TY - JOUR AU - Rotz, C. AU - Montes, F. AU - Chianese, D. PY - 2010 DA - 2010// TI - The carbon footprint of dairy production systems through partial life cycle assessment JO - J Dairy Sci VL - 93 UR - https://doi.org/10.3168/jds.2009-2162 DO - 10.3168/jds.2009-2162 ID - Rotz2010 ER - TY - STD TI - Assessment ALC: Greenhouse Gas Emissions from the Dairy Sector. ID - ref2 ER - TY - JOUR AU - Wang, Z. AU - Gerstein, M. AU - Snyder, M. PY - 2009 DA - 2009// TI - RNA-Seq: a revolutionary tool for transcriptomics JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2484 DO - 10.1038/nrg2484 ID - Wang2009 ER - TY - JOUR AU - Herd, R. AU - Arthur, P. PY - 2009 DA - 2009// TI - Physiological basis for residual feed intake JO - J Anim Sci VL - 87 UR - https://doi.org/10.2527/jas.2008-1345 DO - 10.2527/jas.2008-1345 ID - Herd2009 ER - TY - STD TI - Varga G, Dechow C, Eastridge M. Can We Use Residual Feed Intake to Enhance Dairy Production Efficiency? In: Proceedings of the 22nd Tri-State Dairy Nutrition Conference, Fort Wayne, Indiana, USA, 23-24 April 2013: 2013. Michigan State University; 2013. p. 131-140. ID - ref5 ER - TY - BOOK AU - Hutjens, M. PY - 2012 DA - 2012// TI - Feed efficiency and its impact on feed intake. eXtension Dairy ID - Hutjens2012 ER - TY - JOUR AU - Bionaz, M. PY - 2014 DA - 2014// TI - Nutrigenomics Approaches to Fine-Tune Metabolism and Milk Production: Is This the Future of Ruminant Nutrition? JO - Adv Dairy Res VL - 24 ID - Bionaz2014 ER - TY - JOUR AU - Heyen, D. AU - Weller, J. AU - Ron, M. AU - Band, M. AU - Beever, J. AU - Feldmesser, E. AU - Da, Y. AU - Wiggans, G. AU - VanRaden, P. AU - Lewin, H. PY - 1999 DA - 1999// TI - A genome scan for QTL influencing milk production and health traits in dairy cattle JO - Physiol Genomics VL - 1 ID - Heyen1999 ER - TY - JOUR AU - Loor, J. J. AU - Everts, R. E. AU - Bionaz, M. AU - Dann, H. M. AU - Morin, D. E. AU - Oliveira, R. AU - Rodriguez-Zas, S. L. AU - Drackley, J. K. AU - Lewin, H. A. PY - 2007 DA - 2007// TI - Nutrition-induced ketosis alters metabolic and signaling gene networks in liver of periparturient dairy cows JO - Physiol Genomics VL - 32 UR - https://doi.org/10.1152/physiolgenomics.00188.2007 DO - 10.1152/physiolgenomics.00188.2007 ID - Loor2007 ER - TY - JOUR AU - McCabe, M. AU - Waters, S. AU - Morris, D. AU - Kenny, D. AU - Lynn, D. AU - Creevey, C. PY - 2012 DA - 2012// TI - RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-193 DO - 10.1186/1471-2164-13-193 ID - McCabe2012 ER - TY - JOUR AU - McCarthy, S. D. AU - Waters, S. M. AU - Kenny, D. A. AU - Diskin, M. G. AU - Fitzpatrick, R. AU - Patton, J. AU - Wathes, D. C. AU - Morris, D. G. PY - 2010 DA - 2010// TI - Negative energy balance and hepatic gene expression patterns in high-yielding dairy cows during the early postpartum period: a global approach JO - Physiol Genomics VL - 42 UR - https://doi.org/10.1152/physiolgenomics.00118.2010 DO - 10.1152/physiolgenomics.00118.2010 ID - McCarthy2010 ER - TY - JOUR AU - Berry, D. AU - Crowley, J. PY - 2012 DA - 2012// TI - Residual intake and body weight gain: a new measure of efficiency in growing cattle JO - J Anim Sci VL - 90 UR - https://doi.org/10.2527/jas.2011-4245 DO - 10.2527/jas.2011-4245 ID - Berry2012 ER - TY - JOUR AU - Lin, Z. AU - Macleod, I. AU - Pryce, J. PY - 2013 DA - 2013// TI - Short communication: estimation of genetic parameters for residual feed intake and feeding behavior traits in dairy heifers JO - J Dairy Sci VL - 96 UR - https://doi.org/10.3168/jds.2012-6134 DO - 10.3168/jds.2012-6134 ID - Lin2013 ER - TY - JOUR AU - Tempelman, R. AU - Spurlock, D. AU - Coffey, M. AU - Veerkamp, R. AU - Armentano, L. AU - Weigel, K. AU - Haas, Y. AU - Staples, C. AU - Connor, E. AU - Lu, Y. PY - 2015 DA - 2015// TI - Heterogeneity in genetic and nongenetic variation and energy sink relationships for residual feed intake across research stations and countries JO - J Dairy Sci VL - 98 UR - https://doi.org/10.3168/jds.2014.8510 DO - 10.3168/jds.2014.8510 ID - Tempelman2015 ER - TY - JOUR AU - Connor, E. AU - Hutchison, J. AU - Norman, H. AU - Olson, K. AU - Tassell, C. AU - Leith, J. AU - Baldwin, R. PY - 2013 DA - 2013// TI - Use of residual feed intake in Holsteins during early lactation shows potential to improve feed efficiency through genetic selection JO - J Anim Sci VL - 91 UR - https://doi.org/10.2527/jas.2012-5977 DO - 10.2527/jas.2012-5977 ID - Connor2013 ER - TY - JOUR AU - Koch, R. M. AU - Swiger, L. A. AU - Chambers, D. AU - Gregory, K. PY - 1963 DA - 1963// TI - Efficiency of feed use in beef cattle JO - J Anim Sci VL - 22 UR - https://doi.org/10.2527/jas1963.222486x DO - 10.2527/jas1963.222486x ID - Koch1963 ER - TY - JOUR AU - Kennedy, B. AU - Werf, J. AU - Meuwissen, T. PY - 1993 DA - 1993// TI - Genetic and statistical properties of residual feed intake JO - J Anim Sci VL - 71 ID - Kennedy1993 ER - TY - JOUR AU - Pryce, J. AU - Arias, J. AU - Bowman, P. AU - Davis, S. AU - Macdonald, K. AU - Waghorn, G. AU - Wales, W. AU - Williams, Y. AU - Spelman, R. AU - Hayes, B. PY - 2012 DA - 2012// TI - Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers JO - J Dairy Sci VL - 95 UR - https://doi.org/10.3168/jds.2011-4628 DO - 10.3168/jds.2011-4628 ID - Pryce2012 ER - TY - JOUR AU - Connor, E. AU - Hutchison, J. AU - Olson, K. AU - Norman, H. PY - 2012 DA - 2012// TI - Triennial lactation symposium: Opportunities for improving milk production efficiency in dairy cattle JO - J Anim Sci VL - 90 UR - https://doi.org/10.2527/jas.2011-4528 DO - 10.2527/jas.2011-4528 ID - Connor2012 ER - TY - JOUR AU - Do, D. N. AU - Ostersen, T. AU - Strathe, A. B. AU - Mark, T. AU - Jensen, J. AU - Kadarmideen, H. N. PY - 2014 DA - 2014// TI - Genome-wide association and systems genetic analyses of residual feed intake, daily feed consumption, backfat and weight gain in pigs JO - BMC Genet VL - 15 UR - https://doi.org/10.1186/1471-2156-15-27 DO - 10.1186/1471-2156-15-27 ID - Do2014 ER - TY - JOUR AU - Do, D. N. AU - Strathe, A. B. AU - Ostersen, T. AU - Pant, S. D. AU - Kadarmideen, H. N. PY - 2014 DA - 2014// TI - Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake JO - Front Genet VL - 5 UR - https://doi.org/10.3389/fgene.2014.00307 DO - 10.3389/fgene.2014.00307 ID - Do2014 ER - TY - JOUR AU - Berry, D. AU - Crowley, J. PY - 2013 DA - 2013// TI - Cell biology symposium: genetics of feed efficiency in dairy and beef cattle JO - J Anim Sci VL - 91 UR - https://doi.org/10.2527/jas.2012-5862 DO - 10.2527/jas.2012-5862 ID - Berry2013 ER - TY - JOUR AU - Partridge, C. G. AU - Fawcett, G. L. AU - Wang, B. AU - Semenkovich, C. F. AU - Cheverud, J. M. PY - 2014 DA - 2014// TI - The effect of dietary fat intake on hepatic gene expression in LG/J AND SM/J mice JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-99 DO - 10.1186/1471-2164-15-99 ID - Partridge2014 ER - TY - JOUR AU - Kadarmideen, H. N. PY - 2014 DA - 2014// TI - Genomics to systems biology in animal and veterinary sciences: progress, lessons and opportunities JO - Livest Sci VL - 166 UR - https://doi.org/10.1016/j.livsci.2014.04.028 DO - 10.1016/j.livsci.2014.04.028 ID - Kadarmideen2014 ER - TY - JOUR AU - Suravajhala, P. AU - Kogelman, L. J. AU - Kadarmideen, H. N. PY - 2016 DA - 2016// TI - Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare JO - Genet Sel Evol VL - 48 UR - https://doi.org/10.1186/s12711-016-0217-x DO - 10.1186/s12711-016-0217-x ID - Suravajhala2016 ER - TY - JOUR AU - Zhang, Z. H. AU - Jhaveri, D. J. AU - Marshall, V. M. AU - Bauer, D. C. AU - Edson, J. AU - Narayanan, R. K. AU - Robinson, G. J. AU - Lundberg, A. E. AU - Bartlett, P. F. AU - Wray, N. R. PY - 2014 DA - 2014// TI - A comparative study of techniques for differential expression analysis on RNA-Seq data JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0103207 DO - 10.1371/journal.pone.0103207 ID - Zhang2014 ER - TY - JOUR AU - Drackley, J. K. AU - Overton, T. R. AU - Douglas, G. N. PY - 2001 DA - 2001// TI - Adaptations of glucose and long-chain fatty acid metabolism in liver of dairy cows during the periparturient period JO - J Dairy Sci VL - 84 UR - https://doi.org/10.3168/jds.S0022-0302(01)70204-4 DO - 10.3168/jds.S0022-0302(01)70204-4 ID - Drackley2001 ER - TY - JOUR AU - Alexandre, P. A. AU - Kogelman, L. J. AU - Santana, M. H. AU - Passarelli, D. AU - Pulz, L. H. AU - Fantinato-Neto, P. AU - Silva, P. L. AU - Leme, P. R. AU - Strefezzi, R. F. AU - Coutinho, L. L. PY - 2015 DA - 2015// TI - Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-2292-8 DO - 10.1186/s12864-015-2292-8 ID - Alexandre2015 ER - TY - JOUR AU - Yi, G. AU - Yuan, J. AU - Bi, H. AU - Yan, W. AU - Yang, N. AU - Qu, L. PY - 2015 DA - 2015// TI - In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0136765 DO - 10.1371/journal.pone.0136765 ID - Yi2015 ER - TY - JOUR AU - Kantartzis, K. AU - Machicao, F. AU - Machann, J. AU - Schick, F. AU - Fritsche, A. AU - Häring, H. -. U. AU - Stefan, N. PY - 2009 DA - 2009// TI - The DGAT2 gene is a candidate for the dissociation between fatty liver and insulin resistance in humans JO - Clin Sci VL - 116 UR - https://doi.org/10.1042/CS20080306 DO - 10.1042/CS20080306 ID - Kantartzis2009 ER - TY - JOUR AU - Paradis, F. AU - Yue, S. AU - Grant, J. AU - Stothard, P. AU - Basarab, J. AU - Fitzsimmons, C. PY - 2015 DA - 2015// TI - Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers JO - J Anim Sci VL - 93 UR - https://doi.org/10.2527/jas.2015-8975 DO - 10.2527/jas.2015-8975 ID - Paradis2015 ER - TY - JOUR AU - Ozuna, A. C. AU - Rowland, R. R. AU - Nietfeld, J. C. AU - Kerrigan, M. A. AU - Dekkers, J. AU - Wyatt, C. R. PY - 2012 DA - 2012// TI - Preliminary findings of a previously unrecognized porcine primary immunodeficiency disorder JO - Vet Pathol Online VL - 2012 ID - Ozuna2012 ER - TY - JOUR AU - Kogelman, L. J. AU - Cirera, S. AU - Zhernakova, D. V. AU - Fredholm, M. AU - Franke, L. AU - Kadarmideen, H. N. PY - 2014 DA - 2014// TI - Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model JO - BMC Med Genomics VL - 7 UR - https://doi.org/10.1186/1755-8794-7-57 DO - 10.1186/1755-8794-7-57 ID - Kogelman2014 ER - TY - JOUR AU - Do, D. N. AU - Strathe, A. B. AU - Ostersen, T. AU - Jensen, J. AU - Mark, T. AU - Kadarmideen, H. N. PY - 2013 DA - 2013// TI - Genome-wide association study reveals genetic architecture of eating behavior in pigs and its implications for humans obesity by comparative mapping JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0071509 DO - 10.1371/journal.pone.0071509 ID - Do2013 ER - TY - JOUR AU - Almeida Santana, M. H. AU - Junior, G. A. O. AU - Cesar, A. S. M. AU - e Silva, S. L. AU - Freua, M. C. AU - Costa Gomes, R. AU - Leme, P. R. AU - Fukumasu, H. AU - Carvalho, M. E. AU - Ventura, R. V. PY - 2016 DA - 2016// TI - Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle JO - J Appl Genet VL - 2016 ID - Almeida Santana2016 ER - TY - JOUR AU - Santana, M. AU - Ventura, R. AU - Utsunomiya, Y. AU - Neves, H. AU - Alexandre, P. AU - Oliveira Junior, G. AU - Gomes, R. AU - Bonin, M. AU - Coutinho, L. AU - Garcia, J. PY - 2015 DA - 2015// TI - A genomewide association mapping study using ultrasound‐scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle JO - J Anim Breed Genet VL - 132 UR - https://doi.org/10.1111/jbg.12167 DO - 10.1111/jbg.12167 ID - Santana2015 ER - TY - JOUR AU - Grasfeder, L. L. AU - Gaillard, S. AU - Hammes, S. R. AU - Ilkayeva, O. AU - Newgard, C. B. AU - Hochberg, R. B. AU - Dwyer, M. A. AU - Chang, C. -. y. AU - McDonnell, D. P. PY - 2009 DA - 2009// TI - Fasting-induced hepatic production of DHEA is regulated by PGC-1α, ERRα, and HNF4α JO - Mol Endocrinol VL - 23 UR - https://doi.org/10.1210/me.2009-0024 DO - 10.1210/me.2009-0024 ID - Grasfeder2009 ER - TY - JOUR AU - Chen, Y. AU - Gondro, C. AU - Quinn, K. AU - Herd, R. AU - Parnell, P. AU - Vanselow, B. PY - 2011 DA - 2011// TI - Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake JO - Anim Genet VL - 42 UR - https://doi.org/10.1111/j.1365-2052.2011.02182.x DO - 10.1111/j.1365-2052.2011.02182.x ID - Chen2011 ER - TY - JOUR AU - Tizioto, P. C. AU - Coutinho, L. L. AU - Decker, J. E. AU - Schnabel, R. D. AU - Rosa, K. O. AU - Oliveira, P. S. AU - Souza, M. M. AU - Mourão, G. B. AU - Tullio, R. R. AU - Chaves, A. S. PY - 2015 DA - 2015// TI - Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1464-x DO - 10.1186/s12864-015-1464-x ID - Tizioto2015 ER - TY - JOUR AU - Costa, A. S. H. AU - Pires, V. M. R. AU - Fontes, C. M. G. A. AU - Prates, J. A. M. PY - 2013 DA - 2013// TI - Expression of genes controlling fat deposition in two genetically diverse beef cattle breeds fed high or low silage diets JO - BMC Vet Res VL - 9 UR - https://doi.org/10.1186/1746-6148-9-118 DO - 10.1186/1746-6148-9-118 ID - Costa2013 ER - TY - JOUR AU - Sumner-Thomson, J. AU - Vierck, J. AU - McNamara, J. PY - 2011 DA - 2011// TI - Differential expression of genes in adipose tissue of first-lactation dairy cattle JO - J Dairy Sci VL - 94 UR - https://doi.org/10.3168/jds.2010-3447 DO - 10.3168/jds.2010-3447 ID - Sumner-Thomson2011 ER - TY - JOUR AU - Grala, T. M. AU - Kay, J. K. AU - Phyn, C. V. AU - Bionaz, M. AU - Walker, C. G. AU - Rius, A. G. AU - Snell, R. G. AU - Roche, J. R. PY - 2013 DA - 2013// TI - Reducing milking frequency during nutrient restriction has no effect on the hepatic transcriptome of lactating dairy cattle JO - Physiol Genomics VL - 45 UR - https://doi.org/10.1152/physiolgenomics.00134.2013 DO - 10.1152/physiolgenomics.00134.2013 ID - Grala2013 ER - TY - JOUR AU - Yu, Y. H. AU - Ginsberg, H. PY - 2004 DA - 2004// TI - The role of acyl‐CoA: diacylglycerol acyltransferase (DGAT) in energy metabolism JO - Ann Med VL - 36 UR - https://doi.org/10.1080/07853890410028429 DO - 10.1080/07853890410028429 ID - Yu2004 ER - TY - JOUR AU - Chen, H. C. AU - Farese, R. V. PY - 2000 DA - 2000// TI - DGAT and triglyceride synthesis: a new target for obesity treatment? JO - Trends Cardiovasc Med VL - 10 UR - https://doi.org/10.1016/S1050-1738(00)00066-9 DO - 10.1016/S1050-1738(00)00066-9 ID - Chen2000 ER - TY - STD TI - GeneCards. http://www.genecards.org/. Accessed 15 Mar 2017. UR - http://www.genecards.org/ ID - ref45 ER - TY - JOUR AU - Li, B. AU - Fikse, W. AU - Lassen, J. AU - Lidauer, M. AU - Løvendahl, P. AU - Mäntysaari, P. AU - Berglund, B. PY - 2016 DA - 2016// TI - Genetic parameters for dry matter intake in primiparous Holstein, Nordic Red, and Jersey cows in the first half of lactation JO - J Dairy Sci VL - 99 UR - https://doi.org/10.3168/jds.2015-10669 DO - 10.3168/jds.2015-10669 ID - Li2016 ER - TY - BOOK AU - Andrews S: Fast, Q. C. PY - 2010 DA - 2010// TI - A quality control tool for high throughput sequence data ID - Andrews S: Fast2010 ER - TY - JOUR AU - Martin, M. PY - 2011 DA - 2011// TI - Cutadapt removes adapter sequences from high-throughput sequencing reads JO - EMBnet J VL - 17 UR - https://doi.org/10.14806/ej.17.1.200 DO - 10.14806/ej.17.1.200 ID - Martin2011 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. AU - Batut, P. AU - Chaisson, M. AU - Gingeras, T. R. PY - 2013 DA - 2013// TI - STAR: ultrafast universal RNA-seq aligner JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Okonechnikov, K. AU - Conesa, A. AU - García-Alcalde, F. PY - 2016 DA - 2016// TI - Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data JO - Bioinformatics VL - 32 ID - Okonechnikov2016 ER - TY - JOUR AU - Anders, S. AU - Pyl, P. T. AU - Huber, W. PY - 2014 DA - 2014// TI - HTSeq-a Python framework to work with high-throughput sequencing data JO - Bioinformatics VL - 2014 ID - Anders2014 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Young, M. D. AU - Wakefield, M. J. AU - Smyth, G. K. AU - Oshlack, A. PY - 2010 DA - 2010// TI - Gene ontology analysis for RNA-seq: accounting for selection bias JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-2-r14 DO - 10.1186/gb-2010-11-2-r14 ID - Young2010 ER - TY - JOUR AU - Mootha, V. K. AU - Lindgren, C. M. AU - Eriksson, K. -. F. AU - Subramanian, A. AU - Sihag, S. AU - Lehar, J. AU - Puigserver, P. AU - Carlsson, E. AU - Ridderstråle, M. AU - Laurila, E. PY - 2003 DA - 2003// TI - PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes JO - Nat Genet VL - 34 UR - https://doi.org/10.1038/ng1180 DO - 10.1038/ng1180 ID - Mootha2003 ER - TY - JOUR AU - Subramanian, A. AU - Tamayo, P. AU - Mootha, V. K. AU - Mukherjee, S. AU - Ebert, B. L. AU - Gillette, M. A. AU - Paulovich, A. AU - Pomeroy, S. L. AU - Golub, T. R. AU - Lander, E. S. PY - 2005 DA - 2005// TI - Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles JO - Proc Natl Acad Sci VL - 102 UR - https://doi.org/10.1073/pnas.0506580102 DO - 10.1073/pnas.0506580102 ID - Subramanian2005 ER - TY - JOUR AU - Irizarry, R. A. AU - Wang, C. AU - Zhou, Y. AU - Speed, T. P. PY - 2009 DA - 2009// TI - Gene set enrichment analysis made simple JO - Stat Methods Med Res VL - 18 UR - https://doi.org/10.1177/0962280209351908 DO - 10.1177/0962280209351908 ID - Irizarry2009 ER - TY - JOUR AU - Szklarczyk, D. AU - Franceschini, A. AU - Wyder, S. AU - Forslund, K. AU - Heller, D. AU - Huerta-Cepas, J. AU - Simonovic, M. AU - Roth, A. AU - Santos, A. AU - Tsafou, K. P. PY - 2014 DA - 2014// TI - STRING v10: protein-protein interaction networks, integrated over the tree of life JO - Nucleic Acids Res VL - 43 ID - Szklarczyk2014 ER -