Publications & Works

Publication Network
Journal articles indexed in SCI, SSCI, and AHCI 23

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

YILMAZ A., Ari Yuka S.
Journal of Molecular Medicine , vol.103, no.1, pp.33-49, 2025 (SCI-Expanded) identifier identifier

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

Arı Yuka S., Yilmaz A.
BIODATA MINING , vol.17, no.1, pp.11, 2024 (SCI-Expanded) Sustainable Development identifier identifier

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 , vol.38, no.1, 2024 (SCI-Expanded) identifier

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

Luleci H. B., Yuka S. A., YILMAZ A.
Interdisciplinary Sciences - Computational Life Sciences , 2024 (SCI-Expanded) identifier identifier

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 , vol.8, no.40, pp.36835-36844, 2023 (SCI-Expanded) identifier identifier

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 , vol.46, no.4, pp.713-727, 2023 (SCI-Expanded) identifier identifier

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

Lüleci H. B., YILMAZ A.
BioData Mining , vol.15, no.1, 2022 (SCI-Expanded) identifier identifier

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

Ari Yuka S., Yilmaz A.
PeerJ , vol.9, no.e12370, 2021 (SCI-Expanded) Sustainable Development identifier identifier identifier

Network based multifactorial modelling of miRNA-target interactions

Ari Yuka S., Yilmaz A.
PEERJ , vol.9, 2021 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

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 , vol.5, 2015 (SCI-Expanded) Creative Commons License identifier identifier identifier

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 , vol.110, no.24, 2013 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

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 , vol.26, no.15, pp.1685-1690, 2012 (SCI-Expanded) Creative Commons License identifier identifier identifier

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 , vol.24, no.7, pp.2745-2764, 2012 (SCI-Expanded) Creative Commons License identifier identifier identifier

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 , vol.8, no.3, 2012 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

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 , vol.39, 2011 (SCI-Expanded) Creative Commons License identifier identifier identifier

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 , vol.463, no.7282, pp.763-768, 2010 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

Components and Mechanisms of Regulation of Gene Expression

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

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 , vol.10, 2009 (SCI-Expanded) Creative Commons License identifier identifier identifier

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 , vol.149, no.1, pp.171-180, 2009 (SCI-Expanded) identifier identifier identifier

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 , vol.6, no.1, pp.39-54, 2008 (SCI-Expanded) Creative Commons License identifier identifier identifier

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 , vol.35, no.8, pp.2629-2642, 2007 (SCI-Expanded) Creative Commons License identifier identifier identifier

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

Yilmaz A., BOLINGER C., BORIS-LAWRIE K.
CURRENT HIV RESEARCH , vol.4, no.2, pp.131-139, 2006 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier

Coordinate enhancement of transgene transcription and translation in a lentiviral vector

Yilmaz A., FERNANDEZ S., LAIRMORE M. D., BORIS-LAWRIE K.
RETROVIROLOGY , vol.3, 2006 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier
Articles Published in Other Journals 4

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 , vol.26, no.1, pp.1-12, 2022 (Peer-Reviewed Journal) Sustainable Development identifier

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) , vol.4, no.2, pp.136-141, 2021 (Peer-Reviewed Journal) Creative Commons License Sustainable Development identifier

Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors

YILMAZ A.
Zeki Sistemler Teori ve Uygulamaları Dergisi , vol.3, no.1, pp.1-6, 2020 (Peer-Reviewed Journal) Creative Commons License

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 , vol.2011, 2011 (Scopus) identifier identifier
Papers Presented at Peer-Reviewed Scientific Conferences 29

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, Russia, 1 - 04 December 2020, pp.274-281 identifier

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, Turkey, 17 - 18 October 2019, pp.222-223

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, Turkey, 17 - 18 October 2019, pp.219

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, Turkey, 17 - 18 October 2019, pp.218 Sustainable Development

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, Turkey, 17 - 18 October 2019, pp.230, (Summary Text) Sustainable Development

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, Turkey, 1 - 04 November 2018, pp.30 Sustainable Development

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, Turkey, 3 - 05 October 2018, pp.87

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, Turkey, 17 - 18 May 2017 Sustainable Development

Darendeli B. N., Al-Qabbani H., Yılmaz A.
1.Temel Onkoloji Sempozyumu, İzmir, Turkey, 9 - 11 May 2018, pp.48 Sustainable Development

Öztürk R., Yılmaz A.
1.Temel Onkoloji Sempozyumu, İzmir, Turkey, 9 - 11 May 2018, pp.30 Sustainable Development

Pinpointing the importance of compounds in human metabolic network

Öztürk E. R., Yılmaz A.
7th International Molecular Biology and Biotechnology Congress, Konya, Turkey, 25 - 27 April 2018, pp.160

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, Turkey, 25 - 27 April 2018, pp.401 Sustainable Development

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, Bosnia And Herzegovina, 25 - 29 October 2017, (Summary Text)

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, Bosnia And Herzegovina, 25 - 29 October 2017 Sustainable Development

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, Cyprus (Kktc), 28 June 2017 Sustainable Development

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

KALYON O., YILMAZ A.
10th International Symposium on Health Informatics and Bioinformatics, Güzelyurt, Cyprus (Kktc), 28 June 2017, (Full Text) Sustainable Development

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

Özel C., Yılmaz A.
IVEK 3rd International Convention of Pharmaceuticals and Pharmacies, İstanbul, Turkey, 26 April 2017, pp.338 Sustainable Development

Robust and Rigorous Classification of Tissue Specific Genes

KONUK H. B., YILMAZ A.
INTERNATIONAL DNA DAY AND GENOME CONGRESS (IDDGC) 2017, Kırşehir, Turkey, 24 April 2017

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 October 2016

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, Iran, 20 - 21 October 2016, pp.200-204 identifier identifier

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, United States Of America, 16 - 20 August 2016, pp.3076-3079 identifier identifier identifier

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, Turkey, 16 - 17 October 2015

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 July 2015

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 December 2014

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 December 2014

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 March 2014, (Full Text)

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 September 2013

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 June 2009

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 June 2009
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59

Publication (WoS)

18

Publication (Scopus)

27

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2004

H-Index (WoS)

11

Citation (Scopus)

2154

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12

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4

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2

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9

Thesis Advisory

12

Open Access

24
UN Sustainable Development Goals