

8. Effect of SARS-CoV-2 infection on host competing endogenous RNA and miRNA network.

Ari Yuka S., Yilmaz A.
PeerJ , cilt.9, sa.e12370, 2021 (SCI-Expanded) Sürdürülebilir Kalkınma identifier identifier identifier

9. Network based multifactorial modelling of miRNA-target interactions

Ari Yuka S., Yilmaz A.
PEERJ , cilt.9, 2021 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma identifier identifier identifier

10. Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq)

Ouma W. Z., Mejia-Guerra M. K., YILMAZ A., PAREJA-TOBES P., Li W., Doseff A. I., et al.
SCIENTIFIC REPORTS , cilt.5, 2015 (SCI-Expanded) Creative Commons License identifier identifier identifier

11. Molecular basis for the action of a dietary flavonoid revealed by the comprehensive identification of apigenin human targets

Arango D., Morohashi K., Yilmaz A., Kuramochi K., Parihar A., Brahimaj B., et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , cilt.110, sa.24, 2013 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma identifier identifier identifier

12. Unraveling the KNOTTED1 regulatory network in maize meristems

Bolduc N., Yilmaz A., Mejia-Guerra M. K., Morohashi K., O'Connor D., Grotewold E., et al.
GENES & DEVELOPMENT , cilt.26, sa.15, ss.1685-1690, 2012 (SCI-Expanded) Creative Commons License identifier identifier identifier

13. A Genome-Wide Regulatory Framework Identifies Maize Pericarp Color1 Controlled Genes

Morohashi K., Casas M. I., Falcone Ferreyra L., Mejia-Guerra M. K., Pourcel L., Yilmaz A., et al.
PLANT CELL , cilt.24, sa.7, ss.2745-2764, 2012 (SCI-Expanded) Creative Commons License identifier identifier identifier

14. Thriving under Stress: Selective Translation of HIV-1 Structural Protein mRNA during Vpr-Mediated Impairment of eIF4E Translation Activity

Sharma A., Yilmaz A., Marsh K., Cochrane A., Boris-Lawrie K.
PLOS PATHOGENS , cilt.8, sa.3, 2012 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma identifier identifier identifier

15. AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

Yilmaz A., Mejia-Guerra M. K., Kurz K., Liang X., Welch L., Grotewold E.
NUCLEIC ACIDS RESEARCH , cilt.39, 2011 (SCI-Expanded) Creative Commons License identifier identifier identifier

16. Genome sequencing and analysis of the model grass Brachypodium distachyon

Vogel J. P., Garvin D. F., Mockler T. C., Schmutz J., Rokhsar D., Bevan M. W., et al.
NATURE , cilt.463, sa.7282, ss.763-768, 2010 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma identifier identifier identifier

17. Components and Mechanisms of Regulation of Gene Expression

YILMAZ A., Grotewold E.
COMPUTATIONAL BIOLOGY OF TRANSCRIPTION FACTOR BINDING , cilt.674, ss.23-32, 2010 (SCI-Expanded) identifier identifier identifier

18. The word landscape of the non-coding segments of the Arabidopsis thaliana genome

Lichtenberg J., Yilmaz A., Welch J. D., Kurz K., Liang X., Drews F., et al.
BMC GENOMICS , cilt.10, 2009 (SCI-Expanded) Creative Commons License identifier identifier identifier

19. GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

Yilmaz A., Nishiyama M. Y., Fuentes B. G., Souza G. M., Janies D., Gray J., et al.
PLANT PHYSIOLOGY , cilt.149, sa.1, ss.171-180, 2009 (SCI-Expanded) identifier identifier identifier

20. NOD/SCID mouse model of canine T-cell lymphoma with humoral hypercalcaemia of malignancy: cytokine gene expression profiling and in vivo bioluminescent imaging

Nadella M. V. P., Kisseberth W. C., Nadella K. S., Thudi N. K., Thamm D. H., McNiel E. A., et al.
VETERINARY AND COMPARATIVE ONCOLOGY , cilt.6, sa.1, ss.39-54, 2008 (SCI-Expanded) Creative Commons License identifier identifier identifier

21. RNA helicase A interacts with divergent lymphotropic retroviruses and promotes translation of human T-cell leukemia virus type 1

Bolinger C., Yilmaz A., Hartman T. R., Kovacic M. B., Fernandez S., Ye J., et al.
NUCLEIC ACIDS RESEARCH , cilt.35, sa.8, ss.2629-2642, 2007 (SCI-Expanded) Creative Commons License identifier identifier identifier

22. Retrovirus translation initiation: Issues and hypotheses derived from study of HIV-1

Yilmaz A., BOLINGER C., BORIS-LAWRIE K.
CURRENT HIV RESEARCH , cilt.4, sa.2, ss.131-139, 2006 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma identifier identifier

23. Coordinate enhancement of transgene transcription and translation in a lentiviral vector

Yilmaz A., FERNANDEZ S., LAIRMORE M. D., BORIS-LAWRIE K.
RETROVIROLOGY , cilt.3, 2006 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma identifier identifier identifier
Diğer Dergilerde Yayınlanan Makaleler 4

1. Balıkesir/Antandros Antik Kenti Kazısı Toprak Örneklerinin Metagenomik Analizi

Bal D., Balci B., Yilmaz A., Polat G., Arican E.
Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi , cilt.26, sa.1, ss.1-12, 2022 (Hakemli Dergi) Sürdürülebilir Kalkınma identifier

2. Convolutional Neural Network Approach to Predict Tumor Samples Using Gene Expression Data

DARENDELİ KİRAZ B. N., YILMAZ A.
Zeki sistemler teori ve uygulamaları dergisi (Online) , cilt.4, sa.2, ss.136-141, 2021 (Hakemli Dergi) Creative Commons License Sürdürülebilir Kalkınma identifier

3. Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors

YILMAZ A.
Zeki Sistemler Teori ve Uygulamaları Dergisi , cilt.3, sa.1, ss.1-6, 2020 (Hakemli Dergi) Creative Commons License

4. POPcorn: An Online resource providing access to distributed and diverse maize project data

Cannon E. K., Birkett S. M., Braun B. L., Kodavali S., Jennewein D. M., Yilmaz A., et al.
International Journal of Plant Genomics , cilt.2011, 2011 (Scopus) identifier identifier
Hakemli Bilimsel Toplantılarda Yayımlanmış Bildiriler 29

1. A New Network-Based Tool to Analyse Competing Endogenous RNAs

Yuka S., Yılmaz A.
16th International Symposium on Bioinformatics Research and Applications, ISBRA 2020, Moscow, Rusya, 1 - 04 Aralık 2020, ss.274-281, (Tam Metin Bildiri) identifier

2. Reduction of Depression Symptoms via the Metabolites of Gut Microbiota

Mawaldı I., Yılmaz A.
12th International Symposium on Health Informatics and Bioinformatics (HIBIT) 2019, İzmir, Türkiye, 17 - 18 Ekim 2019, ss.218, (Özet Bildiri) Sürdürülebilir Kalkınma

3. Prediction of Mutation Susceptibility Based on Solely DNA Sequences with Word2Vec

Darendeli B. N., Kalyon O., Yılmaz A.
12th International Symposium on Health Informatics and Bioinformatics (HIBIT) 2019, İzmir, Türkiye, 17 - 18 Ekim 2019, ss.222-223, (Özet Bildiri)

4. Constructing Accurate Compound Networks for Reliable Network Analysis

Alpaydın D., Öztürk R., Yılmaz A.
12th International Symposium on Health Informatics and Bioinformatics (HIBIT) 2019, İzmir, Türkiye, 17 - 18 Ekim 2019, ss.230, (Özet Bildiri) Sürdürülebilir Kalkınma

5. Automation of Genetic Screening and Reporting with Snakemake

Kalyon O., Müslümanoğlu M. H., Yılmaz A.
12th International Symposium on Health Informatics and Bioinformatics (HIBIT) 2019, İzmir, Türkiye, 17 - 18 Ekim 2019, ss.219, (Özet Bildiri)

6. Breast cancer gene expression profile analysis in terms of genes specific to non- breast tissues

Konuk H. B., Yılmaz A.
1st International Conference of Genomics and Bioinformatics (ICGB), Aydın, Türkiye, 1 - 04 Kasım 2018, ss.30, (Özet Bildiri) Sürdürülebilir Kalkınma

7. Batch Analyis of RNA-Seq Data with Docker in AWS Cloud

Yılmaz A.
ICAMLS 2018 International Conference on Applied Mathematics, Modeling and Life Science Problems, İstanbul, Türkiye, 3 - 05 Ekim 2018, ss.87, (Özet Bildiri)

8. What is the relationship between cancer DEGs and tissue specific genes

Konuk H. B., Cesur M. R., Yılmaz A.
Lisansüstü Araştırmalar Sempozyumu ve Tanıtım Günleri, Kocaeli, Türkiye, 17 - 18 Mayıs 2017, (Özet Bildiri) Sürdürülebilir Kalkınma

9. Kanserde İfadesi Değişen Genlerin Metabolit Ağı Açısından Değerlendirilmesi

Öztürk R., Yılmaz A.
1.Temel Onkoloji Sempozyumu, İzmir, Türkiye, 9 - 11 Mayıs 2018, ss.30, (Özet Bildiri) Sürdürülebilir Kalkınma

10. Kanser Teşhisinde Derin Öğrenme ile Sınıflandırma

Darendeli B. N., Al-Qabbani H., Yılmaz A.
1.Temel Onkoloji Sempozyumu, İzmir, Türkiye, 9 - 11 Mayıs 2018, ss.48, (Özet Bildiri) Sürdürülebilir Kalkınma

11. Pinpointing the importance of compounds in human metabolic network

Öztürk E. R., Yılmaz A.
7th International Molecular Biology and Biotechnology Congress, Konya, Türkiye, 25 - 27 Nisan 2018, ss.160, (Özet Bildiri)

12. Multifactorial Modelling of MicroRNA Associated Repression and Its Subsequent Effects on Gene Expression in MicroRNA:Target Network

Arı S., Yılmaz A.
7th International Molecular Biology and Biotechnology Congress, Konya, Türkiye, 25 - 27 Nisan 2018, ss.401, (Özet Bildiri) Sürdürülebilir Kalkınma

13. GENERATING LOSSLESS COMPRESSION OF GENOME SCALE K-MER FREQUENCY TABLE AS RASTER IMAGE

KONUK H. B., YILMAZ A.
International Congress on Advances in Bioscience and Biotechnology, Saraybosna, Bosna-Hersek, 25 - 29 Ekim 2017, (Özet Bildiri)

14. RIGOROUS IDENTIFICATION OF TISSUE SPECIFIC GENES IN SILICO: REVEALING THE INTERPLAY BETWEEN CANCER SPECIFIC EXPRESSION AND TISSUE SPECIFIC EXPRESSION

KONUK H. B., YILMAZ A.
International Congress on Advances in Bioscience and Biotechnology, Saraybosna, Bosna-Hersek, 25 - 29 Ekim 2017, (Özet Bildiri) Sürdürülebilir Kalkınma

15. SURVEY OF CHIMERIC mRNAs IN HIV INFECTED PATIENT RNA-SEQ DATA

KALYON O., YILMAZ A.
10th International Symposium on Health Informatics and Bioinformatics, Güzelyurt, Kıbrıs (Kktc), 28 Haziran 2017, (Tam Metin Bildiri) Sürdürülebilir Kalkınma

16. IDENTIFICATION of TISSUE SPECIFIC GENES and ASSESMENT of THEIR INTERSECTION WITH DIFFERENTIALY EXPRESSED GENES in CANCER DATA to UNDERSTAND TUMOR HETEROGENEITY IN SILICO

Konuk H. B., Cesur M. R., Yılmaz A.
10 th International Symposium on Health Informatics and Bioinformatics, Güzelyurt, Kıbrıs (Kktc), 28 Haziran 2017, (Özet Bildiri) Sürdürülebilir Kalkınma

17. Robust and Rigorous Classification of Tissue Specific Genes

KONUK H. B., YILMAZ A.
INTERNATIONAL DNA DAY AND GENOME CONGRESS (IDDGC) 2017, Kırşehir, Türkiye, 24 Nisan 2017, (Tam Metin Bildiri)

18. Prebiotics and Probiotics: Break the ‘Self-Domino Effect’ for obesity Treatment

Özel C., Yılmaz A.
IVEK 3rd International Convention of Pharmaceuticals and Pharmacies, İstanbul, Türkiye, 26 Nisan 2017, ss.338, (Özet Bildiri) Sürdürülebilir Kalkınma

19. Prediction of splice site using AdaBoost with a new sequence encoding approach

Pashaei E., YILMAZ A., ÖZEN M., AYDIN N.
2016 IEEE International Conference onSystems, Man, and Cybernetics, 9 - 12 Ekim 2016, (Tam Metin Bildiri)

20. A Combined SVM and Markov Model approach for Splice Site Identification

Pashaei E., YILMAZ A., Aydini N.
6th International Conference on Computer and Knowledge Engineering (ICCKE), Mashhad, İran, 20 - 21 Ekim 2016, ss.200-204, (Tam Metin Bildiri) identifier identifier

21. A Novel Method for Splice Sites Prediction Using Sequence Component and Hidden Markov Model

Pashaei E., YILMAZ A., Ozen M., AYDIN N.
38th Annual International Conference of the IEEE-Engineering-in-Medicine-and-Biology-Society (EMBC), Florida, Amerika Birleşik Devletleri, 16 - 20 Ağustos 2016, ss.3076-3079, (Tam Metin Bildiri) identifier identifier identifier

22. Utilization of Multiple Mapped Sequences in Next Generation Sequencing Especially in Chip Seq Experiments

ZOR S., YILMAZ A.
International Health Informatics and Bioinformatics Symposium, Muğla, Türkiye, 16 - 17 Ekim 2015

23. Computational Identification of miRNA Targets Using Olive Library

Ömeroğlu Ulu Z., ÜN C., ÖZTABAK K. Ö., YILMAZ A., ÖZDEMİR ÖZGENTÜRK N.
Post-Transcriptional Gene Regulation in Plants, Paris, 10 - 11 Temmuz 2015

24. Molecular Analysis of Lipid Transfer Gene Selected from Olıve Olea europaea ESTs Expressed Sequence Tags Collection

Ömeroğlu Ulu Z., ÜN C., ÖZTABAK K. Ö., YILMAZ A., ÖZDEMİR ÖZGENTÜRK N.
International Symposium on Molecular Chemistry, 18 - 19 Aralık 2014

25. Construction and Comparison of EST Library for Expressed Genes in Normal and Tumoral Mammary Gland Tissue of the Terrier Dog

Ömeroğlu Ulu Z., ÜN C., ÖZTABAK K. Ö., YILMAZ A., ÖZDEMİR ÖZGENTÜRK N.
International Symposium on Molecular Chemistry, 18 - 19 Aralık 2014

26. Design and synthesis of small peptide sequences to detect concentrations of free transition metal ions

YÜCESAN G., Yılmaz A., Adıyaman R.
American Chemical Society, 01 Mart 2014, (Tam Metin Bildiri)

27. Analyses of EST Collection from Prenatal and Postnatal Mammary Tissue of Sheep

Ömeroğlu Ulu Z., ÜN C., ÖZTABAK K. Ö., YILMAZ A., ÖZDEMİR ÖZGENTÜRK N.
HIBIT 2013 The 8th International Symposium on Health Informatics and Bioinformatics, 25 - 27 Eylül 2013

28. Discovery of regulatory networks in plants by linking promoter and transcription factor databases.

YILMAZ A., Palaniswamy S., Davuluri R., Grotewold E.
Proceedings of the Ohio Collaborative Conference on Bioinformatics, 01 Haziran 2009

29. Construction of genomic regulatory encyclopedias: Strategies and case studies

Alam M., Bitterman T., Drews F., Ecker K., Elnitski L., Evans S., et al.
Proceedings of the Ohio Collaborative Conference on Bioinformatics, 01 Haziran 2009
Metrikler

Yayın

60

Yayın (WoS)

18

Yayın (Scopus)

27

Atıf (WoS)

2004

H-İndeks (WoS)

11

Atıf (Scopus)

2160

H-İndeks (Scopus)

13

Atıf (Scholar)

4

H-İndeks (Scholar)

2

Proje

9

Tez Danışmanlığı

12

Açık Erişim

24
BM Sürdürülebilir Kalkınma Amaçları