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  1. 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

  2. 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

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  8. Burkholderia cenocepacia is a member of the Burkholderia cepacia complex group of bacteria that cause infections in individuals with cystic fibrosis. B. cenocepacia isolate J2315 has been genome sequenced and is ...

    Authors: Andrea Sass, Angela Marchbank, Elizabeth Tullis, John J LiPuma and Eshwar Mahenthiralingam
    Citation: BMC Genomics 2011 12:373
    Content type: Research article Published on:

  9. Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence pheno...

    Authors: Ping Yu, Caihong Wang, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang, Shengxiang Tang and Xinghua Wei
    Citation: BMC Genomics 2011 12:372
    Content type: Research article Published on:

  11. Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many a...

    Authors: Prabin Bajgain, Bryce A Richardson, Jared C Price, Richard C Cronn and Joshua A Udall
    Citation: BMC Genomics 2011 12:370
    Content type: Research article Published on:

  12. Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock t...

    Authors: Christopher A Saski, Zhigang Li, Frank A Feltus and Hong Luo
    Citation: BMC Genomics 2011 12:369
    Content type: Research article Published on:

  13. Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single re...

    Authors: Emilie Chancerel, Camille Lepoittevin, Grégoire Le Provost, Yao-Cheng Lin, Juan Pablo Jaramillo-Correa, Andrew J Eckert, Jill L Wegrzyn, Diana Zelenika, Anne Boland, Jean-Marc Frigerio, Philippe Chaumeil, Pauline Garnier-Géré, Christophe Boury, Delphine Grivet, Santiago C González-Martínez, Pierre Rouzé…
    Citation: BMC Genomics 2011 12:368
    Content type: Research article Published on:

  14. MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in development and stress response in plants by negatively affecting gene expression post-transcriptionally. Identification of...

    Authors: Tianzuo Wang, Lei Chen, Mingui Zhao, Qiuying Tian and Wen-Hao Zhang
    Citation: BMC Genomics 2011 12:367
    Content type: Research article Published on:

  15. Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the ...

    Authors: Noé Fernández-Pozo, Javier Canales, Darío Guerrero-Fernández, David P Villalobos, Sara M Díaz-Moreno, Rocío Bautista, Arantxa Flores-Monterroso, M Ángeles Guevara, Pedro Perdiguero, Carmen Collada, M Teresa Cervera, Álvaro Soto, Ricardo Ordás, Francisco R Cantón, Concepción Avila, Francisco M Cánovas…
    Citation: BMC Genomics 2011 12:366
    Content type: Database Published on:

  16. The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor (TF) that mediates responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Integration of TCDD-induced genome-wide AhR enrichment, d...

    Authors: Edward Dere, Raymond Lo, Trine Celius, Jason Matthews and Timothy R Zacharewski
    Citation: BMC Genomics 2011 12:365
    Content type: Research article Published on:

  17. Understanding animal development and physiology at a molecular-biological level has been advanced by the ability to determine at high resolution the repertoire of mRNA molecules by whole transcriptome resequen...

    Authors: Peter L Chang, Joseph P Dunham, Sergey V Nuzhdin and Michelle N Arbeitman
    Citation: BMC Genomics 2011 12:364
    Content type: Research article Published on:

  18. Amaranthus hypochondriacus, a grain amaranth, is a C4 plant noted by its ability to tolerate stressful conditions and produce highly nutritious seeds. These possess an optimal amino acid balance and constitute a ...

    Authors: John P Délano-Frier, Hamlet Avilés-Arnaut, Kena Casarrubias-Castillo, Gabriela Casique-Arroyo, Paula A Castrillón-Arbeláez, Luis Herrera-Estrella, Julio Massange-Sánchez, Norma A Martínez-Gallardo, Fannie I Parra-Cota, Erandi Vargas-Ortiz and María G Estrada-Hernández
    Citation: BMC Genomics 2011 12:363
    Content type: Research article Published on:

  19. Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androsten...

    Authors: Eli Grindflek, Sigbjørn Lien, Hanne Hamland, Marianne HS Hansen, Matthew Kent, Maren van Son and Theo HE Meuwissen
    Citation: BMC Genomics 2011 12:362
    Content type: Research article Published on:

  20. Shine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation signal in prokaryotes. Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have been s...

    Authors: Xiaobin Zheng, Gang-Qing Hu, Zhen-Su She and Huaiqiu Zhu
    Citation: BMC Genomics 2011 12:361
    Content type: Research article Published on:

  21. Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. In addition to the ecological significance, Phalaenopsis has been considered as an economic...

    Authors: Yu-Yun Hsiao, Yun-Wen Chen, Shi-Ching Huang, Zhao-Jun Pan, Chih-Hsiung Fu, Wen-Huei Chen, Wen-Chieh Tsai and Hong-Hwa Chen
    Citation: BMC Genomics 2011 12:360
    Content type: Research article Published on:

  22. One of the major tasks of the post-genomic era is "reading" genomic sequences in order to extract all the biological information contained in them. Although a wide variety of techniques is used to solve the ge...

    Authors: Lian Zhou, Frank-Jörg Vorhölter, Yong-Qiang He, Bo-Le Jiang, Ji-Liang Tang, Yuquan Xu, Alfred Pühler and Ya-Wen He
    Citation: BMC Genomics 2011 12:359
    Content type: Research article Published on:

  23. Database searching is the most frequently used approach for automated peptide assignment and protein inference of tandem mass spectra. The results, however, depend on the sequences in target databases and on s...

    Authors: Kung-Yen Chang and David C Muddiman
    Citation: BMC Genomics 2011 12:358
    Content type: Research article Published on:

  24. The cell suicide pathway of apoptosis is a necessary event in the life of multicellular organisms. It is involved in many biological processes ranging from development to the immune response. Evolutionarily co...

    Authors: Juliette Courtiade, Yannick Pauchet, Heiko Vogel and David G Heckel
    Citation: BMC Genomics 2011 12:357
    Content type: Research article Published on:

  26. Cellular senescence is an irreversible cell cycle arrest that normal cells undergo in response to progressive shortening of telomeres, changes in telomeric structure, oncogene activation or oxidative stress an...

    Authors: Emilie Rovillain, Louise Mansfield, Christopher J Lord, Alan Ashworth and Parmjit S Jat
    Citation: BMC Genomics 2011 12:355
    Content type: Research article Published on:

  27. Bacterial artificial chromosome (BAC) libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they prov...

    Authors: Razvan Anistoroaei, Boudewijn ten Hallers, Michael Nefedov, Knud Christensen and Pieter de Jong
    Citation: BMC Genomics 2011 12:354
    Content type: Research article Published on:

  28. Transcription factors in disease-relevant pathways represent potential drug targets, by impacting a distinct set of pathways that may be modulated through gene regulation. The influence of transcription factor...

    Authors: Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi and Eivind Hovig
    Citation: BMC Genomics 2011 12:353
    Content type: Methodology article Published on:

  29. Eight diverse sorghum (Sorghum bicolor L. Moench) accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs). Two strategies were used for...

    Authors: James C Nelson, Shichen Wang, Yuye Wu, Xianran Li, Ginny Antony, Frank F White and Jianming Yu
    Citation: BMC Genomics 2011 12:352
    Content type: Research article Published on:

  30. Bacterial Artificial Chromosomes (BACs) have been widely used as transgenes in vertebrate model systems such as mice and zebrafish, for a variety of studies. BAC transgenesis has been a powerful tool to study ...

    Authors: Leighcraft A Shakes, Gembu Abe, Mugtaba A Eltayeb, Hope M Wolf, Koichi Kawakami and Pradeep K Chatterjee
    Citation: BMC Genomics 2011 12:351
    Content type: Methodology article Published on:

  31. Single nucleotide polymorphisms (SNPs) are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analys...

    Authors: Yuanhong Han, Yun Kang, Ivone Torres-Jerez, Foo Cheung, Christopher D Town, Patrick X Zhao, Michael K Udvardi and Maria J Monteros
    Citation: BMC Genomics 2011 12:350
    Content type: Research article Published on:

  32. The gene content of a diverse group of 183 unique Escherichia coli and Shigella isolates was determined using the Affymetrix GeneChip®E. coli Genome 2.0 Array, originally designed for transcriptome analysis, as a...

    Authors: Scott A Jackson, Isha R Patel, Tammy Barnaba, Joseph E LeClerc and Thomas A Cebula
    Citation: BMC Genomics 2011 12:349
    Content type: Research article Published on:

  33. High-pathogenic Y. enterocolitica ssp. enterocolitica caused several human outbreaks in Northern America. In contrast, low pathogenic Y. enterocolitica ssp. palearctica serobiotype O:3/4 is responsible for sporad...

    Authors: Julia Batzilla, Uladzimir Antonenka, Dirk Höper, Jürgen Heesemann and Alexander Rakin
    Citation: BMC Genomics 2011 12:348
    Content type: Research article Published on:

  34. Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speci...

    Authors: Ted Cosart, Albano Beja-Pereira, Shanyuan Chen, Sarah B Ng, Jay Shendure and Gordon Luikart
    Citation: BMC Genomics 2011 12:347
    Content type: Methodology article Published on:

  35. The role of coastal nutrient sources in the persistence of Karenia brevis red tides in coastal waters of Florida is a contentious issue that warrants investigation into the regulation of nutrient responses in thi...

    Authors: Jeanine S Morey, Emily A Monroe, Amanda L Kinney, Marion Beal, Jillian G Johnson, Gary L Hitchcock and Frances M Van Dolah
    Citation: BMC Genomics 2011 12:346
    Content type: Research article Published on:

  36. Oct4 is a key factor of an expanded transcriptional network (Oct4-TN) that governs pluripotency and self-renewal in embryonic stem cells (ESCs) and in the inner cell mass from which ESCs are derived. A pending...

    Authors: Maurizio Zuccotti, Valeria Merico, Michele Bellone, Francesca Mulas, Lucia Sacchi, Paola Rebuzzini, Alessandro Prigione, Carlo A Redi, Riccardo Bellazzi, James Adjaye and Silvia Garagna
    Citation: BMC Genomics 2011 12:345
    Content type: Research article Published on:

  37. Interactions among genetic loci are believed to play an important role in disease risk. While many methods have been proposed for detecting such interactions, their relative performance remains largely unclear...

    Authors: Li Chen, Guoqiang Yu, Carl D Langefeld, David J Miller, Richard T Guy, Jayaram Raghuram, Xiguo Yuan, David M Herrington and Yue Wang
    Citation: BMC Genomics 2011 12:344
    Content type: Methodology article Published on:

  38. Siraitia grosvenorii (Luohanguo) is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chi...

    Authors: Qi Tang, Xiaojun Ma, Changming Mo, Iain W Wilson, Cai Song, Huan Zhao, Yanfang Yang, Wei Fu and Deyou Qiu
    Citation: BMC Genomics 2011 12:343
    Content type: Research article Published on:

  39. Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree ...

    Authors: Melissa ML Wong, Charles H Cannon and Ratnam Wickneswari
    Citation: BMC Genomics 2011 12:342
    Content type: Research article Published on:

  40. The Ras superfamily plays an important role in the control of cell signalling and division. Mutations in the Ras genes convert them into active oncogenes. The Ras oncogenes form a major thrust of global cancer...

    Authors: Umay Kulsum, Vishwadeep Singh, Sujata Sharma, A Srinivasan, Tej P Singh and Punit Kaur
    Citation: BMC Genomics 2011 12:341
    Content type: Database Published on:

  41. Autoantibodies against self-antigens have been associated not only with autoimmune diseases, but also with cancer and are even found in healthy individuals. The mechanism causing the autoantibody response rema...

    Authors: Christina Backes, Nicole Ludwig, Petra Leidinger, Christian Harz, Jana Hoffmann, Andreas Keller, Eckart Meese and Hans-Peter Lenhof
    Citation: BMC Genomics 2011 12:340
    Content type: Research article Published on:

  42. Modern dog breeds display traits that are either breed-specific or shared by a few breeds as a result of genetic bottlenecks during the breed creation process and artificial selection for breed standards. Sele...

    Authors: Javier Quilez, Andrea D Short, Verónica Martínez, Lorna J Kennedy, William Ollier, Armand Sanchez, Laura Altet and Olga Francino
    Citation: BMC Genomics 2011 12:339
    Content type: Research article Published on:

  44. Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylu...

    Authors: Aiyou Huang, Linwen He and Guangce Wang
    Citation: BMC Genomics 2011 12:337
    Content type: Research article Published on:

  45. Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-ac...

    Authors: Beth Holloway, Stanley Luck, Mary Beatty, J-Antoni Rafalski and Bailin Li
    Citation: BMC Genomics 2011 12:336
    Content type: Research article Published on:

  46. The mitochondrion is an essential organelle which plays important roles in diverse biological processes, such as metabolism, apoptosis, signal transduction and cell cycle. Characterizing protein-protein intera...

    Authors: Zuguang Gu, Jie Li, Song Gao, Ming Gong, Junling Wang, Hua Xu, Chenyu Zhang and Jin Wang
    Citation: BMC Genomics 2011 12:335
    Content type: Database Published on:

  47. Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. Acco...

    Authors: Kuo-Hsiang Tang, Kerrie Barry, Olga Chertkov, Eileen Dalin, Cliff S Han, Loren J Hauser, Barbara M Honchak, Lauren E Karbach, Miriam L Land, Alla Lapidus, Frank W Larimer, Natalia Mikhailova, Samuel Pitluck, Beverly K Pierson and Robert E Blankenship
    Citation: BMC Genomics 2011 12:334
    Content type: Research article Published on:

  48. Benzo[a]pyrene (BaP) is a widespread environmental genotoxic carcinogen that damages DNA by forming adducts. This damage along with activation of the aryl hydrocarbon receptor (AHR) induces complex transcripti...

    Authors: Hamza Hamouchene, Volker M Arlt, Ian Giddings and David H Phillips
    Citation: BMC Genomics 2011 12:333
    Content type: Research article Published on:

  49. Cyanobacteria are potential sources of renewable chemicals and biofuels and serve as model organisms for bacterial photosynthesis, nitrogen fixation, and responses to environmental changes. Anabaena (Nostoc) sp. ...

    Authors: Britt L Flaherty, F Van Nieuwerburgh, Steven R Head and James W Golden
    Citation: BMC Genomics 2011 12:332
    Content type: Research article Published on:

  50. Gross chromosomal rearrangements (GCRs) such as aneuploidy are key factors in genome evolution as well as being common features of human cancer. Their role in tumour initiation and progression has not yet been...

    Authors: Paul P Jung, Emilie S Fritsch, Corinne Blugeon, Jean-Luc Souciet, Serge Potier, Sophie Lemoine, Joseph Schacherer and Jacky de Montigny
    Citation: BMC Genomics 2011 12:331
    Content type: Research article Published on:

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