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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  18. The rate at which a stretch of DNA mutates is determined by the cellular systems for DNA replication and repair, and by the nucleotide sequence of the stretch itself. One sequence feature with a particularly s...

    Authors: Roger M Wanner, Carolin Güthlein, Burkhard Springer, Erik C Böttger and Martin Ackermann
    Citation: BMC Genomics 2008 9:249
    Content type: Research article Published on:

  19. 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:

  20. Bifidobacteria are frequently proposed to be associated with good intestinal health primarily because of their overriding dominance in the feces of breast fed infants. However, clinical feeding studies with ex...

    Authors: Ju-Hoon Lee, VN Karamychev, SA Kozyavkin, D Mills, AR Pavlov, NV Pavlova, NN Polouchine, PM Richardson, VV Shakhova, AI Slesarev, B Weimer and DJ O'Sullivan
    Citation: BMC Genomics 2008 9:247
    Content type: Research article Published on:

  21. Expression levels of mRNA and protein by cell types exhibit a range of correlations for different genes. In this study, we compared levels of mRNA abundance for several cluster designation (CD) genes determine...

    Authors: Laura E Pascal, Lawrence D True, David S Campbell, Eric W Deutsch, Michael Risk, Ilsa M Coleman, Lillian J Eichner, Peter S Nelson and Alvin Y Liu
    Citation: BMC Genomics 2008 9:246
    Content type: Research article Published on:

  22. Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome seque...

    Authors: Wanwipa Vongsangnak, Peter Olsen, Kim Hansen, Steen Krogsgaard and Jens Nielsen
    Citation: BMC Genomics 2008 9:245
    Content type: Research article Published on:

  24. The medfly, Ceratitis capitata, is a highly invasive agricultural pest that has become a model insect for the development of biological control programs. Despite research into the behavior and classical and popul...

    Authors: Ludvik M Gomulski, George Dimopoulos, Zhiyong Xi, Marcelo B Soares, Maria F Bonaldo, Anna R Malacrida and Giuliano Gasperi
    Citation: BMC Genomics 2008 9:243
    Content type: Research article Published on:

  27. Endothelial differentiation occurs during normal vascular development in the developing embryo. This process is recapitulated in the adult when endothelial progenitor cells are generated in the bone marrow and...

    Authors: Vesna Nikolova-Krstevski, Manoj Bhasin, Hasan H Otu, Towia Libermann and Peter Oettgen
    Citation: BMC Genomics 2008 9:240
    Content type: Research article Published on:

  28. Estrogen receptor positive (ER+) breast cancers (BC) are heterogeneous with regard to their clinical behavior and response to therapies. The ER is currently the best predictor of response to the anti-estrogen ...

    Authors: Sherene Loi, Benjamin Haibe-Kains, Christine Desmedt, Pratyaksha Wirapati, Françoise Lallemand, Andrew M Tutt, Cheryl Gillet, Paul Ellis, Kenneth Ryder, James F Reid, Maria G Daidone, Marco A Pierotti, Els MJJ Berns, Maurice PHM Jansen, John A Foekens, Mauro Delorenzi…
    Citation: BMC Genomics 2008 9:239
    Content type: Research article Published on:

  29. Leishmania (L) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex inter...

    Authors: Fatma Z Guerfali, Dhafer Laouini, Lamia Guizani-Tabbane, Florence Ottones, Khadija Ben-Aissa, Alia Benkahla, Laurent Manchon, David Piquemal, Sondos Smandi, Ons Mghirbi, Thérèse Commes, Jacques Marti and Koussay Dellagi
    Citation: BMC Genomics 2008 9:238
    Content type: Research article Published on:

  30. Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C~7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorti...

    Authors: Hana Šimková, Jan Šafář, Pavla Suchánková, Pavlína Kovářová, Jan Bartoš, Marie Kubaláková, Jaroslav Janda, Jarmila Číhalíková, Rohit Mago, Tamas Lelley and Jaroslav Doležel
    Citation: BMC Genomics 2008 9:237
    Content type: Research article Published on:

  31. Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs). Whereas the functional properties of these ml-ncRNAs are beginning to be unra...

    Authors: Shunmin He, Hua Su, Changning Liu, Geir Skogerbø, Housheng He, Dandan He, Xiaopeng Zhu, Tao Liu, Yi Zhao and Runsheng Chen
    Citation: BMC Genomics 2008 9:236
    Content type: Research article Published on:

  34. In recent years, there have been several sialome projects revealing transcripts expressed in the salivary glands of ticks, which are important vectors of several human diseases. Here, we focused on the sialome...

    Authors: Jindřich Chmelař, Jennifer M Anderson, Jianbing Mu, Ryan C Jochim, Jesus G Valenzuela and Jan Kopecký
    Citation: BMC Genomics 2008 9:233
    Content type: Research article Published on:

  36. The selective absorption of nutrients and other food constituents in the small intestine is mediated by a group of transport proteins and metabolic enzymes, often collectively called 'intestinal barrier protei...

    Authors: Heleen M de Vogel-van den Bosch, Meike Bünger, Philip J de Groot, Hanneke Bosch-Vermeulen, Guido JEJ Hooiveld and Michael Müller
    Citation: BMC Genomics 2008 9:231
    Content type: Research article Published on:

  37. Microarray comparative genomic hybridization (aCGH) evaluates the distribution of genes of sequenced bacterial strains among unsequenced strains of the same or related species. As genomic sequences from multip...

    Authors: Francisco R Pinto, Sandra I Aguiar, J Melo-Cristino and Mário Ramirez
    Citation: BMC Genomics 2008 9:230
    Content type: Methodology article Published on:

  38. Photorhabdus luminescens is a Gram-negative luminescent enterobacterium and a symbiote to soil nematodes belonging to the species Heterorhabditis bacteriophora. P.luminescens is simultaneously highly pathogenic t...

    Authors: Anna Münch, Lavinia Stingl, Kirsten Jung and Ralf Heermann
    Citation: BMC Genomics 2008 9:229
    Content type: Research article Published on:

  40. Anopheles innate immunity affects Plasmodium development and is a potential target of innovative malaria control strategies. The extent and distribution of nucleotide diversity in immunity genes might provide ins...

    Authors: Anna Cohuet, Sujatha Krishnakumar, Frédéric Simard, Isabelle Morlais, Anastasios Koutsos, Didier Fontenille, Michael Mindrinos and Fotis C Kafatos
    Citation: BMC Genomics 2008 9:227
    Content type: Research article Published on:

  41. The majority of human non-protein-coding DNA is made up of repetitive sequences, mainly transposable elements (TEs). It is becoming increasingly apparent that many of these repetitive DNA sequence elements enc...

    Authors: Nalini Polavarapu, Leonardo Mariño-Ramírez, David Landsman, John F McDonald and I King Jordan
    Citation: BMC Genomics 2008 9:226
    Content type: Research article Published on:

  42. T-cell activation is an essential step of the immune response and relies on the tightly controlled orchestration of hundreds of genes/proteins, yet the cellular and molecular events underlying this complex pro...

    Authors: Min Wang, Dirk Windgassen and Eleftherios T Papoutsakis
    Citation: BMC Genomics 2008 9:225
    Content type: Research article Published on:

  43. Studying mitochondrial (mt) genomics has important implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. In addition, mt genome sequences have provided useful...

    Authors: Ming-Wei Li, Rui-Qing Lin, Hui-Qun Song, Xiang-Yun Wu and Xing-Quan Zhu
    Citation: BMC Genomics 2008 9:224
    Content type: Research article Published on:

  44. The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage map...

    Authors: Thomas Moen, Ben Hayes, Matthew Baranski, Paul R Berg, Sissel Kjøglum, Ben F Koop, Willie S Davidson, Stig W Omholt and Sigbjørn Lien
    Citation: BMC Genomics 2008 9:223
    Content type: Research article Published on:

  45. The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now class...

    Authors: Hisayuki Nomiyama, Kunio Hieshima, Naoki Osada, Yoko Kato-Unoki, Kaori Otsuka-Ono, Sumio Takegawa, Toshiaki Izawa, Akio Yoshizawa, Yutaka Kikuchi, Sumio Tanase, Retsu Miura, Jun Kusuda, Miki Nakao and Osamu Yoshie
    Citation: BMC Genomics 2008 9:222
    Content type: Research article Published on:

  46. Sensitivity and accuracy are key points when using microarrays to detect alterations in gene expression under different conditions. Critical to the acquisition of reliable results is the preparation of the RNA...

    Authors: Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A Setterquist, Peter JM Rottier and Cornelis AM de Haan
    Citation: BMC Genomics 2008 9:221
    Content type: Methodology article Published on:

  47. The polyadenylation of mRNA is one of the critical processing steps during expression of almost all eukaryotic genes. It is tightly integrated with transcription, particularly its termination, as well as other...

    Authors: Arthur G Hunt, Ruqiang Xu, Balasubrahmanyam Addepalli, Suryadevara Rao, Kevin P Forbes, Lisa R Meeks, Denghui Xing, Min Mo, Hongwei Zhao, Amrita Bandyopadhyay, Lavanya Dampanaboina, Amanda Marion, Carol Von Lanken and Qingshun Quinn Li
    Citation: BMC Genomics 2008 9:220
    Content type: Research article Published on:

  48. Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: ...

    Authors: Antonio Marco and Ignacio Marín
    Citation: BMC Genomics 2008 9:219
    Content type: Research article Published on:

  50. The first systematic study of small non-coding RNAs (sRNA, ncRNA) in Streptomyces is presented. Except for a few exceptions, the Streptomyces sRNAs, as well as the sRNAs in other genera of the Actinomyces group, ...

    Authors: Josef Pánek, Jan Bobek, Karel Mikulík, Marek Basler and Jiří Vohradský
    Citation: BMC Genomics 2008 9:217
    Content type: Research article Published on:

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BMC Genomics

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