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  1. Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers fo...

    Authors: Ikuko N Motoike, Mitsuyo Matsumoto, Inaho Danjoh, Fumiki Katsuoka, Kaname Kojima, Naoki Nariai, Yukuto Sato, Yumi Yamaguchi-Kabata, Shin Ito, Hisaaki Kudo, Ichiko Nishijima, Satoshi Nishikawa, Xiaoqing Pan, Rumiko Saito, Sakae Saito, Tomo Saito…
    Citation: BMC Genomics 2014 15:673
    Content type: Research article Published on:

  2. We have previously proposed transcriptome instability as a genome-wide, pre-mRNA splicing-related characteristic of colorectal cancer. Here, we explore the hypothesis of transcriptome instability being a gener...

    Authors: Anita Sveen, Bjarne Johannessen, Manuel R Teixeira, Ragnhild A Lothe and Rolf I Skotheim
    Citation: BMC Genomics 2014 15:672
    Content type: Research article Published on:

  3. The molecular mechanisms involved in plant tolerance to either drought or cold have been extensively studied in many plant species. However, few studies have focused on their comparisons especially using non-m...

    Authors: Yaqi Wu, Wei Wei, Xinyue Pang, Xuefeng Wang, Huiling Zhang, Bo Dong, Yanping Xing, Xinguo Li and Maoyan Wang
    Citation: BMC Genomics 2014 15:671
    Content type: Research article Published on:

  4. Recent mapping of 5-hydroxymethylcytosine (5hmC) provides a genome-wide view of the distribution of this important chromatin mark. However, the role of 5hmC in specific regulatory regions is not clear, especia...

    Authors: Inchan Choi, Rinho Kim, Hee-Woong Lim, Klaus H Kaestner and Kyoung-Jae Won
    Citation: BMC Genomics 2014 15:670
    Content type: Research article Published on:

  5. Emerging studies demonstrate that single nucleotide polymorphisms (SNPs) resided in the microRNA recognition element seed sites (MRESSs) in 3′UTR of mRNAs are putative biomarkers for human diseases and cancers...

    Authors: Di Wu, Gang Yang, Lifang Zhang, Jiwei Xue, Zhining Wen and Menglong Li
    Citation: BMC Genomics 2014 15:669
    Content type: Research article Published on:

  6. Kaposi’s sarcoma associated herpes virus (KSHV) is associated with tumors of endothelial and lymphoid origin. During latent infection, KSHV expresses miR-K12-11, an ortholog of the human tumor gene hsa-miR-155...

    Authors: Yajie Yang, Isaac W Boss, Lauren M McIntyre and Rolf Renne
    Citation: BMC Genomics 2014 15:668
    Content type: Research article Published on:

  7. Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of thre...

    Authors: Nathan L Bachmann, Tamieka A Fraser, Claire Bertelli, Martina Jelocnik, Amber Gillett, Oliver Funnell, Cheyne Flanagan, Garry S A Myers, Peter Timms and Adam Polkinghorne
    Citation: BMC Genomics 2014 15:667
    Content type: Research article Published on:

  8. Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. Amongst the most...

    Authors: Christophe Regnault, Isabelle AM Worms, Christine Oger-Desfeux, Christelle MelodeLima, Sylvie Veyrenc, Marie-Laure Bayle, Bruno Combourieu, Aurélie Bonin, Julien Renaud, Muriel Raveton and Stéphane Reynaud
    Citation: BMC Genomics 2014 15:666
    Content type: Research article Published on:

  9. Most of the proteins contained in royal jelly (RJ) are secreted from the hypopharyngeal glands (HG) of young bees. Although generic protein composition of RJ has been investigated, little is known about how ag...

    Authors: Ting Ji, Zhenguo Liu, Jie Shen, Fang Shen, Qin Liang, Liming Wu, Guohong Chen and Miguel Corona
    Citation: BMC Genomics 2014 15:665
    Content type: Research article Published on:

  10. Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by tec...

    Authors: Yukuto Sato, Kaname Kojima, Naoki Nariai, Yumi Yamaguchi-Kabata, Yosuke Kawai, Mamoru Takahashi, Takahiro Mimori and Masao Nagasaki
    Citation: BMC Genomics 2014 15:664
    Content type: Software Published on:

  12. Glucocorticoids (GCs) cause apoptosis in malignant cells of lymphoid lineage by transcriptionally regulating a plethora of genes. As a result, GCs are included in almost all treatment protocols for lymphoid ma...

    Authors: Daniel Bindreither, Simone Ecker, Barbara Gschirr, Anita Kofler, Reinhard Kofler and Johannes Rainer
    Citation: BMC Genomics 2014 15:662
    Content type: Research article Published on:

  13. With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases. However, computational...

    Authors: Pubudu Saneth Samarakoon, Hanne Sørmo Sorte, Bjørn Evert Kristiansen, Tove Skodje, Ying Sheng, Geir E Tjønnfjord, Barbro Stadheim, Asbjørg Stray-Pedersen, Olaug Kristin Rødningen and Robert Lyle
    Citation: BMC Genomics 2014 15:661
    Content type: Research article Published on:

  14. Metarhizium anisopliae is an important fungal biocontrol agent of insect pests of agricultural crops. Genomics can aid the successful commercialization of biopesticides by identification of key genes differentiat...

    Authors: Julie A Pattemore, James K Hane, Angela H Williams, Bree AL Wilson, Ben J Stodart and Gavin J Ash
    Citation: BMC Genomics 2014 15:660
    Content type: Research article Published on:

  15. Microgravity facilitates the opportunistic infections by augmenting the pathogenic virulence and suppressing the host resistance. Hence the extraterrestrial infections may activate potentially novel bionetwork...

    Authors: Nabarun Chakraborty, Aarti Gautam, Seid Muhie, Stacy-Ann Miller, Marti Jett and Rasha Hammamieh
    Citation: BMC Genomics 2014 15:659
    Content type: Research article Published on:

  16. Cilia are microtubule-based organelles protruding from almost all mammalian cells which, when dysfunctional, result in genetic disorders called “ciliopathies”. High-throughput studies have revealed that cilia ...

    Authors: Roberto Amato, Manuela Morleo, Laura Giaquinto, Diego di Bernardo and Brunella Franco
    Citation: BMC Genomics 2014 15:658
    Content type: Research article Published on:

  17. Autogenous cis-regulators of ribosomal protein synthesis play a critical role in maintaining the stoichiometry of ribosome components. Structured portions within an mRNA transcript typically interact with specifi...

    Authors: Betty L Slinger, Kaila Deiorio-Haggar, Jon S Anthony, Molly M Gilligan and Michelle M Meyer
    Citation: BMC Genomics 2014 15:657
    Content type: Research article Published on:

  18. Inflammation triggered by infection or injury is tightly controlled by glucocorticoid hormones which signal via a dedicated transcription factor, the Glucocorticoid Receptor (GR), to regulate hundreds of genes...

    Authors: Yurii Chinenov, Maddalena Coppo, Rebecca Gupte, Maria A Sacta and Inez Rogatsky
    Citation: BMC Genomics 2014 15:656
    Content type: Research article Published on:

  19. Teleosts are characterized by a remarkable breadth of sexual mechanisms including various forms of hermaphroditism. Sparidae is a fish family exhibiting gonochorism or hermaphroditism even in closely related s...

    Authors: Tereza Manousaki, Alexandros Tsakogiannis, Jacques Lagnel, Elena Sarropoulou, Jenny Z Xiang, Nikos Papandroulakis, Constantinos C Mylonas and Costas S Tsigenopoulos
    Citation: BMC Genomics 2014 15:655
    Content type: Research article Published on:

  20. Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remar...

    Authors: Bas E Dutilh, Cristiane C Thompson, Ana CP Vicente, Michel A Marin, Clarence Lee, Genivaldo GZ Silva, Robert Schmieder, Bruno GN Andrade, Luciane Chimetto, Daniel Cuevas, Daniel R Garza, Iruka N Okeke, Aaron Oladipo Aboderin, Jessica Spangler, Tristen Ross, Elizabeth A Dinsdale…
    Citation: BMC Genomics 2014 15:654
    Content type: Research article Published on:

  21. Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occ...

    Authors: Long Jin, Zhi Jiang, Yudong Xia, Ping’er Lou, Lei Chen, Hongmei Wang, Lu Bai, Yanmei Xie, Yihui Liu, Wei Li, Bangsheng Zhong, Junfang Shen, An’an Jiang, Li Zhu, Jinyong Wang, Xuewei Li…
    Citation: BMC Genomics 2014 15:653
    Content type: Research article Published on:

  22. The major Gram-positive coccoid pathogens cause similar invasive diseases and show high rates of antimicrobial resistance. Uncharacterised proteins shared by these organisms may be involved in virulence or be ...

    Authors: Antonio J Martín-Galiano, José Yuste, María I Cercenado and Adela G de la Campa
    Citation: BMC Genomics 2014 15:652
    Content type: Research article Published on:

  23. The ATP-binding cassette (ABC) transporter superfamily is one of the largest transporter gene families and is observed in all animal taxa. Although a large set of transcriptomic data was recently assembled for...

    Authors: Chang-Bum Jeong, Bo-Mi Kim, Jae-Seong Lee and Jae-Sung Rhee
    Citation: BMC Genomics 2014 15:651
    Content type: Research article Published on:

  24. Chemical senses are one of the foremost means by which organisms make sense of their environment, among them the olfactory and gustatory sense of vertebrates and arthropods. Both senses use large repertoires o...

    Authors: Adnan S Syed and Sigrun I Korsching
    Citation: BMC Genomics 2014 15:650
    Content type: Research article Published on:

  25. 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:

  26. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  45. 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:

  46. 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:

  47. 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:

  49. 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:

  50. 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:

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BMC Genomics

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