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  1. Trypanosomatids utilise polycistronic transcription for production of the vast majority of protein-coding mRNAs, which operates in the absence of gene-specific promoters. Resolution of nascent transcripts by p...

    Authors: V Lila Koumandou, Senthil Kumar A Natesan, Tatiana Sergeenko and Mark C Field
    Citation: BMC Genomics 2008 9:298
    Content type: Research article Published on:

  2. Ionizing-radiation-resistant bacteria (IRRB) show a surprising capacity for adaptation to ionizing radiation and desiccation. Positive Darwinian selection is expected to play an important role in this trait, b...

    Authors: Haïtham Sghaier, Kaïs Ghedira, Alia Benkahla and Insaf Barkallah
    Citation: BMC Genomics 2008 9:297
    Content type: Research article Published on:

  3. Microsporidia are a group of parasites related to fungi that infect a wide variety of animals and have gained recognition from the medical community in the past 20 years due to their ability to infect immuno-c...

    Authors: Erin E Gill, James J Becnel and Naomi M Fast
    Citation: BMC Genomics 2008 9:296
    Content type: Research article Published on:

  5. Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires so...

    Authors: Hana Šimková, Jan T Svensson, Pascal Condamine, Eva Hřibová, Pavla Suchánková, Prasanna R Bhat, Jan Bartoš, Jan Šafář, Timothy J Close and Jaroslav Doležel
    Citation: BMC Genomics 2008 9:294
    Content type: Methodology article Published on:

  6. The jumonji C (JmjC) domain containing gene 6 (Jmjd6, previously known as phosphatidylserine receptor) has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Giv...

    Authors: Phillip Hahn, Jens Böse, Stefanie Edler and Andreas Lengeling
    Citation: BMC Genomics 2008 9:293
    Content type: Research article Published on:

  7. Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in humans. However, the factors that affect SNP density are poorly understood. The goal of this study was to estimate the re...

    Authors: Ivan P Gorlov, Olga Y Gorlova and Christopher I Amos
    Citation: BMC Genomics 2008 9:292
    Content type: Research article Published on:

  8. Phagocytosis plays a major role in the defense of higher organisms against microbial infection and provides also the basis for antigen processing in the immune response. Cells of the model organism Dictyostelium ...

    Authors: Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens and Salvatore Bozzaro
    Citation: BMC Genomics 2008 9:291
    Content type: Research article Published on:

  9. To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertake...

    Authors: Jean-Simon Brouard, Christian Otis, Claude Lemieux and Monique Turmel
    Citation: BMC Genomics 2008 9:290
    Content type: Research article Published on:

  10. Neurovirulent Venezuelan equine encephalitis virus (VEEV) causes lethal encephalitis in equines and is transmitted to humans by mosquitoes. VEEV is highly infectious when transmitted by aerosol and has been de...

    Authors: Anuj Sharma, Bhaskar Bhattacharya, Raj K Puri and Radha K Maheshwari
    Citation: BMC Genomics 2008 9:289
    Content type: Research article Published on:

  11. Some of the biochemical events that lead to necrosis of the liver are well-known. However, the pathogenesis of necrosis of the liver from exposure to hepatotoxicants is a complex biological response to the inj...

    Authors: Lingkang Huang, Alexandra N Heinloth, Zhao-Bang Zeng, Richard S Paules and Pierre R Bushel
    Citation: BMC Genomics 2008 9:288
    Content type: Research article Published on:

  12. During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from ge...

    Authors: François L Luro, Gilles Costantino, Javier Terol, Xavier Argout, Thierry Allario, Patrick Wincker, Manuel Talon, Patrick Ollitrault and Raphael Morillon
    Citation: BMC Genomics 2008 9:287
    Content type: Research article Published on:

  13. The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in...

    Authors: Wei Zhu, Shu Ouyang, Marina Iovene, Kimberly O'Brien, Hue Vuong, Jiming Jiang and C Robin Buell
    Citation: BMC Genomics 2008 9:286
    Content type: Research article Published on:

  14. The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization of variance due to individual, environmental, and technical factors. Meta-analysis of ...

    Authors: Michael J Boedigheimer, Russell D Wolfinger, Michael B Bass, Pierre R Bushel, Jeff W Chou, Matthew Cooper, J Christopher Corton, Jennifer Fostel, Susan Hester, Janice S Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit and Karol L Thompson
    Citation: BMC Genomics 2008 9:285
    Content type: Research article Published on:

  15. Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the c...

    Authors: Jason M Bechtel, Thomas Wittenschlaeger, Trisha Dwyer, Jun Song, Sasi Arunachalam, Sadeesh K Ramakrishnan, Samuel Shepard and Alexei Fedorov
    Citation: BMC Genomics 2008 9:284
    Content type: Research article Published on:

  16. A pig phenotype characterized by juvenile hairlessness, thin skin and age dependent lung emphysema has been discovered in a Danish pig herd. The trait shows autosomal co-dominant inheritance with all three gen...

    Authors: Camilla S Bruun, Claus B Jørgensen, Lene Bay, Susanna Cirera, Henrik E Jensen, Páll S Leifsson, Jens Nielsen, Knud Christensen and Merete Fredholm
    Citation: BMC Genomics 2008 9:283
    Content type: Research article Published on:

  17. The lycophyte Selaginella moellendorffii is a vascular plant that diverged from the fern/seed plant lineage at least 400 million years ago. Although genomic information for S. moellendorffii is starting to be pro...

    Authors: Agnes P Chan, Admasu Melake-Berhan, Kimberly O'Brien, Stephanie Buckley, Hui Quan, Dan Chen, Matthew Lewis, Jo Ann Banks and Pablo D Rabinowicz
    Citation: BMC Genomics 2008 9:282
    Content type: Research article Published on:

  18. In oviparous species, genes encoding proteins with functions in lipid remodeling, such as specialized lipases, may have evolved to facilitate the assembly and utilization of yolk lipids by the embryo. The mamm...

    Authors: Jani Saarela, Gerlinde Jung, Marcela Hermann, Johannes Nimpf and Wolfgang J Schneider
    Citation: BMC Genomics 2008 9:281
    Content type: Research article Published on:

  19. The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene fun...

    Authors: Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Hye-Sun Kim, Beom-Soon Choi, Seunghoon Baek, Jung Sun Kim, Mina Jin, Jin A Kim, Myung-Ho Lim, Soo In Lee, Ho-Il Kim, Hyungtae Kim, Yong Pyo Lim and Beom-Seok Park
    Citation: BMC Genomics 2008 9:280
    Content type: Research article Published on:

  20. The bite of spiders belonging to the genus Loxosceles can induce a variety of clinical symptoms, including dermonecrosis, thrombosis, vascular leakage, haemolysis, and persistent inflammation. In order to examine...

    Authors: Matheus de F Fernandes-Pedrosa, Inácio de LM Junqueira-de-Azevedo, Rute M Gonçalves-de-Andrade, Leonardo S Kobashi, Diego D Almeida, Paulo L Ho and Denise V Tambourgi
    Citation: BMC Genomics 2008 9:279
    Content type: Research article Published on:

  21. Short non-coding RNAs (ncRNAs) perform their cellular functions in ribonucleoprotein (RNP) complexes, which are also essential for maintaining the stability of the ncRNAs. Depletion of individual protein compo...

    Authors: Muhammad Nauman Aftab, Housheng He, Geir Skogerbø and Runsheng Chen
    Citation: BMC Genomics 2008 9:278
    Content type: Research article Published on:

  22. The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied ...

    Authors: Flavio Mignone, Anna Anselmo, Giacinto Donvito, Giorgio P Maggi, Giorgio Grillo and Graziano Pesole
    Citation: BMC Genomics 2008 9:277
    Content type: Research article Published on:

  23. We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polym...

    Authors: Sun Pyo Hong, Seung Il Ji, Hwanseok Rhee, Soo Kyeong Shin, Sun Young Hwang, Seung Hwan Lee, Soong Deok Lee, Heung-Bum Oh, Wangdon Yoo and Soo-Ok Kim
    Citation: BMC Genomics 2008 9:276
    Content type: Methodology article Published on:

  24. Cultivated watermelon form large fruits that are highly variable in size, shape, color, and content, yet have extremely narrow genetic diversity. Whereas a plethora of genes involved in cell wall metabolism, e...

    Authors: W Patrick Wechter, Amnon Levi, Karen R Harris, Angela R Davis, Zhangjun Fei, Nurit Katzir, James J Giovannoni, Ayelet Salman-Minkov, Alvaro Hernandez, Jyothi Thimmapuram, Yaakov Tadmor, Vitaly Portnoy and Tova Trebitsh
    Citation: BMC Genomics 2008 9:275
    Content type: Research article Published on:

  25. The colonial cyanobacterium Microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. Microcystis blooms are often toxic, potentiall...

    Authors: Lionel Frangeul, Philippe Quillardet, Anne-Marie Castets, Jean-François Humbert, Hans CP Matthijs, Diego Cortez, Andrew Tolonen, Cheng-Cai Zhang, Simonetta Gribaldo, Jan-Christoph Kehr, Yvonne Zilliges, Nadine Ziemert, Sven Becker, Emmanuel Talla, Amel Latifi, Alain Billault…
    Citation: BMC Genomics 2008 9:274
    Content type: Research article Published on:

  26. Studies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing, we sought to use microarrays ...

    Authors: Wan-Lin Su, Barmak Modrek, Debraj GuhaThakurta, Stephen Edwards, Jyoti K Shah, Amit V Kulkarni, Archie Russell, Eric E Schadt, Jason M Johnson and John C Castle
    Citation: BMC Genomics 2008 9:273
    Content type: Research article Published on:

  27. In a traditional electrophoresis mobility shift assay (EMSA) a 32P-labeled double-stranded DNA oligonucleotide or a restriction fragment bound to a protein is separated from the unbound DNA by polyacrylamide gel ...

    Authors: Kristel Kaer, Kert Mätlik, Madis Metsis and Mart Speek
    Citation: BMC Genomics 2008 9:272
    Content type: Methodology article Published on:

  28. Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. Azorhizobium caulinodans ORS571 has the dual capacity to fix nitrogen both as free-living organism ...

    Authors: Kyung-Bum Lee, Philippe De Backer, Toshihiro Aono, Chi-Te Liu, Shino Suzuki, Tadahiro Suzuki, Takakazu Kaneko, Manabu Yamada, Satoshi Tabata, Doris M Kupfer, Fares Z Najar, Graham B Wiley, Bruce Roe, Tim T Binnewies, David W Ussery, Wim D'Haeze…
    Citation: BMC Genomics 2008 9:271
    Content type: Research article Published on:

  30. Target genes of a transcription factor (TF) Pou5f1 (Oct3/4 or Oct4), which is essential for pluripotency maintenance and self-renewal of embryonic stem (ES) cells, have previously been identified based on their r...

    Authors: Alexei A Sharov, Shinji Masui, Lioudmila V Sharova, Yulan Piao, Kazuhiro Aiba, Ryo Matoba, Li Xin, Hitoshi Niwa and Minoru SH Ko
    Citation: BMC Genomics 2008 9:269
    Content type: Research article Published on:

  31. Phenotypically identical cells demonstrate predictable, robust behaviours. However, there is uncertainty as to whether phenotypically identical cells are equally similar at the underlying transcriptional level...

    Authors: Tatiana Subkhankulova, Michael J Gilchrist and Frederick J Livesey
    Citation: BMC Genomics 2008 9:268
    Content type: Research article Published on:

  32. To a greater or lesser extent, eukaryotic nuclear genomes contain fragments of their mitochondrial genome counterpart, deriving from the random insertion of damaged mtDNA fragments. NumtS (Nuclear mt Sequences...

    Authors: Daniela Lascaro, Stefano Castellana, Giuseppe Gasparre, Giovanni Romeo, Cecilia Saccone and Marcella Attimonelli
    Citation: BMC Genomics 2008 9:267
    Content type: Research article Published on:

  33. Natural contamination and anthropogenic pollution of soils are likely to be major determinants of functioning and survival of keystone invertebrate taxa. Soil animals will have both evolutionary adaptation and...

    Authors: Jennifer Owen, B Ann Hedley, Claus Svendsen, Jodie Wren, Martijs J Jonker, Peter K Hankard, Linsey J Lister, Stephen R Stürzenbaum, A John Morgan, David J Spurgeon, Mark L Blaxter and Peter Kille
    Citation: BMC Genomics 2008 9:266
    Content type: Research article Published on:

  34. Accurate mRNA splicing depends on multiple regulatory signals encoded in the transcribed RNA sequence. Many examples of mutations within human splice regulatory regions that alter splicing qualitatively or qua...

    Authors: Victoria Nembaware, Bukiwe Lupindo, Katherine Schouest, Charles Spillane, Konrad Scheffler and Cathal Seoighe
    Citation: BMC Genomics 2008 9:265
    Content type: Research article Published on:

  35. Tumor angiogenesis is a highly regulated process involving intercellular communication as well as the interactions of multiple downstream signal transduction pathways. Disrupting one or even a few angiogenesis...

    Authors: Yuefeng Chen, Tao Wei, Lei Yan, Frank Lawrence, Hui-Rong Qian, Timothy P Burkholder, James J Starling, Jonathan M Yingling and Jianyong Shou
    Citation: BMC Genomics 2008 9:264
    Content type: Research article Published on:

  36. Protozoan parasites of the genus Leishmania are causative agents of a diverse spectrum of human diseases collectively known as leishmaniasis. These eukaryotic pathogens that diverged early from the main eukaryoti...

    Authors: Jose M Requena, Cristina Folgueira, Manuel C López and M Carmen Thomas
    Citation: BMC Genomics 2008 9:263
    Content type: Research article Published on:

  37. Peripheral blood mononuclear cells (PBMCs) are relatively easily obtainable cells in humans. Gene expression profiles of PBMCs have been shown to reflect the pathological and physiological state of a person. R...

    Authors: Mark Bouwens, Lydia A Afman and Michael Müller
    Citation: BMC Genomics 2008 9:262
    Content type: Research article Published on:

  38. Integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can als...

    Authors: Diana R Nemergut, Michael S Robeson, Robert F Kysela, Andrew P Martin, Steven K Schmidt and Rob Knight
    Citation: BMC Genomics 2008 9:261
    Content type: Research article Published on:

  40. Cigarette smoking is a leading cause of preventable death and a significant cause of lung cancer and chronic obstructive pulmonary disease. Prior studies have demonstrated that smoking creates a field of molec...

    Authors: Sriram Sridhar, Frank Schembri, Julie Zeskind, Vishal Shah, Adam M Gustafson, Katrina Steiling, Gang Liu, Yves-Martine Dumas, Xiaohui Zhang, Jerome S Brody, Marc E Lenburg and Avrum Spira
    Citation: BMC Genomics 2008 9:259
    Content type: Research article Published on:

  41. Oligoarrays have become an accessible technique for exploring the transcriptome, but it is presently unclear how absolute transcript data from this technique compare to the data achieved with tag-based quantit...

    Authors: Vigdis Nygaard, Fang Liu, Marit Holden, Winston P Kuo, Jeff Trimarchi, Lucila Ohno-Machado, Connie L Cepko, Arnoldo Frigessi, Ingrid K Glad, Mark A van de Wiel, Eivind Hovig and Heidi Lyng
    Citation: BMC Genomics 2008 9:258
    Content type: Research article Published on:

  42. Metazoan mitochondrial genomes usually consist of the same 37 genes. Such genes contain useful information for phylogenetic analyses and evolution modelling. Although complete mitochondrial genomes have been d...

    Authors: Jin-Shu Yang and Wei-Jun Yang
    Citation: BMC Genomics 2008 9:257
    Content type: Research article Published on:

  43. Rhesus macaques (Macaca mulatta) are the primate most used for biomedical research, but phenotypic differences between Indian-origin and Chinese rhesus macaques have encouraged genetic methods for identifying gen...

    Authors: Jessica A Satkoski, RS Malhi, S Kanthaswamy, RY Tito, VS Malladi and DG Smith
    Citation: BMC Genomics 2008 9:256
    Content type: Research article Published on:

  44. Leishmania parasites cause a diverse spectrum of diseases in humans ranging from spontaneously healing skin lesions (e.g., L. major) to life-threatening visceral diseases (e.g., L. infantum). The high conservatio...

    Authors: Annie Rochette, Frédéric Raymond, Jean-Michel Ubeda, Martin Smith, Nadine Messier, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Marc Ouellette and Barbara Papadopoulou
    Citation: BMC Genomics 2008 9:255
    Content type: Research article Published on:

  45. Systematic search for genes whose gain-of-function by exogenous expression confers an advantage in cell-based selective screenings is a powerful method for unbiased functional exploration of the genome, and ha...

    Authors: Maria Luisa Martelli, Claudio Isella, Alessia Mira, Limin Fu, Daniela Cantarella and Enzo Medico
    Citation: BMC Genomics 2008 9:254
    Content type: Methodology article Published on:

  46. microRNAs (miRNAs) are small (~22 nt) non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloni...

    Authors: Elizabeth J Thatcher, Jordan Bond, Ima Paydar and James G Patton
    Citation: BMC Genomics 2008 9:253
    Content type: Research article Published on:

  47. Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed ...

    Authors: Steve R Bischoff, Shengdar Tsai, Nicholas E Hardison, Abby M York, Brad A Freking, Dan Nonneman, Gary Rohrer and Jorge A Piedrahita
    Citation: BMC Genomics 2008 9:252
    Content type: Methodology article Published on:

  48. Selenium (Se) is a trace element that occurs in proteins in the form of selenocysteine (Sec) and in tRNAs in the form of selenouridine (SeU). Selenophosphate synthetase (SelD) is required for both utilization ...

    Authors: Yan Zhang, Anton A Turanov, Dolph L Hatfield and Vadim N Gladyshev
    Citation: BMC Genomics 2008 9:251
    Content type: Research article Published on:

  50. MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression by targeting messenger RNAs (mRNAs) and causing mRNA cleavage or translation blockage. Of the 355 Arthropod miRNAs that have been identifie...

    Authors: Ping-an He, Zuoming Nie, Jianqing Chen, Jian Chen, Zhengbing Lv, Qing Sheng, Songping Zhou, Xiaolian Gao, Lingyin Kong, Xiangfu Wu, Yongfeng Jin and Yaozhou Zhang
    Citation: BMC Genomics 2008 9:248
    Content type: Research article Published on:

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BMC Genomics

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