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  1. Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In t...

    Authors: Xiao-Wei Wang, Qiong-Yi Zhao, Jun-Bo Luan, Yu-Jun Wang, Gen-Hong Yan and Shu-Sheng Liu
    Citation: BMC Genomics 2012 13:529
  2. In bacteria, the weak correlations at the genome scale between mRNA and protein levels suggest that not all mRNAs are translated with the same efficiency. To experimentally explore mRNA translational level reg...

    Authors: Flora Picard, Hélène Milhem, Pascal Loubière, Béatrice Laurent, Muriel Cocaign-Bousquet and Laurence Girbal
    Citation: BMC Genomics 2012 13:528
  3. Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allel...

    Authors: Marina de Miguel, Nuria de Maria, M Ángeles Guevara, Luis Diaz, Enrique Sáez-Laguna, David Sánchez-Gómez, Emilie Chancerel, Ismael Aranda, Carmen Collada, Christophe Plomion, José-Antonio Cabezas and María-Teresa Cervera
    Citation: BMC Genomics 2012 13:527
  4. Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variable “CYPomes” ranging from one to more tha...

    Authors: Venkatesh Moktali, Jongsun Park, Natalie D Fedorova-Abrams, Bongsoo Park, Jaeyoung Choi, Yong-Hwan Lee and Seogchan Kang
    Citation: BMC Genomics 2012 13:525
  5. Assessing the reliability of experimental replicates (or global alterations corresponding to different experimental conditions) is a critical step in analyzing RNA-Seq data. Pearson’s correlation coefficient r ha...

    Authors: Stefan K Schulze, Rahul Kanwar, Meike Gölzenleuchter, Terry M Therneau and Andreas S Beutler
    Citation: BMC Genomics 2012 13:524
  6. Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing tec...

    Authors: Wanxing Wang, Shunmou Huang, Yumei Liu, Zhiyuan Fang, Limei Yang, Wei Hua, Suxia Yuan, Shengyi Liu, Jifeng Sun, Mu Zhuang, Yangyong Zhang and Aisong Zeng
    Citation: BMC Genomics 2012 13:523
  7. Switchgrass (Panicum virgatum) is a herbaceous crop for the cellulosic biofuel feedstock development in the USA and Europe. As switchgrass is a naturally outcrossing species, accurate identification of selfed pro...

    Authors: Linglong Liu and Yanqi Wu
    Citation: BMC Genomics 2012 13:522
  8. The Guinea pig (Cavia porcellus) is one of the most extensively used animal models to study infectious diseases. However, despite its tremendous contribution towards understanding the establishment, progression a...

    Authors: Ruchi Jain, Bappaditya Dey and Anil K Tyagi
    Citation: BMC Genomics 2012 13:520
  9. The filamentous fungus Aspergillus fumigatus has become the most important airborne fungal pathogen causing life-threatening infections in immuno-compromised patients. Recently developed high-throughput transcrip...

    Authors: Sebastian Müller, Clara Baldin, Marco Groth, Reinhard Guthke, Olaf Kniemeyer, Axel A Brakhage and Vito Valiante
    Citation: BMC Genomics 2012 13:519
  10. Early stages of fruit development from initial set through exponential growth are critical determinants of size and yield, however, there has been little detailed analysis of this phase of development. In this...

    Authors: Kaori Ando, Kevin M Carr and Rebecca Grumet
    Citation: BMC Genomics 2012 13:518
  11. Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced ...

    Authors: Oscar Dias, Andreas K Gombert, Eugénio C Ferreira and Isabel Rocha
    Citation: BMC Genomics 2012 13:517
  12. B-cell non-Hodgkin lymphoma represents a diverse group of hematological malignancies, of which follicular lymphoma (FL) is one of the most common subtypes. Family and epidemiological studies suggest an importa...

    Authors: Christine F Skibola, Lucia Conde, Jia-Nee Foo, Jacques Riby, Keith Humphreys, Fenna CM Sillé, Hatef Darabi, Sylvia Sanchez, Henrik Hjalgrim, Jianjun Liu, Paige M Bracci and Karin E Smedby
    Citation: BMC Genomics 2012 13:516
  13. Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published...

    Authors: Joanne Purves, Matthew Blades, Yasrab Arafat, Salman A Malik, Christopher D Bayliss and Julie A Morrissey
    Citation: BMC Genomics 2012 13:515
  14. Guinea pig (Cavia porcellus) is an important model for human intestinal research. We have characterized the faecal microbiota of 60 guinea pigs using Illumina shotgun metagenomics, and used this data to compile a...

    Authors: Falk Hildebrand, Tine Ebersbach, Henrik Bjørn Nielsen, Xiaoping Li, Si Brask Sonne, Marcelo Bertalan, Peter Dimitrov, Lise Madsen, Junjie Qin, Jun Wang, Jeroen Raes, Karsten Kristiansen and Tine Rask Licht
    Citation: BMC Genomics 2012 13:514
  15. Owing to the low cost of the high throughput Next Generation Sequencing (NGS) technology, more and more species have been and will be sequenced. However, de novo assemblies of large eukaryotic genomes thus produc...

    Authors: Man Rao, Mireille Morisson, Thomas Faraut, Suzanne Bardes, Katia Fève, Emmanuelle Labarthe, Valérie Fillon, Yinhua Huang, Ning Li and Alain Vignal
    Citation: BMC Genomics 2012 13:513
  16. During sexual development, filamentous ascomycetes form complex, three-dimensional fruiting bodies for the protection and dispersal of sexual spores. Fruiting bodies contain a number of cell types not found in...

    Authors: Ines Teichert, Gabriele Wolff, Ulrich Kück and Minou Nowrousian
    Citation: BMC Genomics 2012 13:511
  17. In Gram-negative bacteria, the outer membrane is composed of an asymmetric lipid bilayer of phopspholipids and lipopolysaccharides, and the transmembrane proteins that reside in this membrane are almost exclus...

    Authors: Nagarajan Paramasivam, Michael Habeck and Dirk Linke
    Citation: BMC Genomics 2012 13:510
  18. The events leading to sepsis start with an invasive infection of a primary organ of the body followed by an overwhelming systemic response. Intra-abdominal infections are the second most common cause of sepsis...

    Authors: Minny Bhatty, Ruping Fan, William M Muir, Stephen B Pruett and Bindu Nanduri
    Citation: BMC Genomics 2012 13:509
  19. Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a significant bacterial pathogen that poses considerable clinical and public health challenges. The majority of the CA-MRSA disease...

    Authors: Ryan Tewhey, Christopher R Cannavino, John AD Leake, Vikas Bansal, Eric J Topol, Ali Torkamani, John S Bradley and Nicholas J Schork
    Citation: BMC Genomics 2012 13:508
  20. Genomic and transcriptomic approaches have the potential for unveiling the genome-wide response to environmental perturbations. The abundance of the catadromous European eel (Anguilla anguilla) stock has been dec...

    Authors: Jose Martin Pujolar, Ilaria AM Marino, Massimo Milan, Alessandro Coppe, Gregory E Maes, Fabrizio Capoccioni, Eleonora Ciccotti, Lieven Bervoets, Adrian Covaci, Claude Belpaire, Gordon Cramb, Tomaso Patarnello, Luca Bargelloni, Stefania Bortoluzzi and Lorenzo Zane
    Citation: BMC Genomics 2012 13:507
  21. Genome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as ...

    Authors: Katherine H Fisher, Victoria M Wright, Amy Taylor, Martin P Zeidler and Stephen Brown
    Citation: BMC Genomics 2012 13:506
  22. Metastasis is characterized by spreading of neoplastic cells to an organ other than where they originated and is the predominant cause of death among cancer patients. This holds true for melanoma, whose incide...

    Authors: Jared J Gartner, Sean Davis, Xiaomu Wei, Jimmy C Lin, Niraj S Trivedi, Jamie K Teer, Paul S Meltzer, Steven A Rosenberg and Yardena Samuels
    Citation: BMC Genomics 2012 13:505
  23. The function of RNA from the non-coding (the so called “dark matter”) regions of the genome has been a subject of considerable recent debate. Perhaps the most controversy is regarding the function of RNAs foun...

    Authors: Georges St Laurent, Dmitry Shtokalo, Michael R Tackett, Zhaoqing Yang, Tatyana Eremina, Claes Wahlestedt, Silvio Urcuqui-Inchima, Bernd Seilheimer, Timothy A McCaffrey and Philipp Kapranov
    Citation: BMC Genomics 2012 13:504
  24. Theileria parva is a tick-borne protozoan parasite, which causes East Coast Fever, a disease of cattle in sub-Saharan Africa. Like Plasmodium falciparum, the parasite undergoes a transient diploid life-cycle stag...

    Authors: Sonal Henson, Richard P Bishop, Subhash Morzaria, Paul R Spooner, Roger Pelle, Lucy Poveda, Martin Ebeling, Erich Küng, Ulrich Certa, Claudia A Daubenberger and Weihong Qi
    Citation: BMC Genomics 2012 13:503
  25. Pepper (Capsicum annuum L.) is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site (NBS)-le...

    Authors: Hongjian Wan, Wei Yuan, Qingjing Ye, Rongqing Wang, Meiying Ruan, Zhimiao Li, Guozhi Zhou, Zhuping Yao, Jing Zhao, Shujun Liu and Yuejian Yang
    Citation: BMC Genomics 2012 13:502
  26. Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Und...

    Authors: Manuel Aranda, Michael K DeSalvo, Till Bayer, Monica Medina and Christian R Voolstra
    Citation: BMC Genomics 2012 13:501
  27. Many hypothesis-driven genetic studies require the ability to comprehensively and efficiently target specific regions of the genome to detect sequence variations. Often, sample availability is limited requirin...

    Authors: Abdou ElSharawy, Jason Warner, Jeff Olson, Michael Forster, Markus B Schilhabel, Darren R Link, Stefan Rose-John, Stefan Schreiber, Philip Rosenstiel, James Brayer and Andre Franke
    Citation: BMC Genomics 2012 13:500
  28. Silicon plays important biological roles, but the mechanisms of cellular responses to silicon are poorly understood. We report the first analysis of cell cycle arrest and recovery from silicon starvation in th...

    Authors: Roshan Prakash Shrestha, Benoit Tesson, Trina Norden-Krichmar, Stephen Federowicz, Mark Hildebrand and Andrew E Allen
    Citation: BMC Genomics 2012 13:499
  29. The transformation of a developing epithelium into an adult structure is a complex process, which often involves coordinated changes in cell proliferation, metabolism, adhesion, and shape. To identify genetic ...

    Authors: David D O’Keefe, Sean R Thomas, Kelsey Bolin, Ellen Griggs, Bruce A Edgar and Laura A Buttitta
    Citation: BMC Genomics 2012 13:498
  30. The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Or...

    Authors: Fuyu Xu, Myoung-Ryoul Park, Ai Kitazumi, Venura Herath, Bijayalaxmi Mohanty, Song Joong Yun and Benildo G de los Reyes
    Citation: BMC Genomics 2012 13:497
  31. Ubiquitin-mediated protein modification and degradation are believed to play important roles in mammalian spermatogenesis. The catalogues of ubiquitin activating enzymes, conjugating enzymes, and ligases (E3s)...

    Authors: Xiaojun Hou, Wei Zhang, Zhenyu Xiao, Haiyun Gan, Xiwen Lin, Shangying Liao and Chunsheng Han
    Citation: BMC Genomics 2012 13:495
  32. Broiler breeders fed ad libitum are characterised by multiple ovulation, which leads to poor shell quality and egg production. Multiple ovulation is controlled by food restriction in commercial flocks. However, t...

    Authors: Neil A McDerment, Peter W Wilson, David Waddington, Ian C Dunn and Paul M Hocking
    Citation: BMC Genomics 2012 13:494
  33. Macrophomina phaseolina is one of the most destructive necrotrophic fungal pathogens that infect more than 500 plant species throughout the world. It can grow rapidly in infected plants and subsequently produces ...

    Authors: Md Shahidul Islam, Md Samiul Haque, Mohammad Moinul Islam, Emdadul Mannan Emdad, Abdul Halim, Quazi Md Mosaddeque Hossen, Md Zakir Hossain, Borhan Ahmed, Sifatur Rahim, Md Sharifur Rahman, Md Monjurul Alam, Shaobin Hou, Xuehua Wan, Jennifer A Saito and Maqsudul Alam
    Citation: BMC Genomics 2012 13:493
  34. Bread wheat is one of the world’s most important food crops and considerable efforts have been made to develop genomic resources for this species. This includes an on-going project by the International Wheat G...

    Authors: Andreas W Schreiber, Matthew J Hayden, Kerrie L Forrest, Stephan L Kong, Peter Langridge and Ute Baumann
    Citation: BMC Genomics 2012 13:492
  35. RNA interference (RNAi) is commonly applied in genome-scale gene functional screens. However, a one-on-one RNAi analysis that targets each gene is cost-ineffective and laborious. Previous studies have indicate...

    Authors: Chih-Hung Chang, Hsiang-Iu Wang, Hsiang-Chia Lu, Cheng-En Chen, Hong-Hwa Chen, Hsin-Hung Yeh and Chuan Yi Tang
    Citation: BMC Genomics 2012 13:491
  36. Genome-wide association studies (GWAS) have provided a large set of genetic loci influencing the risk for many common diseases. Association studies typically analyze one specific trait in single populations in...

    Authors: Matthias Arnold, Mara L Hartsperger, Hansjörg Baurecht, Elke Rodríguez, Benedikt Wachinger, Andre Franke, Michael Kabesch, Juliane Winkelmann, Arne Pfeufer, Marcel Romanos, Thomas Illig, Hans-Werner Mewes, Volker Stümpflen and Stephan Weidinger
    Citation: BMC Genomics 2012 13:490
  37. All cows experience bacterial contamination and tissue injury in the uterus postpartum, instigating a local inflammatory immune response. However mechanisms that control inflammation and achieve a physiologica...

    Authors: Cathriona Foley, Aspinas Chapwanya, Christopher J Creevey, Fernando Narciandi, Derek Morris, Elaine M Kenny, Paul Cormican, John J Callanan, Cliona O’Farrelly and Kieran G Meade
    Citation: BMC Genomics 2012 13:489
  38. Lymphocytes act as a major component of the adaptive immune system, taking very crucial responsibility for immunity. Differences in proportions of T-cell subpopulations in peripheral blood among individuals un...

    Authors: Xin Lu, Wei-Xuan Fu, Yan-Ru Luo, Xiang-Dong Ding, Jia-Peng Zhou, Yang Liu, Jian-Feng Liu and Qin Zhang
    Citation: BMC Genomics 2012 13:488
  39. Seaweeds of the Laurencia genus have a broad geographic distribution and are largely recognized as important sources of secondary metabolites, mainly halogenated compounds exhibiting diverse potential pharmacolog...

    Authors: Louisi Souza de Oliveira, Gustavo Bueno Gregoracci, Genivaldo Gueiros Zacarias Silva, Leonardo Tavares Salgado, Gilberto Amado Filho, Marcio Alves-Ferreira, Renato Crespo Pereira and Fabiano L Thompson
    Citation: BMC Genomics 2012 13:487
  40. Prion diseases are neurodegenerative diseases that are characterized by the conversion of the cellular prion protein (PrPc) into a pathogenic isoform (PrPSc). It is known that neurodegeneration is often accompani...

    Authors: Judith Montag, Markus Brameier, Ann-Christin Schmädicke, Sabine Gilch, Hermann M Schätzl and Dirk Motzkus
    Citation: BMC Genomics 2012 13:486
  41. In the post-genomic era several methods of computational genomics are emerging to understand how the whole information is structured within genomes. Literature of last five years accounts for several alignment...

    Authors: Alberto Castellini, Giuditta Franco and Vincenzo Manca
    Citation: BMC Genomics 2012 13:485
  42. RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental...

    Authors: José A Robles, Sumaira E Qureshi, Stuart J Stephen, Susan R Wilson, Conrad J Burden and Jennifer M Taylor
    Citation: BMC Genomics 2012 13:484
  43. Neurodegenerative diseases are progressive and irreversible and they can be initiated by mutations in specific genes. Spalt-like genes (Sall) encode transcription factors expressed in the central nervous system. ...

    Authors: María José Ferreiro, Naiara Rodríguez-Ezpeleta, Coralia Pérez, Michael Hackenberg, Ana María Aransay, Rosa Barrio and Rafael Cantera
    Citation: BMC Genomics 2012 13:483
  44. The analysis of gene promoters is essential to understand the mechanisms of transcriptional regulation required under the effects of physiological processes, nutritional intake or pathologies. In higher eukary...

    Authors: Pierre-Yves Dupont, Audrey Guttin, Jean-Paul Issartel and Georges Stepien
    Citation: BMC Genomics 2012 13:482
  45. MicroRNAs (miRNAs) are small RNAs (sRNAs) approximately 21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. Within this contex...

    Authors: Abdelali Barakat, Aditya Sriram, Joseph Park, Tetyana Zhebentyayeva, Dorrie Main and Albert Abbott
    Citation: BMC Genomics 2012 13:481
  46. Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects app...

    Authors: Kevin Flores, Florian Wolschin, Jason J Corneveaux, April N Allen, Matthew J Huentelman and Gro V Amdam
    Citation: BMC Genomics 2012 13:480
  47. Environmental stresses and inhibitors encountered by Saccharomyces cerevisiae strains are the main limiting factors in bioethanol fermentation. Strains with different genetic backgrounds usually show diverse stre...

    Authors: Dao-Qiong Zheng, Pin-Mei Wang, Jie Chen, Ke Zhang, Tian-Zhe Liu, Xue-Chang Wu, Yu-Dong Li and Yu-Hua Zhao
    Citation: BMC Genomics 2012 13:479

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