Items where Division is "Biological Sciences & Bio Eng." and Year is 2013

Article

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

Atasever Arslan, Belkıs and Erdem-Kuruca, Serap and Karakaş, Zeynep and Erman, Batu and Ergen, Arzu (2013) Effects of micro environmental factors on natural killer activity (NK) of beta thalassemia major patients. Cell Immunology, 282 (2). pp. 93-99. ISSN 0008-8749 (Print) 1090-2163 (Online)

Bakır-Güngör, Burcu and Baykan, B. and İşeri, S. Uğur and Tuncer, F. N. and Sezerman, Uğur (2013) Identifying SNP targeted pathways in partial epilepsies with genome-wide association study data. Epilepsy Research, 105 (1-2). pp. 92-102. ISSN 0920-1211 (Print) 1872-6844 (Online)

Bakır-Güngör, Burcu and Sezerman, Uğur (2013) The identification of pathway markers in intracranial aneurysm using genome-wide association data from two different populations. PLoS One, 8 (3). ISSN 1932-6203

Bakış, Yasin and Otu, Hasan H. and Taşçı, Nivart and Meydan, Cem and Bilgin, Neşe and Yüzbaşıoğlu, Sırrı and Sezerman, Uğur (2013) Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure. BMC Bioinformatics, 14 . ISSN 1471-2105

Bilsborrow, Paul and Cooper, Julia and Tetard-Jones, Catherine and Srednicka-Tober, Dominika and Baraniski, Marcin and Eyre, Mick and Schmidt, Christoph and Shotton, Peter and Volakakis, Nikolaos and Çakmak, İsmail and Öztürk, Levent and Leifert, Carlo and Wilcockson, Steve (2013) The effect of organic and conventional management on the yield and quality of wheat grown in a long-term field trial. European Journal of Agronomy, 51 . pp. 71-80. ISSN 1161-0301 (Print) 1873-7331 (Online)

Bodur, Çağrı and Kütük, Özgür and Karslı, Gizem and Isimjan, Tayirjan T. and Harrison, Paul and Başağa, Hüveyda (2013) Pramanicin analog induces apoptosis in human colon cancer cells: critical roles for Bcl-2, Bim, and p38 MAPK signaling. PLoS One, 8 (2). ISSN 1932-6203

Boonchuay, Panomwan and Çakmak, İsmail and Rerkasem, Benjavan and Prom-U-Thai, Chanakan (2013) Effect of different foliar zinc application at different growth stages on seed zinc concentration and its impact on seedling vigor in rice. Soil Science and Plant Nutrition, 59 (2). pp. 180-188. ISSN 0038-0768 (Print) 1747-0765 (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)

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

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

Daneshbakhsh, Bahareh and Khoshgoftarmanesh, Amir Hossein and Shariatmadari, Hossein and Çakmak, İsmail (2013) Effect of zinc nutrition on salinity-induced oxidative damages in wheat genotypes differing in zinc deficiency tolerance. Acta Physiologiae Plantarum, 35 (3). pp. 881-889. ISSN 0137-5881 (Print) 1861-1664 (Online)

Daneshbakhsh, Bahareh and Khoshgoftarmanesh, Amir Hossein and Shariatmadari, Hossein and Çakmak, İsmail (2013) Phytosiderophore release by wheat genotypes differing in zinc deficiency tolerance grown with Zn-free nutrient solution as affected by salinity. Journal of Plant Physiology, 170 (1). pp. 41-46. ISSN 0176-1617 (Print) 1618-1328 (Online)

Durmaz Timuçin, Emel and Kuyucak, Serdar and Sezerman, Uğur (2013) Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex. Protein Engineering, Design and Selection, 26 (5). pp. 325-333. ISSN 1741-0126 (Print) 1741-0134 (Online)

Durmaz Timuçin, Emel and Sezerman, Uğur (2013) The conserved lid tryptophan, W211, potentiates thermostability and thermoactivity in bacterial thermoalkalophilic lipases. PLoS One, 8 (12). ISSN 1932-6203

Erzurumlu, Yalçın and Aydın, Köse Fadime and Gözen, Oğuz and Gözüaçık, Devrim and Toth, Eric A. and Ballar, Petek (2013) A unique IBMPFD-related P97/VCP mutation with differential binding pattern and subcellular localization. International Journal of Biochemistry and Cell Biology, 45 (4). pp. 773-782. ISSN 1357-2725 (Print) 1878-5875 (Online)

Gün, Gökhan and Dinler Doğanay, Gizem and Yürüm, Yuda (2013) Biodesulfurization of DBT by a hyperthermophilic archaeon sulfolobus solfataricus P2. Current Opinion in Biotechnology, 24 (Supple). S34-S35. ISSN 0958-1669

Hirsh, Stacey L. and McKenzie, David R. and Nosworthy, Neil J. and Denman, John A. and Sezerman, Uğur and Bilek, Marcela M. M. (2013) The Vroman effect: competitive protein exchange with dynamic multilayer protein aggregates. Colloids and Surfaces B: Biointerfaces, 103 . pp. 395-404. ISSN 0927-7765 (Print) 1873-4367 (Online)

İtah, Zeynep and Oral, Özlem and Perk, Osman Yavuz and Şeşen, Muhsincan and Demir, Ebru and Erbil, Seçil and Doğan-Ekici, A. Işın and Ekici, Sinan and Koşar, Ali and Gözüaçık, Devrim (2013) Hydrodynamic cavitation kills prostate cells and ablates benign prostatic hyperplasia tissue. Experimental Biology and Medicine, 238 (11). pp. 1-9. ISSN 1535-3702 (Print) 1535-3699 (Online)

Joddar, Binata and Albayrak, Aydın and Kang, Jeonghwa and Nishihara, Mizuki and Abe, Hiroshi and Ito, Yoshihiro (2013) Sustained delivery of siRNA from dopamine-coated stainless steel surfaces. Acta Biomaterialia, 9 (5). pp. 6753-6761. ISSN 1742-7061 (Print) 1878-7568 (Online)

Karadağ, Birce Naz and Yıldırım, Efe Can and Tekdal, Dilek (2013) The comparison of plant regeneration between Jerusalem artichoke and purple potato cultured on MS media with different concentrations and combinations of plant growth regulators. International Journal of Bioscience, Biochemistry and Bioinformatics, 3 (2). pp. 120-124. ISSN 2010-3638

Kautto, Liisa and Grinyer, Jasmine and Paulsen, Ian and Tetu, Sasha and Pillai, Aneesh and Pardiwalla, Swapneel and Sezerman, Uğur and Bayram Akçapınar, Günseli and Bergquist, Peter and Te'o, Junior and Nevalainen, Helena (2013) Stress effects caused by the expression of a mutant cellobiohydrolase I and proteasome inhibition in trichoderma reesei rut-C30. New Biotechnology, 30 (2). pp. 183-191. ISSN 1871-6784 (Print) 1876-4347 (Online)

Korkmaz, Gözde and Tekirdağ, Kumsal Ayşe and Özturk, Deniz Gülfem and Koşar, Ali and Sezerman, Uğur and Gözüaçık, Devrim (2013) MIR376A is a regulator of starvation-induced autophagy. PLoS One, 8 (12). 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

Mengütay, Melis and Ceylan, Yasemin and Kutman, Ümit Barış and Çakmak, İsmail (2013) Adequate magnesium nutrition mitigates adverse effects of heat stress on maize and wheat. Plant and Soil, 368 (1-2). pp. 57-72. ISSN 0032-079X (Print) 1573-5036 (Online)

Meydan, Cem and Otu, Hasan H. and Sezerman, Uğur (2013) Prediction of peptides binding to MHC class I and II alleles by temporal motif mining. BMC Bioinformatics, 14 (Supple). ISSN 1471-2105

Morgounov, Alexey I. and Belan, Igor and Zelenskiy, Yuriy and Roseeva, Lyudmila and Toemoeskoezi, Sandor and Bekes, Ferenc and Abugalieve, Aygul and Çakmak, İsmail and Vargas, Mateo and Crossa, Jose (2013) Historical changes in grain yield and quality of spring wheat varieties cultivated in Siberia from 1900 to 2010. Canadian Journal of Plant Science, 93 (3). pp. 425-433. ISSN 0008-4220

Palmer, Mike W. and Cooper, Julia and Tetard-Jones, Catherine and Srednicka-Tober, Dominika and Baranski, Marcin and Eyre, Mick and Shotton, Peter N. and Volakakis, Nikolaos and Çakmak, İsmail and Öztürk, Levent and Leifert, Carlo and Wilcockson, Steve J. and Bilsborrow, Paul E. (2013) The influence of organic and conventional fertilisation and crop protection practices, preceding crop, harvest year and weather conditions on yield and quality of potato (Solanum tuberosum) in a long-term management trial. European Journal of Agronomy, 49 . pp. 83-92. ISSN 1161-0301 (Print) 1873-7331 (Online)

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)

Sayers, Zehra (2013) Uncharted territory, untapped potential. Science Omega Review Europe (issue ).

Sayers, Zehra and Özcan, Zuhal (2013) Attitudes towards teaching evolution in Turkey. APS News, 22 (6).

Srednicka-Tober, Dominika and Baranski, Marcin and Gromadzka-Ostrowska, Joanna and Skwarlo-Sonta, Krystyna and Rembialkowska, Ewa and Hajslova, Jana and Schulzova, Vera and Çakmak, İsmail and Öztürk, Levent and Krolikowski, Tomasz and Wisniewska, Katarzyna and Hallmann, Ewelina and Baca, Elzbieta and Eyre, Mick and Steinshamn, Havard and Jordon, Teresa and Leifert, Carlo (2013) Effect of crop protection and fertilization regimes used in organic and conventional production systems on feed composition and physiological parameters in rats. Journal of Agricultural and Food Chemistry, 61 (5). pp. 1017-1029. ISSN 0021-8561 (Print) 1520-5118 (Online)

Tai, Xuguang and Erman, Batu and Alag, Amala and Mu, Jie and Kimura, Motoko and Katz, Gil and Guinter, Terry and McCaughtry, Tom and Etzensperger, Ruth and Feigenbaum, Lionel and Singer, Dinah S. and Singer, Alfred (2013) Foxp3 transcription factor is proapoptotic and lethal to developing regulatory T cells unless counterbalanced by cytokine survival signals. Immunity, 38 (6). pp. 1116-1128. ISSN 1074-7613 (Print) 1097-4180 (Online)

Tekiner, Tugce Ayca and Başağa, Hüveyda (2013) Role of microRNA deregulation in breast cancer cell chemoresistance and stemness. Current Medicinal Chemistry, 20 (27). pp. 3358-3369. ISSN 0929-8673 (Print) 1875-533X (Online)

Tekirdağ, Kumsal Ayşe and Gözüaçık, Devrim (2013) Role of miRNAs in the regulation of autophagy. Pakistan Journal of Clinical and Biomedical Research, 1 (2). pp. 6-10.

Tekirdağ, Kumsal Ayşe and Korkmaz, Gözde and Özturk, Deniz Gülfem and Agami, Reuven and Gözüaçık, Devrim (2013) MIR181A regulates starvation- and rapamycin-induced autophagy through targeting of ATG5. Autophagy, 9 (3). pp. 374-385. ISSN 1554-8627 (Print) 1554-8635 (Online)

Tekirdağ, Kumsal Ayşe and Özturk, Deniz Gülfem and Gözüaçık, Devrim (2013) Alteration in autophagic-lysosomal potential during aging and neurological diseases: the microRNA perspective. Current Pathobiology Reports, 1 (4). pp. 1-36. ISSN 2167-485X

Tiziana, Centofanti and Sayers, Zehra and Cabello-Conejo, Maria Isabel and Kidd, Petra and Nishizawa, Naoko K. and Kakei, Yusuke and Davis, Allen P. and Sicher, Richard C. and Chaney, Rufus L. (2013) Xylem exudate composition and root-to-shoot nickel translocation in Alyssum species. Plant and Soil, 373 (1-2). pp. 59-75. ISSN 0032-079X (Print) 1573-5036 (Online)

Toprak, Erdal and Veres, Adrian and Yıldız, Muhammed Sadık and Pedraza, Juan M. and Chait, Remy and Paulsson, Johan and Kishony, Roy (2013) Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition. Nature Protocols, 8 (3). pp. 555-567. ISSN 1754-2189 (Print) 1750-2799 (Online)

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)

Yılancıoğlu, Kaan and Çetiner, Selim (2013) Rediscovery of historical vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods. Genome, 56 (5). pp. 295-302. ISSN 0831-2796 (Print) 1480-3321 (Online)

Yıldız Kutman, Bahar and Kutman, Ümit Barış and Çakmak, İsmail (2013) Foliar nickel application alleviates detrimental effects of glyphosate drift on yield and seed quality of wheat. Journal of Agricultural and Food Chemistry, 61 (35). pp. 8364-8372. ISSN 0021-8561 (Print) 1520-5118 (Online)

Yıldız Kutman, Bahar and Kutman, Ümit Barış and Çakmak, İsmail (2013) Nickel-enriched seed and externally supplied nickel improve growth and alleviate foliar urea damage in soybean. Plant and Soil, 363 (1-2). pp. 61-75. ISSN 0032-079X (Print) 1573-5036 (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

Zhang, Yue-Qiang and Yazıcı, Mustafa Atilla and Gökmen, Özay Özgür and Çakmak, İsmail and Zhang, Fu-Suo and Zou, Chun-Qin (2013) Comparison of winter wheat genotypes differing in zinc efficiency and origin: the zinc uptake and enzyme activity. Communications in Soil Science and Plant Analysis, 44 (19). pp. 2875-2883. ISSN 0010-3624 (Print) 1532-2416 (Online)

Papers in Conference Proceedings

Açıksöz Özden, Seher Bahar and Öztürk, Levent and Yazıcı, Mustafa Atilla and Çakmak, İsmail (2013) Inclusion of urea in the foliar 59FeEDTA-Solution stimulated leaf penetration and translocation of 59Fe within wheat plants. In: XVII. International Plant Nutrition Colloquium & Boron Satellite Meeting, Istanbul, Turkey

Aslan, Onur Şevket and Kızıltaş, Güllü (2013) Computational design of tissue scaffolds for cartilage repair via the level-set method. In: 11th World Congress of the International Cartilage Repair Society (ICRS 2013), Izmir, Turkey

Aslan, Onur Şevket and Kızıltaş, Güllü (2013) Computational design of tissue scaffolds via the level-set method. In: Tissue Engineering and Regenerative Medicine International Society (TERMIS-EU 2013), Istanbul, Turkey

Candan, Nilgün and Çakmak, İsmail and Öztürk, Levent (2013) High seed zinc concentration assures high seedling vigor and biomass production in durum wheat under zinc deficiency and drought stress. In: XVII. International Plant Nutrition Colloquium & Boron Satellite Meeting, Istanbul, Turkey

Kurtoğlu, Evrim and Kaya, Alihan and Gözüaçık, Devrim and Acar, Funda Yağcı and Koşar, Ali (2013) Heat transfer enhancement with iron oxide nanoparticle based ferrofluids. In: 11th International Conference on Nanochannels, Microchannels, and Minichannels (ICNMM2013), Sapporo, Japan

Küçükgül, Can and Özler, Saime Burçe and Karakaş, Hacer Ezgi and Gözüaçık, Devrim and Koç, Bahattin (2013) 3D hybrid bioprinting of macrovascular structures. In: 3rd ECCOMAS Thematic Conference on Tissue Engineering (ICTE 2013), Leiria, Portugal

Oral, Özlem and Sarafi, Parisa and Yüce, Aysel and Gözüaçık, Devrim and Dökmeci, Serap (2013) Molecular and cellular analysis of autophagy in Gaucher disease (Gaucher hastalığında, otofaji mekanizması ve aktivitesinin moleküler ve hücresel düzeyde incelenmesi). In: XIII. Ulusal Tıbbi Biyoloji ve Genetik Kongresi, Kuşadası, Turkey

Özbey, Arzu and Karimzadehkhouei, Mehrdad and Kurtoğlu, Evrim and Koşar, Ali (2013) Simulation of magnetic actuation of ferrofluids in microtubes. In: 11th International Conference on Nanochannels, Microchannels, and Minichannels (ICNMM2013), Sapporo, Japan

Sayers, Zehra and Aydın, Mert and Bal, Erhan and Yeşilırmak, Filiz and Konarev, Petr V. and Petoukhov, Maxim V. and Roessle, Manfred and Kikhney, Alexey G. and Shang, Weifeng and Svergun, Dmitri I. (2013) Comparative characterization of apo-, reconstituted- and in vivo-folded forms of a durum wheat metallothionein. In: 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA

Tekdal, Dilek and Çetiner, Selim (2013) Ovule-embryo culture and plant regeneration of thermopsis turcica, critically endangered Turkish endemic. In: 2013 In Vitro Biology Meeting, Providence, Rhode Island

Tekdal, Dilek and Çetiner, Selim (2013) Türkiye endemiği thermopsis turcica bitkisinde organogenez aracılığıyla bitki rejenerasyonu. In: İç Anadolu Bölgesi 1. Tarım ve Gıda Kongresi (Targid 2013), Niğde, Türkiye

Toprak, Erdal and Palmer, Adam C. and Kim, Seungsoo and Veres, Adrian and Bershtein, Shimon and Kishony, Roy (2013) Evolution of antibiotic resistance through a multi-peaked adaptive landscape. In: 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA

Yılmaz, Özlem and Altıntaş, Gamze and Çakmak, İsmail and Öztürk, Levent (2013) Zinc uptake and transport in wild emmer and cultivated durum wheat differing in seed zinc concentrations. In: XVII. International Plant Nutrition Colloquium & Boron Satellite Meeting, Istanbul, Turkey

Book Section / Chapter

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)

Eberhart, Karin and Oral, Özlem and Gözüaçık, Devrim (2013) Induction of autophagic cell death by anticancer agents. In: Hayat, M. A., (ed.) Autophagy: Cancer, Other Pathologies, Inflammation, Immunity, and Infection, and Aging. Elsevier, The Netherlands, pp. 179-202. ISBN 9780124055308 (Print) 9780124055353 (Online)

Tekdal, Dilek and Çetiner, Selim (2013) The effects of different combinations and varying concentrations of growth regulators on the regeneration of selected Turkish cultivars of melon. In: Silva-Opps, Marina, (ed.) Current Progress in Biological Research. Agricultural and Biological Sciences. InTech, Acadia, Canada, pp. 257-275. ISBN 978-953-51-1097-2

Volumes Edited / Special Issues

Çakmak, İsmail (2013) Magnesium in crop production, food quality and human health. [Volumes Edited / Special Issues]

Thesis

Akhmetov, Azat (2013) Prediction of drug-drug interactions from chemogenomic and gene-gene interactions and analysis of drug-drug interactions. [Thesis]

Meydan, Cem (2013) Discovering discriminative and class-specific sequence and structural motifs in proteins. [Thesis]

Mollamehmetoğlu, Elif (2013) Cloning and expression of beta subunit (AGB1) of heterotrimeric g-protein complex A.thaliana. [Thesis]

Ova, Emir Ali (2013) Adverse effect of high phosphorus on plant zinc concentration expressed differently in wheat plants grown in soil and nutrient solution. [Thesis]

Öz, Tuğçe (2013) Investigating evolutionary trade-offs for designing novel strategies to slow down evolution of antibiotic resistance. [Thesis]

Şahin, Ebru (2013) Detecting motifs for computational classification of dockerin and cohesin sequences. [Thesis]

Temiz, Şeyda Şaziye (2013) Generation of Xanthomonas derived TALE proteins that inhibit gene transcription. [Thesis]

Yenilmez, Batuhan Orbay (2013) Generation of novel random mutagenesis lipase libraries via directed evolution. [Thesis]

Yıldız Kutman, Bahar (2013) The essential and beneficial roles of nickel In growth of soybean and wheat plants. [Thesis]