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  1. 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
    Content type: Research article Published on:

  2. 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
    Content type: Research article Published on:

  3. 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
    Content type: Research article Published on:

  4. 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
    Content type: Research article Published on:

  5. 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
    Content type: Research article Published on:

  6. 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
    Content type: Research article Published on:

  7. 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
    Content type: Research article Published on:

  8. 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
    Content type: Research article Published on:

  9. 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
    Content type: Research article Published on:

  10. 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
    Content type: Research article Published on:

  11. 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
    Content type: Research article Published on:

  12. 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
    Content type: Research article Published on:

  13. 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
    Content type: Methodology article Published on:

  14. 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
    Content type: Research article Published on:

  15. 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
    Content type: Research article Published on:

  16. 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
    Content type: Research article Published on:

  18. 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
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  20. 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
    Content type: Research article Published on:

  21. 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
    Content type: Research article Published on:

  22. 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
    Content type: Methodology article Published on:

  23. 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
    Content type: Research article Published on:

  24. 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
    Content type: Research article Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Research article Published on:

  27. 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
    Content type: Research article Published on:

  28. 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
    Content type: Methodology article Published on:

  29. 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
    Content type: Research article Published on:

  30. 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
    Content type: Research article Published on:

  31. 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
    Content type: Research article Published on:

  32. 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
    Content type: Research article Published on:

  33. 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
    Content type: Research article Published on:

  34. 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
    Content type: Research article Published on:

  35. While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes. Here, we performed a comparative analysis of the predicted (proved in part) orc/cdc...

    Authors: Zhenfang Wu, Hailong Liu, Jingfang Liu, Xiaoqing Liu and Hua Xiang
    Citation: BMC Genomics 2012 13:478
    Content type: Research article Published on:

  36. A detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of...

    Authors: Dorothee Nickles, Lohith Madireddy, Shan Yang, Pouya Khankhanian, Steve Lincoln, Stephen L Hauser, Jorge R Oksenberg and Sergio E Baranzini
    Citation: BMC Genomics 2012 13:477
    Content type: Research article Published on:

  37. miRNAs are short single-stranded non-coding RNAs involved in post-transcriptional gene regulation that play a major role in normal biological functions and diseases. Little is currently known about how express...

    Authors: Michael J Parsons, Christina Grimm, Jose L Paya-Cano, Cathy Fernandes, Lin Liu, Vivek M Philip, Elissa J Chesler, Wilfried Nietfeld, Hans Lehrach and Leonard C Schalkwyk
    Citation: BMC Genomics 2012 13:476
    Content type: Research article Published on:

  38. Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consen...

    Authors: Xiao Yang, Patrick Charlebois, Sante Gnerre, Matthew G Coole, Niall J Lennon, Joshua Z Levin, James Qu, Elizabeth M Ryan, Michael C Zody and Matthew R Henn
    Citation: BMC Genomics 2012 13:475
    Content type: Methodology article Published on:

  39. The release of oil resulting from the blowout of the Deepwater Horizon (DH) drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread applic...

    Authors: Tzintzuni I Garcia, Yingjia Shen, Douglas Crawford, Marjorie F Oleksiak, Andrew Whitehead and Ronald B Walter
    Citation: BMC Genomics 2012 13:474
    Content type: Research article Published on:

  40. Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is av...

    Authors: Kyung-Do Park, Jongsun Park, Junsu Ko, Byung Chul Kim, Heui-Soo Kim, Kung Ahn, Kyoung-Tag Do, Hansol Choi, Hak-Min Kim, Sanghoon Song, Sunghoon Lee, Sungwoong Jho, Hong-Sik Kong, Young Mok Yang, Byung-Hak Jhun, Chulhong Kim…
    Citation: BMC Genomics 2012 13:473
    Content type: Research article Published on:

  41. Psoriasis is an immune-mediated disease characterised by chronically elevated pro-inflammatory cytokine levels, leading to aberrant keratinocyte proliferation and differentiation. Although certain clinical phe...

    Authors: Chrysanthi Ainali, Najl Valeyev, Gayathri Perera, Andrew Williams, Johann E Gudjonsson, Christos A Ouzounis, Frank O Nestle and Sophia Tsoka
    Citation: BMC Genomics 2012 13:472
    Content type: Research article Published on:

  42. A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400...

    Authors: Jessica E Butler, Nelson D Young, Muktak Aklujkar and Derek R Lovley
    Citation: BMC Genomics 2012 13:471
    Content type: Research article Published on:

  43. Studies conducted with gilthead sea bream (Sparus aurata L.) have determined the maximum dietary replacement of fish meal and oil without compromising growth or product quality. The present study aimed to analyze...

    Authors: Josep A Calduch-Giner, Ariadna Sitjà-Bobadilla, Grace C Davey, Michael T Cairns, Sadasivam Kaushik and Jaume Pérez-Sánchez
    Citation: BMC Genomics 2012 13:470
    Content type: Research article Published on:

  44. Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (...

    Authors: Ervin D Nagy, Yufang Guo, Shunxue Tang, John E Bowers, Rebecca A Okashah, Christopher A Taylor, Dong Zhang, Sameer Khanal, Adam F Heesacker, Nelly Khalilian, Andrew D Farmer, Noelia Carrasquilla-Garcia, R Varma Penmetsa, Douglas Cook, H Thomas Stalker, Niels Nielsen…
    Citation: BMC Genomics 2012 13:469
    Content type: Research article Published on:

  45. Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe chole...

    Authors: Rachel Sealfon, Stephen Gire, Crystal Ellis, Stephen Calderwood, Firdausi Qadri, Lisa Hensley, Manolis Kellis, Edward T Ryan, Regina C LaRocque, Jason B Harris and Pardis C Sabeti
    Citation: BMC Genomics 2012 13:468
    Content type: Research article Published on:

  46. Yersinia enterocolitica is a gastrointestinal foodborne pathogen found worldwide and which especially affects infants and young children. While different bioserotypes have been associated with varying pathogenici...

    Authors: Debora Garzetti, Hicham Bouabe, Juergen Heesemann and Alexander Rakin
    Citation: BMC Genomics 2012 13:467
    Content type: Research article Published on:

  47. Animals co-evolve with their gut microbiota; the latter can perform complex metabolic reactions that cannot be done independently by the host. Although the importance of gut microbiota has been well demonstrat...

    Authors: Hsiao-Pei Lu, Yu-bin Wang, Shiao-Wei Huang, Chung-Yen Lin, Martin Wu, Chih-hao Hsieh and Hon-Tsen Yu
    Citation: BMC Genomics 2012 13:466
    Content type: Research article Published on:

  48. The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A an...

    Authors: Tina Strobel, Arwa Al-Dilaimi, Jochen Blom, Arne Gessner, Jörn Kalinowski, Marta Luzhetska, Alfred Pühler, Rafael Szczepanowski, Andreas Bechthold and Christian Rückert
    Citation: BMC Genomics 2012 13:465
    Content type: Research article Published on:

  49. The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alter...

    Authors: Juliana Mazzuchelli, Thomas David Kocher, Fengtang Yang and Cesar Martins
    Citation: BMC Genomics 2012 13:463
    Content type: Research article Published on:

  50. Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increa...

    Authors: Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, Sylvain Thomas and Christophe Klopp
    Citation: BMC Genomics 2012 13:462
    Content type: Software Published on:

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BMC Genomics

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