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  2. Microarray-based gene expression analysis of peripheral whole blood is a common strategy in the development of clinically relevant biomarker panels for a variety of human diseases. However, the results of such...

    Authors: Mary E Winn, Marian Shaw, Craig April, Brandy Klotzle, Jian-Bing Fan, Sarah S Murray and Nicholas J Schork
    Citation: BMC Genomics 2011 12:412
    Content type: Research article Published on:

  3. Whether myofibers increase with a pulsed-wave mode at particular developmental stages or whether they augment evenly across developmental stages in large mammals is unclear. Additionally, the molecular mechani...

    Authors: Hangxing Ren, Li Li, Hongwei Su, Lingyang Xu, Caihong Wei, Li Zhang, Hongbin Li, Wenzhong Liu and Lixin Du
    Citation: BMC Genomics 2011 12:411
    Content type: Research article Published on:

  4. Virulence acquisition and loss is a dynamic adaptation of pathogens to thrive in changing milieus. We investigated the mechanisms of virulence loss at the whole genome level using Babesia bovis as a model apicomp...

    Authors: Audrey OT Lau, Ananth Kalyanaraman, Ignacio Echaide, Guy H Palmer, Russell Bock, Monica J Pedroni, Meenakshi Rameshkumar, Mariano B Ferreira, Taryn I Fletcher and Terry F McElwain
    Citation: BMC Genomics 2011 12:410
    Content type: Research article Published on:

  5. The species Azospirillum amazonense belongs to a well-known genus of plant growth-promoting bacteria. This bacterium is found in association with several crops of economic importance; however, there is a lack of ...

    Authors: Fernando H Sant'Anna, Luiz GP Almeida, Ricardo Cecagno, Luciano A Reolon, Franciele M Siqueira, Maicon RS Machado, Ana TR Vasconcelos and Irene S Schrank
    Citation: BMC Genomics 2011 12:409
    Content type: Research article Published on:

  6. Genome-wide association analysis is a powerful tool for annotating phenotypic effects on the genome and knowledge of genes and chromosomal regions associated with dairy phenotypes is useful for genome and gene...

    Authors: John B Cole, George R Wiggans, Li Ma, Tad S Sonstegard, Thomas J Lawlor Jr, Brian A Crooker, Curtis P Van Tassell, Jing Yang, Shengwen Wang, Lakshmi K Matukumalli and Yang Da
    Citation: BMC Genomics 2011 12:408
    Content type: Research article Published on:

  8. The Australian sheep blowfly Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae) is a destructive pest of the sheep, a model organism for insecticide resistance research, and a valuable tool for medical and fore...

    Authors: Siu F Lee, Zhenzhong Chen, Annette McGrath, Robert T Good and Philip Batterham
    Citation: BMC Genomics 2011 12:406
    Content type: Research article Published on:

  9. The pattern of gene transcripts in the yeast Saccharomyces cerevisiae is strongly affected by the presence of glucose. An increased activity of protein kinase A (PKA), triggered by a rise in the intracellular con...

    Authors: Daniela Livas, Marinka JH Almering, Jean-Marc Daran, Jack T Pronk and Juana M Gancedo
    Citation: BMC Genomics 2011 12:405
    Content type: Research article Published on:

  10. There are large differences between the sexes at the genetic level; these differences include heterogametic sex chromosomes and/or differences in expression of genes between the sexes. In rainbow trout (Oncorhync...

    Authors: Matthew C Hale, Peng Xu, Julie Scardina, Paul A Wheeler, Gary H Thorgaard and Krista M Nichols
    Citation: BMC Genomics 2011 12:404
    Content type: Research article Published on:

  14. Streptococcus gallolyticus subsp. gallolyticus is an important causative agent of infectious endocarditis, while the pathogenicity of this species is widely unclear. To gain insight into the pathomechanisms and t...

    Authors: Dennis Hinse, Tanja Vollmer, Christian Rückert, Jochen Blom, Jörn Kalinowski, Cornelius Knabbe and Jens Dreier
    Citation: BMC Genomics 2011 12:400
    Content type: Research article Published on:

  15. Allergic contact dermatitis is an inflammatory skin disease that affects a significant proportion of the population. This disease is caused by an adverse immune response towards chemical haptens, and leads to ...

    Authors: Henrik Johansson, Malin Lindstedt, Ann-Sofie Albrekt and Carl AK Borrebaeck
    Citation: BMC Genomics 2011 12:399
    Content type: Research article Published on:

  16. As a mild, highly contagious, respiratory disease, swine influenza always damages the innate immune systems, and increases susceptibility to secondary infections which results in considerable morbidity and mor...

    Authors: Yongtao Li, Hongbo Zhou, Zhibin Wen, Shujuan Wu, Canhui Huang, Guangmin Jia, Huanchun Chen and Meilin Jin
    Citation: BMC Genomics 2011 12:398
    Content type: Research article Published on:

  17. Developing a model for codon substitutions is essential for the analyses of protein sequences. Recent studies on the mutation rates in the non-coding regions have shown that CpG mutation rates in the human gen...

    Authors: Kazuharu Misawa
    Citation: BMC Genomics 2011 12:397
    Content type: Research article Published on:

  18. Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged ...

    Authors: Dawei Li, Hugo E Cuevas, Luming Yang, Yuhong Li, Jordi Garcia-Mas, Juan Zalapa, Jack E Staub, Feishi Luan, Umesh Reddy, Xiaoming He, Zhenhui Gong and Yiqun Weng
    Citation: BMC Genomics 2011 12:396
    Content type: Research article Published on:

  19. Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now...

    Authors: Therese Håfström, Désirée S Jansson and Bo Segerman
    Citation: BMC Genomics 2011 12:395
    Content type: Research article Published on:

  20. The gene composition, gene order and structure of the mitochondrial genome are remarkably stable across bilaterian animals. Lice (Insecta: Phthiraptera) are a major exception to this genomic stability in that ...

    Authors: Stephen L Cameron, Kazunori Yoshizawa, Atsushi Mizukoshi, Michael F Whiting and Kevin P Johnson
    Citation: BMC Genomics 2011 12:394
    Content type: Research article Published on:

  21. Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the ...

    Authors: Daniel Gonzalez-Ibeas, José Blanca, Livia Donaire, Montserrat Saladié, Albert Mascarell-Creus, Ana Cano-Delgado, Jordi Garcia-Mas, Cesar Llave and Miguel A Aranda
    Citation: BMC Genomics 2011 12:393
    Content type: Research article Published on:

  22. The orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide nematode phylogenetic hypo...

    Authors: Joong-Ki Park, Tahera Sultana, Sang-Hwa Lee, Seokha Kang, Hyong Kyu Kim, Gi-Sik Min, Keeseon S Eom and Steven A Nadler
    Citation: BMC Genomics 2011 12:392
    Content type: Research article Published on:

  23. Artemisinin resistance in Plasmodium falciparum malaria has emerged in Western Cambodia. This is a major threat to global plans to control and eliminate malaria as the artemisinins are a key component of antimala...

    Authors: Sachel Mok, Mallika Imwong, Margaret J Mackinnon, Joan Sim, Ramya Ramadoss, Poravuth Yi, Mayfong Mayxay, Kesinee Chotivanich, Kek-Yee Liong, Bruce Russell, Duong Socheat, Paul N Newton, Nicholas PJ Day, Nicholas J White, Peter R Preiser, François Nosten…
    Citation: BMC Genomics 2011 12:391
    Content type: Research article Published on:

  24. The yeast cell wall integrity mitogen-activated protein kinase (CWI-MAPK) pathway is the main regulator of adaptation responses to cell wall stress in yeast. Here, we adopt a genomic approach to shed light on ...

    Authors: Patricia Arias, Sonia Díez-Muñiz, Raúl García, César Nombela, José M Rodríguez-Peña and Javier Arroyo
    Citation: BMC Genomics 2011 12:390
    Content type: Research article Published on:

  25. Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to ...

    Authors: Massimo Iorizzo, Douglas A Senalik, Dariusz Grzebelus, Megan Bowman, Pablo F Cavagnaro, Marta Matvienko, Hamid Ashrafi, Allen Van Deynze and Philipp W Simon
    Citation: BMC Genomics 2011 12:389
    Content type: Research article Published on:

  26. The G protein-coupled receptors (GPCRs) belong to the largest superfamily of integral cell membrane proteins and play crucial roles in physiological processes including behavior, development and reproduction. ...

    Authors: Hua Bai, Fang Zhu, Kapil Shah and Subba Reddy Palli
    Citation: BMC Genomics 2011 12:388
    Content type: Research article Published on:

  27. In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR). Among the few characterized rice mutants affected in root development, crown rootless1 mutant is una...

    Authors: Yoan Coudert, Martine Bès, Thi Van Anh Le, Martial Pré, Emmanuel Guiderdoni and Pascal Gantet
    Citation: BMC Genomics 2011 12:387
    Content type: Research article Published on:

  28. The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, mole...

    Authors: Pablo F Cavagnaro, Sang-Min Chung, Sylvie Manin, Mehtap Yildiz, Aamir Ali, Maria S Alessandro, Massimo Iorizzo, Douglas A Senalik and Philipp W Simon
    Citation: BMC Genomics 2011 12:386
    Content type: Research article Published on:

  29. Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and ...

    Authors: Christof Francke, Tom Groot Kormelink, Yanick Hagemeijer, Lex Overmars, Vincent Sluijter, Roy Moezelaar and Roland J Siezen
    Citation: BMC Genomics 2011 12:385
    Content type: Research article Published on:

  30. Fluctuations in temperature occur naturally during plant growth and reproduction. However, in the hot summers this variation may become stressful and damaging for the molecular mechanisms involved in proper ce...

    Authors: Craita E Bita, Sara Zenoni, Wim H Vriezen, Celestina Mariani, Mario Pezzotti and Tom Gerats
    Citation: BMC Genomics 2011 12:384
    Content type: Research article Published on:

  31. Corynebacterium ulcerans has been detected as a commensal in domestic and wild animals that may serve as reservoirs for zoonotic infections. During the last decade, the frequency and severity of human infections ...

    Authors: Eva Trost, Arwa Al-Dilaimi, Panagiotis Papavasiliou, Jessica Schneider, Prisca Viehoever, Andreas Burkovski, Siomar C Soares, Sintia S Almeida, Fernanda A Dorella, Anderson Miyoshi, Vasco Azevedo, Maria P Schneider, Artur Silva, Cíntia S Santos, Louisy S Santos, Priscila Sabbadini…
    Citation: BMC Genomics 2011 12:383
    Content type: Research article Published on:

  33. The R locus controls the color of pigmented soybean (Glycine max) seeds. However information about its control over seed coat biochemistry and gene expressions remains limited. The seed coats of nearly-isogenic b...

    Authors: Nik Kovinich, Ammar Saleem, John T Arnason and Brian Miki
    Citation: BMC Genomics 2011 12:381
    Content type: Research article Published on:

  34. Triticale is adapted to a wide range of abiotic stress conditions, is an important high-quality feed stock and produces similar grain yield but more biomass compared to other crops. Modern genomic approaches a...

    Authors: Katharina V Alheit, Jochen C Reif, Hans Peter Maurer, Volker Hahn, Elmar A Weissmann, Thomas Miedaner and Tobias Würschum
    Citation: BMC Genomics 2011 12:380
    Content type: Research article Published on:

  35. BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and ...

    Authors: Frank A Feltus, Christopher A Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary Smith, James Ford, Margaret E Staton, Stephen P Ficklin, Barbara P Blackmon, Chun-Huai Cheng, Raymond J Schnell, David N Kuhn and Juan-Carlos Motamayor
    Citation: BMC Genomics 2011 12:379
    Content type: Research article Published on:

  36. Newly microarray technologies yield large-scale datasets. The microarray datasets are usually presented in 2D matrices, where rows represent genes and columns represent experimental conditions. Systematic anal...

    Authors: Junwan Liu, Zhoujun Li, Xiaohua Hu, Yiming Chen and EK Park
    Citation: BMC Genomics 2011 12(Suppl 2):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  37. CpG islands are important regions in DNA. They usually appear at the 5’ end of genes containing GC-rich dinucleotides. When DNA methylation occurs, gene regulation is affected and it sometimes leads to carcino...

    Authors: Leah Spontaneo and Nick Cercone
    Citation: BMC Genomics 2011 12(Suppl 2):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  38. Detecting epistatic interactions plays a significant role in improving pathogenesis, prevention, diagnosis and treatment of complex human diseases. A recent study in automatic detection of epistatic interactio...

    Authors: Bing Han and Xue-wen Chen
    Citation: BMC Genomics 2011 12(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  39. Metagenomic assembly is a challenging problem due to the presence of genetic material from multiple organisms. The problem becomes even more difficult when short reads produced by next generation sequencing te...

    Authors: Anveshi Charuvaka and Huzefa Rangwala
    Citation: BMC Genomics 2011 12(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  40. Genomic read alignment involves mapping (exactly or approximately) short reads from a particular individual onto a pre-sequenced reference genome of the same species. Because all individuals of the same specie...

    Authors: M Oğuzhan Külekci, Wing-Kai Hon, Rahul Shah, Jeffrey Scott Vitter and Bojian Xu
    Citation: BMC Genomics 2011 12(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  41. There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in prom...

    Authors: Michal Wozniak, Limsoon Wong and Jerzy Tiuryn
    Citation: BMC Genomics 2011 12(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  42. Analysing gene expression data from microarray technologies is a very important task in biology and medicine, and particularly in cancer diagnosis. Different from most other popular methods in high dimensional...

    Authors: Zhenyu Wang and Vasile Palade
    Citation: BMC Genomics 2011 12(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  43. A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to ...

    Authors: Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen and Mihai Pop
    Citation: BMC Genomics 2011 12(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  44. Reassortments are events in the evolution of the genome of influenza (flu), whereby segments of the genome are exchanged between different strains. As reassortments have been implicated in major human pandemic...

    Authors: Alisa Yurovsky and Bernard M E Moret
    Citation: BMC Genomics 2011 12(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  45. Proximity-based methods and co-evolution-based phylogenetic profiles methods have been successfully used for the identification of functionally related genes. Proximity-based methods are effective for physical...

    Authors: Vikas Rao Pejaver and Sun Kim
    Citation: BMC Genomics 2011 12(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  46. Strains of Mycobacterium tuberculosis complex (MTBC) can be classified into major lineages based on their genotype. Further subdivision of major lineages into sublineages requires multiple biomarkers along with m...

    Authors: Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bülent Yener and Kristin P Bennett
    Citation: BMC Genomics 2011 12(Suppl 2):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  47. KRAB-ZFPs (Krüppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, K...

    Authors: Sylvain Meylan, Anna C Groner, Giovanna Ambrosini, Nirav Malani, Simon Quenneville, Nadine Zangger, Adamandia Kapopoulou, Annamaria Kauzlaric, Jacques Rougemont, Angela Ciuffi, Frederic D Bushman, Philipp Bucher and Didier Trono
    Citation: BMC Genomics 2011 12:378
    Content type: Research article Published on:

  48. In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline simil...

    Authors: Seán S ÓhÉigeartaigh, David Armisén, Kevin P Byrne and Kenneth H Wolfe
    Citation: BMC Genomics 2011 12:377
    Content type: Research article Published on:

  49. The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources f...

    Authors: Nicolas Blavet, Delphine Charif, Christine Oger-Desfeux, Gabriel AB Marais and Alex Widmer
    Citation: BMC Genomics 2011 12:376
    Content type: Research article Published on:

  50. Recent studies have demonstrated the genetic significance of insertions, deletions, and other more complex structural variants (SVs) in the human population. With the development of the next-generation sequenc...

    Authors: Zhengdong D Zhang, Jiang Du, Hugo Lam, Alex Abyzov, Alexander E Urban, Michael Snyder and Mark Gerstein
    Citation: BMC Genomics 2011 12:375
    Content type: Methodology article Published on:

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