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Peer-reviewed

Selected Peer-reviewed publications from the last 5 years (2011- present):

  • Gianluca Mazzoni and Haja N. Kadarmideen (2016). Computational Methods for Quality Check, Preprocessing and Normalization of RNA-Seq Data for Systems Biology and Analysis. Pages 61-77. In:  Systems Biology in Animal Production and Health, Vol. 2, H.N. Kadarmideen (ed.) DOI 10.1007/978-3-319-43332-5_3. Book Published by Springer International Publishing, Switzerland. http://link.springer.com/book/10.1007/978-3-319-43332-5. Print ISBN: 978-3-319-43330-1 and Online ISBN: 978-3-319-43332-5
  • Lisette J. A. Kogelman and Haja N. Kadarmideen (2016). Applications of Systems Genetics and Biology for Obesity Using Pig Models. Pages 25-42. In: Systems Biology in Animal Production and Health, Vol. 1, H.N. Kadarmideen (ed.). DOI 10.1007/978-3-319-43335-6_2. Book Published by Springer International Publishing, Switzerland. http://link.springer.com/book/10.1007/978-3-319-43335-6. Print ISBN: 978-3-319-43333-2 and Online ISBN: 978-3-319-43335-6
  • Haja N. Kadarmideen (2016). Systems Biology in Animal Production and Health, Vol. 1. Book Published by Springer International Publishing, Switzerland. 164 pages. DOI: 10.1007/978-3-319-43335-6. http://link.springer.com/book/10.1007/978-3-319-43335-6. Print ISBN: 978-3-319-43333-2 and Online ISBN: 978-3-319-43335-6
  • Haja N. Kadarmideen (2016). Systems Biology in Animal Production and Health, Vol. 2. Book Published by Springer International Publishing, Switzerland. 167 pages. DOI: 10.1007/978-3-319-43332-5. http://link.springer.com/book/10.1007/978-3-319-43332-5. Print ISBN: 978-3-319-43330-1 and Online ISBN: 978-3-319-43332-5
  • Santana MH, Freua MC, Do DN, Ventura RV, Kadarmideen HN, Ferraz JB. 2016. Systems genetics and genome-wide association approaches for analysis of feed intake, feed efficiency, and performance in beef cattle. Genet Mol Res. 15(4). doi: 10.4238/gmr15048930.
  • Kogelman, LJA., Jingyuan Fu, Franke,L., Greve, JW., Hofker, M., Rensen, SS and Kadarmideen, HN. 2016. Inter-tissue gene co-expression networks between metabolically healthy and unhealthy obese individuals. PLoS One 11(12): e0167519. doi:10.1371/journal.pone.0167519
  • E. Razza , H. Pedersen, L. Stroebech , M. Machado , M. Nogueira, H. N. Kadarmideen, H. Callesen and P. Hyttel. (2015). Prematuration of bovine cumulus-oocyte complexes with cyclic adenosine monophosphate modulators affects both oocyte and blastocyst ultrastructure. Reproduction, Fertility and Development 28(2) 227-227. http://dx.doi.org/10.1071/RDv28n2Ab192
  • Horikoshi,M., Beaumont, RN., Day,FR., Warrington, NM., Kooijman, MN., Fernandez-Tajes,J., van Zuydam, NR., et al., (2016). Genetic studies of birth weight give biological insights into links with adult disease. Nature 538, 248–252. doi:10.1038/nature19806. Access to full article and supplements (view only, if you do not have subscription): http://rdcu.be/kB9e
  • Madsen, M.B., Kogelman, L.J.A., Kadarmideen, H.N., Rasmussen, H.B., (2016). Systems genetics analysis of pharmacogenomics variation during antidepressant treatment period. The Pharmacogenomics Journal, doi:10.1038/tpj.2016.68
  • Freude,KK., Jan O. Secher, Ahmet Ceylan, Kaveh Mashayekhi, Tong Li, Suchitra Poligari, Gianluca Mazzoni, Troels Tolstrup Nielsen, Shengting Liu, Stoyan Petkov, Yonglun Luou, Dong Li, Lori Thomps, Haja N. Kadarmideen, Andras Dinnyes, Lars Bolund, Henrik Callesen & Poul Hyttel (2015). Naïve versus primed porcine induced pluripotent stem cells – deciphering stemness in a challenging species. Molecular Reproduction and Development (accepted)
  • Pareek, CS., Smoczynski, R., Kadarmideen, HN., Dziuba, P., Blaszczyk, P., et al. (2016). Single nucleotide polymorphism discovery in bovine pituitary gland using RNA-seq technology. PLoS One  11(9): e0161370. doi:10.1371/journal.pone.0161370).
  • Suravajhala, P., Kogelman, LJA., and Kadarmideen, HN. 2016. Multi-omic data integration and analysis using systems genomics approaches: Methods and application in animal production, health and welfare. Genetics Selection Evolution. 48:38. DOI 10.1186/s12711-016-0217-x
  • de Almeida Santana, MH., Junior GA., Cesar, AS., Freu, MC., da Costa Gomes, R., da Luz E Silva, S., Leme, PR., Fukumasu, H., Carvalho, ME., Ventura, RV., Coutinho, LL., Kadarmideen, HN., Ferraz, JB. 2016. Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with feed conversion ratio in beef cattle. Journal of Applied Genetics.  DOI 10.1007/s13353-016-0344-7
  • Felix, JF., Bradfield, JP., Grant, SF., Jaddoe, VWV., and the Early Growth Genetics Consortium (2015). Genome-wide association meta-analysis identifies three new childhood body mass index susceptibility loci. Human Molecular Genetics 25 (2): 389-403   DOI:10.1093/hmg/ddv47
  • Pant, S.D., Karlskov-Mortensen, P., Jacobsen, M.J., Cirera, S., Kogelman, L.J.A., Bruun, C.S., Mark, T., Jørgensen, C.B., Grarup, N., Appel, E.V.R., Galjatovic, E.A.A., Hansen, T., Pedersen, O.B.,   Guerin, M., Huby, T., Lesnik, P., Meuwissen, T.H.E., Kadarmideen, H.N. and Fredholm, M. (2015). Comparative Analyses of QTLs influencing Obesity and Metabolic Phenotypes in Pigs and Humans. PLoS One  10(9): e0137356. doi:10.1371/journal.pone.013735
  • Kogelman, LJA., Zhernakova, DV., Westra, HJ., Cirera, S., Fredholm, M., Franke, L., Kadarmideen, HN (2015). An integrative systems genetics approach reveals potential causal genes and pathways related to obesity. Genome Medicine 7: 105. DOI: 10.1186/s13073-015-0229-0
  • Kadarmideen, HN., Mazzoni,G., Watanabe,YF., Strøbech,L., Baruselli,PS., Meirelles,FV., Callesen,H., Hyttel,P., Ferraz, JBS., and Nogueira, MFG. 2015. Genomic Selection of In vitro Produced and Somatic Cell Nuclear Transfer Embryos for Rapid Genetic Improvement in Cattle Production. Animal Reproduction 12 (3): 389-396
  • Stroebech, L., Mazzoni, G., Pedersen, HS., Freude, KK., Kadarmideen, HN., Callesen, H., and Hyttel, P. (2015). In vitro production of bovine embryos – Revisiting oocyte development and application of systems biology. Animal Reproduction 12 (3): 465-472
  • Suravajhala P., Kogelman L.J.A., Mazzoni G and Kadarmideen H.N. (2015). Potential role of lncRNA cyp2c91-protein interactions on diseases of the immune system. Frontiers in Genetics (Systems Biology): 6: 255. DOI:10.3389/fgene.2015.00255
  • Alexandre, PA., L.J.A. Kogelman, M.H.A. Santana, J.P. Eler, Kadarmideen, H.N. and H. Fukumasu. 2014. System biology approach to detect and assign biological functions and regulator genes to feed efficiency traits in Nellore cattle. BMC Genomics 16: 1073 , DOI: http://dx.doi.org/10.1186/s12864-015-2292-8
  • Mazzoni,G., Kogelman, LJA., Suravajhala, PN., Kadarmideen, HN. (2015). Systems genomics using next-generation sequencing methods. International Journal of Bioscience, Biochemistry and Bioinformatics 5(4): 266-279. doi: 10.17706/ijbbb.2015.5.4.264-279.
  • Do DN, Janss, LLG., Jensen, J., and Kadarmideen HN (2015). SNP annotation-based whole genomic prediction and selection: An application to feed efficiency and its component traits in pigs. Journal of Animal Science. 93 (5): 2056-2063. DOI: http://dx.doi.org/10.2527/jas.2014-8640
  • Ali,AA., Khatkar, MS., Kadarmideen, HN., Thomson, PC. (2015). Additive and epistatic genome-wide association for growth and ultrasound scan measures of carcass-related traits in Brahman cattle. Journal of Animal Breeding and Genetics 132: 187–197.
  • Khanal P, Axel AM, Kongsted AH, Husted SV, Johnsen L, Pandey D, Pedersen KL, Birtwistle M, Markussen B, Kadarmideen HN, Nielsen MO.2014. Late gestation under- and overnutrition have differential impacts when combined with a postnatal obesogenic diet on glucose-lactate-insulin adaptations during metabolic challenges in adolescent sheep. Acta Phyologica 213(2):519-536. doi: 10.1111/apha.12391
  • Do DN, Strathe AB, Ostersen T, Pant SD and Kadarmideen HN (2014) Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake. Frontiers in Genetics (Livestock Genomics). 5:307. doi: 10.3389/fgene.2014.00307
  • Kogelman, L.J.A., S. Cirera, D.V. Zhernakova, M. Fredholm, L. Franke, H.N. Kadarmideen. 2014. Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model. BMC Medical Genomics 7: 57. http://www.biomedcentral.com/1755-8794/7/57
  • Kogelman, L.J. A., Pant,S.D., Fredholm, M., Kadarmideen, H.N. 2014. Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network and pathway analyses. Frontiers in Genetics (Systems biology), 5:214. doi: 10.3389/fgene.2014.00214
  • Kogelman, LJA and Kadarmideen, HN. (2014). Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases using whole genome genotype data. BMC Systems Biology 8(Suppl 2): S5 (http://www.biomedcentral.com/1752-0509/8/S2/S5)
  • Kadarmideen, HN. (2014). Genomics to Systems Biology in Animal and Veterinary Sciences: Progress, Lessons and Opportunities. Livestock Science, 166: 232-248. http://dx.doi.org/10.1016/j.livsci.2014.04.028
  • Duy DN., Ostersen,T., Strathe, A.B., Mark., T., J. Jensen., and Kadarmideen, HN. (2014). Genome-wide associations and systems genetic analyses for residual feed intake, daily feed consumption, backfat and weight gain in pigs. BMC Genetics 15:27 (http://www.biomedcentral.com/1471-2156/15/27)
  • Strathe, A. B., Velander, I. H., Mark, T., Ostersen, T., Hansen, C. and Kadarmideen, H.N. (2013). Genetic Parameters for male fertility and its relationship to Skatole and Androstenone in Danish Landrace Boars. Journal of Animal Science 91(10):4659-4668
  • Lan,PD., Duy, DN., Nam,LQ., Ba,NV., Minh,LTA., Hoan,TX., Cuong, VC., and H.N. Kadarmideen (2013). Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations. Journal of Animal Breeding and Genetics. http://dx.doi.org/10.1111/jbg.12068.
  • Duy, DN., Strathe, AB., Ostersen, T., Jensen, J., Mark, T., and Kadarmideen, HN. (2013). Genome-wide association study reveals genetic architecture of eating behavior in pigs and its implications for humans obesity by comparative mapping. PLoS ONE 8(8): e71509. doi:10.1371/journal.pone.0071509
  • Cirera,S., Jensen, MS, Elbrønd, VS., Moesgaard, SG., Christoffersen, BO., Kadarmideen, HN., Skovgaard,K., Bruun, CV., Karlskov-Mortensen, P., Jørgensen, CB and Fredholm, M. (2013). Expression studies of six human obesity-related genes in seven tissues from divergent pig breeds. Animal Genetics. DOI: 10.1111/age.12082
  • Hou,L., A. H. Kongsted, S. M. Ghoreishi, T. K. Takhtsabzy, M. Friedrichsen, L. I. Hellgren, H.N. Kadarmideen, A. Vaag and M. O. Nielsen (2013). Pre- and early-postnatal nutrition modify gene and protein expressions of muscle energy metabolism markers and phospholipid fatty acid composition in a muscle type specific manner in sheep. PLoS ONE 8(6): e65452. doi:10.1371/journal.pone.0065452
  • Strathe, A. B., Velander, I. H., Mark, T., and Kadarmideen, H.N. (2013). Genetic Parameters for Androstenone and Skatole as indicators of Boar Taint and their relationship to Production and Litter Size Traits in Danish Landrace. Journal of Animal Science 91:2587-2595, doi:10.2527/jas2012-6107
  • Duy DN, Strathe, AB., Jensen, J., Mark,T., Kadarmideen, HN. (2013). Genetic parameters for different measures of feed efficiency and related traits in boars of three pig breeds. Journal of Animal Science 91, 4069-79.
  • Lan,PD., Duy, DN., Binh, NT., Nam,LQ., Ba,NV., Thuy,TTT., Hoan,TX., Cuong, VC., and H.N. Kadarmideen (2013). Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites. Livestock Science 155 (1): 17-22.
  • McDowall, ML, NS Watson Haigh, NM Edwards, HN Kadarmideen, GS Natrass, HA McGrice and PI Hynd (2013). Transient Treatment of Pregnant Merino Ewes with Modulators of Cortisol Biosynthesis Coinciding with Primary Wool Follicle Initiation Alters Lifetime Wool Growth. Animal Production Science. 53(10) 1101-1111
  • Kogelman, LJA., H.N. Kadarmideen, T.Mark, P.Karlskov-Mortensen, C. S. Bruun, S.Cirera, M.J. Jacobsen, C.B. Jørgensen and M. Fredholm (2013). An F2 pig resource population as a model for genetic studies of obesity and obesity-related diseases in humans: design and genetic parameters. Frontiers in Genetics 4:29. doi: 10.3389/fgene.2013.00029
  • Ali, A.A., P. C. Thomson and Kadarmideen, H.N. (2013). Association between microsatellite markers and bovine tuberculosis in Chadian Zebu cattle. Open Journal of Animal Sciences 3 (1): 27-35
  • Mogensen,MS Scheibye-Alsing,K., Karlskov-Mortensen,P., Proschowsky,HF., Jensen, VF., Bak,M., Tommerup, N., Kadarmideen, HN and Fredholm, M. (2012). Validation of genome-wide intervertebral disk calcification associations in dachshund and further investigation of the chromosome 12 susceptibility locus. Frontiers in Genetics, 3: 225. doi: 10.3389/fgene.2012.00225
  • Kadarmideen, H.N. and Watson Haigh, N.S. (2012). Building gene co-expression networks using transcriptomics data for systems biology investigations: Comparison of methods using microarray data. Bioinformation 8 (18): 855-861.
  • Ali, A.A., O’Neill, C., Thomson, P.C., and Kadarmideen, H.N.(2012). Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle. Genetics, Selection, Evolution, 44: 22 doi:10.1186/1297-9686-44-22
  • Karacaören, B., Janss, L.L.G., and Kadarmideen, H.N. (2012). Predicting breeding values in animals by kalman filter: application to body condition scores in dairy cattle. Kafkas Univ Vet Fak Derg.18 (4): 627-632.
  • Watson-Haigh NS, O’Neill, C., and Kadarmideen H.N. (2012). Proximity loggers: data handling and classification for quality control. IEEE Sensors 12 (5): 1611 – 1617
  • Kogelman, LJA., Byrne, K., Vuocolo, T., Watson-Haigh, N.S., Kadarmideen, H.N., Kijas, J.W., Oddy, HVH., Gardiner, GE., Gondro, C., and Tellam, RL. (2011). Genetic architecture of gene expression in ovine skeletal muscle. BMC Genomics 12:607.
  • Kadarmideen, H.N., Ali, A.A., P. C. Thomson, B. Muller and J. Zinsstag (2011). Polymorphisms of the SLC11A1 Gene and Resistance to Bovine Tuberculosis in African Zebu Cattle. Animal Genetics 42:656-658.
  • Kadarmideen H.N, Watson-Haigh NS, Andronicos, N.M. (2011). Systems biology of ovine intestinal parasite resistance: disease gene modules and biomarkers. Molecular BioSystems 7, 235–246