Albrecht T, Auinger H-J, Wimmer V, Ogutu J, Knaak C, Ouzunova M, Piepho H-P,  Schön C-C (2014) Genome-based prediction of maize hybrid performance across genetic groups, testers, locations, and years. Theor Appl Genet 127:1375-1386, DOI: 10.1007/s00122-014-2305-z

Baes CF, Dolezal MA, Koltes JE, Bapst B, Fritz-Waters E, Jansen S, Flury C, Signer-Hasler H, Stricker C, Fernando R, Fries R, Moll J, Garrick DJ, Reecy JM, Gredler B (2014) Evaluation of variant identification methods for whole genome sequencing data in dairy cattle. BMC Genomics 15:948

Böhm J, Schipprack W, Mirdita V, Utz HF, Melchinger AE, (2014) Breeding Potential of European Flint Maize Landraces Evaluated by their Testcross Performance. Crop Sci. 54: 1665-1672

Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brøndum RF, Liao X, Djari A, Rodriguez SC,  Grohs C, Esquerré D, Bouchez O, Rossignol M-N, Klopp C, Rocha D, Fritz S, Eggen A, Bowman PJ, Coote D, Chamberlain AJ, Anderson C, VanTassell C, Hulsegge I, Goddard ME, Guldbrandtsen B, Lund MS, Veerkamp RF, Boichard DA, Fries R, Hayes BJ (2014) Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics 46: 858–865, doi:10.1038/ng.3034

Ehret A, Hochstuhl D, Krattenmacher N, Tetens J, Klein MS, Gronwald W, Thaller G (2014) Short communication: Use of genomic and metabolic information as well as milk performance records for prediction of subclinical ketosis risk via artificial neural networks. Journal of Dairy Science dx.doi.org/10.3168/jds.2014-8602

Ertl J, Edel C, Emmerling R, Pausch H, Fries R, Götz K-U (2014) On the limited increase in validation reliability using HD genotypes in genomic BLUP: observations from Fleckvieh cattle. Journal of Dairy Science 97:487-496

Ertl J, Legarra A, Vitezica ZG, Varona L, Edel C, Emmerling R, Götz K-U (2014) Genomic analysis of dominance effects on milk production and conformation traits in Fleckvieh cattle. Genet. Sel. Evol. 46:40

Estaghvirou SBO, Ogutu JO, Piepho H-P (2014) Influence of outliers on the accuracy estimation in genomic prediction in plant breeding. G3: Genes|Genomes|Genetics 4. doi:10.1534/g3.114.011957

Gholami M, Erbe M, Gärke C, Preisinger R, Weigend A, Weigend S, Simianer H. (2014) Population Genomic Analyses Based on 1 Million SNPs in Commercial Egg Layers. PLoS One, 9(4):e94509

Giraud H, Lehermeier C, Bauer E, Falque M, Segura V, Bauland C, Camisan C, Campo L, Meyer N, Ranc N, Schipprack W, Flament P, Melchinger AE, Menz M, Moreno-González J, Ouzunova M, Charcosset A, Schön C-C, Moreau L (2014) Linkage Disequilibrium with Linkage Analysis of Multi-Line Crosses Reveals Different Multi-Allelic QTL for Hybrid Performance in the Flint and Dent Heterotic Groups of Maize. Genetics doi:10.1534/genetics.114.169367

Gresset S, Westermeier P, Rademacher S, Ouzunova M, Presterl T, Westhoff P, Schön C-C (2014) Stable carbon isotope discrimination is under genetic control in the C4 species maize with several genomic regions influencing trait expression. Plant Physiology 164:131-143, doi: 10.1104/pp.113.224816

Jung S, Pausch H, Langenmayer MC, Schwarzenbacher H, Majzoub-Altweck M, Gollnick NS, Fries R (2014) A nonsense mutation in PLD4 is associated with a zinc deficiency-like syndrome in Fleckvieh cattle. BMC Genomics 15:623

Kramer M, Erbe M, Seefried FR, Gredler B, Bapst B, Bieber A, Simianer H (2014) Accuracy of direct genomic values for functional traits in Brown Swiss cattle. J DAIRY SCI, 97: 1774–1781

Lehermeier C, Krämer N, Bauer E, Bauland C, Camisan C, Campo L, Flament P, Melchinger AE, Menz M, Meyer N, Moreau L, Moreno-Gonzáles J, Ouzunova M, Pausch H, Ranc N, Schipprack W, Schönleben M, Walter H, Charcosset A, Schön C-C (2014) Usefulness of multi-parental populations of maize (Zea mays L.) for genome-based prediction. Genetics. 198:3-16, doi: 10.1534/genetics.114.161943

Lyimo CM, Weigend A, Msoffe PL, Eding H, Simianer H, Weigend S (2014) Global diversity and genetic contributions of chicken populations from Afican, Asian and European regions. Anim Genet. 45(6):836-48. doi: 10.1111/age.12230. Epub 2014 Oct 14

Malik WA, Möhring J, Piepho HP (2014) A clustering-based test for nonadditivity in an unreplicated two-way layout. Communications in Statistics – Simulation and Computation. DOI:10.1080/03610918.2013.870196

Ogutu JO, Piepho H-P (2014) Regularized group regression methods for genomic prediction: Bridge, MCP, SCAD, group bridge, group lasso, sparse group lasso, group MCP and group SCAD. BMC Proceedings 2014, 8(Suppl 5):S7  doi:10.1186/1753-6561-8-S5-S7

Pausch H, Kölle S, Wurmser C, Schwarzenbacher H, Emmerling R, Jansen S, Trottmann M, Fuerst C, Götz K-U, Fries R, (2014) A Nonsense Mutation in TMEM95 Encoding a Nondescript Transmembrane Protein Causes Idiopathic Male Subfertility in Cattle. PLoS Genetics 10, e1004044

Pausch H, Fries R (2014) Genome-wide analysis of complex traits in cattle. Zuechtungskunde, 86(1):47–57

Qanbari S, Pausch H, Jansen S, Somel M, Strom TM, Fries R, Nielsen R, Simianer H (2014) Classic selective sweeps revealed by massive sequencing in cattle. PLOS GENET, 10: e1004148

Qanbari S, Simianer H (2014) Mapping signatures of positive selection in the genome of livestock. LIVEST SCI, 166: 133–143

Simianer H, Erbe M (2014) Genetics, genomics, breeding – why scale matters. J ANIM BREED GENET, 131: 83-84

Technow F, Schrag TA, Schipprack W, Bauer E, Simianer H, Melchinger AE (2014) Genome properties and prospects of genomic prediction of hybrid performance in a breeding program of maize. Genetics 114:1343-1355 doi: 10.1534/genetics.114.165860

Technow F, Schrag TA, Schipprack W, Melchinger AE, (2014) Identification of key ancestors of modern germplasm in a breeding program of maize. Theor. Appl. Genet. 127: 2545-2553

Tellier A, Lemaire C (2014) Coalescence 2.0: a multiple branching of recent theoretical developments and their applications. Molecular Ecology, 23:2637-2652

Tellier A, Moreno-Gámez S, Stephan W (2014) Speed of adaptation and genomic signatures in arms race and trench warfare models of host-parasite coevolution Evolution, 68(8) 2211-2224

Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom TM, Fries R, Pausch H, Bertani C, Davassi A, Mayer KFX, Schön C-C (2014) A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array. BMC Genomics 15:823 doi:10.1186/1471-2164-15-823

Weigend S, Janßen-Tapken U, Erbe M, Ober U, Weigend A, Preisinger R, Simianer H (2014) Biodiversität beim Huhn - Potenziale für die Praxis. Züchtungskunde 86(1) S. 25-41

Zhang Z, Ober U, Erbe M, Zhang H, Gao N, He J, Li J, Simianer H (2014) Improving the accuracy of whole genome prediction for complex traits using the results of genome wide association studies. PLOS ONE, 9: e93017

Boysen T-J, Heuer C, Tetens J, Reinhardt F, Thaller G (2013) Novel use of derived genotype probabilities to discover significant dominance effects for milk production traits in dairy cattle. Genetics 193:431-442

Erbe M, Gredler B, Seefried FR, Bapst B, Simianer H. A function accounting for training set size and marker density to model the average accuracy of genomic prediction. PLoS ONE 8:e81046

Estaghvirou B, Ogutu JO, Schulz-Streeck T, Knaak C, Ouzenova M, Gordillo A, Piepho HP (2013) Evaluation of approaches for estimating prediction accuracy in genomic selection in plant and animal breeding. BMC Genomics 14:860

Frascaroli E,  Schrag TA,  Melchinger AE (2013) Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs. Theoretical and Applied Genetics 126:133-141

Gianola D, Qanbari S, Simianer H (2013) An evaluation of a novel estimator of linkage disequilibrium. Heredity 111:275-285

Günther T, Coop G (2013) Robust identification of local adaptation from allele frequencies. Genetics 195:205-220

Jansen S, Aigner B, Pausch H, Wysocki M, Eck S, Benet-Pagès A, Graf E, Wieland T, Strom TM, Meitinger T, Fries R (2013) Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage. BMC Genomics 14:446

Kranis A, Gheyas AA, Boschiero C, Turner F, Yu L, Smith S, Talbot R, Pirani A, Brew F, Kaiser P, Hocking PM, Fife M, Salmon N, Fulton J, Strom TM, Haberer G, Weigend S, Preisinger R, Gholami M, Qanbari S, Simianer H, Watson KA, Woolliams JA, Burt DW (2013) Development of a high density 600K SNP genotyping array for chicken. BMC Genomics 14:59

Lehermeier C, Wimmer V, Albrecht T, Auinger H-J, Gianola D, Schmid VJ, Schön C-C (2013) Sensitivity to Prior Specification in Bayesian Genome-based Prediction Models. Statistical Applications in Genetics and Molecular Biology 12:375-391

Moreno-Gámez S, Stephan W, Tellier A (2013) Effect of disease prevalence and spatial heterogeneity on polymorphism maintenance in host-parasite interactions. Plant Path 62:133-141

Ober U, Malinowski A, Schlather M, Simianer H (2013) The expected linkage disequilibrium in a finite population revisited. ArXiv e-prints:1304.4856

Pausch H, Aigner B, Emmerling R, Edel C, Götz KU, Fries R (2013) Imputation of high-density genotypes in the Fleckvieh cattle population. Genetics Selection Evolution 45:3

Piepho H-P, Williams ER, Ogutu JO (2013) A two-stage approach to recovery of inter-block information and shrinkage of block effect estimates. Communications in Biometry and Crop Science:10-22

Riedelsheimer C, Endelman JB, Stange M, Sorrells ME, Jannink JL, Melchinger AE (2013) Genomic predictability of interconnected biparental maize populations. Genetics 194:493-503

Riedelsheimer C, Melchinger AE (2013) Optimizing the allocation of resources for genomic selection in one breeding cycle. Theoretical and Applied Genetics 126:2835-2848

Schulz-Streeck T, Ogutu JO, Piepho HP (2013) Comparisons of single-stage and two-stage approaches to genomic selection. Theoretical and Applied Genetics 126:69-82

Schulz-Streeck T, Ogutu JO, Gordillo A, Karaman Z, Knaak C, Piepho H-P (2013) Genomic selection allowing for marker-by-environment interaction. Plant Breeding 132:532-538

Sitzenstock F, Ytournel F, Sharifi AR, Cavero D, Täubert H, Preisinger R, Simianer H (2013) Efficiency of genomic selection in an established Commercial layer breeding program. Genetics Selection Evolution 45:29. Doi:10.1186/1297-9686-45-29

Strigens A, Freitag NM, Gilbert X, Grieder C, Riedelsheimer C, Schrag TA, Messmer R, Melchinger AE (2013) Association mapping for chilling tolerance in elite flint and dent maize inbred lines evaluated in growth chamber and field experiments. Plant, Cell & Environment 36:1871-1887

Technow F, Bürger A, Melchinger AE (2013) Genomic prediction of Northern corn leaf blight resistance in maize with combined or separated training sets for heterotic groups. G3: Genes, Genomes, Genetics 3:197-203

Technow F, Melchinger AE (2013) Genomic prediction of dichotomous traits with Bayesian logistic models. Theoretical and Applied Genetics 126:1133-1143

Venhoranta H, Pausch H, Wysocki M, Szczerbal I, Hänningen R, Taponen J, Uimari P, Flisikowski K, Lohi H, Fries R, Switonski M, Andersson M (2013) Ectopic KIT copy number variation underlies impaired migration of primordial germ cells associated with gonadal hypoplasia in cattle (Bos taurus). PLoS ONE 8:e75659

Wimmer V, Lehermeier C, Albrecht T, Auinger H-J, Wang Y, Schön C-C (2013) Genome-wide prediction of traits with different genetic architecture through efficient variable selection. Genetics 195:573-587

Zhao Y, Gowda M, Liu,W, Würschum T, Maurer HP, Longin FH, Ranc N, Piepho HP, Reif JC (2013): Choice of shrinkage parameter and prediction of genomic breeding values in elite maize breeding populations. Plant Breeding 132:99-106  

Erbe M, Hayes BJ, Matukumalli LK, Goswami S, Bowman PJ, Reich CM, Mason BA, Goddard ME (2012) Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. Journal of Dairy Science 95:4114-4129

Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TFC, Simianer H (2012) Using whole genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genetics 8:e1002685

Ogutu JO, Schulz-Streeck T, Piepho HP (2012) Genomic selection using regularized linear regression models: ridge regression, lasso, elastic net and their extensions. BMC Proceedings 6:S10

Pausch H, Wang X, Jung S, Krogmeier D, Edel C, Emmerling R, Götz K-U, Fries R (2012) Identification of QTL for UV-protective eye area pigmentation in cattle by progeny phenotyping and genome-wide association analysis. PLoS ONE 7:e36346

Piepho HP, Möhring J, Schulz-Streeck T Ogutu JO (2012) A stage-wise approach for analysis of multi-environment trials. Biometrical Journal 54:846-860

Piepho HP, Ogutu JO, Schulz-Streeck T, Estaghvirou B, Gordillo A, Technow F (2012) Efficient computation of Ridge-regression best linear unbiased prediction in genomic selection in plant breeding. Crop Science 52:1093-1104

Qanbari S, Strom TM, Haberer G, Weigend S, Gheyas AA, Turner F, Burt DW, Preisinger R, Gianola D, Simianer H (2012) A high resolution genomewide scan for significant selective sweeps: an application to pooled sequence data in laying chickens. PLoS ONE 7:e49525

Riedelsheimer C, Czedik-Eysenberg A, Grieder C, Lisec J, Technow F, Sulpice R, Altmann T, Stitt M, Willmitzer L, Melchinger AE (2012) Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nature Genetics 44:217-222

Riedelsheimer C, Technow, Melchinger AE (2012) Comparison of whole-genome prediction models for traits with contrasting genetic architecture in a diversity panel of maize inbred lines. BMC Genomics 13:452

Schulz-Streeck T, Ogutu J., Gordillo A, Karaman Z, Knaak C, Piepho HP (2012) Genomic selection using multiple populations. Crop Science 52:2452-2461

Technow F, Riedelsheimer C, Schrag TA, Melchinger AE (2012) Genomic prediction of hybrid performance in maize with models incorporating dominance and population specific marker effects. Theoretical and Applied Genetics 125:1181-1194

Wimmer V, Albrecht T, Auinger HJ, Schön CC (2012) synbreed: A framework for the analysis of genomic prediction data using R. Bioinformatics 28:2086-2087

Ytournel F, Teyssédre S, Roldan D, Erbe M, Simianer H, Boichard D, Gilbert H, Druet T, Legarra A (2012) LDSO: a program to simulate pedigrees and molecular information. Journal of Animal Breeding and Genetics 129:417-421

Albrecht T, Wimmer V, Auinger H-J, Erbe M, Knaak C, Ouzunova M, Simianer H, Schön C-C (2011) Genome-based prediction of testcross values in maize. Theoretical and Applied Genetics 123:339-350

Fries R, Pausch H (2011) Individual genome sequencing of livestock animals - En route to genomic selection 2.0. Züchtungskunde 83:371-381

Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner E-M, Hansen M, Joets J, Le Paslier M-C, McMullen MD, Montalent P, Rose M, Schön C-C, Sun Q, Walter H, Martin OC, Falque M (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE 6:e28334

Ober U, Erbe M, Long N, Porcu E, Schlather M, Simianer H (2011) Predicting genetic values: a kernel-based best linear unbiased prediction with genomic data. Genetics 188:695-708

Ogutu JO, Piepho HP, Schulz-Streeck T (2011) A comparison of random forests, boosting and support vector machines for genomic selection with SNP markers. BMC Proceedings 5:S11

Pimentel E, Erbe M, König S, Simianer H (2011) Genome partitioning of genetic variation for milk production and composition traits in Holstein cattle. Frontiers in Genetics 2:19

Qanbari S, Gianola D, Hayes B, Schenkel F, Miller S, Moore S, Thaller G, Simianer H (2011) Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics 12:318

Schulz-Streeck T, Ogutu JO, Piepho HP (2011) Pre-selection of markers for genomic selection. BMC Proceedings 5:S12

Simko I, Piepho HP (2011) Combining phenotypic data from ordinal rating scales in multiple plant experiments. Trends in Plant Science 16: 235-237

Qanbari S, Hansen M, Weigend S, Preisinger R, Simianer H (2010) Linkage disequilibrium reveals different demographic history in egg laying chickens. BMC Genetics 11:103

Sun G, Zhu C, Kramer MH, Yang SS, Song W, Piepho HP, Yu J (2010) Comparing different R2 statistics for mixed model association mapping. Heredity 105:333-340

Eck SH, Benet-Pages A, Flisikowski K, Meitinger T, Fries R, Strom TM (2009) Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol 10:R82