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  1. Although numerous investigations have compared gene expression microarray platforms, preprocessing methods and batch correction algorithms using constructed spike-in or dilution datasets, there remains a pauci...

    Authors: Arianne C Richard, Paul A Lyons, James E Peters, Daniele Biasci, Shaun M Flint, James C Lee, Eoin F McKinney, Richard M Siegel and Kenneth GC Smith
    Citation: BMC Genomics 2014 15:649
    Content type: Research article Published on:

  2. Gene expression analysis by reverse transcription quantitative PCR (qPCR) is the most widely used method for analyzing the expression of a moderate number of genes and also for the validation of microarray res...

    Authors: Diego Robledo, Jorge Hernández-Urcera, Rosa M Cal, Belén G Pardo, Laura Sánchez, Paulino Martínez and Ana Viñas
    Citation: BMC Genomics 2014 15:648
    Content type: Research article Published on:

  4. Genomic prediction is becoming a daily tool for plant breeders. It makes use of genotypic information to make predictions used for selection decisions. The accuracy of the predictions depends on the number of ...

    Authors: Angela-Maria Bernal-Vasquez, Jens Möhring, Malthe Schmidt, Manfred Schönleben, Chris-Carolin Schön and Hans-Peter Piepho
    Citation: BMC Genomics 2014 15:646
    Content type: Research article Published on:

  5. Human leukocyte antigen (HLA) is a group of genes that are extremely polymorphic among individuals and populations and have been associated with more than 100 different diseases and adverse drug effects. HLA t...

    Authors: Kazuyoshi Hosomichi, Shigeki Mitsunaga, Hideki Nagasaki and Ituro Inoue
    Citation: BMC Genomics 2014 15:645
    Content type: Methodology article Published on:

  6. Little is known about the relationship between miRNA and mRNA expression in Alzheimer’s disease (AD) at early- or late-symptomatic stages. Sequence-based target prediction algorithms and anti-correlation profi...

    Authors: Haneul Noh, Charny Park, Soojun Park, Young Seek Lee, Soo Young Cho and Hyemyung Seo
    Citation: BMC Genomics 2014 15:644
    Content type: Research article Published on:

  7. Strain CPAC 7 (=SEMIA 5080) was recently reclassified into the new species Bradyrhizobium diazoefficiens; due to its outstanding efficiency in fixing nitrogen, it has been used in commercial inoculants for applic...

    Authors: Douglas Fabiano Gomes, Jesiane Stefânia da Silva Batista, Amanda Alves Paiva Rolla, Luciano Paulino da Silva, Carlos Bloch, Lygia Vitoria Galli-Terasawa and Mariangela Hungria
    Citation: BMC Genomics 2014 15:643
    Content type: Research article Published on:

  9. LIM (Lin-11, Isl-1 and Mec-3 domains) genes have been reported to trigger the formation of actin bundles, a major higher-order cytoskeletal assembly, in higher plants; however, the stress resistance related funct...

    Authors: Jong-In Park, Nasar Uddin Ahmed, Hee-Jeong Jung, Senthil Kumar Thamil Arasan, Mi-Young Chung, Yong-Gu Cho, Masao Watanabe and Ill-Sup Nou
    Citation: BMC Genomics 2014 15:641
    Content type: Research article Published on:

  10. The current knowledge of eukaryote signalling originates from phenotypically diverse organisms. There is a pressing need to identify conserved signalling components among eukaryotes, which will lead to the tra...

    Authors: Matthew M Hindle, Sarah F Martin, Zeenat B Noordally, Gerben van Ooijen, Martin E Barrios-Llerena, T Ian Simpson, Thierry Le Bihan and Andrew J Millar
    Citation: BMC Genomics 2014 15:640
    Content type: Research article Published on:

  11. DNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here...

    Authors: Fabian Ripp, Christopher Felix Krombholz, Yongchao Liu, Mathias Weber, Anne Schäfer, Bertil Schmidt, Rene Köppel and Thomas Hankeln
    Citation: BMC Genomics 2014 15:639
    Content type: Methodology article Published on:

  12. The Homeobox (Hox) family complex contains 39 genes, clustered into four groups (A-D) all expressing in sequential manner. The HOX proteins are transcriptional factors involved in regulation of pattern formation ...

    Authors: Monal Sharma, Leena Rawal, Deepak Panwar, Neeta Sehgal and Sher Ali
    Citation: BMC Genomics 2014 15:638
    Content type: Research article Published on:

  13. Gastrointestinal nematodes are one of the most serious causes of disease in domestic ruminants worldwide. There is considerable variation in resistance to gastrointestinal nematodes within and between sheep br...

    Authors: Kathryn M McRae, John C McEwan, Ken G Dodds and Neil J Gemmell
    Citation: BMC Genomics 2014 15:637
    Content type: Research article Published on:

  14. Genome sequencing of Anopheles gambiae was completed more than ten years ago and has accelerated research on malaria transmission. However, annotation needs to be refined and verified experimentally, as most pred...

    Authors: Alejandro Padrón, Alvaro Molina-Cruz, Mariam Quinones, José MC Ribeiro, Urvashi Ramphul, Janneth Rodrigues, Kui Shen, Ashley Haile, José Luis Ramirez and Carolina Barillas-Mury
    Citation: BMC Genomics 2014 15:636
    Content type: Research article Published on:

  15. The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden or Tiger milk mushroom (Polyporales, Basidiomycota) is a valuable folk medicine for indigenous peoples in Southeast Asia. Despite the increasing interest i...

    Authors: Hui-Yeng Y Yap, Yit-Heng Chooi, Mohd Firdaus-Raih, Shin-Yee Fung, Szu-Ting Ng, Chon-Seng Tan and Nget-Hong Tan
    Citation: BMC Genomics 2014 15:635
    Content type: Research article Published on:

  16. Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tole...

    Authors: Jing Xia, Changying Zeng, Zheng Chen, Kevin Zhang, Xin Chen, Yufei Zhou, Shun Song, Cheng Lu, Ruiju Yang, Zi Yang, Junfei Zhou, Hai Peng, Wenquan Wang, Ming Peng and Weixiong Zhang
    Citation: BMC Genomics 2014 15:634
    Content type: Research article Published on:

  17. RNA sequencing methods have already altered our view of the extent and complexity of bacterial and eukaryotic transcriptomes, revealing rare transcript isoforms (circular RNAs, RNA chimeras) that could play an...

    Authors: Verónica Lloréns-Rico, Luis Serrano and Maria Lluch-Senar
    Citation: BMC Genomics 2014 15:633
    Content type: Methodology article Published on:

  18. Both common and rare genetic variants have been shown to contribute to the etiology of complex diseases. Recent genome-wide association studies (GWAS) have successfully investigated how common variants contrib...

    Authors: Wei Guo and Yin Yao Shugart
    Citation: BMC Genomics 2014 15:632
    Content type: Methodology article Published on:

  19. Strand specific RNA sequencing is rapidly replacing conventional cDNA sequencing as an approach for assessing information about the transcriptome. Alongside improved laboratory protocols the development of bio...

    Authors: Benjamín Sigurgeirsson, Olof Emanuelsson and Joakim Lundeberg
    Citation: BMC Genomics 2014 15:631
    Content type: Methodology article Published on:

  21. Fusarium Head Blight (FHB) caused primarily by Fusarium graminearum (Fg) is one of the major diseases of small-grain cereals including bread wheat. This disease both reduces yields and causes quality losses due t...

    Authors: Jean-Claude Pasquet, Séjir Chaouch, Catherine Macadré, Sandrine Balzergue, Stéphanie Huguet, Marie-Laure Martin-Magniette, Floriant Bellvert, Xavier Deguercy, Vincent Thareau, Dimitri Heintz, Patrick Saindrenan and Marie Dufresne
    Citation: BMC Genomics 2014 15:629
    Content type: Research article Published on:

  22. Penaeus monodon nudivirus (PmNV) is the causative agent of spherical baculovirosis in shrimp (Penaeus monodon). This disease causes significant mortalities at the larval stage and early postlarval (PL) stage and ...

    Authors: Yi-Ting Yang, Der-Yen Lee, Yongjie Wang, Jer-Ming Hu, Wen-Hsiung Li, Jiann-Horng Leu, Geen-Dong Chang, Huei-Mien Ke, Shin-Ting Kang, Shih-Shun Lin, Guang-Hsiung Kou and Chu-Fang Lo
    Citation: BMC Genomics 2014 15:628
    Content type: Research article Published on:

  23. Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China. Genome sequencing of the pathogen will provide important information for globally understandi...

    Authors: Shigang Gao, Yaqian Li, Jinxin Gao, Yujuan Suo, Kehe Fu, Yingying Li and Jie Chen
    Citation: BMC Genomics 2014 15:627
    Content type: Research article Published on:

  25. The domestic goat (Capra hircus), an important livestock species, belongs to a clade of Ruminantia, Bovidae, together with cattle, buffalo and sheep. The history of genome evolution and chromosomal rearrangements...

    Authors: Xiaoyong Du, Bertrand Servin, James E Womack, Jianhua Cao, Mei Yu, Yang Dong, Wen Wang and Shuhong Zhao
    Citation: BMC Genomics 2014 15:625
    Content type: Research article Published on:

  26. The Ts1Cje mouse model of Down syndrome (DS) has partial triplication of mouse chromosome 16 (MMU16), which is partially homologous to human chromosome 21. These mice develop various neuropathological features...

    Authors: King-Hwa Ling, Chelsee A Hewitt, Kai-Leng Tan, Pike-See Cheah, Sharmili Vidyadaran, Mei-I Lai, Han-Chung Lee, Ken Simpson, Lavinia Hyde, Melanie A Pritchard, Gordon K Smyth, Tim Thomas and Hamish S Scott
    Citation: BMC Genomics 2014 15:624
    Content type: Research article Published on:

  27. Bovine hereditary zinc deficiency (BHZD) is an autosomal recessive disorder of cattle, first described in Holstein-Friesian animals. Affected calves suffer from severe skin lesions and show a poor general heal...

    Authors: Simone Jung, Hubert Pausch, Martin C Langenmayer, Hermann Schwarzenbacher, Monir Majzoub-Altweck, Nicole S Gollnick and Ruedi Fries
    Citation: BMC Genomics 2014 15:623
    Content type: Research article Published on:

  28. Genome wide association studies (GWAS) are applied to identify genetic loci, which are associated with complex traits and human diseases. Analogous to the evolution of gene expression analyses, pathway analyse...

    Authors: Christina Backes, Frank Rühle, Monika Stoll, Jan Haas, Karen Frese, Andre Franke, Wolfgang Lieb, H-Erich Wichmann, Tanja Weis, Wanda Kloos, Hans-Peter Lenhof, Eckart Meese, Hugo Katus, Benjamin Meder and Andreas Keller
    Citation: BMC Genomics 2014 15:622
    Content type: Research article Published on:

  29. Myogenesis is initiated by myoblast differentiation and fusion to form myotubes and muscle fibres. A population of myoblasts, known as satellite cells, is responsible for post-natal growth of muscle and for it...

    Authors: Vincent Grassot, Anne Da Silva, James Saliba, Abderrahman Maftah, Fabrice Dupuy and Jean-Michel Petit
    Citation: BMC Genomics 2014 15:621
    Content type: Research article Published on:

  30. Insulin producing beta cell and glucagon producing alpha cells are colocalized in pancreatic islets in an arrangement that facilitates the coordinated release of the two principal hormones that regulate glucos...

    Authors: Christopher Benner, Talitha van der Meulen, Elena Cacéres, Kristof Tigyi, Cynthia J Donaldson and Mark O Huising
    Citation: BMC Genomics 2014 15:620
    Content type: Research article Published on:

  31. A convergence of high-throughput sequencing and computational power is transforming biology into information science. Despite these technological advances, converting bits and bytes of sequence information int...

    Authors: Niels W Hanson, Kishori M Konwar, Alyse K Hawley, Tomer Altman, Peter D Karp and Steven J Hallam
    Citation: BMC Genomics 2014 15:619
    Content type: Methodology article Published on:

  32. Powdery mildew (PM) is a major fungal disease of thousands of plant species, including many cultivated Rosaceae. PM pathogenesis is associated with up-regulation of MLO genes during early stages of infection, cau...

    Authors: Stefano Pessina, Stefano Pavan, Domenico Catalano, Alessandra Gallotta, Richard GF Visser, Yuling Bai, Mickael Malnoy and Henk J Schouten
    Citation: BMC Genomics 2014 15:618
    Content type: Research article Published on:

  33. Identification of parasite genes that underlie traits such as drug resistance and host specificity is challenging using classical linkage mapping approaches. Extreme QTL (X-QTL) methods, originally developed b...

    Authors: Frédéric D Chevalier, Claudia LL Valentim, Philip T LoVerde and Timothy JC Anderson
    Citation: BMC Genomics 2014 15:617
    Content type: Research article Published on:

  34. Dictyostelium discoideum, a microbial model for social evolution, is known to distinguish self from non-self and show genotype-dependent behavior during chimeric development. Aside from a small number of cell-cel...

    Authors: Si I Li, Neil J Buttery, Christopher RL Thompson and Michael D Purugganan
    Citation: BMC Genomics 2014 15:616
    Content type: Research article Published on:

  35. Alternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of gene expression. Little is known about how APA sites may evolve in homologous genes in different plant specie...

    Authors: Xiaohui Wu, Bobby Gaffney, Arthur G Hunt and Qingshun Q Li
    Citation: BMC Genomics 2014 15:615
    Content type: Research article Published on:

  37. Lipid polymers in plant cell walls, such as cutin and suberin, build recalcitrant hydrophobic protective barriers. Their degradation is of foremost importance for both plant pathogenic and saprophytic fungi. R...

    Authors: Isabel Martins, Diego O Hartmann, Paula C Alves, Celso Martins, Helga Garcia, Céline C Leclercq, Rui Ferreira, Ji He, Jenny Renaut, Jörg D Becker and Cristina Silva Pereira
    Citation: BMC Genomics 2014 15:613
    Content type: Research article Published on:

  38. All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale ge...

    Authors: Lianhua Guo, Yingnan Chen, Ning Ye, Xiaogang Dai, Wanxu Yang and Tongming Yin
    Citation: BMC Genomics 2014 15:612
    Content type: Research article Published on:

  39. Cadmium (Cd) is a severe detrimental environmental pollutant. To adapt to Cd-induced deleterious effects, plants have evolved sophisticated defence mechanisms. In this study, a genome-wide transcriptome analys...

    Authors: Fangbin Cao, Fei Chen, Hongyan Sun, Guoping Zhang, Zhong-Hua Chen and Feibo Wu
    Citation: BMC Genomics 2014 15:611
    Content type: Research article Published on:

  41. Frankia is a genus of soil actinobacteria forming nitrogen-fixing root-nodule symbiotic relationships with non-leguminous woody plant species, collectively called actinorhizals, from eight dicotyledonous families...

    Authors: Ken-ichi Kucho, Takashi Yamanaka, Hideo Sasakawa, Samira R Mansour and Toshiki Uchiumi
    Citation: BMC Genomics 2014 15:609
    Content type: Research article Published on:

  42. Whole genome sequencing of bisulfite converted DNA (‘methylC-seq’) method provides comprehensive information of DNA methylation. An important application of these whole genome methylation maps is classifying e...

    Authors: Iksoo Huh, Xingyu Yang, Taesung Park and Soojin V Yi
    Citation: BMC Genomics 2014 15:608
    Content type: Methodology article Published on:

  43. Coral reefs worldwide are being harmed through anthropogenic activities. Some coral reefs in Thailand remain well-preserved, including the shallow coral reefs along Kra island, Nakhon Si Thammarat province. In...

    Authors: Naraporn Somboonna, Alisa Wilantho, Anunchai Assawamakin, Somchai Monanunsap, Duangjai Sangsrakru, Sithichoke Tangphatsornruang and Sissades Tongsima
    Citation: BMC Genomics 2014 15:607
    Content type: Research article Published on:

  44. The Brassicaceae family is an exemplary model for studying plant polyploidy. The Brassicaceae knowledge-base includes the well-annotated Arabidopsis thaliana reference sequence; well-established evidence for thre...

    Authors: Jungeun Kim, Jeongyeo Lee, Jae-Pil Choi, Inkyu Park, Kyungbong Yang, Min Keun Kim, Young Han Lee, Ill-Sup Nou, Dae-Soo Kim, Sung Ran Min, Sang Un Park and HyeRan Kim
    Citation: BMC Genomics 2014 15:606
    Content type: Research article Published on:

  46. Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origin...

    Authors: Blake T Hovde, Shawn R Starkenburg, Heather M Hunsperger, Laina D Mercer, Chloe R Deodato, Ramesh K Jha, Olga Chertkov, Raymond J Monnat Jr and Rose Ann Cattolico
    Citation: BMC Genomics 2014 15:604
    Content type: Research article Published on:

  47. Phellinus sulphurascens is a fungal pathogen that causes laminar root rot in conifers, one of the most damaging root diseases in western North America. Despite its importance as a forest pathogen, this fungus is ...

    Authors: Holly L Williams, Rona N Sturrock, Muhammad A Islam, Craig Hammett, Abul K M Ekramoddoullah and Isabel Leal
    Citation: BMC Genomics 2014 15:603
    Content type: Research article Published on:

  49. Helicobacter is a genus of Gram-negative bacteria, possessing a characteristic helical shape that has been associated with a wide spectrum of human diseases. Although much research has been done on Helicobacter a...

    Authors: Siew Woh Choo, Mia Yang Ang, Hanieh Fouladi, Shi Yang Tan, Cheuk Chuen Siow, Naresh VR Mutha, Hamed Heydari, Wei Yee Wee, Jamuna Vadivelu, Mun Fai Loke, Vellaya Rehvathy and Guat Jah Wong
    Citation: BMC Genomics 2014 15:600
    Content type: Database Published on:

  50. The recent increase in human polymorphism data, together with the availability of genome sequences from several primate species, provides an unprecedented opportunity to investigate how natural selection has s...

    Authors: Magdalena Gayà-Vidal and M Mar Albà
    Citation: BMC Genomics 2014 15:599
    Content type: Research article Published on:

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BMC Genomics

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