جعفری احمدآبادی سید علی اصغر، عسکریهمت حشمتاله، محمدآبادی محمدرضا (1402) تاثیر شاهدانه بر بیان ژن DLK1 در بافت قلب بره‌های کرمانی. مجله بیوتکنولوژی کشاورزی، 15(1)، 217-234.
شکری سمیرا، خضری امین، محمدآبادی محمدرضا، خیرالدین حمید (1402) بررسی بیان ژنMYH7 در بافت‌های ران، دست و راسته بره‌های پرواری نژاد کرمانی. مجله بیوتکنولوژی کشاورزی، 15(2)، 217-236.
عبدلی نسب مریم، مرتضوی مجتبی (1400) مطالعه بیوانفورماتیک پروتئینهای LEA درگیر در تحمل به تنش خشکی در جو (Hordum vulgare L.) و برنج (Oryza sativa L.). مجله بیوتکنولوژی کشاورزی، 13(1)، 182-159.
محمدآبادی محمدرضا، خیرالدین حمید، آفاناسنکو ولودیمیر، و همکاران (1403) نقش هوش مصنوعی در ژنومیکس. مجله بیوتکنولوژی کشاورزی، 16(2)، 279-195.
محمدآبادی محمدرضا، گلکار افروز، عسکری حصنی مجید (1402) اثر رازیانه (Foeniculum vulgare) بر بیان ژن فاکتور 1 رشد شبه انسولین در بافت شکمبه گوسفند کرمانی. مجله بیوتکنولوژی کشاورزی، 15(4)، 239-256.
Abdoli Nasab M, Mortezavi M (2021) Bioinformatics study of LEA proteins involved in tolerance to drought stress in barley (Hordium vulgare L.) and rice (Oryza sativa L.). Agric Biotechnol J 13(1), 159-182 (In Persian).
Akbudak MA, Filiz E (2020) Genome-wide investigation of proline transporter (ProT) gene family in tomato: Bioinformatics and expression analyses in response to drought stress. Plant Physiol Biochem 157, 13-22.
Ashoub A, Beckhaus T, Berberich T, et al. (2013) Comparative analysis of barley leaf proteome as affected by drought stress. Planta 237, 771-781.
Attwood TK, Blythe MJ, Flower DR, et al. (2002) PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res 30, 239-241.
Barazandeh A, Mohammadabadi MR, Ghaderi-Zefrehei M, Nezamabadipour H (2016) Predicting CpG Islands and Their Relationship with Genomic Feature in Cattle by Hidden Markov Model Algorithm. Iran J Appl Anim Sci 6 (3), 571-579.
Benetka W, Koranda M, Eisenhaber F (2006) Protein prenylation: An (almost) comprehensive overview on discovery history, enzymology, and significance in physiology and disease. Monatsh. Für Chem 137, 1241-1281.
Blom N, Sicheritz PT, Gupta R, et al. (2004) Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4 (6), 1633-1649.
Bordbar F, Mohammadabadi M, Jensen J, et al. (2022) Identification of candidate genes regulating carcass depth and hind leg circumference in simmental beef cattle using Illumina Bovine Beadchip and next-generation sequencing. Animals 12 (9), e1103
Borden K, Boddy M, Lally J, et al. (1995) The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto‐oncoprotein PML. EMBO J 14, 1532-1541.
Boutet E, Lieberherr D, Tognolli M, et al. (2016) UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view. Methods Mol Biol 1374, 23-54.
Cai D, Liu H, Sang N, et al. (2017) Identification and characterization of CONSTANS-like (COL) gene family in upland cotton (Gossypium hirsutum L.). PLoS One 12, e0179038.
Casaretto J, Ho T-hD (2003) The transcription factors HvABI5 and HvVP1 are required for the abscisic acid induction of gene expression in barley aleurone cells. The Plant Cell 15, 271-284.
Darling AL, Zaslavsky BY, Uversky VN (2019) Intrinsic disorder-based emergence in cellular biology: Physiological and pathological liquid-liquid phase transitions in cells. Polymers 11, e990.
Dhatterwal P, Basu S, Mehrotra S, et al. (2019) Genome wide analysis of W-box element in Arabidopsis thaliana reveals TGAC motif with genes down regulated by heat and salinity. Sci Rep 9, e1681.
Dunn MA, Hughes MA, Zhang L, et al. (1991) Nucleotide sequence and molecular analysis of the low temperature induced cereal gene, BLT4. Mol Gen Genet 229(3), 389-394.
Goddard NJ, Dunn MA, Zhang L, et al. (1993) Molecular analysis and spatial expression pattern of a low-temperature-specific barley gene, blt101. Plant Mol Biol 23(4), 871-879.
Goldstein SA, Miller C (1991) Site-specific mutations in a minimal voltage-dependent K+ channel alter ion selectivity and open-channel block. Neuron 7, 403-408.
Hughes J, Hepworth C, Dutton C, et al. (2017) Reducing Stomatal Density in Barley Improves Drought Tolerance without Impacting on Yield. Plant Physiol 174(2), 776-787.
Jafari Ahmadabadi SAA, Askari-Hemmat H, Mohammadabadi M, et al. (2023) The effect of Cannabis seed on DLK1 gene expression in heart tissue of Kermani lambs. Agric Biotechnol J 15(1), 217-234 (In Persian).
Jofuku KD, Den Boer B, Van Montagu M, et al. (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. The Plant Cell 6, 1211-1225.
Kirchmair J, Markt P, Distinto S, et al. (2008) Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—what can we learn from earlier mistakes? J Comput Aid Mol Des 22, 213-228.
Knox AK, Dhillon T, Cheng H, et al. (2010) CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor Appl Genet 121(1), 21-35.
Köhler C, Merkle T, Neuhaus G (1999) Characterisation of a novel gene family of putative cyclic nucleotide‐and calmodulin‐regulated ion channels in Arabidopsis thaliana. Plant J 18, 97-104.
Kumar S, Shanker A (2018) Bioinformatics Resources for the stress biology of plants. In Book: Biotic and Abiotic Stress Tolerance in Plants pp. 367-386.
Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157(1), 105-132.
Laity JH, Lee BM, Wright PE (2001) Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struc Boil 11, 39-46.
Lamers J, van der Meer T, Testerink C (2020) How plants sense and respond to stressful environments. Plant Physiol. 182, 1624-1635.
Liang M, Hole D, Wu J, et al. (2012) Expression and functional analysis of nuclear factory, subunit B genes in barley. Planta 235, 779-791.
Lipka V, Kwon C, Panstruga R (2007) SNARE-ware: the role of SNARE-domain proteins in plant biology. Annu Rev Cell Dev Biol 23, 147-174.
Liu J, Shabala S, Shabala L, et al. (2019) Tissue-specific regulation of Na+ and K+ transporters explains genotypic differences in salinity stress tolerance in rice. Front. Plant Sci 10, e1361.
Liu Q, Kasuga M, Sakuma Y, et al. (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought-and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10(8), 1391-1406.
Luscombe NM, Greenbaum D, Gerstein M (2001) What is bioinformatics? A proposed definition and overview of the field. Method Inform Med 40, 346-358.
Lyons J, Graham D, Raison JK (1979) Low temperature stress in crop plants: the role of the membrane. Elsevier. pp. 565.
Mahfoozi S, Limin A, Fowler D (2001) Developmental regulation of low-temperature tolerance in winter wheat. Ann Bot 87, 751-757.
Marchler-Bauer A, Lu S, Anderson JB, et al. (2010) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39, D225-D229.
Mayer KF, Waugh R, Brown JW, et al. (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491(7426), 711-716.
Mohammadabadi M, Golkar A, Askari Hesni M (2023) The effect of fennel (Foeniculum vulgare) on insulin-like growth factor 1 gene expression in the rumen tissue of Kermani sheep. Agric Biotechnol J 15(4), 239-256 (In Persian).
Mohammadabadi M, Kheyrodin H, Afanasenko V, et al. (2024) The role of artificial intelligence in genomics. Agric Biotechnol J 16(2), 195-279 (In Persian).
Mohammadinejad F, Mohammadabadi M, Roudbari Z, Sadkowski T (2022) Identification of Key Genes and Biological Pathways Associated with Skeletal Muscle Maturation and Hypertrophy in Bos taurus, Ovis aries, and Sus scrofa. Animals 12(24), e3471 (In Persian).
Møller JV, Juul B, le Maire M (1996) Structural organization, ion transport, and energy transduction of P-type ATPases. Biochim. Biophys. Acta - Biomembr 1286, 1-51.
Moore AD, Björklund ÅK, Ekman D, et al. (2008) Arrangements in the modular evolution of proteins. Trends Biochem Sci 33(9), 444-451.
Nejad FM, M Mohammadabadi, Z Roudbari, et al. (2024) Network visualization of genes involved in skeletal muscle myogenesis in livestock animals. BMC Genomics 25(1), e294
Niwa T, Kondo T, Nishizawa M, et al. (2013) Epidermal patterning factor like5 peptide represses stomatal development by inhibiting meristemoid maintenance in Arabidopsis thaliana. Biosci Biotechnol Biochem 77, 1287-1295.
Pabo CO, Peisach E, Grant RA (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem 70, 313-340.
Rani S, Chaudhary A, Rani K (2018) Management strategies for abiotic stresses in barley. Wheat Barley Res 10, 151-165.
Richardson JS (1981) The anatomy and taxonomy of protein structure. Adv Protein Chem 34, 167-339.
Rodríguez-Gabriel MA, Burns G, McDonald WH, et al. (2003) RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress. EMBO J 22, 6256-6266.
Moller S, Croning MDR, Apweiler R (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17(7), 646-653.
Saadatabadi LM, Mohammadabadi M, Nanaei HA, et al. (2023) Unraveling candidate genes related to heat tolerance and immune response traits in some native sheep using whole genome sequencing data. Small Rumin Res 225, e107018.
Safaei SMH, Dadpasand M, Mohammadabadi M, et al. (2022) An Origanum majorana Leaf Diet Influences Myogenin Gene Expression, Performance, and Carcass Characteristics in Lambs. Animals 13(1), e14
Safaei SMH, Mohammadabadi M, Moradi B, et al. (2024) Role of fennel (foeniculum vulgare) seed powder in increasing testosterone and IGF1 gene expression in the testis of lamb. Gene Express 23(2), 98-105.
Séverine D, Chiara G, Frédérique L, et al. (2021) Expasy, the Swiss bioinformatics resource portal, as designed by its users. Nucleic Acids Res 49(W1), W216-W227.
Shahsavari M, Mohammadabadi M, Khezri A, et al. (2022) Effect of Fennel (Foeniculum Vulgare) Seed Powder Consumption on Insulin-like Growth Factor 1 Gene Expression in the Liver Tissue of Growing Lambs. Gene Expr 21(2), 21-26.
Shen Q, Chen C-N, Brands A, et al. (2001) The stress-and abscisic acid-induced barley gene HVA22: developmental regulation and homologues in diverse organisms. Plant Mol Biol 45, 327-340.
Shen Q, Uknes SJ, Ho TH (1993) Hormone response complex in a novel abscisic acid and cycloheximide-inducible barley gene. J Biol Chem 268(31), 23652-23660.
Shokri S, Khezri A, Mohammadabadi M, Kheyrodin H (2023) The expression of MYH7 gene in femur, humeral muscle and back muscle tissues of fattening lambs of the Kermani breed. Agric Biotechnol J 15(2), 217-236 (In Persian).
Sigrist CJA, Bridge A, Le Mercier P (2020) A potential role for integrins in host cell entry by SARS-CoV-2. Antiviral Res 177, e104759.
Sivamani E, Bahieldin A, Wraith JM, et al. (2000) Improved biomass productivity and water use efficiency under water deficit conditions in transgenic wheat constitutively expressing the barley HVA1 gene. Plant Sci 155, 1-9.
Skinner JS, Szucs P, von Zitzewitz J, et al. (2006) Mapping of barley homologs to genes that regulate low temperature tolerance in Arabidopsis. Theor Appl Genet 112(5), 832-842.
Slocombe SP, Laurie S, Bertini L, et al. (2002) Identification of SnIP1, a novel protein that interacts with SNF1-related protein kinase (SnRK1). Plant Mol Biol 49, 31-44.
Steegmaier M, Yang B, Yoo JS, et al. (1998) Three novel proteins of the syntaxin/SNAP-25 family. J Biol Chem 273(51), 34171-34179.
Turhan H, Baser I (2004) In vitro and in vivo water stress in sunflower (Helianthus Annuus L.)/Estrés Hídrico En Girasol (Helianthus annuus L.) En Las Condiciones in vitro E in vivo/stress D’eau Du Tournesol (Helianthus annus L.) Dans Les Conditions in vitro Et in vivo. Helia 27, 227-236.
Virdi AS, Singh S, Singh P (2015) Abiotic stress responses in plants: roles of calmodulin-regulated proteins. Front. Plant Sci 6, e809.
Wang H, Lu S, Guan X, et al. (2022) Dehydration-responsive element binding protein 1C, 1E, and 1G promote stress tolerance to chilling, heat, drought, and salt in rice. Front Plant Sci 13, e851731.
Wang J, Chitsaz F, Derbyshire
MK, et al. (2023) The conserved domain database in 2023. Nucleic Acids Res 51(D), D384-D388.
Wang Y, Zhang X, Huang G, et al. (2020) Dynamic changes in membrane lipid composition of leaves of winter wheat seedlings in response to PEG-induced water stress. BMC Plant Biol 20, 1-15.
White TC, Simmonds D, Donaldson P, et al. (1994) Regulation of BN115, a low-temperature-responsive gene from winter Brassica napus. Plant Physiol 106, 917-928.
Wilkins MR, Gasteiger E, Bairoch A, et al. (1999) Protein identification and analysis tools on the ExPASy server. Methods Mol Biol 112, 531-552.
Xu Z-S, Ni Z-Y, Li Z-Y, et al. (2009) Isolation and functional characterization of HvDREB1—a gene encoding a dehydration-responsive element binding protein in Hordeum vulgare. J Plant Res 122, 121-130.
Zdobnov EM, Apweiler R (2001) InterProScan–an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847-848.
)