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  1. The immature fiber (im) mutant of Gossypium hirsutum L. is a special cotton fiber mutant with non-fluffy fibers. It has low dry weight and fineness of fibers due to developmental defects in fiber secondary cell w...

    Authors: Cheng Wang, Yuanda Lv, Wentin Xu, Tianzhen Zhang and Wangzhen Guo
    Citation: BMC Genomics 2014 15:94
    Content type: Research article Published on:

  2. Imprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues ...

    Authors: Kory C Douglas, Xu Wang, Madhuri Jasti, Abigail Wolff, John L VandeBerg, Andrew G Clark and Paul B Samollow
    Citation: BMC Genomics 2014 15:89
    Content type: Research article Published on:

  3. MicroRNAs (MiRNA) are small non-coding RNAs that regulate gene expression. The aim of this study was to identify miRNAs differentially expressed between mild and moderately emphysematous lung, as well as their...

    Authors: Santiyagu M Savarimuthu Francis, Morgan R Davidson, Maxine E Tan, Casey M Wright, Belinda E Clarke, Edwina E Duhig, Rayleen V Bowman, Nicholas K Hayward, Kwun M Fong and Ian A Yang
    Citation: BMC Genomics 2014 15:88
    Content type: Research article Published on:

  4. Psoriasis is a common inflammatory skin disease with a known genetic component. Our previously published psoriasis genome-wide association study identified dozens of novel susceptibility loci in Han Chinese. H...

    Authors: Xianyong Yin, Nathan E Wineinger, Hui Cheng, Yong Cui, Fusheng Zhou, Xianbo Zuo, Xiaodong Zheng, Sen Yang, Nicholas J Schork and Xuejun Zhang
    Citation: BMC Genomics 2014 15:87
    Content type: Research article Published on:

  5. The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, th...

    Authors: Christine G Elsik, Kim C Worley, Anna K Bennett, Martin Beye, Francisco Camara, Christopher P Childers, Dirk C de Graaf, Griet Debyser, Jixin Deng, Bart Devreese, Eran Elhaik, Jay D Evans, Leonard J Foster, Dan Graur, Roderic Guigo, Katharina Jasmin Hoff…
    Citation: BMC Genomics 2014 15:86
    Content type: Research article Published on:

  6. The reduction in the cost of sequencing a human genome has led to the use of genotype sampling strategies in order to impute and infer the presence of sequence variants that can then be tested for associations...

    Authors: Chris Bizon, Michael Spiegel, Scott A Chasse, Ian R Gizer, Yun Li, Ewa P Malc, Piotr A Mieczkowski, Josh K Sailsbery, Xiaoshu Wang, Cindy L Ehlers and Kirk C Wilhelmsen
    Citation: BMC Genomics 2014 15:85
    Content type: Research article Published on:

  7. Personal genome assembly is a critical process when studying tumor genomes and other highly divergent sequences. The accuracy of downstream analyses, such as RNA-seq and ChIP-seq, can be greatly enhanced by us...

    Authors: Sean R Landman, Tae Hyun Hwang, Kevin AT Silverstein, Yingming Li, Scott M Dehm, Michael Steinbach and Vipin Kumar
    Citation: BMC Genomics 2014 15:84
    Content type: Software Published on:

  8. Cylindrospermopsis raciborskii is an invasive filamentous freshwater cyanobacterium, some strains of which produce toxins. Sporadic toxicity may be the result of gene deletion events, the horizontal transfer of t...

    Authors: Rati Sinha, Leanne A Pearson, Timothy W Davis, Julia Muenchhoff, Ryanbi Pratama, Aaron Jex, Michele A Burford and Brett A Neilan
    Citation: BMC Genomics 2014 15:83
    Content type: Research article Published on:

  9. Chromothripsis is a recently discovered phenomenon of genomic rearrangement, possibly arising during a single genome-shattering event. This could provide an alternative paradigm in cancer development, replacin...

    Authors: Haoyang Cai, Nitin Kumar, Homayoun C Bagheri, Christian von Mering, Mark D Robinson and Michael Baudis
    Citation: BMC Genomics 2014 15:82
    Content type: Research article Published on:

  10. Genetic variation associated with human leukocyte antigen (HLA) genes has immunological functions and is associated with autoimmune diseases. To date, large-scale studies involving classical HLA genes have been l...

    Authors: Ai-Ru Hsieh, Su-Wei Chang, Pei-Lung Chen, Chen-Chung Chu, Ching-Lin Hsiao, Wei-Shiung Yang, Chien-Ching Chang, Jer-Yuarn Wu, Yuan-Tsong Chen, Tien-Chun Chang and Cathy SJ Fann
    Citation: BMC Genomics 2014 15:81
    Content type: Research article Published on:

  11. ChIP-Seq is widely used to detect genomic segments bound by transcription factors (TF), either directly at DNA binding sites (BSs) or indirectly via other proteins. Currently, there are many software tools imp...

    Authors: Victor G Levitsky, Ivan V Kulakovskiy, Nikita I Ershov, Dmitry Yu Oshchepkov, Vsevolod J Makeev, T C Hodgman and Tatyana I Merkulova
    Citation: BMC Genomics 2014 15:80
    Content type: Research article Published on:

  12. Induced pluripotent stem cells (iPSCs) derived from somatic cells have enormous potential for clinical applications. Notably, it was recently reported that reprogramming from somatic cells to iPSCs can induce ...

    Authors: Yulin Chen, Lin Guo, Jiekai Chen, Xiangjie Zhao, Weichen Zhou, Cheng Zhang, Jiucun Wang, Li Jin, Duanqing Pei and Feng Zhang
    Citation: BMC Genomics 2014 15:79
    Content type: Research article Published on:

  13. Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxta...

    Authors: Shuo Zhang, Chanjuan Tang, Qiang Zhao, Jing Li, Lifang Yang, Lufeng Qie, Xingke Fan, Lin Li, Ning Zhang, Meicheng Zhao, Xiaotong Liu, Yang Chai, Xue Zhang, Hailong Wang, Yingtao Li, Wen Li…
    Citation: BMC Genomics 2014 15:78
    Content type: Research article Published on:

  14. Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cult...

    Authors: Yong-Mei Bi, Ann Meyer, Gregory S Downs, Xuejiang Shi, Ashraf El-kereamy, Lewis Lukens and Steven J Rothstein
    Citation: BMC Genomics 2014 15:77
    Content type: Research article Published on:

  16. In social groups, dominant individuals may socially inhibit reproduction of subordinates using aggressive interactions or, in the case of highly eusocial insects, pheromonal communication. It has been hypothes...

    Authors: Amy L Toth, John F Tooker, Srihari Radhakrishnan, Robert Minard, Michael T Henshaw and Christina M Grozinger
    Citation: BMC Genomics 2014 15:75
    Content type: Research article Published on:

  17. Deregulation of Wnt/β-catenin signaling is a hallmark of the majority of sporadic forms of colorectal cancer and results in increased stability of the protein β-catenin. β-catenin is then shuttled into the nuc...

    Authors: Andreas Herbst, Vindi Jurinovic, Stefan Krebs, Susanne E Thieme, Helmut Blum, Burkhard Göke and Frank T Kolligs
    Citation: BMC Genomics 2014 15:74
    Content type: Research article Published on:

  18. Plant natural products have been co-opted for millennia by humans for various uses such as flavor, fragrances, and medicines. These compounds often are only produced in relatively low amounts and are difficult...

    Authors: Wei Gao, Hai-Xi Sun, Hongbin Xiao, Guanghong Cui, Matthew L Hillwig, Alana Jackson, Xiao Wang, Ye Shen, Nan Zhao, Liangxiao Zhang, Xiu-Jie Wang, Reuben J Peters and Luqi Huang
    Citation: BMC Genomics 2014 15:73
    Content type: Research article Published on:

  19. Oocytes mature in ovarian follicles surrounded by granulosa cells. During follicle growth, granulosa cells replicate and secrete hormones, particularly steroids close to ovulation. However, most follicles ceas...

    Authors: Claire Glister, Nicholas Hatzirodos, Katja Hummitzsch, Philip G Knight and Raymond J Rodgers
    Citation: BMC Genomics 2014 15:72
    Content type: Research article Published on:

  20. The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading ...

    Authors: Derek J Stefanik, Tristan J Lubinski, Brian R Granger, Allyson L Byrd, Adam M Reitzel, Lukas DeFilippo, Allison Lorenc and John R Finnerty
    Citation: BMC Genomics 2014 15:71
    Content type: Database Published on:

  21. MicroRNAs (miRNAs) are small regulatory molecules which post-transcriptionally regulate mRNA stability and translation. Several microRNAs have received attention due to their role as key metabolic regulators. ...

    Authors: Jan A Mennigen, Christopher J Martyniuk, Iban Seiliez, Stéphane Panserat and Sandrine Skiba-Cassy
    Citation: BMC Genomics 2014 15:70
    Content type: Research article Published on:

  22. Paclitaxel (Taxolâ„¢) is an important anticancer drug with a unique mode of action. The biosynthesis of paclitaxel had been considered restricted to the Taxus species until it was discovered in Taxomyces andreanae,...

    Authors: Yanfang Yang, Hainan Zhao, Roberto A Barrero, Baohong Zhang, Guiling Sun, Iain W Wilson, Fuliang Xie, Kevin D Walker, Joshua W Parks, Robert Bruce, Guangwu Guo, Li Chen, Yong Zhang, Xin Huang, Qi Tang, Hongwei Liu…
    Citation: BMC Genomics 2014 15:69
    Content type: Research article Published on:

  23. Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throug...

    Authors: Andrew C Clarke, Stefan Prost, Jo-Ann L Stanton, W Timothy J White, Matthew E Kaplan and Elizabeth A Matisoo-Smith
    Citation: BMC Genomics 2014 15:68
    Content type: Methodology article Published on:

  24. Wheat is an excellent plant species for nuclear mitochondrial interaction studies due to availability of large collection of alloplasmic lines. These lines exhibit different vegetative and physiological proper...

    Authors: Andrzej K Noyszewski, Farhad Ghavami, Loai M Alnemer, Ali Soltani, Yong Q Gu, Naxin Huo, Steven Meinhardt, Penny MA Kianian and Shahryar F Kianian
    Citation: BMC Genomics 2014 15:67
    Content type: Research article Published on:

  25. A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense res...

    Authors: Danielle C Cardoso, Juliana C Martinati, Poliana F Giachetto, Ramon O Vidal, Marcelo F Carazzolle, Lilian Padilha, Oliveiro Guerreiro-Filho and Mirian P Maluf
    Citation: BMC Genomics 2014 15:66
    Content type: Research article Published on:

  26. The relationships between bacterial genomes are complicated by rampant horizontal gene transfer, varied selection pressures, acquisition of new genes, loss of genes, and divergence of genes, even in closely re...

    Authors: Joe Rokicki, David Knox, Robin D Dowell and Shelley D Copley
    Citation: BMC Genomics 2014 15:65
    Content type: Software Published on:

  27. The copy number variation (CNV) in beta-defensin genes (DEFB) on human chromosome 8p23 has been proposed to contribute to the phenotypic differences in inflammatory diseases. However, determination of exact DE...

    Authors: Xianghong Zhang, Sebastian Müller, Michael Möller, Klaus Huse, Stefan Taudien, Malte Book, Frank Stuber, Matthias Platzer and Marco Groth
    Citation: BMC Genomics 2014 15:64
    Content type: Methodology article Published on:

  28. A close match of the HLA alleles between donor and recipient is an important prerequisite for successful unrelated hematopoietic stem cell transplantation. To increase the chances of finding an unrelated donor...

    Authors: Vinzenz Lange, Irina Böhme, Jan Hofmann, Kathrin Lang, Jürgen Sauter, Bianca Schöne, Patrick Paul, Viviane Albrecht, Johanna M Andreas, Daniel M Baier, Jochen Nething, Ulf Ehninger, Carmen Schwarzelt, Julia Pingel, Gerhard Ehninger and Alexander H Schmidt
    Citation: BMC Genomics 2014 15:63
    Content type: Methodology article Published on:

  29. Genome wide association studies (GWAS) in most cattle breeds result in large genomic intervals of significant associations making it difficult to identify causal mutations. This is due to the extensive, low-le...

    Authors: Lesley-Ann Raven, Benjamin G Cocks and Ben J Hayes
    Citation: BMC Genomics 2014 15:62
    Content type: Research article Published on:

  30. Sequence alignment has become an indispensable tool in modern molecular biology research, and probabilistic sequence alignment models have been shown to provide an effective framework for building accurate seq...

    Authors: Byung-Jun Yoon
    Citation: BMC Genomics 2014 15(Suppl 1):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  31. Hepatocellular carcinoma (HCC) is one of the most highly malignant and lethal cancers of the world. Its pathogenesis has been reported to be multi-factorial, and the molecular carcinogenesis of HCC can not be ...

    Authors: Lin Wei, Baofeng Lian, Yuannv Zhang, Wei Li, Jianren Gu, Xianghuo He and Lu Xie
    Citation: BMC Genomics 2014 15(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  32. Taxonomic annotation of reads is an important problem in metagenomic analysis. Existing annotation tools, which rely on the approach of aligning each read to the taxonomic structure, are unable to annotate man...

    Authors: Yi Wang, Henry Chi Ming Leung, Siu Ming Yiu and Francis Yuk Lun Chin
    Citation: BMC Genomics 2014 15(Suppl 1):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  33. Due to the importance of Penicillium chrysogenum holding in medicine, the genome of low-penicillin producing laboratorial strain Wisconsin54-1255 had been sequenced and fully annotated. Through classical mutagene...

    Authors: Fu-Qiang Wang, Jun Zhong, Ying Zhao, Jingfa Xiao, Jing Liu, Meng Dai, Guizhen Zheng, Li Zhang, Jun Yu, Jiayan Wu and Baoling Duan
    Citation: BMC Genomics 2014 15(Suppl 1):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  34. In order to have a better understanding of unexplained heritability for complex diseases in conventional Genome-Wide Association Studies (GWAS), aggregated association analyses based on predefined functional r...

    Authors: Meng Lu, Hye-Seung Lee, David Hadley, Jianhua Z Huang and Xiaoning Qian
    Citation: BMC Genomics 2014 15(Suppl 1):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  35. In mass spectrometry-based proteomics, the statistical significance of a peptide-spectrum or protein-spectrum match is an important indicator of the correctness of the peptide or protein identification. In bot...

    Authors: Xiaowen Liu, Matthew W Segar, Shuai Cheng Li and Sangtae Kim
    Citation: BMC Genomics 2014 15(Suppl 1):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  36. During eukaryotic genome evolution, tandem gene duplication is the most frequent event giving rise to clustered gene families. However, how expression divergence between tandemly duplicated genes has emerged a...

    Authors: Ben-Yang Liao and Andrew Ying-Fei Chang
    Citation: BMC Genomics 2014 15(Suppl 1):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  37. Histone proteins are subject to various posttranslational modifications (PTMs). Elucidating their functional relationships is crucial toward understanding many biological processes. Bayesian network (BN)-based...

    Authors: Ngoc Tu Le, Tu Bao Ho, Bich Hai Ho and Dang Hung Tran
    Citation: BMC Genomics 2014 15(Suppl 1):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  38. Gene set enrichment analysis (GSEA) is an important approach to the analysis of coordinate expression changes at a pathway level. Although many statistical and computational methods have been proposed for GSEA...

    Authors: Yinglei Lai, Fanni Zhang, Tapan K Nayak, Reza Modarres, Norman H Lee and Timothy A McCaffrey
    Citation: BMC Genomics 2014 15(Suppl 1):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  40. Reliable prediction of stability changes induced by a single amino acid substitution is an important aspect of computational protein design. Several machine learning methods capable of predicting stability cha...

    Authors: Lukas Folkman, Bela Stantic and Abdul Sattar
    Citation: BMC Genomics 2014 15(Suppl 1):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  41. Tuberculosis has become a major health problem being the second leading cause of death worldwide. Mycobacterium tuberculosis secretes a virulence factor, protein tyrosine phosphatase B (mPTPB) in the cytoplasm of...

    Authors: Jaspreet Kaur Dhanjal, Sonam Grover, Sudhanshu Sharma, Ajeet Kumar Singh and Abhinav Grover
    Citation: BMC Genomics 2014 15(Suppl 1):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  42. Prediction of the structural classes of proteins can provide important information about their functionalities as well as their major tertiary structures. It is also considered as an important step towards pro...

    Authors: Abdollah Dehzangi, Kuldip Paliwal, James Lyons, Alok Sharma and Abdul Sattar
    Citation: BMC Genomics 2014 15(Suppl 1):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  43. Post-translational modification (PTM) of transcriptional factors and chromatin remodelling proteins is recognized as a major mechanism by which transcriptional regulation occurs. Chromatin immunoprecipitation ...

    Authors: Chia-Yang Cheng, Chia-Han Chu, Hung-Wei Hsu, Fang-Rong Hsu, Chung Yi Tang, Wen-Ching Wang, Hsing-Jien Kung and Pei-Ching Chang
    Citation: BMC Genomics 2014 15(Suppl 1):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  44. The gynoecium is one of the most complex organs of angiosperms specialized for seed production and dispersal, but only several genes important for ovule or embryo sac development were identified by using femal...

    Authors: Wen-qin Fu, Zhi-gang Zhao, Xian-hong Ge, Li Ding and Zai-yun Li
    Citation: BMC Genomics 2014 15:61
    Content type: Research article Published on:

  46. Prion diseases are characterized by the accumulation of the pathogenic PrPSc protein, mainly in the brain and the lymphoreticular system. Although prions multiply/accumulate in the lymph nodes without any detecta...

    Authors: Hicham Filali, Inmaculada Martín-Burriel, Frank Harders, Luis Varona, Carlos Hedman, Diego R Mediano, Marta Monzón, Alex Bossers, Juan J Badiola and Rosa Bolea
    Citation: BMC Genomics 2014 15:59
    Content type: Research article Published on:

  47. Mycobacterium avium subsp. avium (Maa) and M. avium subsp. hominissuis (Mah) are environmental mycobacteria and significant opportunistic pathogens. Mycobacterium avium infections in humans and pigs are mainly du...

    Authors: Angelika Agdestein, Anya Jones, Arnar Flatberg, Tone B Johansen, Inger Austrheim Heffernan, Berit Djønne, Anthony Bosco and Ingrid Olsen
    Citation: BMC Genomics 2014 15:58
    Content type: Research article Published on:

  48. Klebsiella pneumoniae is an important opportunistic pathogen associated with nosocomial and community-acquired infections. A wide repertoire of virulence and antimicrobial resistance genes is present in K. pneumo...

    Authors: Pablo Ivan Pereira Ramos, Renata Christina Picão, Luiz Gonzaga Paula de Almeida, Nicholas Costa B Lima, Raquel Girardello, Ana Carolina P Vivan, Danilo E Xavier, Fernando G Barcellos, Marsileni Pelisson, Eliana C Vespero, Claudine Médigue, Ana Tereza Ribeiro de Vasconcelos, Ana Cristina Gales and Marisa Fabiana Nicolás
    Citation: BMC Genomics 2014 15:54
    Content type: Research article Published on:

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BMC Genomics

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