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  1. The NF-κB family plays a prominent role in the innate immune response, cell cycle activation or cell apoptosis. Upon stimulation by pathogen-associated patterns, such as viral RNA a kinase cascade is activated...

    Authors: Marta Iwanaszko, Allan R Brasier and Marek Kimmel
    Citation: BMC Genomics 2012 13:182
    Content type: Research article Published on:

  2. The gilthead sea bream (Sparus aurata L.) occurs around the Mediterranean and along Eastern Atlantic coasts from Great Britain to Senegal. It is tolerant of a wide range of temperatures and salinities and is ofte...

    Authors: Daniel Garcia de la serrana, Alicia Estévez, Karl Andree and Ian A Johnston
    Citation: BMC Genomics 2012 13:181
    Content type: Research article Published on:

  3. The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. ...

    Authors: Tim Kahlke, Alexander Goesmann, Erik Hjerde, Nils Peder Willassen and Peik Haugen
    Citation: BMC Genomics 2012 13:179
    Content type: Research article Published on:

  4. Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic m...

    Authors: Mikkel Schubert, Aurelien Ginolhac, Stinus Lindgreen, John F Thompson, Khaled AS AL-Rasheid, Eske Willerslev, Anders Krogh and Ludovic Orlando
    Citation: BMC Genomics 2012 13:178
    Content type: Methodology article Published on:

  5. Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and ext...

    Authors: Aurelien Ginolhac, Julia Vilstrup, Jesper Stenderup, Morten Rasmussen, Mathias Stiller, Beth Shapiro, Grant Zazula, Duane Froese, Kathleen E Steinmann, John F Thompson, Khaled AS AL-Rasheid, Thomas MP Gilbert, Eske Willerslev and Ludovic Orlando
    Citation: BMC Genomics 2012 13:177
    Content type: Methodology article Published on:

  6. Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chro...

    Authors: Jong-Kuk Na, Jianping Wang, Jan E Murray, Andrea R Gschwend, Wenli Zhang, Qingyi Yu, Rafael Navajas‒ Pérez, F Alex Feltus, Cuixia Chen, Zdenek Kubat, Paul H Moore, Jiming Jiang, Andrew H Paterson and Ray Ming
    Citation: BMC Genomics 2012 13:176
    Content type: Research article Published on:

  7. The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostas...

    Authors: Vitthal T Barvkar, Varsha C Pardeshi, Sandip M Kale, Narendra Y Kadoo and Vidya S Gupta
    Citation: BMC Genomics 2012 13:175
    Content type: Research article Published on:

  8. At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoi...

    Authors: Luisa Berná, Ankita Chaurasia, Claudia Angelini, Concetta Federico, Salvatore Saccone and Giuseppe D'Onofrio
    Citation: BMC Genomics 2012 13:174
    Content type: Research article Published on:

  9. Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21) is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB) disease in many...

    Authors: Won Kyong Cho, Jisuk Yu, Kyung-Mi Lee, Moonil Son, Kyunghun Min, Yin-Won Lee and Kook-Hyung Kim
    Citation: BMC Genomics 2012 13:173
    Content type: Research article Published on:

  10. The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious dev...

    Authors: Maria A Nilsson, Axel Janke, Elizabeth P Murchison, Zemin Ning and Björn M Hallström
    Citation: BMC Genomics 2012 13:172
    Content type: Research article Published on:

  11. Fungal plant pathogens cause serious agricultural losses worldwide. Alternaria arborescens is a major pathogen of tomato, with its virulence determined by the presence of a conditionally dispensable chromosome (C...

    Authors: Jinnan Hu, Chenxi Chen, Tobin Peever, Ha Dang, Christopher Lawrence and Thomas Mitchell
    Citation: BMC Genomics 2012 13:171
    Content type: Research article Published on:

  12. Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype. ~Omics datasets are often very larg...

    Authors: Jumamurat R Bayjanov, Douwe Molenaar, Vesela Tzeneva, Roland J Siezen and Sacha A F T van Hijum
    Citation: BMC Genomics 2012 13:170
    Content type: Methodology article Published on:

  13. microRNAs (miRNAs) are key regulators of gene expression and play important roles in many aspects of plant biology. The role(s) of miRNAs in nitrogen-fixing root nodules of leguminous plants such as soybean is...

    Authors: Marie Turner, Oliver Yu and Senthil Subramanian
    Citation: BMC Genomics 2012 13:169
    Content type: Research article Published on:

  14. Vegetables of the genus Allium are widely consumed but remain poorly understood genetically. Genetic mapping has been conducted in intraspecific crosses of onion (Allium cepa L.), A. fistulosum and interspecific ...

    Authors: John McCallum, Samantha Baldwin, Masayoshi Shigyo, Yanbo Deng, Sjaak van Heusden, Meeghan Pither-Joyce and Fernand Kenel
    Citation: BMC Genomics 2012 13:168
    Content type: Database Published on:

  15. While studying long-lived mutants has advanced our understanding of the processes involved in ageing, the mechanisms underlying natural variation in lifespan and ageing rate remain largely unknown. Here, we ch...

    Authors: Agnieszka Doroszuk, Martijs J Jonker, Nicolien Pul, Timo M Breit and Bas J Zwaan
    Citation: BMC Genomics 2012 13:167
    Content type: Research article Published on:

  16. Mitochondrial (mt) markers are successfully applied in evolutionary biology and systematics because mt genomes often evolve faster than the nuclear genomes. In addition, they allow robust phylogenetic analysis...

    Authors: Angelo Duò, Rémy Bruggmann, Stefan Zoller, Matthias Bernt and Christoph R Grünig
    Citation: BMC Genomics 2012 13:166
    Content type: Research article Published on:

  17. Natrialba magadii is an aerobic chemoorganotrophic member of the Euryarchaeota and is a dual extremophile requiring alkaline conditions and hypersalinity for optimal growth. The genome sequence of Nab. magadii ty...

    Authors: Shivakumara Siddaramappa, Jean F Challacombe, Rosana E DeCastro, Friedhelm Pfeiffer, Diego E Sastre, María I Giménez, Roberto A Paggi, John C Detter, Karen W Davenport, Lynne A Goodwin, Nikos Kyrpides, Roxanne Tapia, Samuel Pitluck, Susan Lucas, Tanja Woyke and Julie A Maupin-Furlow
    Citation: BMC Genomics 2012 13:165
    Content type: Research article Published on:

  18. Various aspects of genome organization have been explored based on data from distinct technologies, including histone modification ChIP-Seq, 3C, and its derivatives. Recently developed Hi-C techniques enable t...

    Authors: Lin Liu, Yiqian Zhang, Jianxing Feng, Ning Zheng, Junfeng Yin and Yong Zhang
    Citation: BMC Genomics 2012 13:164
    Content type: Methodology article Published on:

  19. As a human replacement, the crab-eating macaque (Macaca fascicularis) is an invaluable non-human primate model for biomedical research, but the lack of genetic information on this primate has represented a signif...

    Authors: Jae-Won Huh, Young-Hyun Kim, Sang-Je Park, Dae-Soo Kim, Sang-Rae Lee, Kyoung-Min Kim, Kang-Jin Jeong, Ji-Su Kim, Bong-Seok Song, Bo-Woong Sim, Sun-Uk Kim, Sang-Hyun Kim and Kyu-Tae Chang
    Citation: BMC Genomics 2012 13:163
    Content type: Research article Published on:

  20. The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of nitrogen fixation in microbes requires species-sp...

    Authors: Patricia C Dos Santos, Zhong Fang, Steven W Mason, João C Setubal and Ray Dixon
    Citation: BMC Genomics 2012 13:162
    Content type: Research article Published on:

  21. Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces ...

    Authors: Bo-Ruei Chen, Devin C Hale, Peter J Ciolek and Kurt W Runge
    Citation: BMC Genomics 2012 13:161
    Content type: Methodology article Published on:

  22. Aberrant activation of signaling pathways downstream of epidermal growth factor receptor (EGFR) has been hypothesized to be one of the mechanisms of cetuximab (a monoclonal antibody against EGFR) resistance in...

    Authors: Elana J Fertig, Qing Ren, Haixia Cheng, Hiromitsu Hatakeyama, Adam P Dicker, Ulrich Rodeck, Michael Considine, Michael F Ochs and Christine H Chung
    Citation: BMC Genomics 2012 13:160
    Content type: Research article Published on:

  24. Sireviruses are an ancient genus of the Copia superfamily of LTR retrotransposons, and the only one that has exclusively proliferated within plant genomes. Based on experimental data and phylogenetic analyses, Si...

    Authors: Alexandros Bousios, Evangelia Minga, Nikoleta Kalitsou, Maria Pantermali, Aphrodite Tsaballa and Nikos Darzentas
    Citation: BMC Genomics 2012 13:158
    Content type: Database Published on:

  25. Microorganisms able to grow under artificial culture conditions comprise only a small proportion of the biosphere's total microbial community. Until recently, scientists have been unable to perform thorough an...

    Authors: Chi-Ching Lee, Wei-Cheng Lo, Szu-Ming Lai, Yi-Ping Phoebe Chen, Chuan Yi Tang and Ping-Chiang Lyu
    Citation: BMC Genomics 2012 13:157
    Content type: Research article Published on:

  26. The weight that gene copy number plays in transcription remains controversial; although in specific cases gene expression correlates with copy number, the relationship cannot be inferred at the global level. W...

    Authors: Tara L Spivey, Valeria De Giorgi, Yingdong Zhao, Davide Bedognetti, Zoltan Pos, Qiuzhen Liu, Sara Tomei, Maria Libera Ascierto, Lorenzo Uccellini, Jennifer Reinboth, Lotfi Chouchane, David F Stroncek, Ena Wang and Francesco M Marincola
    Citation: BMC Genomics 2012 13:156
    Content type: Research article Published on:

  27. Interferon inducible transmembrane proteins (IFITMs) have diverse roles, including the control of cell proliferation, promotion of homotypic cell adhesion, protection against viral infection, promotion of bone...

    Authors: Danielle Hickford, Stephen Frankenberg, Geoff Shaw and Marilyn B Renfree
    Citation: BMC Genomics 2012 13:155
    Content type: Research article Published on:

  28. MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression implicated in multiple cellular processes. Cyclic stretch of alveoli is characteristic of mechanical ventilation, and is postulated to ...

    Authors: Nadir Yehya, Adi Yerrapureddy, John Tobias and Susan S Margulies
    Citation: BMC Genomics 2012 13:154
    Content type: Research article Published on:

  29. The fetal and adult globin genes in the human β-globin cluster on chromosome 11 are sequentially expressed to achieve normal hemoglobin switching during human development. The pharmacological induction of feta...

    Authors: Biaoru Li, Lianghao Ding, Wei Li, Michael D Story and Betty S Pace
    Citation: BMC Genomics 2012 13:153
    Content type: Research article Published on:

  30. Epigenetic modifications, transcription factor (TF) availability and differences in chromatin folding influence how the genome is interpreted by the transcriptional machinery responsible for gene expression. E...

    Authors: Chih-yu Chen, Quaid Morris and Jennifer A Mitchell
    Citation: BMC Genomics 2012 13:152
    Content type: Research article Published on:

  31. Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available...

    Authors: Gina A Garzón-Martínez, Z Iris Zhu, David Landsman, Luz S Barrero and Leonardo Mariño-Ramírez
    Citation: BMC Genomics 2012 13:151
    Content type: Research article Published on:

  33. Adaptive divergence driven by environmental heterogeneity has long been a fascinating topic in ecology and evolutionary biology. The study of the genetic basis of adaptive divergence has, however, been greatly...

    Authors: Jui-Hua Chu, Rong-Chien Lin, Chia-Fen Yeh, Yu-Cheng Hsu and Shou-Hsien Li
    Citation: BMC Genomics 2012 13:149
    Content type: Research article Published on:

  34. Taxol® (paclitaxel) promotes microtubule assembly and stabilization and therefore is a potent chemotherapeutic agent against wide range of cancers. Methyl jasmonate (MJ) elicited Taxus cell cultures provide a sus...

    Authors: Sangram K Lenka, Nadia Boutaoui, Bibin Paulose, Kham Vongpaseuth, Jennifer Normanly, Susan C Roberts and Elsbeth L Walker
    Citation: BMC Genomics 2012 13:148
    Content type: Research article Published on:

  35. The transcription factor Pax8 is essential for the differentiation of thyroid cells. However, there are few data on genes transcriptionally regulated by Pax8 other than thyroid-related genes. To better underst...

    Authors: Sergio Ruiz-Llorente, Enrique Carrillo Santa de Pau, Ana Sastre-Perona, Cristina Montero-Conde, Gonzalo Gómez-López, James A Fagin, Alfonso Valencia, David G Pisano and Pilar Santisteban
    Citation: BMC Genomics 2012 13:147
    Content type: Research article Published on:

  36. Chicken meat and eggs can be a source of human zoonotic pathogens, especially Salmonella species. These food items contain a potential hazard for humans. Chickens lines differ in susceptibility for Salmonella ...

    Authors: Marinus FW te Pas, Ina Hulsegge, Dirkjan Schokker, Mari A Smits, Mark Fife, Rima Zoorob, Marie-Laure Endale and Johanna MJ Rebel
    Citation: BMC Genomics 2012 13:146
    Content type: Research article Published on:

  37. Many species of filarial nematodes depend on Wolbachia endobacteria to carry out their life cycle. Other species are naturally Wolbachia-free. The biological mechanisms underpinning Wolbachia-dependence and indep...

    Authors: Samantha N McNulty, Andrew S Mullin, Jefferson A Vaughan, Vasyl V Tkach, Gary J Weil and Peter U Fischer
    Citation: BMC Genomics 2012 13:145
    Content type: Research article Published on:

  38. Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for ...

    Authors: Torsten Hain, Rohit Ghai, André Billion, Carsten Tobias Kuenne, Christiane Steinweg, Benjamin Izar, Walid Mohamed, Mobarak Abu Mraheil, Eugen Domann, Silke Schaffrath, Uwe Kärst, Alexander Goesmann, Sebastian Oehm, Alfred Pühler, Rainer Merkl, Sonja Vorwerk…
    Citation: BMC Genomics 2012 13:144
    Content type: Research article Published on:

  39. Infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) infection causes high mortality and huge economic losses in the poultry industry. To protect chickens against ILTV infection, chicken-embryo orig...

    Authors: Jeongyoon Lee, Walter G Bottje and Byung-Whi Kong
    Citation: BMC Genomics 2012 13:143
    Content type: Research article Published on:

  40. Miscanthus (subtribe Saccharinae, tribe Andropogoneae, family Poaceae) is a genus of temperate perennial C4 grasses whose high biomass production makes it, along with its close relatives sugarcane and sorghum, at...

    Authors: Kankshita Swaminathan, Won Byoung Chae, Therese Mitros, Kranthi Varala, Liang Xie, Adam Barling, Katarzyna Glowacka, Megan Hall, Stanislaw Jezowski, Ray Ming, Matthew Hudson, John A Juvik, Daniel S Rokhsar and Stephen P Moose
    Citation: BMC Genomics 2012 13:142
    Content type: Research article Published on:

  41. Corynebacterium resistens was initially recovered from human infections and recognized as a new coryneform species that is highly resistant to antimicrobial agents. Bacteremia associated with this organism in imm...

    Authors: Jasmin Schröder, Irena Maus, Katja Meyer, Stephanie Wördemann, Jochen Blom, Sebastian Jaenicke, Jessica Schneider, Eva Trost and Andreas Tauch
    Citation: BMC Genomics 2012 13:141
    Content type: Research article Published on:

  42. Single nucleotide polymorphisms (SNPs) are increasingly becoming the DNA marker system of choice due to their prevalence in the genome and their ability to be used in highly multiplexed genotyping assays. Alth...

    Authors: Bruno Studer, Stephen Byrne, Rasmus O Nielsen, Frank Panitz, Christian Bendixen, Md Shofiqul Islam, Matthias Pfeifer, Thomas Lübberstedt and Torben Asp
    Citation: BMC Genomics 2012 13:140
    Content type: Methodology article Published on:

  43. The mitochondrial genome is important for studying genome evolution as well as reconstructing the phylogeny of organisms. Complete mitochondrial genome sequences have been reported for more than 2200 metazoans...

    Authors: Hai-Xia Chen, Shi-Chun Sun, Per Sundberg, Wei-Cheng Ren and Jon L Norenburg
    Citation: BMC Genomics 2012 13:139
    Content type: Research article Published on:

  44. Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed i...

    Authors: Melinda E Clark, Zhili He, Alyssa M Redding, Marcin P Joachimiak, Jay D Keasling, Jizhong Z Zhou, Adam P Arkin, Aindrila Mukhopadhyay and Matthew W Fields
    Citation: BMC Genomics 2012 13:138
    Content type: Research article Published on:

  45. Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ance...

    Authors: Douglas S Domingues, Guilherme MQ Cruz, Cushla J Metcalfe, Fabio TS Nogueira, Renato Vicentini, Cristiane de S Alves and Marie-Anne Van Sluys
    Citation: BMC Genomics 2012 13:137
    Content type: Research article Published on:

  46. Microsatellites or simple sequence repeats (SSRs) in expressed sequence tags (ESTs) are useful resources for genome analysis because of their abundance, functionality and polymorphism. The advent of commercial...

    Authors: Saneyoshi Ueno, Yoshinari Moriguchi, Kentaro Uchiyama, Tokuko Ujino-Ihara, Norihiro Futamura, Tetsuya Sakurai, Kenji Shinohara and Yoshihiko Tsumura
    Citation: BMC Genomics 2012 13:136
    Content type: Research article Published on:

  47. Miniature inverted repeat transposable element (MITE) is one type of transposable element (TE), which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only f...

    Authors: Hai-Tao Dong, Lu Zhang, Kang-Le Zheng, Hai-Gen Yao, Jack Chen, Feng-Chi Yu, Xiao-Xing Yu, Bi-Zeng Mao, Dong Zhao, Jian Yao and De-Bao Li
    Citation: BMC Genomics 2012 13:135
    Content type: Research article Published on:

  48. Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel protei...

    Authors: Van Du T Tran, Philippe Chassignet, Saad Sheikh and Jean-Marc Steyaert
    Citation: BMC Genomics 2012 13(Suppl 2):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  49. Many important biological problems can be modeled as contagion diffusion processes over interaction networks. This article shows how the EpiSimdemics interaction-based simulation system can be applied to the g...

    Authors: Keith R Bisset, Ashwin M Aji, Madhav V Marathe and Wu-chun Feng
    Citation: BMC Genomics 2012 13(Suppl 2):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  50. During alternative splicing, the inclusion of an exon in the final mRNA molecule is determined by nuclear proteins that bind cis-regulatory sequences in a target pre-mRNA molecule. A recent study suggested tha...

    Authors: Patricia Buendia, John Tyree, Robert Loredo and Shu-Ning Hsu
    Citation: BMC Genomics 2012 13(Suppl 2):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

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