Jorge Fernandes
2023
150. Konstantinidis I., Sætrom P., Brieuc M.S.O., Jakobsen K.S., Liedtke H., Pohlmann C., Tsoulia T. & Fernandes J.M.O. (2023). DNA hydroxymethylation differences underlie early phenotypic divergence of somatic growth in Nile tilapia reared in common garden. Epigenetics (accepted), doi: 10.1080/15592294.2023.2282323.
149. Shankregowda A.M., Siriyappagouder P., Kuizenga M., Bal T.M.P., Abdelhafiz Y., Eizaguirre C., Fernandes J.M.O., Viswanath K. & Raeymaekers J.A.M. (2023). Host habitat rather than evolutionary history explains gut microbiome diversity in sympatric stickleback species. Frontiers in Microbiology 14: 1232358.
148. Alesci A., Albano M., Fumia A., Messina E., Miller A., Fresco D., Fernandes J.M.O., Spanò N., Savoca S. & Capillo G. (2023). Shell formation in two species of bivalves: the role of mantle cells and haemocytes. Zoological Journal of the Linnean Society doi.org/10.1093/zoolinnean/zlad099.
147. Gora A.H., Rehman S., Dias J., Fernandes J.M.O., Olsvik P.A., Sørensen M. & Kiron V. (2023). Microbial oil, alone or paired with β-glucans, can control hypercholesterolemia in a zebrafish model. BBA - Molecular and Cell Biology of Lipids 1868(11): 159383.
146. Viswanath K., Abdelhafiz Y., Gora A.H., Rehman S., Chowdhury S., Saraswathy B., Verlhac-Trichet V.P., Fernandes J.M.O., Sørensen M. (2023). Fish as the lesser-known counterpart to mammalian models to explore the biofunctionality of polyphenols. Journal of Functional Foods 107: 105654.
145. Sharko F., Rbbani G., Siriyappagouder P., Raeymaekers J.A.M., Galindo-Villegas J., Nedoluzhko A. & Fernandes J.M.O. (2023). CircPrime: a web-based platform for design of specific circular RNA primers. BMC Bioinformatics 24: 205.
144. Gora A.H., Rehman S., Dias J., Fernandes J.M.O., Olsvik P.O., Sørensen M. & Kiron V. (2023). Protective mechanisms of a microbial oil against hypercholesterolemia: evidence from a zebrafish model. Frontiers in Nutrition 10:1161119.
143. Rehman S., Gora A.H., Dias J., Abdelhafiz Y., Pierre R., Fernandes J.M.O., Sørensen M., Brugman S. & Kiron V. (2023). Potential of algae-derived alginate oligosaccharides and β-glucan to counter inflammation in adult zebrafish intestine. Frontiers in Immunology 14: 1183701.
142. Rbbani G., Nedoluzhko A., Siriyappagouder P., Sharko F., Raeymaekers J.A.M., Galindo-Villegas J., Joshi R. & Fernandes J.M.O. (2023). The novel circular RNA CircMef2c is positively associated with muscle growth in Nile tilapia. Genomics 115(3): 110598.
141. Pinninti L.R., Maurstad M.F., Hoff S.N.K., Kristensen T., Noble L.R., Jentoft S. & Fernandes J.M.O. (2023). The complete mitochondrial genome of the Atlantic spiny lumpsucker Eumicrotremus spinosus (Fabricius, 1776). Mitochondrial DNA Part B 8(3): 364-367.
140. Konstantinidis I., Sætrom P. & Fernandes J.M.O. (2023). Genome-wide hydroxymethylation profiles in liver of Nile tilapia with distinct growth performance. Scientific Data 10: 114.
139. Zaccone G., Alesci A., Mokhtar D.M., Aragona M., Guerrera M.C., Capillo G., Albano M., Fernandes J.M.O., Viswanath K., Sayed R.K.A., Hussein M.M., Lo Cascio P., Kuciel M., Zuwala K., Germanà A., Icardo J.M. & Lauriano E.R. (2023). Localization of acetylcholine, alpha 7-nAChR and the antimicrobial peptide piscidin 1 in the macrophages of fish gut: Evidence for a cholinergic system, diverse macrophage populations and polarization of immune responses. Fishes 8: 43.
138. Boulygina E., Sharko F., Cheprasov M., Gladysheva-Azgari M., Slobodova N., Tsygankova S., Rastorguev S., Grigorieva L., Kopp M., Fernandes J.M.O., Novgo-Rodov G., Boeskorov G., Protopopov A., Hwang W.-S., Tikhonov A. & Nedoluzhko A. (2022). Ancient DNA reveals maternal philopatry of the Northeast Eurasian brown bear (Ursus arctos) population during the Holocene. Genes 13(11): 1961.
2022
137. Albano M., D'Iglio C., Spanò N., Fernandes J.M.O., Savoca S. & Capillo G. (2022). Distribution of the order Lampriformes in the Mediterranean Sea with notes on their biology, morphology, and taxonomy. Biology (accepted).
136. Rehman S., Gora A.H., Varshney S., Dias J., Brugman S., Olsvik P.A., Fernandes J.M.O. & Kiron V. (2022). Developmental defects and behavioural changes in a diet-induced inflammation model of zebrafish. Frontiers in Immunology (accepted).
135. Jafari O., Ebrahimi M., Hedayati S.A., Zeinalabedini M., Poorbagher H., Pourmoghadam M.N. & Fernandes J.M.O. (2022). Integration of morphometrics and machine learning enables accurate distinction between wild and farmed common carp. Life 12: 957.
134. Abdelhafiz Y., Fernandes J.M.O., Donati C., Pindo M. & Kiron V. (2022). Intergenerational transfer of persistent communities in female Nile tilapia. Frontiers in Microbiology 13:879990.
133. Geraerts M., Vangestel C., Artois T., Fernandes J.M.O., Jorissen M., Chocha M.A., Mizani C:D., Smeets K., Snoeks J., Sonet G., Yang T., Van Steenberge M., Vreven E., Wamuini S.L., Vanhove M. & Huyse T. (2022). Population genomics of introduced Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) in the Democratic Republic of the Congo: repeated introductions since colonial times with multiple sources. Molecular Ecology 31: 3304-3322.
132. Jafari O., Zeinolabedini M., Robledo D., Fernandes J.M.O., Hedayati S.A.-A. & Arefnezhad B. (2022). Genotyping-by-sequencing reveals the impact of a restocking programme on wild common carp (Cyprinus carpio) populations of the southern Caspian basin. Frontiers in Ecology and Evolution 10:872176.
131. Konstantinidis I., Firmino J., Ruiz A., Iñarra B., Martin D.S., Estévez A., Fernandes J.M.O., Gisbert E. (2022). Brewer's spent dry yeast modulates immunity in gilthead sea bream (Sparus aurata). Frontiers in Marine Science 9:857592.
130. Zaccone G., Capillo G., Fernandes J.M.O., Kiron V., Lauriano E.R., Alesci A., Cascio P.L., Guerrera M.C., Kuciel M., Zuwala K., Icardo J.M., Ishimatsu A., Murata R., Amagai T., Germanà A. & Aragona M. (2022). Expression of the antimicrobial peptide Piscidin 1 and neuropeptides in fish gill and skin: A potential participation in neuro-immune interaction. Marine Drugs 20: 145.
129. Saito T., Whatmore P., Taylor J.F., Fernandes J.M.O., Adam A.-C., Tocher D.R., Espe M. & Skjærven K.H. (2022). Micronutrient supplementation affects DNA methylation in male gonads with potential intergenerational epigenetic inheritance involving the embryonic development through glutamate receptor-associated genes. BMC Genomics 23: 115.
128. Maina J.N., Icardo J.M., Zaccone G., Lauriano E.R., Aragona M.L., Guerrera C., Germana A., Fernandes J.M.O., Kiron V. & Capillo G. (2022). Immunohistochemical and ultrastructural study of the immune cell system and epithelial surfaces of the respiratory organs in the bimodally breathing African sharptooth catfish (Clarias gariepinus Burchell, 1822). Anatomical Record 305(11): 3212-3229.
127. Kiron V., Kathiresan P., Fernandes J.M.O., Sørensen M., Vasanth G.K., Qingsong L., Kwang L.T., Dahle D., Dias J. & Trichet V.V. (2022). Clues from the intestinal mucus proteome of Atlantic salmon to counter inflammation. Journal of Proteomics 255: 104487.
126. Gora A.H., Rehman S., Kiron V., Dias J., Fernandes J.M.O., Olsvik P.A., Siriyappagouder P., Vatsos I., Schmid-Staiger U., Frick K. & Pestana P. (2022). Management of hypercholesterolemia through dietary ß-glucans - insights from a zebrafish model. Frontiers in Nutrition 8: 797452.
125. Podgorniak T., Dhanasiri A., Chen X., Ren X., Kuan P. & Fernandes J.M.O. (2022). Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype. Epigenetics 17(10): 1281-1298.
2021
124. Park Y., Zhang Q., Fernandes J.M.O., Wiegertjes G.F. & Kiron V. (2021). Macrophage heterogeneity in the intestinal cells of salmon: Hints from transcriptomic and imaging data. Frontiers in Immunology 12: 798156.
123. Abdelhafiz Y.A., Fernandes J.M.O., Stefani E., Albanese D., Donati C. & Kiron V. (2021). Power play of commensal bacteria in the buccal cavity of female Nile tilapia. Frontiers in Microbiology 12: 773351.
122. Lauriano E.R., Capillo G., Icardo J.M., Fernandes J.M.O., Kiron V., Kuciel M., Zuwala K., Guerrera M.C., Aragona M.L., Germana A. & Zaccone G. (2021). Neuroepithelial cells (NECs) and mucous cells express a variety of neurotransmitters and neurotransmitter receptors in the gill and respiratory air-sac of the catfish Heteropneustes fossilis (Siluriformes, Heteropneustidae): a possible role in local immune defence. Zoology 148: 125958.
121. Abdelhafiz Y., Fernandes J.M.O., Larger S., Albanese D., Donati C., Jafari O., Nedoluzhko A. & Kiron V. (2021). Breeding strategy shapes the composition of bacterial communities in female Nile tilapia reared in a recirculating aquaculture system. Frontiers in Microbiology 12: 709611.
120. Nedoluzhko A., Mjelle R., Renström M., Skjærven K.H., Piferrer F. & Fernandes J.M.O. (2021). The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation. Genomics 113: 3050-3057.
119. Capillo G., Lauriano E.R., Icardo J.M., Siriyappagouder P., Kuciel M., Karapanagiotis S., Zaccone G. & Fernandes J.M.O. (2021). Structural identification of the pacemaker cells and expression of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in the heart of the wild Atlantic cod, Gadus morhua (Linnaeus, 1758). International Journal of Molecular Sciences 22(14): 7539.
118. Adam A.-C., Saito T., Espe M., Whatmore P., Fernandes J.M.O., Vikeså V., Skjaerven K.H. (2021). Metabolic and molecular signatures of improved growth in Atlantic salmon (Salmo salar) fed surplus levels of methionine, folic acid, vitamin B6 and B12 throughout smoltification. British Journal of Nutrition doi: 10.1017/S0007114521002336.
117. Rbbani M.G., Nedoluzhko A., Galindo-Villegas J. & Fernandes J.M.O. (2021). Function of circular RNAs in fish and their potential application as biomarkers. International Journal of Molecular Sciences 22 (13): 7119.
116. Konstantinidis I., Anastasiadi D., Sætrom P., Nedoluzhko A.V., Mjelle R., Podgorniak T., Piferrer F. & Fernandes J.M.O. (2021). Epigenetic mapping of the somatotropic axis in Nile tilapia reveals differential DNA hydroxymethylation marks associated with growth. Genomics 113 (5): 2953-2964.
115. Shalgimbayeva G.M., Volkov A.A., Slobodova N.V., Sharko F.S., Tsygankova S.V., Boulygina E.S., Nguyen V.Q., Pham T., Nguyen T.D., Assylbekova S.Z., Alekseev Y., Nedoluzhko A.V., Fernandes J.M.O. & Rastorguev S.M. (2021). Genetic investigation of Aral wild common carp population (Cyprinus carpio) using ddRAD sequencing. Diversity 13: 295.
114. Rehman S., Gora A.H., Siriyappagouder P., Fernandes J.M.O., Dias J. & Kiron V. (2021). Zebrafish intestinal transcriptome highlights subdued inflammatory responses and the efficacy of yeast -glucan. Journal of Fish Diseases 44 (10): 1619-1637.
113. Martínez-Llorens S., Falk-Petersen I.B., Godoy-Olmos S., Ulleberg L.O., Tomás-Vidal A., Puvanendran V., Odei D.K., Hagen Ø., Fernandes J.M.O., Jobling M. & Peruzzi S. (2021). Digestive tract morphology and enzyme activities of juvenile diploid and triploid Atlantic salmon (Salmo salar) fed fishmeal-based diets with or without fish protein hydrolysates. PLoS One 16(1): e0245216.
112. Capillo G., Zaccone G., Cupello C., Fernandes J.M.O., Kiron V., Kuciel M., Zuwala K., Guerrera M.C., Aragona M., Icardo J.M. & Lauriano E.R. (2021). Expression of acetylcholine, its contribution to regulation of immune function and O2 sensing and phylogenetic interpretations of the African butterfly fish Pantodon buchholzi (Osteoglossiformes, Pantodontidae). Fish and Shellfish Immunology 111: 189-200.
2020
111. Kiron V., Park Y., Siriyappagouder P., Dahle D., Vasanth G., Dias J., Fernandes J.M.O., Sørensen M. & Verlhac-Trichet V. (2020). Intestinal transcriptome analysis reveals soy derivative-linked changes in Atlantic salmon. Frontiers in Immunology 11: 596514.
110. López-Cánovas A.E., Cabas I., Chaves-Pozo E., Ros-Chumillas M., Navarro-Segura L., López-Gómez A., & Fernandes J.M.O., Galindo-Villegas J. & García Ayala A. (2020). Nanoencapsulated clove oil applied as an anaesthetic at slaughtering decreases stress, extends the freshness, and lengthens shelf life of cultured fish. Foods 9: 1750.
109. Oliveira C.C.V., Fatsini E., Fernández I., Anjos C., Chauvigné F., Cerdà J., Mjelle R., Fernandes J.M.O., Cabrita E. (2020). Kisspeptin influences the reproductive axis and circulating levels of microRNAs in the flatfish Senegalese sole. International Journal of Molecular Sciences 21(23): 9051.
108. Saito T., Whatmore P., Taylor J.F., Fernandes J.M.O., Bock C., Adam A.-C., Espe M. & Skjærven K.H. (2020). Micronutrient supplementation affects transcriptional and epigenetic regulation of lipid metabolism in Atlantic salmon liver. Epigenetics doi: 10.1080/15592294.2020.1859867.
107. Dhanasiri A.K.S., Johny A., Xue X., Berge G.M., Bogevik A.S., Rise M.L., Fæste C.K. & Fernandes J.M.O. (2020). Plant-based diets induce transcriptomic changes in muscle of zebrafish and Atlantic salmon. Frontiers in Genetics 11: 575237.
106. Park Y., Zhang Q., Wiegertjes G.F., Fernandes J.M.O. & Kiron V. (2020). Adherent intestinal cells from Atlantic salmon show phagocytic ability and express macrophage-specific genes. Frontiers in Cell and Developmental Biology 8: 580848.
105. Odei D.K., Hagen Ø., Peruzzi S., Falk-Petersen I.-B. & Fernandes J.M.O. (2020). Transcriptome sequencing and histology reveal dosage compensation in the liver of triploid pre-smolt Atlantic salmon. Scientific Reports 10: 16836.
104. Santos C.A., Andrade S.C.S., Fernandes J.M.O. & Freitas P.D. (2020). Shedding the light on Litopenaeus vannamei differential muscle and hepatopancreas immune responses in white spot syndrome virus (WSSV) exposure. Genes 11: 805.
103. Chen X., Zhang Z., Fernandes J.M.O., Gao Y., Yin P., Liu Y., Tian L., Xie S. & Niu J. (2020). Beneficial effects on growth, haematic indicators, immune status, antioxidant function and gut health in Juvenile Nile tilapia (Oreochromis niloticus) by dietary administration of a multi-strain probiotic. Aquaculture Nutrition 26 (4): 1369-1382.
102. Siriyappagouder P., Galindo-Villegas J., Dhanasiri A.K. S., Zhang Q., Mulero V., Kiron V. & Fernandes J.M.O. (2020). Pseudozyma priming influences expression of genes involved in metabolic pathways and immunity in zebrafish larvae. Frontiers in Immunology 11: 978.
101. Nedoluzhko A.V., Slobodova N.V., Sharko F.S.2, Shalgimbayeva G.M., Tsygankova S.V., Boulygina E.S., Jeney Z., Nguyen V.Q., Pham T.T., Nguyen D.T., Volkov A.A., Fernandes J.M.O. & Rastorguev S.M. (2020). A new strain group of common carp: the genetic differences and admixture events between Cyprinus carpio breeds. Ecology and Evolution 10: 5431-5439.
100. Konstantinidis I., Sætrom P., Mjelle R., Nedoluzhko A.V., Robledo D. & Fernandes J.M.O. (2020). Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Epigenetics 15 (10): 1052-1067.
99. Dhanasiri A.K.S., Chen X., Dahle D., Siriyappagouder P., Fæste C.K. & Fernandes J.M.O. (2020). Dietary inclusion of plant ingredients induces epigenetic changes in the intestine of zebrafish. Epigenetics 15 (10): 1035-1051.
98. Nedoluzhko A., Sharko F., Rbbani G., Teslyuk A., Konstantinidis I. & Fernandes J.M.O. (2020). CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. Peer J 8: e8757.
2019
97. Pourmoghadam M., Poorbagher H., Fernandes J.M.O. & Jafari O. (2019). Diazinon negatively affects the integrity of environmental DNA stability, a case study with common carp (Cyprinus carpio). Environmental Monitoring and Assessment 191:672.
96. Gupta S., Lokesh J., Abdelhafiz Y.A., Siriyappagouder P., Pierre R., Sørensen M., Fernandes J.M.O. & Kiron V. (2019). Macroalga-derived alginate oligosaccharide alters intestinal bacteria of Atlantic salmon. Frontiers in Microbiology 10: 2037.
95. Jafari O., Fernandes J.M.O., Hedayati A.-A., Shabany A. & Pourmoghadam M.N. (2019). Microsatellite analysis of five populations of Alosa braschnikowi (Borodin, 1904) across the southern coast of the Caspian Sea. Frontiers in Genetics 10: 760.
94. Gupta S., Fernandes J.M.O. & Kiron V. (2019). Antibiotic-induced perturbations are manifested in the dominant intestinal bacterial phyla of Atlantic salmon. Microorganisms 7: 233.
93. Podgorniak T., Brockmann S., Konstantinidis I. & Fernandes J.M.O. (2019). Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication. Epigenetics 14(8): 818-836.
92. Johny A., Fæste C.K., Bogevik A., Berge G.M., Fernandes J.M.O. & Ivanova L. (2019). Development and validation of a liquid chromatography high-resolution mass spectrometry method for the simultaneous determination of 25 mycotoxins and phytoestrogens in plant-based fish feed and exposed fish. Toxins 11: 222.
91. Qiu H., Fernandes J.M.O., Hong W., Wu H.X., Zhang Y.T., Huang S., Liu D.T., Yu H., Wang Q., You X. & Chen S.X. (2019). Paralogues from the expanded Tlr11 gene family in mudskipper (Boleophthalmus pectinirostris) are under positive selection and respond differently to LPS/poly(I:C) challenge. Frontiers in Immunology 10: 343.
90. Gupta S., Fečkaninová A., Lokesh J., Koščová J., Sørensen M., Fernandes J.M.O. & Kiron V. (2019). Lactobacillus dominate in the intestine of atlantic salmon fed dietary probiotics. Frontiers in Microbiology 9: 3247.
89. Fernandez I., Fernandes J.M.O., Roberto V.P., Koop M., Oliveira C., Riesco M.F., Dias J., Cox C.J., Cancela L., Cabrita E., Gavaia P.J. (2019). Circulating small non-coding RNAs provide new insights into vitamin K nutrition and reproductive physiology in teleost fish. BBA - General Subjects 1863(1): 39-51.
2018
88. Siriyappagouder P., Galindo-Villegas J., Lokesh J., Mulero V., Fernandes J.M.O. & Kiron V. (2018). Exposure to yeast shapes the intestinal bacterial community assembly in zebrafish larvae. Frontiers in Microbiology 9: 1868.
87. Lokesh J., Kiron V., Sipkema D., Fernandes J.M.O. & Moum T. (2018). Succession of embryonic and intestinal bacterial communities of Atlantic salmon. MicrobiologyOpen e672.
86. Peruzzi S., Puvanendran V., Riesen G., Seim R.R., Hagen Ø., Martínez-Llorens S., Falk-Petersen I.-B., Fernandes J.M.O. & Jobling M. (2018). Growth and development of skeletal anomalies in diploid and triploid Atlantic salmon (Salmo salar) fed phosphorus-rich diets with fish meal and hydrolyzed fish protein. PLoS One 13(3): e0194340.
85. Canada P., Engrola S., Mira S., Teodósio R., Yust M.M., Sousa V., Pedroche J., Fernandes J.M.O., Conceição L.E.C. & Valente L.M.P. (2018). Larval dietary protein complexity affects regulation of muscle growth and expression of DNA methyltransferases in Senegalese sole. Aquaculture 491: 28-38.
84. Zhang Q., Kopp M., Babiak I. & Fernandes J.M.O. (2018). Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide. Scientific Reports 8: 4142.
83. Siriyappagouder P., Kiron V., Lokesh J., Rajeish M., Kopp M. & Fernandes J.M.O. (2018). The intestinal mycobiota in wild zebrafish comprises mainly Dothideomycetes while Saccharomycetes predominate in their laboratory-reared counterparts. Frontiers in Microbiology 9: 387.
82. Skjærven K.H., Jakt L.M., Fernandes J.M.O., Dahl J.A., Adam A.C. & Espe M. (2018). Parental micronutrient deficiency distorts liver DNA methylation and expression of lipid genes associated with a fatty-liver-like phenotype in offspring. Scientific Reports 8: 3055.
2017
81. Canada P., Mira S., Teodósio R., Fernandes J.M.O., Barrios C., Millán F., Pedroche J., Valente L.M.P. & Engrola S. (2017). Dietary protein complexity modulates growth, protein utilisation and the expression of protein digestion-related genes in Senegalese sole larvae. Aquaculture 479: 273-284.
80. Presslauer C., Bizuayehu T.T., Kopp M., Fernandes J.M.O. & Babiak I. (2017). Dynamics of miRNA transcriptome during gonadal development of zebrafish. Scientific Reports 7: 43850.
79. Micallef G., Cash P., Fernandes J.M.O., Rajan B., Tinsley J.W., Bickerdike R., Martin S.A.M. & Bowman A.S. (2017). Dietary yeast cell wall extract alters the proteome of the skin mucous barrier in Atlantic salmon (Salmo salar): increased abundance and expression of a calreticulin-like protein. PLoS ONE 12(1): e0169075.
2016
78. Skjærven K.H., Jakt L.M., Dahl J.A., Espe M., Aanes H., Hamre K. & Fernandes J.M.O. (2016). Parental vitamin deficiency affects the embryonic gene expression of immune -, lipid transport - and apolipoprotein genes. Scientific Reports 6: 34535.
77. Presslauer C., Bizuayehu T.T., Razmi K., Fernandes J.M.O. & Babiak I (2016). See-Thru-Gonad zebrafish line: Developmental and functional validation. Reproduction 152(5): 507-517.
76. Batista S., Medina A., Pires M.A., Moriñigo M.A., Sansuwan K., Fernandes J.M.O., Valente L.M.P. & Ozório R.O.A. (2016). Innate immune response, intestinal morphology and microbiota changes in Senegalese sole fed plant protein diets with probiotics or autolyzed yeast. Applied Microbiology and Biotechnology 100(16):7223-7238.
75. Canada P., Engrola S., Mira S., Teodósio R., Fernandes J.M.O., Sousa V., Barriga-Negra L., Conceição L.E.C. & Valente L.M.P. (2016). The supplementation of a microdiet with crystalline indispensable amino-acids affects muscle growth and the expression pattern of related genes in Senegalese sole (Solea senegalensis) larvae. Aquaculture 458: 158–169.
74. Batista S., Ozório R.O., Kollias S., Dhanasiri A.K., Lokesh J., Kiron V., Valente L.M.P. & Fernandes J.M.O. (2016). Changes in intestinal microbiota, immune- and stress-related transcript levels in Senegalese sole (Solea senegalensis) fed plant ingredients diets intercropped with probiotics. Aquaculture 458: 149-157.
73. Nagasawa K., Sarropoulou E., Edvardsen V. & Fernandes J.M.O. (2016). Substantial downregulation of myogenic transcripts in skeletal muscle of Atlantic cod during the spawning period. PLoS One 11(2): e0148374.
72. Valente L.M.P., Cabral E.M., Sousa V.F., Cunha L.M. & Fernandes J.M.O. (2016). Plant protein blends in diets for Senegalese sole affect skeletal muscle growth, flesh texture and the expression of related genes. Aquaculture 453: 77-85.
71. Katan T., Nash G.W., Rise M.L., Hall J.A., Fernandes J.M.O., Boyce D., Johnsen C.A. and Gamperl A.K. (2016). A little goes long way: improved growth in Atlantic cod (Gadus morhua) fed small amounts of wild zooplankton. Aquaculture 451: 271-282.
2015
70. Smolina I., Kollias S., Møller E.F., Lindeque P., Sundaram A.Y.M., Fernandes J.M.O., Roncalli V., Lenz P. & Hoarau G. (2015). Contrasting transcriptome response to thermal stress in two key zooplankton species, Calanus finmarchicus and C. glacialis. Marine Ecology Progress Series 534: 79-93.
69. Kitani Y., Fernandes J.M.O. & and Kiron V. (2015). Identification of the Atlantic cod L-amino acid oxidase and its alterations following bacterial exposure. Developmental and Comparative Immunology 50: 116-120.
2014
68. Presslauer C., Nagasawa K., Dahle D., Babiak J., Fernandes J.M.O. & Babiak I. (2014). Induced autoimmunity against gonadal proteins affects gonadal development in juvenile zebrafish. PLoS One 9(12): e114209.
67. Mommens M., Fernandes J.M.O., Tollefsen K.E., Johnston I.A. & Babiak I. (2014). Profiling of the embryonic Atlantic halibut (Hippoglossus hippoglossus L.) transcriptome reveals maternal transcripts as potential markers of embryo quality. BMC Genomics 15: 829.
66. Lazado C.C., Kumaratunga H.P.S., Nagasawa K., Babiak I., Caipang C.M.A. & Fernandes J.M.O. (2014). In vitro and ex vivo models indicate that the molecular clock in fast skeletal muscle of Atlantic cod is not autonomous. Molecular Biology Reports 41(10): 6679-6689.
65. Kulkarni A.D., Caipang C.M.A., Kiron V., Rombout J.H.W.M., Fernandes J.M.O. & Brinchmann M.F. (2014). Evaluation of the immune gene response using an RNAi approach in vaccinated Penaeus monodon during oral WSSV infection. Marine Genomics 18: 55-65.
64. Lazado C.C., Kumaratunga H.P.S., Nagasawa K., Babiak I., Giannetto A. & Fernandes J.M.O. (2014). Daily rhythmicity of clock gene transcripts in Atlantic cod fast skeletal muscle. PLoS One 9(6): e99172.
63. Campos C., Sundaram A.Y.M., Valente L.M.P., Conceição L.E.C, Engrola S. & Fernandes J.M.O. (2014). Thermal plasticity of the miRNA transcriptome during Senegalese sole development. BMC Genomics 15: 525.
62. Lazado C.C., Nagasawa K., Babiak I., Kumaratunga H.P.S. & Fernandes J.M.O. (2014). Circadian rhythmicity and photoperiodic plasticity of myosin gene transcription in fast skeletal muscle of Atlantic cod (Gadus morhua). Marine Genomics doi: 10.1016/j.margen.2014.04.011.
61. Kulkarni A., Kiron Viswanath, Rombout J.H.W.M., Brinchmann M.F., Fernandes J.M.O., Sudheer N.S. & Singh B.I.S. (2014). Protein profiling in the gut of Penaeus monodon gavaged with oral WSSV-vaccines and live white spot syndrome virus. Proteomics doi: 10.1002/pmic.201300405.
60. Campos C., Valente L.M.P., Conceição L.E.C., Engrola S. & Fernandes J.M.O. (2014). Molecular regulation of muscle development and growth in Senegalese sole larvae exposed to temperature fluctuations. Aquaculture doi: 10.1016/j.aquaculture.2014.04.035.
59. Nagasawa K., Presslauer C., Kirtiklis L., Babiak I. & Fernandes J.M.O. (2014). Sexually dimorphic transcription of estrogen receptors in cod gonads throughout a reproductive cycle. Journal of Molecular Endocrinology 52(3): 357-371.
58. Andersen Ø., Rosa M.C., Yadav P., Pirolli D., Fernandes J.M.O., Berg PR, Jentoft S. & Andrè C. (2014). The conserved Phe GH5 of importance for hemoglobin intersubunit contact is mutated in gadoid fish. BMC Evolutionary Biology 14:54.
57. Jueterbock A., Kollias S., Smolina I., Fernandes J.M.O., Coyer J.A., Olsen J.L. & Hoarau G. (2014). Thermal stress resistance of the brown alga Fucus serratus along the North-Atlantic coast: acclimatization potential to climate change. Marine Genomics 13: 27-36.
56. Fernandes J.M.O., Giannetto A., Nagasawa K., Mauceri A., Maisano M., Domenico E., Cappello T., Oliva S. & Fasulo S. (2014). Influence of continuous light treatment on expression of stress biomarkers in Atlantic cod. Developmental and Comparative Immunology 44(1): 30-34.
2013
55. Campos C., Fernandes J.M.O., Conceição L.E.C., Engrola S., Sousa V. & Valente L.M.P. (2013). Thermal conditions during larval pelagic phase influence subsequent somatic growth of Senegalese sole by modulating gene expression and muscle growth dynamics. Aquaculture 414-415: 46-55.
54. Dhanasiri A.K.S., Fernandes J.M.O. & Kiron V. (2013). Liver transcriptome changes in zebrafish during adaptation to transport-associated stress. PLoS One 8(6): e65028.
53. Lanes C.F.C., Bizuayehu T.T., Fernandes J.M.O., Kiron V. & Babiak I. (2013). Transcriptome of Atlantic cod (Gadus morhua) early embryos from farmed and wild broodstocks. Marine Biotechnology 15(6): 677-694.
52. Campos C., Castanheira M.F., Engrola S., Valente L.M.P., Fernandes J.M.O. & Conceição L. (2013). Rearing temperature affects Senegalese sole (Solea senegalensis) larvae protein metabolic capacity. Fish Physiology and Biochemistry 39(6):1485-1496.
51. Ruangsri J., Kitani Y., Kiron V., Jeppinamogeru L., Brinchmann M.F., Karlsen B.O. & Fernandes J.M.O. (2013). A novel beta-defensin antimicrobial peptide in Atlantic cod with stimulatory effect on phagocytic activity. PLoS One 8(4): e62302.
50. Bizuayehu T.T., Fernandes J.M.O., Johansen S.D. & Babiak I. (2013). Characterization of novel precursor miRNAs using next generation sequencing and prediction of miRNA targets in Atlantic halibut. PLoS One 8(4): e61378.
49. Campos C., Valente L.M.P., Conceição L., Engrola S. & Fernandes J.M.O. (2013). Temperature affects methylation of the myogenin putative promoter, its expression and muscle cellularity in Senegalese sole larvae. Epigenetics 8(4): 389-397.
48. Giannetto A., Nagasawa K. & Fernandes J.M.O. (2013). Influence of photoperiod on the expression of DNA (cytosine-5) methyltransferases in Atlantic cod. Gene 519: 222-230.
47. Dhanasiri A.K.S., Fernandes J.M.O. & Kiron V. (2013). Acclimation of zebrafish to transport stress. Zebrafish 10(1): 87-98.
46. Rajan B., Kiron V., Fernandes J.M.O., Rombout J.H.W.M. and Brinchmann M.F. (2013). Localization and immune characteristics of two galectin-1 proteins in Atlantic cod (Gadus morhua) mucosal tissues. Developmental and Comparative Immunology 40(2): 83-93.
45. Ruangsri J., Lokesh J., Fernandes J.M.O. & Kiron V. (2013). Transcriptional regulation of antimicrobial peptides in mucosal tissues of Atlantic cod Gadus morhua L. in response to different stimuli. Aquaculture Research doi:10.1111/are.12136.
44. Campos C., Valente L.M.P., Conceição L., Engrola S., Sousa V., Rocha E., & Fernandes J.M.O. (2013). Incubation temperature induces changes in muscle cellularity and gene expression in Senegalese sole (Solea senegalensis). Gene 516: 209-217.
43. Valente L.M.P., Moutou K.A., Conceição L., Engrola S., Fernandes J.M.O. & Johnston I. A. (2013). What determines growth potential and juvenile quality of farmed fish species? Reviews in Aquaculture (accepted).
42. Nagasawa K., Fernandes J.M.O., Yoshizaki G., Miwa M. & Babiak I. (2013). Identification and migration of primordial germ cells in Atlantic salmon, Salmo salar: characterization of vasa, dead end, and lymphocyte antigen 75 genes. Molecular Reproduction and Development 80: 118-131.
2012
41. Sundaram A.Y.M., Kiron V., Dopazo J. & Fernandes J.M.O. (2012). Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua. BMC Evolutionary Biology 12: 256.
40. Lanes C.F.C., Fernandes J.M.O., Kiron V. & Babiak I. (2012). Profiling of key apoptotic, stress and immune-related transcripts during embryonic and post-embryonic development of Atlantic cod (Gadus morhua L.) originating from wild or farmed broodstocks. Theriogenology 78: 1583-1596.
39. Dhanasiri A.K.S., Fernandes J.M.O. & Kiron V. (2012). Glutamine synthetase activity and the expression of three glul paralogues in zebrafish during transport. Comparative Biochemistry and Physiology B 163:274-284.
38. Lokesh J., Fernandes J.M.O., Korsnes K., Bergh Ø., Brinchmann M.F. & Kiron V. (2012). Transcriptional regulation of cytokines in the intestine of Atlantic cod fed yeast derived mannan oligosaccharide or beta-glucan and challenged with Vibrio anguillarum. Fish and Shellfish Immunology 33(3): 626-631.
37. Sundaram A., Consuegra S., Kiron V. & Fernandes J.M.O. (2012). Positive selection within teleost toll-like receptors tlr21 and tlr22 subfamilies and their response to temperature stress and microbial components in zebrafish. Molecular Biology Reports 39(9): 8965-8975.
36. Bizuayehu T.T., Babiak J., Norberg B., Fernandes J.M.O., Johansen S.D. & Babiak I. (2012). Sex-biased expression of miRNAs in Atlantic halibut (Hippoglossus hippoglossus) brain and gonads. Sexual Development 6: 257-266.
35. Presslauer C., Nagasawa K., Fernandes J.M.O. & Babiak I. (2012). Expression of vasa and nanos3 during primordial germ cell formation and migration in Atlantic cod (Gadus morhua L.). Theriogenology 78: 1262-1277.
34. Lanes C.C., Bolla S., Fernandes J.M.O., Nicolaisen O., Kiron V. & Babiak I. (2012). Nucleotide-enrichment of live feed: a promising protocol for rearing of Atlantic cod Gadus morhua larvae. Marine Biotechnology 14(5):544-558.
33. Nagasawa K., Giannetto A. & Fernandes J.M.O. (2012). Photoperiod influences growth and mll (mixed-lineage leukaemia) expression in Atlantic cod. PLoS ONE 7(5):e36908.
32. Ruangsri J., Fernandes J.M.O., Rombout J.H.W.M., Brinchmann M. & Kiron V. (2012). Ubiquitous presence of piscidin-1 in Atlantic cod as evidenced by immunolocalisation. BMC Veterinary Research 8:46.
31. Micallef G., Bickerdike R., Reiff C., Fernandes J.M.O., Bowman A.S. & Martin S.A.M. (2012). Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defensive organ. Marine Biotechnology 14(5):559-569.
30. Campos C., Valente L.M.P. & Fernandes J.M.O. (2012). Molecular evolution of zebrafish dnmt3 genes and thermal plasticity of their expression during embryonic development. Gene 500: 93-100.
29. Bizuayehu T.T., Lanes C.F.C., Furmanek T., Karlsen B.O., Fernandes J.M.O., Johansen S.D. & Babiak I. (2012). Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development. BMC Genomics 13:11.
28. Ruangsri J., Caipang C., Kiron V. & Fernandes J.M.O. (2012). Differential expression and biological activity of two piscidin paralogues and a novel splice variant in Atlantic cod (Gadus morhua L). Fish and Shellfish Immunology 32: 396-406.
27. Lanes C.F.C, Bizuayehu T.T., Bolla S., Martins C., Fernandes J.M.O., Viswanath K., Bianchini A. & Babiak I. (2012). Biochemical composition and performance of Atlantic cod (Gadus morhua L.) eggs and larvae obtained from farmed and wild broodstocks. Aquaculture 324-325: 267-275.
2011
26. Rajan B., Fernandes J.M.O., Caipang C., Kiron V., Rombout J. & Brinchmann M. (2011). Proteome reference map of the skin mucus of Atlantic cod (Gadus morhua) revealing immune competent molecules. Fish and Shellfish Immunology 31: 224-231.
25. Dhanasiri A., Kiron V., Fernandes J.M.O., Bergh Ø. & Powell M. (2011). Novel application of nitrifying bacterial consortia to ease ammonia toxicity in ornamental fish transport units: trials with zebrafish. Journal of Applied Microbiology 11(2): 278-292.
24. Noga E.J., Ullal A.J., Corrales J. & Fernandes J.M.O. (2011). Application of antimicrobial polypeptide host defenses to aquaculture: exploitation of downregulation and upregulation responses. Comparative Biochemistry and Physiology D 6(1): 44-54.
23. Sarropoulou E. & Fernandes J.M.O. (2011). Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species. Comparative Biochemistry and Physiology D 6(1): 92-102.
2010
22. Mommens M., Fernandes J.M.O., Bizuayehu T.T., Bolla S.L., Johnston I.A. & Babiak I. (2010). Maternal mRNAs as molecular markers for egg quality in Atlantic halibut (Hippoglossus hippoglossus L.). BMC Research Notes 3: 138.
21. Fernandes J.M.O., Ruangsri J. & Kiron V. (2010). Atlantic cod piscidin and its diversification through positive selection. PLoS ONE 5(3): e9501.
20. Ruangsri J., Fernandes J.M.O., Brinchmann M. & Kiron V. (2010). Antimicrobial activity in the tissues of Atlantic cod (Gadus morhua L.). Fish and Shellfish Immunology 28: 879-886.
19. Campos C., Valente L.M.P., Borges P., Bizuayehua T. & Fernandes J.M.O. (2010). Dietary lipid levels have a remarkable impact on the expression of growth-related genes in Senegalese sole (Solea senegalensis Kaup). Journal of Experimental Biology 213:200-209.
18. Sarropoulou E., Fernandes J.M.O., Mittera K., Magoulas A., Mulero V., Sepulcre P., Figueras A., Novoa B. & Kotoulas G. (2010). Evolution of a multifunctional gene: The warm temperature acclimation protein Wap65 in the European seabass Dicentrarchus labrax. Molecular Phylogenetics and Evolution 55:640-649.
2000-2009
17. Hagen Ø., Fernandes J.M.O., Solberg C. & Johnston I.A. (2009). Expression of growth-related genes during fasting and refeeding in juvenile Atlantic halibut, Hippoglossus hippoglossus L. Comparative Biochemistry and Physiology B 152: 47-53.
16. Fernandes J.M.O., Mommens M., Hagen Ø., Babiak I. & Solberg C. (2008). Selection of suitable reference genes for real-time PCR studies of Atlantic halibut. Comparative Biochemistry and Physiology B 150: 23-32.
15. Smith V.J., Fernandes J.M.O., Kemp G.D. & Hauton C. (2008). Crustins: enigmatic WAP domain-containing antibacterial proteins from crustaceans. Developmental and Comparative Immunology 32: 758-772.
14. Fernandes J.M.O., Macqueen D., Lee H.-T. & Johnston I.A. (2008). Genomic, evolutionary and expression analyses of cee, an ancient gene involved in normal growth and development. Genomics 91: 315-325.
13. Fernandes J.M.O., MacKenzie M., Kinghorn J.R. & Johnston I.A. (2007). FoxK1 splice variants show developmental stage-specific plasticity of expression with temperature in the tiger pufferfish. Journal of Experimental Biology 210: 3461-3472.
12. Fernandes J.M.O., Kinghorn J.R. & Johnston I.A. (2007). Differential expression of multiple alternatively spliced transcripts of MyoD. Gene 391:178-185.
11. Fernandes J.M.O., Kinghorn J.R. & Johnston I.A. (2007). Characterization of two paralogous muscleblind-like genes from the tiger pufferfish (Takifugu rubripes). Comparative Biochemistry and Physiology B 146: 180-186.
10. Bai J., Solberg C., Fernandes J.M.O. & Johnston I.A. (2007). Profiling of maternal and developmental-stage specific mRNA transcripts in Atlantic halibut Hippoglossus hippoglossus. Gene 386: 202-210.
9. Fernandes J.M.O., MacKenzie M.G., Wright P., Steele S., Suzuki Y., Kinghorn J.R. & Johnston I.A. (2006). Myogenin in model puffer fish species: comparative genomic analysis and thermal plasticity of expression during early development. Comparative Biochemistry and Physiology D 1(1): 35-45.
8. Fernandes J.M.O., MacKenzie M., Elgar G., Suzuki Y., Watabe S., Kinghorn J.R. & Johnston I.A. (2005). A genomic approach to reveal novel genes associated with myotube formation in the model teleost, Takifugu rubripes. Physiological Genomics 22: 327-338.
7. Fernandes J.M.O., Kemp G.D. & Smith V.J. (2004). Two novel muramidases from skin mucosa of rainbow trout, Oncorhynchus mykiss. Comparative Biochemistry and Physiology B 138(1): 53-64.
6. Fernandes J.M.O., Molle G., Kemp G.D. & Smith V.J. (2004). Isolation and characterisation of oncorhyncin II, a histone H1-derived antimicrobial peptide from skin secretions of rainbow trout, Oncorhynchus mykiss. Developmental and Comparative Immunology 28: 127-138.
5. Fernandes J.M.O. & Smith V.J. (2004). Partial purification of antibacterial proteinaceous factors from erythrocytes of Oncorhynchus mykiss. Fish and Shellfish Immunology 16: 1-9.
4. Fernandes J.M.O., Saint N., Kemp G.D. & Smith V.J. (2003). Oncorhyncin III: a potent antimicrobial peptide derived from the non-histone chromosomal protein H6 of rainbow trout, Oncorhynchus mykiss. Biochemical Journal 373(Pt 2): 621-628.
3. Fernandes J.M.O., Kemp G.D., Molle G. & Smith V.J. (2002). Antimicrobial properties of a histone H2A-like protein from skin secretions of rainbow trout, Oncorhynchus mykiss. Biochemical Journal 368(Pt 2): 611-620.
2. Fernandes J.M.O. & Smith V.J. (2002). A novel antimicrobial function for a ribosomal peptide from rainbow trout skin. Biochemical Biophysical Research Communications 296(1): 167-171.
1. Smith V.J., Fernandes J.M.O., Jones S.J. Kemp, G.D. & Tatner M.F. (2000). Antibacterial proteins in rainbow trout, Oncorhynchus mykiss. Fish and Shellfish Immunology 10 (3): 243-260.
I have published 150 papers in international scientific journals with peer-review, which have attracted over 6900 citations.
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Updated on 08/11/2023
