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Research article Composite likelihood estimation of demographic parameters Daniel Garrigan PMCID: PMC2783031 Hypermethylation of the DLC1 CpG island does not alter gene expression in canine lymphoma Jeffrey N Bryan, Mohamed Jabbes, Linda M Berent, Gerald L Arthur, Kristen H Taylor, Kerry C Rissetto, Carolyn J Henry, Farah Rahmatpanah, Wendi V Rankin, Jose A Villamil, Michael R Lewis, and Charles W Caldwell PMCID: PMC2784477 A modifier screen in the Drosophila eye reveals that aPKC interacts with Glued during central synapse formation Lisha Ma, Louise A Johns, and Marcus J Allen PMCID: PMC2789099 Software LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs Hsueh-Wei Chang, Li-Yeh Chuang, Yan-Jhu Chang, Yu-Huei Cheng, Yu-Chen Hung, Hsiang-Chi Chen, and Cheng-Hong Yang PMCID: PMC2709117 Parallelization and optimization of genetic analyses in isolation by distance web service Julia L Turner, Scott T Kelley, James S Otto, Faramarz Valafar, and Andrew J Bohonak PMCID: PMC2713274 Automating approximate Bayesian computation by local linear regression Kevin R Thornton PMCID: PMC2712468 Research Articles Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations C Berthouly, G Leroy, T Nhu Van, H Hoang Thanh, B Bed'Hom, B Trong Nguyen, C Vu Chi, F Monicat, M Tixier-Boichard, E Verrier, J-C Maillard, and X Rognon PMCID: PMC2628941 Mapping of five candidate sex-determining loci in rainbow trout (Oncorhynchus mykiss) Mahmoud A Alfaqih, Joseph P Brunelli, Robert E Drew, and Gary H Thorgaard PMCID: PMC2633016 Novel mutations in the VKORC1 gene of wild rats and mice – a response to 50 years of selection pressure by warfarin? Simone Rost, Hans-Joachim Pelz, Sandra Menzel, Alan D MacNicoll, Vanina León, Ki-Joon Song, Thomas Jäkel, Johannes Oldenburg, and Clemens R Müller PMCID: PMC2644709 Genome-wide QTL mapping for three traits related to teat number in a White Duroc × Erhualian pig resource population Nengshui Ding, Yuanmei Guo, Christoph Knorr, Junwu Ma, Huirong Mao, Lütao Lan, Shijun Xiao, Huashui Ai, Chris S Haley, Bertram Brenig, and Lusheng Huang PMCID: PMC2672953 Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean Lorraine Pariset, Stephane Joost, Paolo Ajmone Marsan, Alessio Valentini, and Econogene Consortium (EC) PMCID: PMC2663570 Mitochondrial DNA haplogroup H structure in North Africa Hajer Ennafaa, Vicente M Cabrera, Khaled K Abu-Amero, Ana M González, Mohamed B Amor, Rym Bouhaha, Nduna Dzimiri, Amel B Elgaaïed, and José M Larruga PMCID: PMC2657161 Full sib pens of pigs are not suitable to identify variance component of associative effect: a simulation study using Gibbs Sampling Jiqiu Cheng, Steven Janssens, and Nadine Buys PMCID: PMC2678166 Identification and association of the single nucleotide polymorphisms in calpain3 (CAPN3) gene with carcass traits in chickens Zeng-Rong Zhang, Yi-Ping Liu, Yong-Gang Yao, Xiao-Song Jiang, Hua-Rui Du, and Qing Zhu PMCID: PMC2656522 Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies Thaung Hlaing, Willoughby Tun-Lin, Pradya Somboon, Duong Socheat, To Setha, Sein Min, Moh Seng Chang, and Catherine Walton PMCID: PMC2660364 A mouse chromosome 4 balancer ENU-mutagenesis screen isolates eleven lethal lines Melissa K Boles, Bonney M Wilkinson, Andrea Maxwell, Lihua Lai, Alea A Mills, Ichiko Nishijima, Andrew P Salinger, Ivan Moskowitz, Karen K Hirschi, Bin Liu, Allan Bradley, and Monica J Justice PMCID: PMC2670824 Monoallelic maternal expression of STAT5A affects embryonic survival in cattle Hasan Khatib, Christian Maltecca, Ricky L Monson, Valerie Schutzkus, and Jack J Rutledge PMCID: PMC2662876 Mutations in genes involved in nonsense mediated decay ameliorate the phenotype of sel-12 mutants with amber stop mutations in Caenorhabditis elegans Alisson M Gontijo, Sylvie Aubert, Ingele Roelens, and Bernard Lakowski PMCID: PMC2678165 Copy number variation in African Americans Joseph P McElroy, Matthew R Nelson, Stacy J Caillier, and Jorge R Oksenberg PMCID: PMC2674062 Big mountains but small barriers: Population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China Aibin Zhan, Cheng Li, and Jinzhong Fu PMCID: PMC2679764 A high density linkage map of the bovine genome Juan A Arias, Mike Keehan, Paul Fisher, Wouter Coppieters, and Richard Spelman PMCID: PMC2680908 High-resolution haplotype block structure in the cattle genome Rafael Villa-Angulo, Lakshmi K Matukumalli, Clare A Gill, Jungwoo Choi, Curtis P Van Tassell, and John J Grefenstette PMCID: PMC2684545 Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon Karim Gharbi, Kevin A Glover, Louise C Stone, Elizabeth S MacDonald, Louise Matthews, Unni Grimholt, and Michael J Stear PMCID: PMC2680909 Novel mutations in TLR genes cause hyporesponsiveness to Mycobacterium avium subsp. paratuberculosis infection Mangesh R Bhide, Rastislav Mucha, Ivan Mikula, Jr, Lucia Kisova, Rostislav Skrabana, Michal Novak, and Ivan Mikula, sr PMCID: PMC2705378 Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum Jennifer A Brisson, Sergey V Nuzhdin, and David L Stern PMCID: PMC2695480 Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis Atsunori Higashino, Naoki Osada, Yumiko Suto, Makoto Hirata, Yosuke Kameoka, Ichiro Takahashi, and Keiji Terao PMCID: PMC2702342 Pairing and recombination features during meiosis in Cebus paraguayanus (Primates: Platyrrhini) Raquel Garcia-Cruz, Pedro Robles, Eliana R Steinberg, Nuria Camats, Miguel A Brieño, Montserrat Garcia-Caldés, and Marta D Mudry PMCID: PMC2702343 Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies Ke Hao, Eugene Chudin, Joshua McElwee, and Eric E Schadt PMCID: PMC2709633 Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman Phillip Endicott, Juan J Sanchez, Irene Pichler, Paul Brotherton, Jerome Brooks, Eduard Egarter-Vigl, Alan Cooper, and Peter Pramstaller PMCID: PMC2717998 Screening of variants for lactase persistence/non-persistence in populations from South Africa and Ghana Suvi Torniainen, M Iqbal Parker, Ville Holmberg, Elisa Lahtela, Collet Dandara, and Irma Jarvela PMCID: PMC2713916 Association between SNPs within candidate genes and compounds related to boar taint and reproduction Maren Moe, Sigbjørn Lien, Torunn Aasmundstad, Theo HE Meuwissen, Marianne HS Hansen, Christian Bendixen, and Eli Grindflek PMCID: PMC2723134 The scurs inheritance: new insights from the French Charolais breed Aurélien Capitan, Cécile Grohs, Mathieu Gautier, and André Eggen PMCID: PMC2719667 Comparative chromosome mapping of repetitive sequences. Implications for genomic evolution in the fish, Hoplias malabaricus Marcelo B Cioffi, Cesar Martins, and Luiz AC Bertollo PMCID: PMC2713275 Significance of common variants on human chromosome 8q24 in relation to the risk of prostate cancer in native Japanese men Miao Liu, Takayuki Kurosaki, Motofumi Suzuki, Yutaka Enomoto, Hiroaki Nishimatsu, Tomio Arai, Motoji Sawabe, Takayuki Hosoi, Yukio Homma, and Tadaichi Kitamura PMCID: PMC2719668 Whole genome microarray analysis, from neonatal blood cards Jill Hardin, Richard H Finnell, David Wong, Michael E Hogan, Joy Horovitz, Jenny Shu, and Gary M Shaw PMCID: PMC2722673 An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels Rami Nassir, Roman Kosoy, Chao Tian, Phoebe A White, Lesley M Butler, Gabriel Silva, Rick Kittles, Marta E Alarcon-Riquelme, Peter K Gregersen, John W Belmont, Francisco M De La Vega, and Michael F Seldin PMCID: PMC2728728 QTL analyses of temporal and intensity components of home-cage activity in KJR and C57BL/6J strains Juzoh Umemori, Akinori Nishi, Arimantas Lionikas, Takayuki Sakaguchi, Satoshi Kuriki, David A Blizard, and Tsuyoshi Koide PMCID: PMC2723135 Population study of 1311 C/T polymorphism of Glucose 6 Phosphate Dehydrogenase gene in Pakistan – an analysis of 715 X-chromosomes Bushra Moiz, Amna Nasir, Tariq Moatter, Zulfiqar Ali Naqvi, and Mohammad Khurshid PMCID: PMC2725355 A strong association of axillary osmidrosis with the wet earwax type determined by genotyping of the ABCC11 gene Motoi Nakano, Nobutomo Miwa, Akiyoshi Hirano, Koh-ichiro Yoshiura, and Norio Niikawa PMCID: PMC2731057 Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate Kouji Setoguchi, Masako Furuta, Takashi Hirano, Tomoko Nagao, Toshio Watanabe, Yoshikazu Sugimoto, and Akiko Takasuga PMCID: PMC2736976 Handling linkage disequilibrium in qualitative trait linkage analysis using dense SNPs: a two-step strategy Kelly Cho and Josée Dupuis PMCID: PMC2731784 Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites Josiemer Mattei, Laurence D Parnell, Chao-Qiang Lai, Bibiana Garcia-Bailo, Xian Adiconis, Jian Shen, Donna Arnett, Serkalem Demissie, Katherine L Tucker, and Jose M Ordovas PMCID: PMC2734553 Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: Conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss) Ruth B Phillips, Kimberly A Keatley, Matthew R Morasch, Abigail B Ventura, Krzysztof P Lubieniecki, Ben F Koop, Roy G Danzmann, and William S Davidson PMCID: PMC2734554 Missense and nonsense mutations in melanocortin 1 receptor (MC1R) gene of different goat breeds: association with red and black coat colour phenotypes but with unexpected evidences Luca Fontanesi, Francesca Beretti, Valentina Riggio, Stefania Dall'Olio, Elena Gómez González, Raffaella Finocchiaro, Roberta Davoli, Vincenzo Russo, and Baldassare Portolano PMCID: PMC2748843 Genetic diversity and the emergence of ethnic groups in Central Asia Evelyne Heyer, Patricia Balaresque, Mark A Jobling, Lluis Quintana-Murci, Raphaelle Chaix, Laure Segurel, Almaz Aldashev, and Tanya Hegay PMCID: PMC2745423 Identification of a two-marker-haplotype on Bos taurus autosome 18 associated with somatic cell score in German Holstein cattle Bodo Brand, Christine Baes, Manfred Mayer, Norbert Reinsch, and Christa Kühn PMCID: PMC2753619 Atlantic cod (Gadus morhua) hemoglobin genes: multiplicity and polymorphism Tudor Borza, Cynthia Stone, A Kurt Gamperl, and Sharen Bowman PMCID: PMC2757024 Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor β on mRNA stability and translatability Milica Putnik, Chunyan Zhao, Jan-Åke Gustafsson, and Karin Dahlman-Wright PMCID: PMC2759954 Genetic variation for body weight change in mice in response to physical exercise Larry J Leamy, Daniel Pomp, and J Timothy Lightfoot PMCID: PMC2760581 Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions Khaled K Abu-Amero, Ali Hellani, Ana M González, Jose M Larruga, Vicente M Cabrera, and Peter A Underhill PMCID: PMC2759955 Characterization of the chromosomal inversion associated with the Koa mutation in the mouse revealed the cause of skeletal abnormalities Kentaro Katayama, Sayaka Miyamoto, Aki Furuno, Kouyou Akiyama, Sakino Takahashi, Hiroetsu Suzuki, Takehito Tsuji, and Tetsuo Kunieda PMCID: PMC2758895 Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed Magdalena Serrano, Jorge H Calvo, Marta Martínez, Ane Marcos-Carcavilla, Javier Cuevas, Carmen González, Juan J Jurado, and Paloma Díez de Tejada PMCID: PMC2761942 Haplotype frequencies at the DRD2 locus in populations of the East European Plain Olga V Flegontova, Andrey V Khrunin, Olga I Lylova, Larisa A Tarskaia, Victor A Spitsyn, Alexey I Mikulich, and Svetlana A Limborska PMCID: PMC2765450 Molecular cloning and characterization of the porcine prostaglandin transporter (SLCO2A1): evaluation of its role in F4 mediated neonatal diarrhoea Mario Van Poucke, Vesna Melkebeek, Tim Erkens, Alex Van Zeveren, Eric Cox, and Luc J Peelman PMCID: PMC2763009 Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation Angélica Cibrián-Jaramillo, Christine D Bacon, Nancy C Garwood, Richard M Bateman, Meredith M Thomas, Steve Russell, C Donovan Bailey, William J Hahn, Samuel GM Bridgewater, and Rob DeSalle PMCID: PMC2770526 Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3 Nikolai P Kandul and Mohamed AF Noor PMCID: PMC2767349 Microsatellite markers of water buffalo, Bubalus bubalis - development, characterisation and linkage disequilibrium studies Muniyandi Nagarajan, Niraj Kumar, Gopala Nishanth, Ramachandran Haribaskar, Karthikeyani Paranthaman, Jalaj Gupta, Manish Mishra, R Vaidhegi, Shantanu Kumar, Amresh K Ranjan, and Satish Kumar PMCID: PMC2773805 Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans Paula Kersbergen, Kate van Duijn, Ate D Kloosterman, Johan T den Dunnen, Manfred Kayser, and Peter de Knijff PMCID: PMC2775748 Optimization of selection contribution and mate allocations in monoecious tree breeding populations Jon Hallander and Patrik Waldmann PMCID: PMC2776599 Methodology Articles Impact of genotyping errors on the type I error rate and the power of haplotype-based association methods Vivien Marquard, Lars Beckmann, Iris M Heid, Claudia Lamina, and Jenny Chang-Claude PMCID: PMC2648998 Determining the effectiveness of High Resolution Melting analysis for SNP genotyping and mutation scanning at the TP53 locus Sonia Garritano, Federica Gemignani, Catherine Voegele, Tú Nguyen-Dumont, Florence Le Calvez-Kelm, Deepika De Silva, Fabienne Lesueur, Stefano Landi, and Sean V Tavtigian PMCID: PMC2648999 Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta Peter Brooks, Charles Marcaillou, Maud Vanpeene, Jean-Paul Saraiva, Daniel Stockholm, Stephan Francke, Reyna Favis, Nadine Cohen, Francis Rousseau, Frédéric Tores, Pierre Lindenbaum, Jörg Hager, and Anne Philippi PMCID: PMC2679057 Modelling dominance in a flexible intercross analysis Lars Rönnegård, Francois Besnier, and Örjan Carlborg PMCID: PMC2716366 A strategy for constructing aneuploid yeast strains by transient nondisjunction of a target chromosome Kirk R Anders, Julie R Kudrna, Kirstie E Keller, BreAnna Kinghorn, Elizabeth M Miller, Daniel Pauw, Anders T Peck, Christopher E Shellooe, and Isaac JT Strong PMCID: PMC2725114 Single-feature polymorphism discovery by computing probe affinity shape powers Wayne Wenzhong Xu, Seungho Cho, S Samuel Yang, Yung-Tsi Bolon, Hatice Bilgic, Haiyan Jia, Yanwen Xiong, and Gary J Muehlbauer PMCID: PMC2746803 Contribution of genetic effects to genetic variance components with epistasis and linkage disequilibrium Tao Wang and Zhao-Bang Zeng PMCID: PMC2754994 Improving power in genetic-association studies via wavelet transformation Renfang Jiang, Jianping Dong, and Yilin Dai PMCID: PMC2759953 Assessment of global phase uncertainty in case-control studies Hae-Won Uh, Jeanine J Houwing-Duistermaat, Hein Putter, and Hans C van Houwelingen PMCID: PMC2760579 Regression-based approach for testing the association between multi-region haplotype configuration and complex trait Yanling Hu, Sinnwell Jason, Qishan Wang, Yuchun Pan, Xiangzhe Zhang, Hongbo Zhao, Changlong Li, and Libin Sun PMCID: PMC2760580 A genetic algorithm based method for stringent haplotyping of family data Francois Besnier and Örjan Carlborg PMCID: PMC2754495 High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity Weiyin Zhou, Margaret A Calciano, Heather Jordan, Michael Brenner, Seth Johnson, Darong Wu, Lin Lei, Diego Pallares, Pascale Beurdeley, Fabien Rouet, Pritmohinder S Gill, Laurent Bracco, Cyril Soucaille, and Richard Einstein PMCID: PMC2768739 Automated DNA mutation detection using universal conditions direct sequencing: application to ten muscular dystrophy genes Richard R Bennett, Hal E Schneider, Elicia Estrella, Stephanie Burgess, Andrew S Cheng, Caitlin Barrett, Va Lip, Poh San Lai, Yiping Shen, Bai-Lin Wu, Basil T Darras, Alan H Beggs, and Louis M Kunkel PMCID: PMC2781300 Other Issues: Journal List
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