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Statistical and computational genetics

This section incorporates all aspects of statistical and computational genetics, including but not limited to: methods and applications for the analysis of all types of genetic data.

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  1. Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed t...

    Authors: Takumi Miura, Satoshi Yasuda and Yoji Sato

    Citation: BMC Genomic Data 2021 22:8

    Content type: Methodology article

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  2. Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the mol...

    Authors: Hua Liu, Chang Luo, Dongliang Chen, Yaqin Wang, Shuang Guo, Xiaoxi Chen, Jingyi Bai, Mingyuan Li, Xinlei Huang, Xi Cheng and Conglin Huang

    Citation: BMC Genomic Data 2021 22:2

    Content type: Research article

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  5. Genome-wide association studies (GWAS) have successfully identified genetic susceptible variants for complex diseases. However, the underlying mechanism of such association remains largely unknown. Most diseas...

    Authors: Yuchen Zhu, Jiadong Ji, Weiqiang Lin, Mingzhuo Li, Lu Liu, Huanhuan Zhu, Fuzhong Xue, Xiujun Li, Xiang Zhou and Zhongshang Yuan

    Citation: BMC Genetics 2020 21:90

    Content type: Research article

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  6. Lesion-mimic and premature aging (lmpa) mutant lmpa1 was identified from the ethyl methane sulfonate (EMS) mutant library in the bread wheat variety Keda 527 (KD527) background. To reveal the genetic basis of lmp...

    Authors: Weiwei Kong, Liming Wang, Pei Cao, Xingfeng Li, Jingjing Ji, Puhui Dong, Xuefang Yan, Chunping Wang, Honggang Wang and Jiaqiang Sun

    Citation: BMC Genetics 2020 21:88

    Content type: Research article

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  7. Stenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. sec...

    Authors: Ying Luo, Xiujie Zhang, Jiahong Xu, Yao Zheng, Shouqin Pu, Zhizhen Duan, Zhihao Li, Guodao Liu, Jinhui Chen and Zhiyong Wang

    Citation: BMC Genetics 2020 21:86

    Content type: Research article

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  8. Biological pathways play an important role in the occurrence, development and recovery of complex diseases, such as cancers, which are multifactorial complex diseases that are generally caused by mutation of m...

    Authors: Hongkai Li, Zhi Geng, Xiaoru Sun, Yuanyuan Yu and Fuzhong Xue

    Citation: BMC Genetics 2020 21:85

    Content type: Methodology article

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  10. POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondri...

    Authors: Yousuf A. Khan, Irwin Jungreis, James C. Wright, Jonathan M. Mudge, Jyoti S. Choudhary, Andrew E. Firth and Manolis Kellis

    Citation: BMC Genetics 2020 21:25

    Content type: Research article

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  12. Effective matching of genotypes and environments is required for the species to reach optimal productivity and act effectively for carbon sequestration. A common garden experiment across five different environ...

    Authors: Jaroslav Klápště, Dean Meason, Heidi S. Dungey, Emily J. Telfer, Paul Silcock and Simon Rapley

    Citation: BMC Genetics 2020 21:15

    Content type: Research Article

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  14. To satisfy an increasing demand for dietary protein, the poultry industry has employed genetic selection to increase the growth rate of broilers by over 400% in the past 50 years. Although modern broilers reac...

    Authors: Angela Zou, Kerry Nadeau, Pauline W. Wang, Jee Yeon Lee, David S. Guttman, Shayan Sharif, Doug R. Korver, John H. Brumell and John Parkinson

    Citation: BMC Genetics 2020 21:5

    Content type: Research article

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  15. Forest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majorit...

    Authors: Jaroslav Klápště, Mari Suontama, Heidi S Dungey, Emily J Telfer and Grahame T Stovold

    Citation: BMC Genetics 2019 20:81

    Content type: Research Article

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  17. Various biological materials unrelated to humans are found at crime scenes and it is often important to elucidate the origin of these materials. A genetic locus common to several species is conventionally PCR-...

    Authors: Takako Kinebuchi, Nozomi Idota, Hajime Tsuboi, Marin Takaso, Risa Bando and Hiroshi Ikegaya

    Citation: BMC Genetics 2019 20:50

    Content type: Research article

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  20. It becomes clear that the increase in the density of marker panels and even the use of sequence data didn’t result in any meaningful increase in the accuracy of genomic selection (GS) using either regression (...

    Authors: Ling-Yun Chang, Sajjad Toghiani, Samuel E. Aggrey and Romdhane Rekaya

    Citation: BMC Genetics 2019 20:21

    Content type: Research article

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  21. Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA ba...

    Authors: Prabina Kumar Meher, Tanmaya Kumar Sahu, Shachi Gahoi, Ruchi Tomar and Atmakuri Ramakrishna Rao

    Citation: BMC Genetics 2019 20:2

    Content type: Research article

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  22. X chromosome inactivation (XCI) is an important gene regulation mechanism in females to equalize the expression levels of X chromosome between two sexes. Generally, one of two X chromosomes in females is rando...

    Authors: Si-Qi Xu, Yu Zhang, Peng Wang, Wei Liu, Xian-Bo Wu and Ji-Yuan Zhou

    Citation: BMC Genetics 2018 19:109

    Content type: Methodology article

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  25. SNPs are informative to estimate genomic breed composition (GBC) of individual animals, but selected SNPs for this purpose were not made available in the commercial bovine SNP chips prior to the present study....

    Authors: Jun He, Yage Guo, Jiaqi Xu, Hao Li, Anna Fuller, Richard G. Tait Jr, Xiao-Lin Wu and Stewart Bauck

    Citation: BMC Genetics 2018 19:56

    Content type: Research article

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  26. The central tenet of ‘genome content’ has been that the ‘non-coding’ parts are highly enriched with ‘microsatellites’ or ‘Simple Sequence Repeats’ (SSRs). We presume that the presence and change in number of r...

    Authors: Nisha Joy, Y. P. Maimoonath Beevi and E. V. Soniya

    Citation: BMC Genetics 2018 19:29

    Content type: Research article

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  27. The availability of high-density (HD) marker panels, genome wide variants and sequence data creates an unprecedented opportunity to dissect the genetic basis of complex traits, enhance genomic selection (GS) a...

    Authors: Ling-Yun Chang, Sajjad Toghiani, Ashley Ling, Sammy E. Aggrey and Romdhane Rekaya

    Citation: BMC Genetics 2018 19:4

    Content type: Research article

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    The Correction to this article has been published in BMC Genetics 2018 19:13

  28. Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign w...

    Authors: Anke Hüls, Ursula Krämer, Christopher Carlsten, Tamara Schikowski, Katja Ickstadt and Holger Schwender

    Citation: BMC Genetics 2017 18:115

    Content type: Methodology article

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  29. Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil pa...

    Authors: Qi Bin Kwong, Chee Keng Teh, Ai Ling Ong, Fook Tim Chew, Sean Mayes, Harikrishna Kulaveerasingam, Martti Tammi, Suat Hui Yeoh, David Ross Appleton and Jennifer Ann Harikrishna

    Citation: BMC Genetics 2017 18:107

    Content type: Research article

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  30. When testing for SNP (single nucleotide polymorphism) associations in related individuals, observations are not independent. Simple linear regression assuming independent normally distributed residuals results...

    Authors: Arnd Gross, Anke Tönjes and Markus Scholz

    Citation: BMC Genetics 2017 18:104

    Content type: Methodology article

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  31. Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species....

    Authors: Daniel J. Shea, Motoki Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto and Keiichi Okazaki

    Citation: BMC Genetics 2017 18:101

    Content type: Methodology article

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  32. Undirected graphical models or Markov random fields have been a popular class of models for representing conditional dependence relationships between nodes. In particular, Markov networks help us to understand...

    Authors: Hosik Choi, Jungsoo Gim, Sungho Won, You Jin Kim, Sunghoon Kwon and Changyi Park

    Citation: BMC Genetics 2017 18:93

    Content type: Methodology article

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  33. For dichotomous traits, the generalized disequilibrium test with the moment estimate of the variance (GDT-ME) is a powerful family-based association method. Genomic imprinting is an important epigenetic phenom...

    Authors: Jian-Long Li, Peng Wang, Wing Kam Fung and Ji-Yuan Zhou

    Citation: BMC Genetics 2017 18:90

    Content type: Methodology article

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  34. Genome-wide association studies involve detecting association between millions of genetic variants and a trait, which typically use univariate regression to test association between each single variant and the...

    Authors: Jaron Arbet, Matt McGue, Snigdhansu Chatterjee and Saonli Basu

    Citation: BMC Genetics 2017 18:70

    Content type: Methodology Article

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  35. Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding...

    Authors: Honglin Chen, Lixia Wang, Xiaoyan Liu, Liangliang Hu, Suhua Wang and Xuzhen Cheng

    Citation: BMC Genetics 2017 18:65

    Content type: Research article

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  36. For the analysis of gene-environment (GxE) interactions commonly single nucleotide polymorphisms (SNPs) are used to characterize genetic susceptibility, an approach that mostly lacks power and has poor reprodu...

    Authors: Anke Hüls, Katja Ickstadt, Tamara Schikowski and Ursula Krämer

    Citation: BMC Genetics 2017 18:55

    Content type: Methodology article

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    The Erratum to this article has been published in BMC Genetics 2017 18:73

  37. The use of multiple genetic backgrounds across years is appealing for genomic prediction (GP) because past years’ data provide valuable information on marker effects. Nonetheless, single-year GP models are les...

    Authors: Angela-Maria Bernal-Vasquez, Andres Gordillo, Malthe Schmidt and Hans-Peter Piepho

    Citation: BMC Genetics 2017 18:51

    Content type: Research Article

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  38. Over the past decades, the prevalence of type 2 diabetes mellitus (T2D) has been steadily increasing around the world. Despite large efforts devoted to better understand the genetic basis of the disease, the i...

    Authors: Jie Ren, Tao He, Ye Li, Sai Liu, Yinhao Du, Yu Jiang and Cen Wu

    Citation: BMC Genetics 2017 18:44

    Content type: Methodology article

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  39. Most genome-wide association studies assumed an additive model of inheritance which may result in significant loss of power when there is a strong departure from additivity. The General Regression Model (GRM),...

    Authors: Marie-Hélène Dizier, Florence Demenais and Flavie Mathieu

    Citation: BMC Genetics 2017 18:24

    Content type: Research article

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  40. The evaluation and interpretation of forensic DNA mixture evidence faces greater interpretational challenges due to increasingly complex mixture evidence. Such challenges include: casework involving low quanti...

    Authors: Frederick R. Bieber, John S. Buckleton, Bruce Budowle, John M. Butler and Michael D. Coble

    Citation: BMC Genetics 2016 17:125

    Content type: Methodology article

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  41. mRNA expression in a cell or subcellular organelle is precisely regulated for the purpose of gene function regulation. The 3’ untranslated region (3’UTR) of mRNA is the binding target of microRNA and RNA bindi...

    Authors: Tian Li, Yaoyun Kuang and Bin Li

    Citation: BMC Genetics 2016 17:111

    Content type: Research article

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  42. Japanese larch (Larix kaempferi) as a successful exotic species has become one of the most important economic and ecological conifers in China. In order to broaden the genetic resource of Larix kaempferi, an effo...

    Authors: Shu Diao, Yimei Hou, Yunhui Xie and Xiaomei Sun

    Citation: BMC Genetics 2016 17:104

    Content type: Research article

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  43. Lynch syndrome is a hereditary cancer syndrome associated with high risks of colorectal and endometrial cancer that is caused by pathogenic variants in the mismatch repair genes (MLH1, MSH2, MSH6, PMS2, EPCAM). A...

    Authors: Brian Morris, Elisha Hughes, Eric Rosenthal, Alexander Gutin and Karla R. Bowles

    Citation: BMC Genetics 2016 17:99

    Content type: Research article

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  45. Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci (QTL) mapping, gene...

    Authors: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar and Juan Zalapa

    Citation: BMC Genetics 2016 17:62

    Content type: Software

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  46. We propose a novel Markov Blanket-based repeated-fishing strategy (MBRFS) in attempt to increase the power of existing Markov Blanket method (DASSO-MB) and maintain its advantages in omic data analysis.

    Authors: Hongkai Li, Zhongshang Yuan, Jiadong Ji, Jing Xu, Tao Zhang, Xiaoshuai Zhang and Fuzhong Xue

    Citation: BMC Genetics 2016 17:51

    Content type: Methodology article

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  47. Core collections are important tools in genetic resources research and administration. At present, most core collection selection criteria are based on one of the following item characteristics: passport data,...

    Authors: Ernesto Borrayo, Ryoko Machida-Hirano, Masaru Takeya, Makoto Kawase and Kazuo Watanabe

    Citation: BMC Genetics 2016 17:42

    Content type: Methodology Article

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  48. The genetic variants identified by Genome-wide association study (GWAS) can only account for a small proportion of the total heritability for complex disease. The existence of gene-gene joint effects which con...

    Authors: Jing Xu, Zhongshang Yuan, Jiadong Ji, Xiaoshuai Zhang, Hongkai Li, Xuesen Wu, Fuzhong Xue and Yanxun Liu

    Citation: BMC Genetics 2016 17:31

    Content type: Methodology article

    Published on:

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