Research Articles

Selcen Ari Yuka, Alper Yilmaz (2021). Effect of SARS-CoV-2 infection on host competing endogenous RNA and miRNA network. PeerJ.

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Busra Nur Darendeli, Alper Yilmaz (2021). Convolutional Neural Network Approach to Predict Tumor Samples Using Gene Expression Data. Journal of Intelligent Systems: Theory and Applications.

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Selcen Ari Yuka, Alper Yilmaz (2021). Network based multifactorial modelling of miRNA-target interactions. PeerJ.

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Alper Yilmaz (2020). Assessment of mutation susceptibility in DNA sequences with word vectors. Journal of Intelligent Systems: Theory and Applications.

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, Robert Ford (2015). An example journal article. Journal of Source Themes, 1(1).

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Wilberforce Zachary Ouma, Maria Katherine Mejia-Guerra, Alper Yilmaz, Pablo Pareja-Tobes, Wei Li, Andrea I Doseff, Erich Grotewold (2015). Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq). Scientific Reports.

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Daniel Arango, Kengo Morohashi, Alper Yilmaz, Kouji Kuramochi, Arti Parihar, Bledi Brahimaj, Erich Grotewold, Andrea I Doseff (2013). Molecular basis for the action of a dietary flavonoid revealed by the comprehensive identification of apigenin human targets. Proc Natl Acad Sci U S A.

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Nathalie Bolduc, Alper Yilmaz, Maria Katherine Mejia-Guerra, Kengo Morohashi, Devin O'Connor, Erich Grotewold, Sarah Hake (2012). Unraveling the KNOTTED1 regulatory network in maize meristems. Genes & Development.

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Kengo Morohashi, María Isabel Casas, Maria Lorena Falcone Ferreyra, Lorena Falcone Ferreyra, Maria Katherine Mejia-Guerra, Lucille Pourcel, Alper Yilmaz, Antje Feller, Bruna Carvalho, Julia Emiliani, Eduardo Rodriguez, Silvina Pellegrinet, Michael McMullen, Paula Casati, Erich Grotewold (2012). A genome-wide regulatory framework identifies maize pericarp color1 controlled genes. The Plant Cell.

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Amit Sharma, Alper Yilmaz, Kim Marsh, Alan Cochrane, Kathleen Boris-Lawrie (2012). Thriving under stress: selective translation of HIV-1 structural protein mRNA during Vpr-mediated impairment of eIF4E translation activity. PLoS Pathogens.

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Ethalinda K S Cannon, Scott M Birkett, Bremen L Braun, Sateesh Kodavali, Douglas M Jennewein, Alper Yilmaz, Valentin Antonescu, Corina Antonescu, Lisa C Harper, Jack M Gardiner, Mary L Schaeffer, Darwin A Campbell, Carson M Andorf, Destri Andorf, Damon Lisch, Karen E Koch, Donald R McCarty, John Quackenbush, Erich Grotewold, Carol M Lushbough, Taner Z Sen, Carolyn J Lawrence (2011). POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data. International Journal of Plant Genomics.

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Jens Lichtenberg, Alper Yilmaz, Kyle Kurz, Xiaoyu Liang, Chase Nelson, Thomas Bitterman, Eric Stockinger, Erich Grotewold, Lonnie R. Welch (2011). Encyclopedias of DNA Elements for Plant Genomes. Advances in Genomic Sequence Analysis and Pattern Discovery.

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Alper Yilmaz, Maria Katherine Mejia-Guerra, Kyle Kurz, Xiaoyu Liang, Lonnie Welch, Erich Grotewold (2011). AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Res.

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The International Brachypodium Initiative (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature.

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Alper Yilmaz, Erich Grotewold (2010). Components and mechanisms of regulation of gene expression. Methods in Molecular Biology (Clifton, N.J.).

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Jens Lichtenberg, Alper Yilmaz, Joshua D Welch, Kyle Kurz, Xiaoyu Liang, Frank Drews, Klaus Ecker, Stephen S Lee, Matt Geisler, Erich Grotewold, Lonnie R Welch (2009). The word landscape of the non-coding segments of the Arabidopsis thaliana genome. BMC Genomics.

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Alper Yilmaz, Ramana Davuluri, Saranyan Palaniswamy, Erich Grotewold (2009). Discovery of Regulatory Networks in Plants by Linking Promoter and Transcription Factor Databases. 2009 Ohio Collaborative Conference on Bioinformatics.

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Jens Lichtenberg, Mohit Alam, Thomas Bitterman, Frank Drews, Klaus Ecker, Laura Elnitski, Susan Evans, Matt Geisler, Erich Grotewold, Dazhang Gu, Edwin Jacox, Kyle Kurz, Stephen S. Lee, Xiaoyu Liang, Pooja M. Majmudar, Paul Morris, Chase Nelson, Eric Stockinger, Joshua D. Welch, Sarah Wyatt, Alper Yilmaz, Lonnie R. Welch (2009). Construction of Genomic Regulatory Encyclopedias: Strategies and Case Studies. 2009 Ohio Collaborative Conference on Bioinformatics.

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Alper Yilmaz, Milton Y Nishiyama, Bernardo Garcia Fuentes, Glaucia Mendes Souza, Daniel Janies, John Gray, Erich Grotewold (2009). GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol.

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M V P Nadella, W C Kisseberth, K S Nadella, N K Thudi, D H Thamm, E A McNiel, A Yilmaz, K Boris-Lawrie, T J Rosol (2008). NOD/SCID mouse model of canine T-cell lymphoma with humoral hypercalcaemia of malignancy: cytokine gene expression profiling and in vivo bioluminescent imaging. Veterinary and Comparative Oncology.

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Cheryl Bolinger, Alper Yilmaz, Tiffiney Roberts Hartman, Melinda Butsch Kovacic, Soledad Fernandez, Jianxin Ye, Mary Forget, Patrick L Green, Kathleen Boris-Lawrie (2007). RNA helicase A interacts with divergent lymphotropic retroviruses and promotes translation of human T-cell leukemia virus type 1. Nucleic Acids Res.

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Alper Yilmaz, Soledad Fernandez, Michael D Lairmore, Kathleen Boris-Lawrie (2006). Coordinate enhancement of transgene transcription and translation in a lentiviral vector. Retrovirology.

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Alper Yilmaz, Cheryl Bolinger, Kathleen Boris-Lawrie (2006). Retrovirus Translation Initiation: Issues and Hypotheses Derived from Study of HIV-1. Current HIV Research.

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