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  1. AU="Hikmet Budak"
  2. AU=Kurd Ramzi
  3. AU=Szefel Jaros?aw
  4. AU="Vaisse, Christian"
  5. AU="Jean-Baptiste Poline"
  6. AU="Halekoh, Ulrich"
  7. AU="H. Fayaz"
  8. AU="Saddam Hussain"
  9. AU="Leary, Steven"
  10. AU="Schuit, Ewoud"
  11. AU=Sun Bingbing
  12. AU=d'Arminio Monforte Antonella
  13. AU="Sylvain Latour"
  14. AU="Velhal, S"
  15. AU="Lutz, Richard A"
  16. AU="Raveesh Kumar"
  17. AU="Andreas von Deimling"
  18. AU="Erik MeersauthorLaboratory of Analytical and Applied Ecochemistry, Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium"
  19. AU="Thakkar, Nitya"
  20. AU="Hongtao Tie"
  21. AU="Bhati, Saurabh Kumar"
  22. AU="Choi, Hyunho"
  23. AU="Jayaprakash, Balamuralikrishna"
  24. AU="Lee, Brian H"
  25. AU="May, Susann"
  26. AU="Remondes-Costa, Sónia"
  27. AU="Lauren Sauer"
  28. AU="G Saiz, Paula"
  29. AU="Stoica, George"
  30. AU=Odorizzi Pamela M.
  31. AU=Pollaers Katherine
  32. AU="Stefanova, Veselina"
  33. AU="Geraldine M. O’Connor"
  34. AU="Jim E. Banta"
  35. AU="Marti-Bonmati, Luis"
  36. AU="Doris Kampner"
  37. AU="Luca Soraci"

Suchergebnis

Treffer 1 - 10 von insgesamt 42

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  1. Artikel ; Online: G4Boost

    H. Busra Cagirici / Hikmet Budak / Taner Z. Sen

    BMC Bioinformatics, Vol 23, Iss 1, Pp 1-

    a machine learning-based tool for quadruplex identification and stability prediction

    2022  Band 18

    Abstract: Abstract Background G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, ... ...

    Abstract Abstract Background G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decision tree-based prediction tool, G4Boost, to identify G4 motifs and predict their secondary structure folding probability and thermodynamic stability based on their sequences, nucleotide compositions, and estimated structural topologies. Results G4Boost predicted the quadruplex folding state with an accuracy greater then 93% and an F1-score of 0.96, and the folding energy with an RMSE of 4.28 and R2 of 0.95 only by the means of sequence intrinsic feature. G4Boost was successfully applied and validated to predict the stability of experimentally-determined G4 structures, including for plants and humans. Conclusion G4Boost outperformed the three machine-learning based prediction tools, DeepG4, Quadron, and G4RNA Screener, in terms of both accuracy and F1-score, and can be highly useful for G4 prediction to understand gene regulation across species including plants and humans.
    Schlagwörter G-quadruplex ; Machine learning ; Topology ; Stability ; Energy ; Plants ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 006
    Sprache Englisch
    Erscheinungsdatum 2022-06-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Genome-wide discovery of G-quadruplexes in barley

    H. Busra Cagirici / Hikmet Budak / Taner Z. Sen

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Band 15

    Abstract: Abstract G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are ... ...

    Abstract Abstract G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Erscheinungsdatum 2021-04-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses

    Bala Ani Akpinar / Tugdem Muslu / Gadi V. P. Reddy / Munevver Dogramaci / Hikmet Budak

    International Journal of Molecular Sciences, Vol 24, Iss 2226, p

    2023  Band 2226

    Abstract: Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. ... ...

    Abstract Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates the identification and annotation of lncRNAs at a large scale. Wheat is among the leading food staples worldwide whose production is threatened by both biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a major source of defense against wheat stem sawfly, a devastating insect pest. We also analyzed and annotated lncRNAs from two bread wheat varieties, resistant and susceptible to another destructive pest, orange wheat blossom midge, with and without infestation. Several putative lncRNAs contained potential precursor sequences and/or target regions for microRNAs, another type of regulatory noncoding RNAs, which may indicate functional networks. Interestingly, in contrast to lncRNAs themselves, microRNAs with potential precursors within the lncRNA sequences appeared to be highly conserved at the sequence and family levels. We also observed a few putative lncRNAs that have perfect to near-perfect matches to organellar genomes, supporting the recent observations that organellar genomes may contribute to the noncoding transcript pool of the cell.
    Schlagwörter long noncoding RNAs ; gene regulation ; wheat ; microRNA ; stress response ; insect resistance ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Thema/Rubrik (Code) 571
    Sprache Englisch
    Erscheinungsdatum 2023-01-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: The complete genome sequence of elite bread wheat cultivar, “Sonmez” [version 1; peer review

    Hikmet Budak / Valerie Barbe / Nathan Watson-Haigh / Ute Baumann / Bala Ani Akpinar / Philippe Leroy

    F1000Research, Vol

    3 approved]

    2022  Band 11

    Abstract: High-yielding crop varieties will become critical in meeting the future food demand in the face of worsening weather extremes and threatening biotic stressors. The bread wheat cultivar Sonmez-2001 is a registered variety that is notable for its ... ...

    Abstract High-yielding crop varieties will become critical in meeting the future food demand in the face of worsening weather extremes and threatening biotic stressors. The bread wheat cultivar Sonmez-2001 is a registered variety that is notable for its performance under low-irrigation conditions, which further improves upon irrigation. Additionally, Sonmez-2001 is resilient against certain biotic stressors, particularly soil-borne pathogens. Here, we provide a reference-guided whole genome sequence of Sonmez-2001, assembled into 21 chromosomes of the A, B and D genomes and totaling 13.3 gigabase-pairs in length. Additionally, a de novo assembly of an additional 1.05 gigabase-pairs was generated that represents either Sonmez-specific sequences or sequences that considerably diverged between Sonmez and Chinese Spring. Within this de novo assembly, we identified 35 gene models, of which 11 were high-confidence, that may contribute to the favorable traits of this high-performing variety. We identified up to 24 million sequence variants, of which up to 2.4% reside in coding sequences, that can be used to develop molecular markers that should be of immediate use to the cereal community.
    Schlagwörter Wheat ; genome sequencing ; Triticum aestivum ; yield ; Sonmez ; eng ; Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 571
    Sprache Englisch
    Erscheinungsdatum 2022-06-01T00:00:00Z
    Verlag F1000 Research Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: Author Correction

    Babar Hussain / Stuart James Lucas / Levent Ozturk / Hikmet Budak

    Scientific Reports, Vol 10, Iss 1, Pp 1-

    Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stage in wheat

    2020  Band 3

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2020-10-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes

    Tugdem Muslu / Bala Ani Akpinar / Sezgi Biyiklioglu-Kaya / Meral Yuce / Hikmet Budak

    International Journal of Molecular Sciences, Vol 22, Iss 12349, p

    2021  Band 12349

    Abstract: Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple ... ...

    Abstract Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple food crops; among all, wheat stem sawfly ( Cephus cinctus Norton) and orange wheat blossom midge ( Sitodiplosis mosellana ) are two of the most economically and agronomically harmful insect pests which cause yield loss in cereals, especially in wheat in North America. There is no effective strategy for suppressing this pest damage yet, and only the plants with intrinsic tolerance mechanisms such as solid stem phenotypes for WSS and antixenosis and/or antibiosis mechanisms for OWBM can limit damage. A major QTL and a causal gene for WSS resistance were previously identified in wheat, and 3 major QTLs and a causal gene for OWBM resistance. Here, we present a comparative analysis of coding and non-coding features of these loci of wheat across important cereal crops, barley, rye, oat, and rice. This research paves the way for our cloning and editing of additional WSS and OWBM tolerance gene(s), proteins, and metabolites.
    Schlagwörter WSS ; OWBM ; resistance ; genome organization ; wheat ; cereals ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Thema/Rubrik (Code) 571
    Sprache Englisch
    Erscheinungsdatum 2021-11-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing

    H. Busra Cagirici / Bala Ani Akpinar / Taner Z. Sen / Hikmet Budak

    International Journal of Molecular Sciences, Vol 22, Iss 10400, p

    2021  Band 10400

    Abstract: The highly challenging hexaploid wheat ( Triticum aestivum ) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. ... ...

    Abstract The highly challenging hexaploid wheat ( Triticum aestivum ) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. Although the process of variant calling is relatively straightforward, selection of the best combination of the computational tools for read alignment and variant calling stages of the analysis and efficient filtering of the false variant calls are not always easy tasks. Previous studies have analyzed the impact of methods on the quality metrics in diploid organisms. Given that variant identification in wheat largely relies on accurate mining of exome data, there is a critical need to better understand how different methods affect the analysis of whole exome sequencing (WES) data in polyploid species. This study aims to address this by performing whole exome sequencing of 48 wheat cultivars and assessing the performance of various variant calling pipelines at their suggested settings. The results show that all the pipelines require filtering to eliminate false-positive calls. The high consensus among the reference SNPs called by the best-performing pipelines suggests that filtering provides accurate and reproducible results. This study also provides detailed comparisons for high sensitivity and precision at individual and population levels for the raw and filtered SNP calls.
    Schlagwörter wheat ; SNPs ; WES ; variants ; BCFtools ; STAR ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Sprache Englisch
    Erscheinungsdatum 2021-09-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel: Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors

    Alptekin, Burcu / Hikmet Budak

    Functional & integrative genomics. 2017 May, v. 17, no. 2-3

    2017  

    Abstract: MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and ... ...

    Abstract MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet. With the advent of the next generation sequencing technologies considerably decreasing sequencing costs per base-pair, genomic, and transcriptomic data from several wheat species, including the progenitors and wild relatives have become available. In this study, we performed in silico identification and comparative analysis of microRNA repertoires of bread wheat (Triticum aestivum L.) and its diploid progenitors and relatives, Aegilops sharonensis, Aegilops speltoides, Aegilops tauschii, Triticum monococcum, and Triticum urartu through the utilization of publicly available transcriptomic data. Over 200 miRNA families were identified, majority of which have not previously been reported. Ancestral relationships expanded our understanding of wheat miRNA evolution, while T. monococcum miRNAs delivered important clues on the effects of domestication on miRNA expression. Comparative analyses on wild Ae. sharonensis accessions highlighted candidate miRNAs that can be linked to stress tolerance. The miRNA repertoires of bread wheat and its diploid progenitors and relatives provide important insight into the diversification and distribution of miRNA genes, which should contribute to the elucidation of miRNA evolution of Poaceae family. A thorough understanding of the convergent and divergent expression profiles of miRNAs in different genetic backgrounds can provide unique opportunities to modulation of gene regulation for better crop performance.
    Schlagwörter Aegilops sharonensis ; Aegilops speltoides ; Aegilops tauschii ; Triticum aestivum ; Triticum monococcum ; Triticum urartu ; diploidy ; domestication ; evolution ; genes ; genetic background ; high-throughput nucleotide sequencing ; human nutrition ; microRNA ; stress tolerance ; temperate zones ; transcriptomics ; wheat ; wild relatives
    Sprache Englisch
    Erscheinungsverlauf 2017-05
    Umfang p. 171-187.
    Erscheinungsort Springer Berlin Heidelberg
    Dokumenttyp Artikel
    ZDB-ID 2014670-X
    ISSN 1438-7948 ; 1438-793X
    ISSN (online) 1438-7948
    ISSN 1438-793X
    DOI 10.1007/s10142-016-0487-y
    Datenquelle NAL Katalog (AGRICOLA)

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  9. Artikel ; Online: RNA Sequencing and Co-expressed Long Non-coding RNA in Modern and Wild Wheats

    Halise Busra Cagirici / Burcu Alptekin / Hikmet Budak

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Band 16

    Abstract: Abstract There is an urgent need for the improvement of drought-tolerant bread and durum wheat. The huge and complex genome of bread wheat (BBAADD genome) stands as a vital obstruction for understanding the molecular mechanism underlying drought ... ...

    Abstract Abstract There is an urgent need for the improvement of drought-tolerant bread and durum wheat. The huge and complex genome of bread wheat (BBAADD genome) stands as a vital obstruction for understanding the molecular mechanism underlying drought tolerance. However, tetraploid wheat (Triticum turgidum ssp., BBAA genome) is an ancestor of modern bread wheat and offers an important model for studying the drought response due to its less complex genome. Additionally, several wild relatives of tetraploid wheat have already shown a significant drought tolerance. We sequenced root transcriptome of three tetraploid wheat varieties with varying stress tolerance profiles, and built differential expression library of their transcripts under control and drought conditions. More than 5,000 differentially expressed transcripts were identified from each genotype. Functional characterization of transcripts specific to drought-tolerant genotype, revealed their association with osmolytes production and secondary metabolite pathways. Comparative analysis of differentially expressed genes and their non-coding RNA partners, long noncoding RNAs and microRNAs, provided valuable insight to gene expression regulation in response to drought stress. LncRNAs as well as coding transcripts share similar structural features in different tetraploid species; yet, lncRNAs slightly differ from coding transcripts. Several miRNA-lncRNA target pairs were detected as differentially expressed in drought stress. Overall, this study suggested an important pool of transcripts where their manipulations confer a better performance of wheat varieties under drought stress.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 572
    Sprache Englisch
    Erscheinungsdatum 2017-09-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel: CRISPR/Cas9 genome editing in wheat

    Kim, Dongjin / Burcu Alptekin / Hikmet Budak

    Functional & integrative genomics. 2018 Jan., v. 18, no. 1

    2018  

    Abstract: Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) ... ...

    Abstract Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile tool for genome editing which enables editing of multiple genes based on the guidance of small RNAs. Even though the efficiency of CRISPR/Cas9 system has been shown with several studies from diploid plants, its application remains a challenge for plants with polyploid and complex genome. Here, we applied CRISPR/Cas9 genome editing system in wheat protoplast to conduct the targeted editing of stress-responsive transcription factor genes, wheat dehydration responsive element binding protein 2 (TaDREB2) and wheat ethylene responsive factor 3 (TaERF3). Targeted genome editing of TaDREB2 and TaERF3 was achieved with transient expression of small guide RNA and Cas9 protein in wheat protoplast. The effectiveness of mutagenesis in wheat protoplast was confirmed with restriction enzyme digestion assay, T7 endonuclease assay, and sequencing. Furthermore, several off-target regions for designed sgRNAs were analyzed, and the specificity of genome editing was confirmed with amplicon sequencing. Overall results suggested that CRISPR/Cas9 genome editing system can easily be established on wheat protoplast and it has a huge potentiality for targeted manipulation of wheat genome for crop improvement purposes.
    Schlagwörter RNA ; Triticum aestivum ; binding proteins ; diploidy ; gene editing ; genes ; molecular biology ; mutagenesis ; polyploidy ; protoplasts ; restriction endonucleases ; transcription (genetics) ; transcription factors ; wheat
    Sprache Englisch
    Erscheinungsverlauf 2018-01
    Umfang p. 31-41.
    Erscheinungsort Springer Berlin Heidelberg
    Dokumenttyp Artikel
    ZDB-ID 2014670-X
    ISSN 1438-7948 ; 1438-793X
    ISSN (online) 1438-7948
    ISSN 1438-793X
    DOI 10.1007/s10142-017-0572-x
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