Haja Kadarmideen

2022

Host Genome–Metagenome Analyses Using Combinatorial Network Methods Reveal Key Metagenomic and Host Genetic Features for Methane Emission and Feed Efficiency in Cattle

Cardinale, S. & Kadarmideen, H. N., 2022, In: Frontiers in Genetics. 13, 12 p., 795717.

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In vitro- and in vivo-produced male dairy calves show molecular differences in the hepatic and muscular energy regulation

Rabaglino, M. B., Secher, J. B. M., Hyttel, P. & Kadarmideen, H., 2022, In: Biology of Reproduction. 107, 4, p. 1113–1124

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2021

Analysis of SNP rs1800796 association with risk of rheumatoid arthritis in Pakistani population: A case control study

Nisar, H., Pasha, U., Hanif, K., Abid, R., Sherwani, R. A. K., Kadarmideen, H. N. & Sadaf, S., Apr 2021, In: Pakistan Journal of Zoology. 53, 2, p. 529-535

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Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos

Rabaglino, M. B., O’Doherty, A., Secher, J. B. M., Lonergan, P., Hyttel, P., Fair, T. & Kadarmideen, H. N., May 2021, In: PLOS ONE. 16, 5 May, 17 p., e0252096.

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Bovine in-vitro produced embryos: Development of embryo proper and associated membranes from day 26 to 47 of gestation

Pedersen, H. S., Mazzoni, G., Pihl, M., Kadarmideen, H. N., Hyttel, P. & Callesen, H., 2021, In: Reproductive Biology. 20, 4, p. 595-599

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Epigenomic and transcriptomic analyses reveal early activation of the HPG axis in in vitro-produced male dairy calves

Rabaglino, M. B., Bojsen-Møller Secher, J., Sirard, M-A., Hyttel, P. & Kadarmideen, H. N., 2021, In: FASEB Journal. 35, 10, 19 p., e21882.

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2020

Characterization of Global DNA Methylation in Different Gene Regions Reveals Candidate Biomarkers in Pigs with High and Low Levels of Boar Taint

Wang, X. & Kadarmideen, H., 2020, In: Veterinary Sciences. 7, 2, 18 p., 77.

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Characterization of the endometrial transcriptome in early diestrus influencing pregnancy status in dairy cattle after transfer of in vitro-produced embryos

Mazzoni, G., Pedersen, H. S., Rabaglino, M. B., Hyttel, P., Callesen, H. & Kadarmideen, H. N., 1 Jan 2020, In: Physiological Genomics. 52, 7, p. 269-279

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Comparisons of improved genomic predictions generated by different imputation methods for genotyping by sequencing data in livestock populations

Wang, X., Su, G., Hao, D., Sandø Lund, M. & N. Kadarmideen, H., 2020, In: Journal of Animal Science and Biotechnology. 11, 3, 12 p.

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Copy Number Variations and Expression Levels of Guanylate-Binding Protein 6 Gene Associated with Growth Traits of Chinese Cattle

Hao, D., Wang, X., Thomsen, B., Kadarmideen, H., Wang, X., Lan, X., Huang, Y., Qi, X. & Chen, H., 2020, In: Animals. 10, 4, 17 p., 566.

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Differential impacts of late gestational over-and undernutrition on adipose tissue traits and associated visceral obesity risk upon exposure to a postnatal high-fat diet in adolescent sheep

Khanal, P., Pandey, D., Binti Ahmad, S., Safayi, S., Kadarmideen, H. N. & Nielsen, M. O., 2020, In: Physiological Reports. 8, 3, 21 p., e14359.

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GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis

Wang, X., Hao, D. & Kadarmideen, H. N., 2020, In: Journal of Computational Biology. 28, 13 p.

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Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle

Grigoletto, L., Santana, M. H. A., Bressan, F. F., Eler, J. P., Nogueira, M. F. G., Kadarmideen, H. N., Baruselli, P. S., Ferraz, J. B. S. & Brito, L. F., 2020, In: Animals. 10, 7, 15 p., 1185.

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Genetic variations (eQTLs) in muscle transcriptome and mitochondrial genes, and trans-eQTL molecular pathways in feed efficiency from Danish breeding pigs

Carmelo, V. A. O. & Kadarmideen, H. N., 2020, In: PLOS ONE. 15, 9, 18 p., e0239143.

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Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs

Carmelo, V. A. O. & N. Kadarmideen, H., 2020, In: Frontiers in Genetics. 11, 16 p., 650.

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Genome-Wide Epistatic Interaction Networks Affecting Feed Efficiency in Duroc and Landrace Pigs

Banerjee, P., Carmelo, V. A. O. & N. Kadarmideen, H., 2020, In: Frontiers in Genetics. 11, 121.

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Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy

Pierzchała, M., Pierzchała, D., Ogłuszka, M., Poławska, E., Blicharski, T., Roszczyk, A., Nawrocka, A., Urbański, P., Stepanow, K., Ciepłoch, A., Korwin-Kossakowska, A., F.W. te Pas, M., Slaska, B., Buszewska-Forajta, M., M. Jaśkowski, J., Sachajko, M., Herudzińska, M., M. Jaśkowski, B., Niżański, W., Fraser, L., & 3 othersCzarnik, U., N. Kadarmideen, H. & S. Pareek, C., 2020, In: Life. 10, 33 p., 68.

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Impact of IL-17F 7488T/C Functional Polymorphism on Progressive Rheumatoid Arthritis: Novel Insight from the Molecular Dynamic Simulations

Nisar, H., Pasha, U., Mirza, M. U., Abid, R., Hanif, K., Kadarmideen, H. N. & Sadaf, S., 16 Jun 2020, In: Immunological Investigations. p. 1-11 11 p.

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Integrative analysis of metabolomic and transcriptomic profiles uncovers biological pathways of feed efficiency in pigs

Banerjee, P., Carmelo, V. A. O. & Kadarmideen, H. N., Jul 2020, In: Metabolites. 10, 7, p. 1-17 275.

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Interplay among miR-29 family, mineral metabolism, and gene regulation in Bos indicus muscle

da Silva Diniz, W. J., Banerjee, P., Mazzoni, G., Coutinho, L. L., Cesar, A. S. M., Afonso, J., Gromboni, C. F., Nogueira, A. R. A., Kadarmideen, H. N. & de Almeida Regitano, L. C., 1 Jan 2020, In: Molecular Genetics and Genomics. 295, p. 1113–1127

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Machine learning approach to integrated endometrial transcriptomic datasets reveals biomarkers predicting uterine receptivity in cattle at seven days after estrous

Rabaglino, M. B. & Kadarmideen, H. N., 2020, In: Scientific Reports. 10, 1, 10 p., 16981.

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Metabolite Genome-Wide Association Study (mGWAS) and Gene-Metabolite Interaction Network Analysis Reveal Potential Biomarkers for Feed Efficiency in Pigs

Wang, X. & Kadarmideen, H. N., 2020, In: Metabolites. 10, 19 p., 201.

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Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs

Carmelo, V. A. O., Banerjee, P., da Silva Diniz, W. J. & Kadarmideen, H. N., 2020, In: Scientific Reports. 10, 1, 14 p., 255.

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Transcriptomic changes in bovine skeletal muscle cells after resveratrol treatment

Hao, D., Wang, X., Wang, X., Thomsen, B., Kadarmideen, H. N., Lan, X., Huang, Y. & Chen, H., 5 Jun 2020, In: Gene. 754, 9 p., 144849.

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2019

An Epigenome-Wide DNA Methylation Map of Testis in Pigs for Study of Complex Traits

Wang, X. & Kadarmideen, H., 2019, In: Frontiers in Genetics. 10, 13 p., 405.

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Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis

Drag, M. H., Kogelman, L. J. A., Maribo, H., Meinert, L., Thomsen, P. D. & Kadarmideen, H. N., 1 Oct 2019, In: Physiological Genomics. 51, 10, p. 488-499

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Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle

Diniz, W. J. S., Mazzoni, G., Coutinho, L. L., Banerjee, P., Geistlinger, L., Cesar, A. S. M., Bertolini, F., Afonso, J., de Oliveira, P. S. N., Tizioto, P. C., Kadarmideen, H. & Regitano, L. C. A., 2019, In: Frontiers in Genetics. 10, 12 p., 210.

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Genome-wide DNA methylation analysis using next-generation sequencing to reveal candidate genes responsible for boar taint in pigs

Wang, X. & Kadarmideen, H. N., 1 Jan 2019, In: Animal Genetics. 50, p. 644-59

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Genomic analyses suggest adaptive differentiation of Northern European native cattle breeds

Stronen, A. V., Pertoldi, C., Iacolina, L., Kadarmideen, H. N. & Kristensen, T. N., 2019, In: Evolutionary Applications. 12, 6, p. 1096-1113

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Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations

Wang, X., Lund, M. S., Ma, P., Janss, L., Kadarmideen, H. & Su, G., 2019, In: Journal of Animal Science and Biotechnology. 10, 10 p., 8.

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Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors

Warrington, N. M., Beaumont, R. N., Horikoshi, M., Day, F. R., Helgeland, Ø., Laurin, C., Bacelis, J., Peng, S., Hao, K., Feenstra, B., Wood, A. R., Mahajan, A., Tyrrell, J., Robertson, N. R., Rayner, N. W., Qiao, Z., Moen, G-H., Vaudel, M., Marsit, C. J., Chen, J. J. J., & 189 othersNodzenski, M., Schnurr, T. M., Zafarmand, M. H., Bradfield, J. P., Grarup, N., Kooijman, M. N., Li-Gao, R., Geller, F., Ahluwalia, T. S., Paternoster, L., Rueedi, R., Huikari, V., Hottenga, J-J., Lyytikäinen, L-P., Cavadino, A., Metrustry, S., Cousminer, D. L., Wu, Y., Thiering, E., Wang, C. A., Have, C. T., Vilor-Tejedor, N., Joshi, P. K., Painter, J. N., Ntalla, I., Myhre, R., Pitkänen, N., van Leeuwen, E. M., Joro, R., Lagou, V., Richmond, R. C., Espinosa, A., Barton, S. J., Inskip, H. M., Holloway, J. W., Santa-Marina, L., Estivill, X., Ang, W., Marsh, J. A., Reichetzeder, C., Marullo, L., Hocher, B., Lunetta, K. L., Murabito, J. M., Relton, C. L., Kogevinas, M., Chatzi, L., Allard, C., Bouchard, L., Hivert, M-F., Zhang, G., Muglia, L. J., Heikkinen, J., Consortium, EGG., Morgen, C. S., van Kampen, A. H. C., van Schaik, B. D. C., Mentch, F. D., Langenberg, C., Luan, J., Scott, R. A., Zhao, J. H., Hemani, G., Ring, S. M., Bennett, A. J., Gaulton, K. J., Fernandez-Tajes, J., van Zuydam, N. R., Medina-Gomez, C., de Haan, H. G., Rosendaal, F. R., Kutalik, Z., Marques-Vidal, P., Das, S., Willemsen, G., Mbarek, H., Müller-Nurasyid, M., Standl, M., Appel, E. V. R., Fonvig, C. E., Trier, C., van Beijsterveldt, C. E. M., Murcia, M., Bustamante, M., Bonas-Guarch, S., Hougaard, D. M., Mercader, J. M., Linneberg, A., Schraut, K. E., Lind, P. A., Medland, S. E., Shields, B. M., Knight, B. A., Chai, J-F., Panoutsopoulou, K., Bartels, M., Sánchez, F., Stokholm, J., Torrents, D., Vinding, R. K., Willems, S. M., Atalay, M., Chawes, B. L., Kovacs, P., Prokopenko, I., Tuke, M. A., Yaghootkar, H., Ruth, K. S., Jones, S. E., Loh, P-R., Murray, A., Weedon, M. N., Tönjes, A., Stumvoll, M., Michaelsen, K. F., Eloranta, A-M., Lakka, T. A., van Duijn, C. M., Kiess, W., Körner, A., Niinikoski, H., Pahkala, K., Raitakari, O. T., Jacobsson, B., Zeggini, E., Dedoussis, G. V., Teo, Y-Y., Saw, S-M., Montgomery, G. W., Campbell, H., Wilson, J. F., Vrijkotte, T. G. M., Vrijheid, M., de Geus, E. J. C. N., Hayes, M. G., Kadarmideen, H. N., Holm, J-C., Beilin, L. J., Pennell, C. E., Heinrich, J., Adair, L. S., Borja, J. B., Mohlke, K. L., Eriksson, J. G., Widén, E. E., Hattersley, A. T., Spector, T. D., Kähönen, M., Viikari, J. S., Lehtimäki, T., Boomsma, D. I., Sebert, S., Vollenweider, P., Sørensen, T. I. A., Bisgaard, H. F., Bønnelykke, K., Murray, J. C., Melbye, M., Nohr, E. A., Mook-Kanamori, D. O., Rivadeneira, F., Hofman, A., Felix, J. F., Jaddoe, V. W. V., Hansen, T., Pisinger, C., Vaag, A. A., Pedersen, O., Uitterlinden, A. G., Järvelin, M-R., Power, C., Hyppönen, E., Scholtens, D. M., Lowe, W. L., Davey Smith, G., Timpson, N. J., Morris, A. P., Wareham, N. J., Hakonarson, H., Grant, S. F. A., Frayling, T. M., Lawlor, D. A., Njølstad, P. R., Johansson, S., Ong, K. K., McCarthy, M. I., Perry, J. R. B., Evans, D. M. & Freathy, R. M., 2019, In: Nature Genetics. 51, 5, p. 804-814

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Metabolomics Analyses in High-Low Feed Efficient Dairy Cows Reveal Novel Biochemical Mechanisms and Predictive Biomarkers

Wang, X. & Kadarmideen, H. N., 2019, In: Metabolites. 9, 7, 16 p., 151.

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Transcriptomics–genomics data integration and expression quantitative trait loci analyses in oocyte donors and embryo recipients for improving in vitro production of dairy cattle embryos

Kadarmideen, H. & Mazzoni, G., 2019, In: Reproduction, Fertility and Development. 31, p. 55–67

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2018

An adult-based insulin resistance genetic risk score associates with insulin resistance, metabolic traits and altered fat distribution in Danish children and adolescents who are overweight or obese

Graae, A-S., Hollensted, M., Kloppenborg, J. T., Mahendran, Y., Schnurr, T. M., Appel, E. V. R., Rask, J., Nielsen, T. R. H., Johansen, M. Ø., Linneberg, A., Jørgensen, M. E., Grarup, N., Kadarmideen, H. N., Holst, B., Pedersen, O., Holm, J-C. & Hansen, T., 2018, In: Diabetologia. 61, 8, p. 1769-1779 11 p.

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Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency

Salleh, S. M., Mazzoni, G., Løvendahl, P. & Kadarmideen, H., 2018, In: B M C Bioinformatics. 19, 15 p., 513.

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Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils

Sabino, M., Carmelo, V. A. O., Mazzoni, G., Cappelli, K., Capomaccio, S., Ajmone-Marsan, P., Verini-Supplizi, A., Trabalza-Marinucci, M. & Kadarmideen, H. N., 2018, In: B M C Genomics. 19, 1, 15 p., 236.

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Genetic Susceptibility for Childhood BMI has no Impact on Weight Loss Following Lifestyle Intervention in Danish Children: Childhood Obesity Gene Risk: Intervention Outcome

Hollensted, M., Fogh, M., Schnurr, T. M., Kloppenborg, J. T., Have, C. T., Ruest Haarmark Nielsen, T., Rask, J., Asp Vonsild Lund, M., Frithioff-Bøjsøe, C., Østergaard Johansen, M., Vincent Rosenbaum Appel, E., Mahendran, Y., Grarup, N., Kadarmideen, H. N., Pedersen, O., Holm, J-C. & Hansen, T., 2018, In: Obesity. 26, 12, p. 1915-1922

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Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics

Salleh, MS., Mazzoni, G., Nielsen, M. O., Løvendahl, P. & Kadarmideen, H., 2018, In: Journal of Genetics and Genome Research. 5, 1, 14 p.

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Simulated physiological oocyte maturation has side effects on bovine oocytes and embryos

Razza, E. M., Pedersen, H. S., Stroebech, L., Fontes, P. K., Kadarmideen, H. N., Callesen, H., Pihl, M., Nogueira, M. F. G. & Hyttel, P., 2018, In: Journal of Assisted Reproduction and Genetics. 36, 3, p. 413–424

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Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

Drag, M., Hansen, M. B. & Kadarmideen, H. N., 2018, In: P L o S One. 13, 2, 30 p., e0192673.

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Transcription factor co-expression networks of adipose RNA-Seq data reveal regulatory mechanisms of obesity

Skinkyte-Juskiene, R., Kogelman, L. J. A. & Kadarmideen, H. N., 1 May 2018, In: Current Genomics. 19, 4, p. 289-299

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WISH-R- a fast and efficient tool for construction of epistatic networks for complex traits and diseases

Carmelo, V. A. O., Kogelman, L. J. A., Madsen, M. B. & Kadarmideen, H. N., 2018, In: B M C Bioinformatics. 19, 7 p., 277.

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2017

A genome-wide association study of thyroid stimulating hormone and free thyroxine in Danish children and adolescents

Nielsen, T. R. H., Appel, E. V. R., Svendstrup, M., Ohrt, J. D., Dahl, M., Fonvig, C. E., Hollensted, M., Have, C. T., Kadarmideen, H. N., Pedersen, O., Hansen, T., Holm, J-C., Grarup, N. & Meyre, D. (ed.), 2017, In: P L o S One. 12, 3, e0174204.

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Differential expression and co-expression gene networks reveal candidate biomarkers of boar taint in non-castrated pigs

Drag, M., Skinkyté-Juskiené, R., Do, D. N., Kogelman, L. J. A. & Kadarmideen, H. N., 2017, In: Scientific Reports. 7, 1, 18 p., 12205.

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Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

Oliveira Junior, G. A., Perez, B. C., Cole, J. B., Santana, M. H. A., Silveira, J., Mazzoni, G., Ventura, R. V., Santana Junior, M. L., Kadarmideen, H., Garrick, D. J. & Ferraz, J. B. S., 2017, In: Journal of Animal Science. 95, 11, p. 4796-4812 17 p.

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Identification of potential biomarkers in donor cows for in vitro embryo production by granulosa cell transcriptomics

Mazzoni, G., Salleh, S. M., Freude, K., Pedersen, H. S., Stroebech, L., Callesen, H., Hyttel, P., Kadarmideen, H. N. & Óvilo, C. (ed.), 2017, In: P L o S One. 12, 4, 27 p., e0175464.

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RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

Salleh, M. S., Mazzoni, G., Höglund, J. K., Olijhoek, D. W., Lund, P., Løvendahl, P. & Kadarmideen, H., 2017, In: B M C Genomics. 18, 1, 17 p., 258.

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Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology

Pareek, C. S., Błaszczyk, P., Dziuba, P., Czarnik, U., Fraser, L., Sobiech, P., Pierzchała, M., Feng, Y., Kadarmideen, H. N. & Kumar, D., 2017, In: P L o S One. 12, 2, 26 p., e0172687.

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Haja Kadarmideen

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