Items where Author is "Budak, Hikmet"

Article

Hussain, Babar and Akpınar, Bala A. and Alaux, Michael and Algharib, Ahmed M. and Sehgal, Deepmala and Ali, Zulfiqar and Aradottir, Gudbjorg I. and Batley, Jacqueline and Bellec, Arnaud and Bentley, Alison R. and Cagirici, Halise B. and Cattivelli, Luigi and Choulet, Fred and Cockram, James and Desiderio, Francesca and Devaux, Pierre and Dogramaci, Münevver and Dorado, Gabriel and Dreisigacker, Susanne and Edwards, David and El-Hassouni, Khaoula and Eversole, Kellye and Fahima, Tzion and Figueroa, Melania and Gálvez, Sergio and Gill, Kulvinder S. and Govta, Liubov and Gul, Alvina and Hensel, Goetz and Hernandez, Pilar and Crespo-Herrera, Leonardo Abdiel and Ibrahim, Amir and Kilian, Benjamin and Korzun, Viktor and Krugman, Tamar and Li, Yinghui and Liu, Shuyu and Mahmoud, Amer F. and Morgounov, Alexey and Muslu, Tuğdem and Naseer, Faiza and Ordon, Frank and Paux, Etienne and Perovic, Dragan and Reddy, Gadi V.P. and Reif, Jochen Christoph and Reynolds, Matthew and Roychowdhury, Rajib and Rudd, Jackie and Sen, Taner Z. and Sukumaran, Sivakumar and Ozdemir, Bahar Sogutmaz and Tiwari, Vijay Kumar and Ullah, Naimat and Unver, Turgay and Yazar, Selami and Appels, Rudi and Budak, Hikmet (2022) Capturing wheat phenotypes at the genome level. Frontiers in Plant Science, 13 . ISSN 1664-462X (Print) 1664-462X (Online)

Muslu, Tuğdem and Akpinar, Bala Ani and Kaya, Sezgi and Yüce, Meral and Budak, Hikmet (2021) Comparative analysis of coding and non-coding features within insect tolerance loci in wheat with their homologs in cereal genomes. International Journal of Molecular Sciences, 22 (22). ISSN 1661-6596 (Print) 1422-0067 (Online)

Gogolev, Yuri V. and Ahmar, Sunny and Akpinar, Bala Ani and Budak, Hikmet and Kiryushkin, Alexey S. and Gorshkov, Vladimir Y. and Hensel, Goetz and Demchenko, Kirill N. and Kovalchuk, Igor and Mora-Poblete, Freddy and Muslu, Tuğdem and Tsers, Ivan D. and Yadav, Narendra Singh and Korzun, Viktor (2021) Omics, epigenetics, and genome editing techniques for food and nutritional security. Plants, 10 (7). ISSN 2223-7747

Muslu, Tuğdem and Kaya, Sezgi and Akpinar, Bala Ani and Yüce, Meral and Budak, Hikmet (2021) Pan-genome mirnomics in brachypodium. Plants, 10 (5). ISSN 2223-7747

Rabanus-Wallace, M. Timothy and Hackauf, Bernd and Mascher, Martin and Lux, Thomas and Wicker, Thomas and Gundlach, Heidrun and Baez, Mariana and Houben, Andreas and Mayer, Klaus F.X. and Guo, Liangliang and Poland, Jesse and Pozniak, Curtis J. and Walkowiak, Sean and Melonek, Joanna and Praz, Coraline R. and Schreiber, Mona and Budak, Hikmet and Heuberger, Matthias and Steuernagel, Burkhard and Wulff, Brande and Börner, Andreas and Byrns, Brook and Čížková, Jana and Fowler, D. Brian and Fritz, Allan and Himmelbach, Axel and Kaithakottil, Gemy and Keilwagen, Jens and Keller, Beat and Konkin, David and Larsen, Jamie and Li, Qiang and Myśków, Beata and Padmarasu, Sudharsan and Rawat, Nidhi and Sesiz, Uğur and Kaya, Sezgi and Sharpe, Andy and Šimková, Hana and Small, Ian and Swarbreck, David and Toegelová, Helena and Tsvetkova, Natalia and Voylokov, Anatoly V. and Vrána, Jan and Bauer, Eva and Bolibok-Bragoszewska, Hanna and Doležel, Jaroslav and Hall, Anthony and Jia, Jizeng and Korzun, Viktor and Laroche, André and Ma, Xue Feng and Ordon, Frank and Özkan, Hakan and Rakoczy-Trojanowska, Monika and Scholz, Uwe and Schulman, Alan H. and Siekmann, Dörthe and Stojałowski, Stefan and Tiwari, Vijay K. and Spannagl, Manuel and Stein, Nils (2021) Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential. Nature Genetics, 53 (4). pp. 564-573. ISSN 1061-4036 (Print) 1546-1718 (Online)

Çağırıcı, Halise Büşra and Galvez, S. and Sen, Taner Z. and Budak, Hikmet (2021) LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants. Functional and Integrative Genomics, 21 (2). pp. 195-204. ISSN 1438-793X (Print) 1438-7948 (Online)

Hussain, Babar and Lucas, Stuart J. and Öztürk, Levent and Budak, Hikmet (2020) Author Correction: Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stage in wheat (Scientific Reports, (2017), 7, 1, (15662), 10.1038/s41598-017-15726-6). Scientific Reports, 10 (1). ISSN 2045-2322

Budak, Hikmet and Kaya, Sezgi and Çağırıcı, Halise Büşra (2020) Long non-coding RNA in plants in the era of reference sequences. Frontiers in Plant Science, 11 . ISSN 1664-462X

Kurt, Hasan and Eyüpoğlu, Alp Ertunga and Sütlü, Tolga and Budak, Hikmet and Yüce, Meral (2019) Plasmonic selection of ssDNA aptamers against fibroblast growth factor receptor. ACS Combinatorial Science, 21 (8). pp. 578-587. ISSN 2156-8952 (Print) 2156-8944 (Online)

Khan, Zaeema and Karamahmutoğlu, Hande and Elitaş, Meltem and Yüce, Meral and Budak, Hikmet (2019) Through the looking glass: real-time imaging in brachypodium roots and osmotic stress analysis. Plants, 8 (1). ISSN 2223-7747

Hussain, Babar and Lucas, Stuart J. and Budak, Hikmet (2018) CRISPR/Cas9 in plants: at play in the genome and at work for crop improvement. Briefings in Functional Genomics, 17 (5). pp. 319-328. ISSN 2041-2649 (Print) 2041-2657 (Online)

Yüce, Meral and Kurt, Hasan and Hussain, Babar and Ow-Yang, Cleva W. and Budak, Hikmet (2018) Exploiting stokes and anti-stokes type emission profiles of aptamer-functionalized luminescent nanoprobes for multiplex sensing applications. Chemistry Select, 3 (21). pp. 5814-5823. ISSN 2365-6549

Ullah, Naimat and Yüce, Meral and Gökçe, Z. Neslihan Öztürk and Budak, Hikmet (2017) Comparative metabolite profiling of drought stress in roots and leaves of seven Triticeae species. BMC Genomics, 18 . ISSN 1471-2164

Hussain, Babar and Lucas, Stuart J. and Öztürk, Levent and Budak, Hikmet (2017) Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stage in wheat. Scientific Reports, 7 . ISSN 2045-2322

Lucas, Stuart J. and Salantur, Ayten and Yazar, Selami and Budak, Hikmet (2017) High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Functional and Integrative Genomics . ISSN 1438-793X (Print) 1438-7948 (Online) Published Online First http://dx.doi.org/10.1007/s10142-017-0563-y

Alptekin, Burcu and Budak, Hikmet (2017) Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors. Functional & Integrative Genomics, 17 (2-3). pp. 171-187. ISSN 1438-793X (Print) 1438-7948 (Online)

Elitaş, Meltem and Yüce, Meral and Budak, Hikmet (2017) Microfabricated tools for quantitative plant biology. Analyst, 142 (6). pp. 835-848. ISSN 0003-2654 (Print) 1364-5528 (Online)

Akpınar, Bala Anı and Lucas, Stuart J. and Budak, Hikmet (2017) A large-scale chromosome-specific SNP discovery guideline. Functional and Integrative Genomics, 17 (1). pp. 97-105. ISSN 1438-793X (Print) 1438-7948 (Online)

Kurt, Hasan and Yüce, Meral and Hussain, Babar and Budak, Hikmet (2016) Dual-excitation upconverting nanoparticle and quantum dot aptasensor for multiplexed food pathogen detection. Biosensors and Bioelectronics, 81 . pp. 280-286. ISSN 0956-5663 (Print) 1873-4235 (Online)

Mokkapati, V. R. S. S. and Taşlı, Neslihan P. and Khan, Zaeema and Tufani, Ali and Pandit, Santosh and Budak, Hikmet and Şahin, Fikrettin (2016) NaB integrated graphene oxide membranes for enhanced cell viability and stem cell properties of human adipose stem cells. RSC Advances, 6 (61). pp. 56159-56165. ISSN 2046-2069 (Print) 2046-2069 (Online)

Akpınar, Bala Anı and Budak, Hikmet (2016) Dissecting miRNAs in wheat d genome progenitor, aegilops tauschii. Frontiers in Plant Science, 7 . ISSN 1664-462X (Print) 1664-462X (Online)

Klionsky, Daniel J. and Gözüaçık, Devrim and Budak, Hikmet and Autophagy, Consortium (2016) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy, 12 (1). pp. 1-222. ISSN 1554-8627 (Print) 1554-8635 (Online)

Budak, Hikmet and Hussain, Babar and Khan, Zaeema and Öztürk, Neslihan Z. and Ullah, Naimat (2015) From genetics to functional genomics: improvement in drought signaling and tolerance in wheat. Frontiers in Plant Science, 6 . ISSN 1664-462X (Print) 1664-462X (Online)

Kippes, Nestor and Debernardi, Juan M. and Vasquez-Gross, Hans A. and Akpınar, Bala Anı and Budak, Hikmet and Kato, Kenji and Chao, Shiaoman and Akhunov, Eduard and Dubcovsky, Jorge (2015) Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia. Proceedings of the National Academy of Sciences, 112 (39). E5401-E5410. ISSN 0027-8424 (Print) 1091-6490 (Online)

Khaksefidi, Reyhaneh Ebrahimi and Mirlohi, Shirin and Khalaji, Fahimeh and Fakhari, Zahra and Shiran, Behrouz and Fallahi, Hossein and Rafiei, Fariba and Budak, Hikmet and Ebrahimie, Esmaeil (2015) Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus. Frontiers in Plant Science, 6 . ISSN 1664-462X (Print) 1664-462X (Online)

Yüce, Meral and Uysal, Ebru and Budak, Hikmet (2015) Amplification yield enhancement of short DNA templates using bulk and surface-attached amine-functionalized single-wall carbon nanotubes. Applied Surface Science, 349 . pp. 147-155. ISSN 0169-4332 (Print) 1873-5584 (Online)

Budak, Hikmet and Akpınar, Bala Anı (2015) Plant miRNAs: biogenesis, organization and origins. Functional and Integrative Genomics, 15 (5). pp. 523-531. ISSN 1438-793X (Print) 1438-7948 (Online)

Akpınar, Bala Anı and Kantar, Melda and Budak, Hikmet (2015) Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress. Functional and Integrative Genomics, 15 (5). pp. 587-598. ISSN 1438-793X (Print) 1438-7948 (Online)

Akpınar, Bala Anı and Lucas, Stuart J. and Vrana, Jan and Dolezel, Jaroslav and Budak, Hikmet (2015) Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum). Plant Biotechnology Journal, 13 (6). pp. 740-752. ISSN 1467-7644 (Print) 1467-7652 (Online)

Khan, Zaeema and Budak, Hikmet (2015) A short overview on the latest updates on cereal crop plant genome sequencing with an emphasis on cereal crops and their wild relatives. Ekin Journal of Crop Breeding and Genetics, 1 (2). pp. 1-7. ISSN 2149-1275 (Print) 2459-069X (Online)

Budak, Hikmet and Bulut, Reyyan Fatima and Kantar, Melda and Alptekin, Burcu (2015) MicroRNA nomenclature and the need for a revised naming prescription. Briefings in Functional Genomics (Sl) . ISSN 2041-2649 (Print) 2041-2657 (Online)

Budak, Hikmet and Kantar, Melda (2015) Harnessing NGS and big data optimally: comparison of miRNA prediction from assembled versus non-assembled sequencing data—the case of the grass aegilops tauschii complex genome. OMICS: A Journal of Integrative Biology, 19 (7). pp. 407-415. ISSN 1536-2310

Akpınar, Bala Anı and Yüce, Meral and Lucas, Stuart J. and Vrana, Jan and Buresova, Veronika and Dolezel, Jaroslav and Budak, Hikmet (2015) Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides. Scientific Reports, 5 . ISSN 2045-2322

Akpınar, Bala Anı and Magni, Federica and Yüce, Meral and Lucas, Stuart J. and Simkova, Hana and Safar, Jan and Vautrin, Sonia and Berges, Helene and Cattonaro, Federica and Dolezel, Jaroslav and Budak, Hikmet (2015) The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements. BMC Genomics, 16 . ISSN 1471-2164

Yüce, Meral and Ullah, Naimat and Budak, Hikmet (2015) Trends in aptamer selection methods and applications. Analyst, 140 (16). pp. 5379-5399. ISSN 0003-2654 (Print) 1364-5528 (Online)

Budak, Hikmet and Kantar, Melda and Bulut, Reyyan Fatima and Akpınar, Bala Anı (2015) Stress responsive miRNAs and isomiRs in cereals. Plant Science, 235 . pp. 1-13. ISSN 0168-9452

Yüce, Meral and Budak, Hikmet (2014) Dispersion quality of amine functionalized multiwall carbon nanotubes plays critical roles in polymerase chain reaction enhancement. Journal of Nanoparticle Research, 16 (12). ISSN 1388-0764 (Print) 1572-896X (Online)

Lucas, Stuart J. and Akpınar, Bala Anı and Simkova, Hana and Kubalakova, Marie and Dolezel, Jaroslav and Budak, Hikmet (2014) Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications. BMC Genomics, 15 . ISSN 1471-2164

Budak, Hikmet and Yüce, Meral (2014) Dispersion quality of amine functionalized multiwall carbon nanotubes plays critical roles in PCR enhancement. Journal of Nanoparticle Research . ISSN 1388-0764 (Print) 1572-896X (Online) Published Online First http://dx.doi.org/10.1007/s11051-014-2768-5

Yüce, Meral and Kurt, Hasan and Budak, Hikmet (2014) Characterization of a dual biotin tag for improved single stranded dna production. Analytical Methods, 6 (2). pp. 548-557. ISSN 1759-9660 (Print) 1759-9679 (Online)

Yüce, Meral and Kurt, Hasan and Mokkapati, Raghu Sarma and Budak, Hikmet (2014) Employment of nanomaterials in polymerase chain reaction: insight into the impacts and putative operating mechanisms of nano-additives in PCR. RSC Advances, 4 (69). pp. 36800-36814. ISSN 2046-2069 (Print) 2046-2069 (Online)

Gordon, Sean P. and Priest, Henry and Marais, David L. Des and Schackwitz, Wendy and Figueroa, Melania and Martin, Joel and Bragg, Jennifer N. and Tyler, Ludmila and Lee, Cheng-Ruei and Bryant, Doug and Wang, Wenqin and Messing, Joachim and Manzaneda, Antonio J. and Barry, Kerrie and Garvin, David F. and Budak, Hikmet and Tuna, Metin and Mitchell-Olds, Thomas and Pfender, William F. and Juenger, Thomas E. and Mockler, Todd C. and Vogel, John (2014) Genome diversity in brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant Journal, 79 (3). pp. 361-374. ISSN 0960-7412 (Print) 1365-313X (Online)

Mayer, Klaus F. X. and Budak, Hikmet (2014) A chromosome-based draft sequence of the hexaploid bread wheat (triticum aestivum) genome. Science (SI), 345 (6194). ISSN 0036-8075 (Print) 1095-9203 (Online)

Marcussen, Thomas and Sandve, Simen R. and Heier, Lise and Spannagl, Manuel and Pfeifer, Matthias and Jakobsen, Kjetill S. and Wulff, Brande B. H. and Steuernagel, Burkhard and Mayer, Klaus F. X. and Olsen, Odd-Arne and Budak, Hikmet and Group Author(s), Int Wheat Genome Sequencing (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science (SI), 345 (6194). ISSN 0036-8075 (Print) 1095-9203 (Online)

Pfeifer, Matthias and Kugler, Karl G. and Sandve, Simen R. and Zhan, Bujie and Rudi, Heidi and Hvidsten, Torgeir R. and Mayer, Klaus F. X. and Olsen, Odd-Arne and Budak, Hikmet and Group Author(s), Int Wheat Genome Sequencing (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. Science (SI), 345 (6194). ISSN 0036-8075 (Print) 1095-9203 (Online)

Budak, Hikmet and Khan, Zaeema and Kantar, Melda (2014) History and current status of wheat miRNAs using next-generation sequencing and their roles in development and stress. Briefings in Functional Genomics (Sl) . ISSN 2041-2649 (Print) 2041-2657 (Online)

Yucebilgili, Kuaybe and Kantar, Melda and Budak, Hikmet (2014) New wheat microRNA using whole-genome sequence. Functional and Integrative Genomics, 14 (2). pp. 363-379. ISSN 1438-793X (Print) 1438-7948 (Online)

Lucas, Stuart J. and Baştaş, Kubilay and Budak, Hikmet (2014) Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection. Gene, 536 (2). pp. 254-264. ISSN 0378-1119 (Print) 1879-0038 (Online)

Budak, Hikmet and Kantar, Melda (2013) New wheat micro RNA using whole genome sequences. (Accepted)

Pont, Caroline and Murat, Florent and Guizard, Sebastien and Flores, Raphael and Foucrier, Severine and Bidet, Yannick and Quraishi, Umar Masood and Alaux, Michael and Dolezel, Jaroslav and Fahima, Tzion and Budak, Hikmet and Keller, Beat and Salvi, Silvio and Maccaferri, Marco and Steinbach, Delphine and Feuillet, Catherine and Quesneville, Hadi and Salse, Jerome (2013) Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant Journal, 76 (6). pp. 1030-1044. ISSN 0960-7412 (Print) 1365-313X (Online)

Budak, Hikmet and Akpınar, Bala Anı and Ünver, Turgay and Türktaş, Mine (2013) Proteome changes in wild and modern wheat leaves upon drought stress by two-dimensional electrophoresis and nanoLC-ESI-MS/MS. Plant Molecular Biology, 83 (1-2). pp. 89-103. ISSN 0167-4412 (Print) 1573-5028 (Online)

Yucebilgili, Kuaybe and Kantar, Melda and Lucas, Stuart J. and Budak, Hikmet (2013) Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing. PLoS One, 8 (7). ISSN 1932-6203

Lucas, Stuart J. and Akpınar, Bala Anı and Kantar, Melda and Weinstein, Zohar Bat-El and Aydınoğlu, Fatma and Safar, Jan and Simkova, Hana and Frenkel, Zeev and Korol, Abraham and Magni, Federica and Cattonaro, Federica and Vautrin, Sonia and Bellec, Arnaud and Berges, Helene and Dolezel, Jaroslav and Budak, Hikmet (2013) Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A. PLoS One, 8 (4). ISSN 1932-6203

Unver, Turgay and Türktaş, Mine and Budak, Hikmet (2013) In planta evidence for the involvement of a ubiquitin conjugating enzyme (UBC E2 clade) in negative regulation of disease resistance. Plant Molecular Biology Reporter, 31 (2). pp. 323-334. ISSN 0735-9640 (Print) 1572-9818 (Online)

Budak, Hikmet and Kantar, Melda and Yucebilgili, Kuaybe (2013) Drought tolerance in modern and wild wheat. Scientific World Journal . ISSN 1537-744X

Akpınar, Bala Anı and Lucas, Stuart J. and Budak, Hikmet (2013) Genomics approaches for crop improvement against abiotic stress. Scientific World Journal . ISSN 1537-744X

Kantar, Melda and Akpınar, Bala Anı and Valarik, Miroslav and Lucas, Stuart J. and Dolezel, Jaroslav and Hernandez, Pilar and Budak, Hikmet (2012) Subgenomic analysis of microRNAs in polyploid wheat. Functional and Integrative Genomics, 12 (3). pp. 465-479. ISSN 1438-793X (Print) 1438-7948 (Online)

Lucas, Stuart J. and Budak, Hikmet (2012) Sorting the wheat from the chaff: identifying miRNAs in genomic survey sequences of triticum aestivum chromosome 1AL. PLoS One, 7 (7). ISSN 1932-6203

Kuzuoğlu, Duygu and Cebeci Yalçınkaya, Özge and Akpınar, Bala Anı and Mitou, Geraldine and Korkmaz, Gözde and Gözüaçık, Devrim and Budak, Hikmet (2012) Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. Planta, 236 (4). pp. 1081-1092. ISSN 0032-0935 (Print) 1432-2048 (Online)

Lucas, Stuart J. and Simkova, Hana and Safar, Jan and Jurman, Irena and Cattonaro, Federica and Vautrin, Sonia and Bellec, Arnaud and Berges, Helene and Dolezel, Jaroslav and Budak, Hikmet (2012) Functional features of a single chromosome arm in wheat (1AL) determined from its structure. Functional and Integrative Genomics, 12 (1). pp. 173-182. ISSN 1438-793X (Print) 1438-7948 (Online)

Akpınar, Bala Anı and Avşar, Bihter and Lucas, Stuart J. and Budak, Hikmet (2012) Plant abiotic stress signaling. Plant Signaling & Behavior, 7 (11). pp. 1450-1455. ISSN 1559-2316 (Print) 1559-2324 (Online)

Budak, Hikmet (2012) Plant abiotic stress signalling. (Accepted)

Budak, Hikmet and Akpınar, Bala Anı (2011) Dehydration stress-responsive miRNA in brachypodium distachyon: evident by genome-wide screening of microRNAs expression. OMICS: A Journal of Integrative Biology, 15 (11). pp. 791-799. ISSN 1536-2310

Lucas, Stuart J. and Doğan, Esen and Budak, Hikmet (2011) TMPIT1 from wild emmer wheat: first characterisation of a stress-inducible integral membrane protein. Gene, 483 (1-2). pp. 22-28. ISSN 0378-1119

Brkljacic, Jelena and Grotewold, Erich and Scholl, Randy and Mockler, Todd and Garvin, David F. and Vain, Philippe and Brutnell, Thomas and Sibout, Richard and Bevan, Michael and Budak, Hikmet and Caicedo, Ana L. and Gao, Caixia and Gu, Yong and Hazen, Samuel P. and Holt, Ben F. and Hong, Shin-Young and Jordan, Mark and Manzaneda, Antonio J. and Mitchell-Olds, Thomas and Mochida, Keiichi and Mur, Luis A. J. and Park, Chung-Mo and Sedbrook, John and Watt, Michelle and Zheng, Shao Jian and Vogel, John P. (2011) Brachypodium as a model for the grasses: today and the future. Plant Physiology, 157 (1). pp. 3-13. ISSN 0032-0889

Durmaz, Emel and Çoruh, Ceyda and Dinler, Gizem and Grusak, Micheal A. and Peleg, Zvika and Saranga, Yashua and Fahima, Tzion and Yazıcı, Mustafa Atilla and Öztürk, Levent and Çakmak, İsmail and Budak, Hikmet (2011) Expression and cellular localization of ZIP1 transporter under zinc deficiency in wild emmer wheat. Plant Molecular Biology Reporter, 29 (3). pp. 582-596. ISSN 0735-9640

Wicker, Thomas and Mayer, Klaus F. X. and Gundlach, Heidrun and Martis, Mihaela and Steuernagel, Burkhard and Scholz, Uwe and Simkova, Hana and Kubalakova, Marie and Choulet, Frederic and Taudien, Stefan and Platzer, Matthias and Feuillet, Catherine and Fahima, Tzion and Budak, Hikmet and Dolezel, Jaroslav and Keller, Beat and Stein, Nils (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell, 23 (5). pp. 1706-1718. ISSN 1040-4651

Kantar, Melda and Lucas, Stuart J. and Budak, Hikmet (2011) MiRNA expression patterns of triticum dicoccoides in response to shock drought stress. Planta, 233 (3). pp. 471-484. ISSN 0032-0935 (Print) 1432-2048 (Online)

Lucas, Stuart J. and Durmaz, Emel and Akpınar, Bala Anı and Budak, Hikmet (2011) The drought response displayed by a DRE-binding protein from Triticum dicoccoides. Plant Physiology and Biochemistry, 49 (3). pp. 346-351. ISSN 0981-9428

Mahmoud, Amer Faiz Ahmed and Budak, Hikmet (2011) First report of charcoal rot caused by macrophomina phaseolina in sunflower in Turkey. Plant Disease, 95 (2). p. 223. ISSN 0191-2917

Kantar, Melda and Lucas, Stuart J. and Budak, Hikmet (2011) Drought stress: molecular genetics and genomics approaches. Advances in Botanical Research, 57 . pp. 445-493. ISSN 0065-2296

Kantar, Melda and Ünver, Turgay and Budak, Hikmet (2010) Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Functional and Integrative Genomics, 10 (4). pp. 493-507. ISSN 1438-793X (Print) 1438-7948 (Online)

Akfırat, F. S. and Aydın, Y. and Ertuğrul, F. and Hasancebi, S. and Budak, Hikmet and Akan, K. and Mert, Z. and Bolat, N. and Uncuoğlu, A. A. (2010) A microsatellite marker for yellow rust resistance in wheat. Cereal Research Communications, 38 (2). pp. 203-210. ISSN 0133-3720 (Print) 1788-9170 (Online)

Choulet, Frederic and Wicker, Thomas and Rustenholz, Camille and Paux, Etienne and Salse, Jerome and Leroy, Philippe and Schlub, Stephane and Le Paslier, Marie-Christine and Magdelenat, Ghislaine and Gonthier, Catherine and Couloux, Arnaud and Budak, Hikmet and Breen, James and Pumphrey, Michael and Liu, Sixin and Kong, Xiuying and Jia, Jizeng and Gut, Marta and Brunel, Dominique and Anderson, James A. and Gill, Bikram S. and Appels, Rudi and Keller, Beat and Feuillet, Catherine (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell, 22 (6). pp. 1686-1701. ISSN 1040-4651

Morgounov, A. and Zykin, V. and Belan, I. and Roseeva, L. and Zelenskiy, Yu and Gomez Becerra, Hugo Ferney and Budak, Hikmet and Bekes, F. (2010) Genetic gains for grain yield in high latitude spring wheat grown in Western Siberia in 1900-2008. Field Crops Research, 117 (1). pp. 101-112. ISSN 0378-4290

Ünver, Turgay and Bakar, Mine and Shearman, Robert C. and Budak, Hikmet (2010) Genome-wide profiling and analysis of Festuca arundinacea miRNAs and transcriptomes in response to foliar glyphosate application. Molecular Genetics and Genomics, 283 (4). pp. 397-413. ISSN 1617-4615 (Print) 1617-4623 (Online)

Vogel, John P. and Garvin, David F. and Mockler, Todd J. and Schmutz, Jeremy and Rokhsar, Dan and Bevan, Michael W. and Barry, Kerrie and Lucas, Susan and Harmon-Smith, Miranda and Lail, Kathleen and Tice, Hope and Grimwood, Jane and McKenzie, Neil and Huo, Naxin and Gu, Yong Q and Lazo, Gerard R. and Anderson, Olin D. and You, Frank M. and Luo, Ming-Cheng and Dvorak, Jan and Wright, Jan and Febrer, Melanie and Idziak, Dominika and Hasterok, Robert and Lindquist, Scott A. and Wang, Mei and Fox, Samuel E. and Priest, Henry D. and Filichkin, Sergei A. and Givan, Scott A. and Bryant, Douglas W. and Chang, Jeff H. and Wu, Haiyan and Wu, Wei and Hsia, An-Ping and Schnable, Patrick S. and Kalyanaraman, Anantharaman and Baarbazuk, Brad and Michael, Todd P. and Hazen, Samuel P. and Bragg, Jennifer N. and Laudencia-Chingcuanco, Debbie and Weng, Yiqun and Haberer, Georg and Spannagl, Mianuel and Mayer, Klaus and Rattei, Thomas and Mitros, Therese and Lee, Sang-Jik and Rose, Jocelyn K. C. and Mueller, Lukas A. and York, Thomas L. and Wicker, Thomas and Buchmann, Jan P. and Tanskanen, Jaakko and Schulman, Alan H. and Gundlach, Heidrun and de Oliveira, Antonio Costa and Maia, Luciano da C. and Belknap, William and Jiang, Ning and Lai, Jinsheng and Zhu, Liucun and Ma, Jianxin and Sun, Cheng and Pritham, Ellen and Salse, Jerome and Murat, Florent and Abrouk, Michael and Bruggmann, Remy and Messing, Joachim and You, Frank M. and Fahlgren, Noah and Sullivan, Christopher M. and Carrington, James C. and Chapman, Elisabeth J. and May, Greg D. and Zhai, Jixian and Ganssmann, Matthias and Gurazada, Sai Guna Ranjan and German, Marcelo and Meyers, Blake C. and Green, Pamela J. and Tyler, Ludmila and Wu, Jiajie and Lazo, Gerard R. and Thomson, James and Hazen, Samuel P. and Chen, Shan and Scheller, Henrik V. and Harholt, Jesper and Ulvskov, Peter and Kimbrel, Jeffrey A. and Chang, Jeff H. and Bartley, Laura E. and Cao, Peijian and Jung, Ki-Hong and Sharma, Manoj K. and Vega-Sanchez, Miguel and Ronald, Pamela and Dardick, Christopher D. and De Bodt, Stefanie and Verelst, Wim and Inze, Dirk and Heese, Maren and Schnittger, Arp and Yang, Xiaohan and Kalluri, Udaya C. and Tuskan, Gerald A. and Hua, Zhihua and Vierstra, Richard D. and Cui, Yu and Ouyang, Shuhong and Sun, Qixin and Liu, Zhiyong and Yılmaz, Alper and Grotewold, Erich and Sibout, Richard and Hematy, Kian and Mouille, Gregory and Hoefte, Herman and Pelloux, Jerome and O'Connor, Devin and Schbnable, James and Rowe, Scott and Harmon, Frank and Cass, Cynthia L. and Sedbrook, John C. and Byrne, Mary E. and Walsh, Sean and Higgins, Janet and Li, Pinghua and Brutnell, Thomas and Ünver, Turgay and Budak, Hikmet and Belcram, Harry and Charles, Mathieu and Chalhoub, Boulos and Baxter, Ivan (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463 (7282). pp. 763-768. ISSN 0028-0836

Gomez Becerra, Hugo Ferney and Yazıcı, Mustafa Atilla and Öztürk, Levent and Budak, Hikmet and Peleg, Zvi and Morgounov, Alexey and Fahima, Tzion and Saranga, Yehoshua and Çakmak, İsmail (2010) Genetic variation and environmental stability of grain mineral nutrient concentrations in Triticum dicoccoides under five environments. Euphytica, 171 (1). pp. 39-52. ISSN 0014-2336 (Print) 1573-5060 (Online)

Dizkırıcı, Ayten and Kaya, Zeki and Güren, H. Elif and Budak, Hikmet (2010) Barley germplasms developed for scald disease resistance exhibited a high level of genetic diversity based on SRAP markers. Turkish Journal of Biology, 34 (3). pp. 271-279. ISSN 1300-0152

Castillo, A. and Budak, Hikmet and Martin, A. C. and Dorado, G. and Börner, A. and Röder, M. and Hernandez, P. (2010) Interspecies and intergenus transferability of barley and wheat D-genome microsatellite markers. Annals of Applied Biology, 156 (3). pp. 347-356. ISSN 0003-4746 (Print) 1744-7348 (Online)

Filiz, E. and Özdemir, B. S. and Budak, F. and Vogel, J. P. and Tuna, M. and Budak, Hikmet (2009) Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome, 52 (10). pp. 876-890. ISSN 0831-2796

Ünver, Turgay and Budak, Hikmet (2009) Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta, 230 (4). pp. 659-669. ISSN 0032-0935 (Print) 1432-2048 (Online)

Mitou, Geraldine and Budak, Hikmet and Gözüaçık, Devrim (2009) Techniques to study autophagy in plants. International Journal of Plant Genomics, 2009 . pp. 1-14. ISSN 1687-5370

Ergen, Zahide Neslihan and Thimmapuram, Jyothi and Bohnert, Hans J. and Budak, Hikmet (2009) Transcriptome pathways unique to dehydration tolerant relatives of modern wheat. Functional and Integrative Genomics, 9 (3). pp. 377-396. ISSN 1438-793X (Print) 1438-7948 (Online)

Vogel, John P. and Tuna, Metin and Budak, Hikmet and Huo, Naxin and Gu, Yong Q. and Steinwand, Michael A. (2009) Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biology, 9 . ISSN 1471-2229

Su, Y. Senem and Öztürk, Levent and Çakmak, İsmail and Budak, Hikmet (2009) Turfgrass species response exposed to increasing rates of glyphosate application. European Journal of Agronomy, 31 (3 Sp. ). pp. 120-125. ISSN 1161-0301

Peleg, Zvi and Çakmak, İsmail and Öztürk, Levent and Yazıcı, M. Atilla and Jun, Yan and Budak, Hikmet and Korol, Abraham B. and Fahima, Tzion and Saranga, Yehoshua (2009) Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat 3 wild emmer wheat RIL population. Theoretical and Applied Genetics, 119 (2). pp. 353-369. ISSN 0040-5752

Ergen, Zahide Neslihan and Budak, Hikmet (2009) Sequencing over 13 000 expressed sequence tags from six subtractive cDNA libraries of wild and modern wheats following slow drought stress. Plant Cell and Environment, 32 (3). pp. 220-236. ISSN 0140-7791

Cebeci Yalçınkaya, Özge and Budak, Hikmet (2009) Global expression patterns of three festuca species exposed to different doses of glyphosate using the affymetrix geneChip wheat genome array. Comparative and Functional Genomics, 2009 . ISSN 1531-6912

Unver, Turgay and Namuth-Covert, Deena M. and Budak, Hikmet (2009) Review of current methodological approaches for characterizing microRNAs in plants. International Journal of Plant Genomics, 2009 . ISSN 1687-5370

Unver, Turgay and Budak, Hikmet (2009) Virus induced gene silencing, a post transcriptional gene silencing method. International Journal of Plant Genomics, 2009 . ISSN 1687-5370

Cebeci, Özge and Köktürk, B. and Ergen, Neslihan and Öztürk, Levent and Çakmak, İsmail and Budak, Hikmet (2008) Differential expression of wheat transcriptomes in response to varying cadmium concentrations. Biologia Plantarum, 52 (4). pp. 703-708. ISSN 0006-3134 (Print) 1573-8264 (Online)

Dinler-Doğanay, Gizem and Budak, Hikmet (2008) Analysis of expressed sequence tags (ESTs) from Agrostis species obtained using sequence related amplified polymorphism. Biochemical Genetics, 46 (9-10). pp. 663-676. ISSN 0006-2928 (Print) 1573-4927 (Online)

Ilbagi, H. and Rabenstein, F. and Habekuss, A. and Ordon, F. and Citir, A. and Cebeci, O. and Budak, Hikmet (2008) Molecular, serological and transmission electron microscopic analysis of the barley yellow dwarf virus- PAV and the cereal yellow dwarf virus-RPV in canary seed (Phalaris canariensis L.). Cereal Research Communications, 36 (2). pp. 225-234. ISSN 0133-3720 (Print) 1788-9170 (Online)

Özdemir, Bahar Soğutmaz and Hernandez, Pilar and Filiz, Ertuğrul and Budak, Hikmet (2008) Brachypodium genomics. International Journal of Plant Genomics . ISSN 1687-5370 (Print) 1687-5389 (Online)

Castillo, lmudena and Budak, Hikmet and Varshney, Rajeev K. and Dorado, Gabriel and Graner, Andreas and Hernandez, Pilar (2008) Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC Plant Biology, 8 (97). ISSN 1471-2229

Aydın, Nevzat and Gökmen, Sabri and Yıldırım, Ahmet and Öz, Ahmet and Figliuolo, Giovanni and Budak, Hikmet (2007) Estimating genetic variation among dent corn inbred lines and topcrosses using multivariate analysis. Journal of Applied Biological Sciences, 1 (2). pp. 63-70. ISSN 1307-1130

Distelfeld, Assaf and Çakmak, İsmail and Peleg, Zvi and Öztürk, Levent and Yazıcı, Mustafa Atilla and Budak, Hikmet and Saranga, Yehoshua and Fahima, Tzion (2007) Multiple QTL-effects of wheat Gpc-B1 locus on grain protein and micronutrient concentrations. Physiologia plantarum, 129 (3). pp. 635-643. ISSN 0031-9317

Neslihan Z., Ergen and Dinler-Doğanay, Gizem and Shearman, Robert C. and Budak, Hikmet (2007) Identifying, cloning and structural analysis of differentially expressed genes upon Puccinia infection of Festuca rubra var. rubra. Gene, 393 (1-2). pp. 145-152. ISSN 0378-1119

Işık, Zeynep and Parmaksızoğlu, İskender and Çoruh, Ceyda and Geylan-Su, Y.S. and Cebeci, O. and Beecher, B. and Budak, Hikmet (2007) Organellar genome analysis of rye (Secale cereale) representing diverse geographic regions. Genome, 50 (8). pp. 724-734. ISSN 1480-3321

Erayman, Mustafa and Abeyo, Bekele Geleta and Baenziger, P. Stephen and Budak, Hikmet and Eskridge, Kent M. (2006) Evaluation of seedling characteristics of wheat (triticum aestivum L.) through canonical correlation analysis. Cereal Research Communications, 34 (4). pp. 1231-1238. ISSN 0133-3720 (Print) 1788-9170 (Online)

Budak, Hikmet and Kasap, Zeynep and Shearman, Robert C. and Dweikat, İsmail and Sezerman, Uğur and Mahmood, Abid (2006) Molecular characterization of cDNA encoding resistance gene-like sequences in Buchloe dactyloides. Molecular biotechnology, 34 (3). pp. 293-301. ISSN 1073-6085 (Print) 1559-0305 (Online)

Budak, Hikmet and Su, Senem Yaşasın and Ergen, Neslihan (2006) Revealing constitutively-expressed resistance genes in Agrostis species using PCR-based motif directed RNA fingerprinting. Genetical Research, 88 (3). pp. 165-175. ISSN 0016-6723

Budak, Hikmet and Shearman, Robert C. and Gülşen, Osman and Dweikat, İsmail (2005) Understanding ploidy complex and geographic origin of Buchloe dactyloides genome using cytoplasmic and nuclear marker systems. (Accepted)

Budak, Hikmet and Shearman, Robert C. and Dweikat, İsmail (2005) Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes. Genome, 48 (3). pp. 411-416. ISSN 0831-2796

Papers in Conference Proceedings

Lucas, Stuart J. and Sezer, A. and Boztepe, Ö. and Kahraman, Kadriye and Budak, Hikmet (2018) Genetic analysis of powdery mildew disease in Turkish hazelnut. In: IX International Congress on Hazelnut, Atakum, Samsun, Turkey

Akpınar, Bala Anı and Canlı, Özge and Budak, Hikmet (2015) Zn-deficiency responsive transcripts in Agrostis species revealed by mRNA differential display. In: 8th International Symposium on the Molecular Breeding of Forage and Turf, İstanbul, Turkey

Yücebilgili Kurtoğlu, Kuaybe and Kantar, Melda and Lucas, Stuart J. and Budak, Hikmet (2014) Dissecting microRNAs in wheat chromosome 5D using next generation sequencing data. In: XXII. Plant and Animal Genome Meeting, San Diego, CA

Gordon, Sean and Priest, Henry D. and Des Marais, David L. and Schackwitz, Wendy and Figueroa, Melania and Martin, Joel and Bragg, Jennifer and Tyler, Ludmila and Lee, Cheng-Ruei and Bryant, Doug and Wang, Wenqin and Messing, Joachim and Manzaneda, Antonio and Barry, Kerrie W. and Garvin, David F. and Budak, Hikmet and Tuna, Metin and Mitchell-Olds, Thomas and Pfender, William F. and Jeunger, Thomas and Mockler, Todd C. and Vogel, John (2014) Genome diversity in brachypodium distachyon: deep sequencing of highly diverse inbred lines. In: XXII. Plant and Animal Genome Meeting, San Diego, CA

Kantar, Melda and Avşar, Bihter and Budak, Hikmet (2014) Introgression of drought related QTLs into elite cultivars. In: XXII. Plant and Animal Genome Meeting, San Diego, CA

Aksoy, S. and Hekimbaşı, T. and Eyidoğan, F. and Öktem, H. and Budak, Hikmet (2009) Application of fiber-fish methods for transgene analysis in transgenic plants. In: 7th European Cytogenetics Conference, Stockholm, Sweden

Filiz, Ertuğrul and Özdemir, Bahar Soğutmaz and Tuna, Metin and Budak, Hikmet (2009) Diploid brachypodium distachyon of Turkey: molecular and morphological analysis. In: 5th International Molecular Breeding of Forage and Turf, Sapporo, Japan

Uncuoğlu, Ahu Altınkut and Yumurtacı, Ayşen and Aydın, Yıldız and Çakmak, İsmail and Ünal, Meral and Yeşil, Emel and Karanlık, Sema and Budak, Hikmet (2006) Data mining of ests for genetic improvement of salt tolerance in wheat. In: International Conference on Bioinformatics and Computational Biology, Las Vegas, Nevada, USA

Haker, Duygu and Ertuğrul, Fahriye and Çakmak, İsmail and Budak, Hikmet and Sayers, Zehra (2005) Bugday arpa ve celtikte WRKY gen ailesinin izole edilmesi ve sekanslanması. In: XIV Ulusal Biotechnology Conference, Eskişehir, Turkey

Budak, Hikmet and Yavuz, Y. F. (2005) Comparative sequence analysis to identify functional elements for functional genomics. In: International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS 05), Las Vegas, Nevada, USA

Book

Budak, Hikmet (2006) BIOCOMP'06: the 2006 International Conference on Bioinformatics & Computational Biology. CSR, Las Vegas, Nevada, USA. ISBN 1601320027

Book Section / Chapter

Dorado, Gabriel and Gálvez, Sergio and Budak, Hikmet and Unver, Turgay and Hernández, Pilar (2019) Nucleic-acid sequencing. In: Narayan, Roger, (ed.) Encyclopedia of Biomedical Engineering. Elsevier, Amsterdam, pp. 443-460. ISBN 9780128048290 (Print) 9780128051443 (Online)

Sogutmaz Ozdemir, Bahar and Budak, Hikmet (2018) Application of tissue culture and transformation techniques in model species Brachypodium distachyon. In: Sablok, Gaurav and Budak, Hikmet and Ralph, Peter J., (eds.) Brachypodium Genomics: Methods and Protocols. Methods in Molecular Biology, 1667. Humana, New York, NY, pp. 289-310. ISBN 978-1-4939-8439-8 (Print) 978-1-4939-7278-4 (Online)

Yüce, Meral and Kurt, Hasan and Hussain, Babar and Budak, Hikmet (2018) Systematic evolution of ligands by exponential enrichment for aptamer selection. In: Sarmento, Bruno and Neves, José Das, (eds.) Biomedical Applications of Functionalized Nanomaterials: Concepts, Development and Clinical Translation. Elsevier, Amsterdam, pp. 211-243. ISBN 9780323508780 (Print) 9780323508797 (Online)

Hussain, Babar and Yüce, Meral and Ullah, Naimat and Budak, Hikmet (2016) Bioconjugated nanomaterials for monitoring food contamination. In: Grumezescu, Alexandru, (ed.) Nanobiosensors. Elsevier, Amsterdam, pp. 93-123. ISBN 9780128043011 (Print) 9780128043721 (Online)

Budak, Hikmet (2013) Analysis and exploitation of cereal genomes with the aid of brachypodium. In: Tuberosa, Roberto, (ed.) Genomics of Plant Genetic Resources. Springer, Springer Science+Business Media Dordrecht. (Accepted)

Budak, Hikmet (2010) Plant genetic reseources: effective utilization. In: Call, A., (ed.) Encyclopedia of Agricultural, Food and Biological Engineering. Taylor & Francis, USA. (Accepted)

Monograph

Shearman, Robert C. and Riordan, T.P. and Abeyo, B.G. and Heng-Moss, T.M. and Lee, D.J. and Gaussoin, R.E. and Gulsen, O. and Budak, Hikmet and Serba, D. D. (2006) Buffalograss: though native turfgrass. Monograph. USGA Turfgrass and Environmental Research, USA.

Volumes Edited / Special Issues

Budak, Hikmet (2009) Wet lab tools widely used in plant genomics. [Volumes Edited / Special Issues]