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  1. Many biological networks show some characteristics of scale-free networks. Scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. In...

    Authors: Sara Light, Per Kraulis and Arne Elofsson
    Citation: BMC Genomics 2005 6:159
  2. Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present ...

    Authors: Elisa Giuntini, Alessio Mengoni, Carlotta De Filippo, Duccio Cavalieri, Nadia Aubin-Horth, Christian R Landry, Anke Becker and Marco Bazzicalupo
    Citation: BMC Genomics 2005 6:158
  3. Prader-Willi and Angelman syndrome (PWS and AS) patients typically have an ~5 Mb deletion of human chromosome 15q11-q13, of opposite parental origin. A mouse model of PWS and AS has a transgenic insertion-dele...

    Authors: Mihaela Stefan, Kathryn C Claiborn, Edyta Stasiek, Jing-Hua Chai, Tohru Ohta, Richard Longnecker, John M Greally and Robert D Nicholls
    Citation: BMC Genomics 2005 6:157
  4. Progranulin is an epithelial tissue growth factor (also known as proepithelin, acrogranin and PC-cell-derived growth factor) that has been implicated in development, wound healing and in the progression of man...

    Authors: Benoît Cadieux, Babykumari P Chitramuthu, David Baranowski and Hugh PJ Bennett
    Citation: BMC Genomics 2005 6:156
  5. SSH has emerged as a widely used technology to identify genes that are differentially regulated between two biological situations. Because it includes a normalisation step, it is used for preference to clone l...

    Authors: LC Bui, RD Léandri, JP Renard and V Duranthon
    Citation: BMC Genomics 2005 6:155
  6. It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotran...

    Authors: Thewarach Laha, Nonglack Kewgrai, Alex Loukas and Paul J Brindley
    Citation: BMC Genomics 2005 6:154
  7. large scale and reliable proteins' functional annotation is a major challenge in modern biology. Phylogenetic analyses have been shown to be important for such tasks. However, up to now, phylogenetic annotatio...

    Authors: N Balandraud, P Gouret, EGJ Danchin, M Blanc, D Zinn, J Roudier and P Pontarotti
    Citation: BMC Genomics 2005 6:153
  8. Regulatory functions of nitric oxide (NO) that bypass the second messenger cGMP are incompletely understood. Here, cGMP-independent effects of NO on gene expression were globally examined in U937 cells, a human...

    Authors: Xiaolin Cui, Jianhua Zhang, Penglin Ma, Daniela E Myers, Ilana G Goldberg, Kelly J Sittler, Jennifer J Barb, Peter J Munson, Ana del Pilar Cintron, J Philip McCoy, Shuibang Wang and Robert L Danner
    Citation: BMC Genomics 2005 6:151
  9. High throughput microarray-based single nucleotide polymorphism (SNP) genotyping has revolutionized the way genome-wide linkage scans and association analyses are performed. One of the key features of the arra...

    Authors: Matthew J Huentelman, David W Craig, Albert D Shieh, Jason J Corneveaux, Diane Hu-Lince, John V Pearson and Dietrich A Stephan
    Citation: BMC Genomics 2005 6:149
  10. Global mRNA amplification has become a widely used approach to obtain gene expression profiles from limited material. An important concern is the reliable reflection of the starting material in the results obt...

    Authors: Vigdis Nygaard, Marit Holden, Anders Løland, Mette Langaas, Ola Myklebost and Eivind Hovig
    Citation: BMC Genomics 2005 6:147
  11. In contrast to other agents able to induce apoptosis of cultured cells, Ca2+ ionophore A23187 was shown to elicit direct activation of intracellular signal(s). The phenotype of the cells derived from patients hav...

    Authors: Detlef Kozian, Valérie Proulle, Almut Nitsche, Marie Galitzine, Marie-Carmen Martinez, Beatrice Schumann, Dominique Meyer, Matthias Herrmann, Jean-Marie Freyssinet and Danièle Kerbiriou-Nabias
    Citation: BMC Genomics 2005 6:146
  12. iTRAQ™ technology for protein quantitation using mass spectrometry is a recent, powerful means of determining relative protein levels in up to four samples simultaneously. Although protein identification of sa...

    Authors: Ian P Shadforth, Tom PJ Dunkley, Kathryn S Lilley and Conrad Bessant
    Citation: BMC Genomics 2005 6:145
  13. The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near fu...

    Authors: Nathalie Pavy, Charles Paule, Lee Parsons, John A Crow, Marie-Josee Morency, Janice Cooke, James E Johnson, Etienne Noumen, Carine Guillet-Claude, Yaron Butterfield, Sarah Barber, George Yang, Jerry Liu, Jeff Stott, Robert Kirkpatrick, Asim Siddiqui…
    Citation: BMC Genomics 2005 6:144
  14. Ginkgo biloba L. is the only surviving member of one of the oldest living seed plant groups with medicinal, spiritual and horticultural importance worldwide. As an evolutionary relic, it displays many characters ...

    Authors: Eric D Brenner, Manpreet S Katari, Dennis W Stevenson, Stephen A Rudd, Andrew W Douglas, Walter N Moss, Richard W Twigg, Suzan J Runko, Giulia M Stellari, WR McCombie and Gloria M Coruzzi
    Citation: BMC Genomics 2005 6:143
  15. The molecular determinants of carcinogenesis, tumor progression and patient prognosis can be deduced from simultaneous comparison of thousands of genes by microarray analysis. However, the presence of stroma c...

    Authors: Elza C de Bruin, Simone van de Pas, Esther H Lips, Ronald van Eijk, Minke MC van der Zee, Marcel Lombaerts, Tom van Wezel, Corrie AM Marijnen, J Han JM van Krieken, Jan Paul Medema, Cornelis JH van de Velde, Paul HC Eilers and Lucy TC Peltenburg
    Citation: BMC Genomics 2005 6:142
  16. A yeast strain lacking the two genes SSA1 and SSA2, which encode cytosolic molecular chaperones, acquires thermotolerance as well as the mild heat-shocked wild-type yeast strain. We investigated the genomic respo...

    Authors: Rena Matsumoto, Kuniko Akama, Randeep Rakwal and Hitoshi Iwahashi
    Citation: BMC Genomics 2005 6:141
  17. As a result of high-throughput genotyping methods, millions of human genetic variants have been reported in recent years. To efficiently identify those with significant biological functions, a practical strate...

    Authors: Yongjian Guo and D Curtis Jamison
    Citation: BMC Genomics 2005 6:140
  18. ADP-ribosylation is an enzyme-catalyzed posttranslational protein modification in which mono(ADP-ribosyl)transferases (mARTs) and poly(ADP-ribosyl)transferases (pARTs) transfer the ADP-ribose moiety from NAD o...

    Authors: Helge Otto, Pedro A Reche, Fernando Bazan, Katharina Dittmar, Friedrich Haag and Friedrich Koch-Nolte
    Citation: BMC Genomics 2005 6:139
  19. Pooling genomic DNA samples within clinical classes of disease followed by genotyping on whole-genome SNP microarrays, allows for rapid and inexpensive genome-wide association studies. Key to the success of th...

    Authors: David W Craig, Matthew J Huentelman, Diane Hu-Lince, Victoria L Zismann, Michael C Kruer, Anne M Lee, Erik G Puffenberger, John M Pearson and Dietrich A Stephan
    Citation: BMC Genomics 2005 6:138
  20. Eukaryotic organisms contain mitochondria, organelles capable of producing large amounts of ATP by oxidative phosphorylation. Each cell contains many mitochondria with many copies of mitochondrial DNA in each ...

    Authors: Patrick C Bradshaw, Anand Rathi and David C Samuels
    Citation: BMC Genomics 2005 6:136
  21. Microarray transcript profiling has the potential to illuminate the molecular processes that are involved in the responses of cattle to disease challenges. This knowledge may allow the development of strategie...

    Authors: Laurelea Donaldson, Tony Vuocolo, Christian Gray, Ylva Strandberg, Antonio Reverter, Sean McWilliam, YongHong Wang, Keren Byrne and Ross Tellam
    Citation: BMC Genomics 2005 6:135
  22. Independent identification of genes in different organisms and assays has led to a multitude of names for each gene. This balkanization makes it difficult to use gene names to locate genomic resources, homolog...

    Authors: Andrew J Olson, Tim Tully and Ravi Sachidanandam
    Citation: BMC Genomics 2005 6:134
  23. The gene(s) encoding the ETEC F4ab/ac receptors, involved in neonatal diarrhoea in pigs (a disease not yet described in humans), is located close to the TF locus on Sscr13. In order to reveal and characterize ...

    Authors: Mario Van Poucke, David Bourry, François Piumi, Marc Mattheeuws, Alex Van Zeveren, Patrick Chardon and Luc J Peelman
    Citation: BMC Genomics 2005 6:133
  24. Severe acute respiratory syndrome (SARS), a recent epidemic human disease, is caused by a novel coronavirus (SARS-CoV). First reported in Asia, SARS quickly spread worldwide through international travelling. A...

    Authors: Yun-Shien Lee, Chun-Houh Chen, Angel Chao, En-Shih Chen, Min-Li Wei, Lung-Kun Chen, Kuender D Yang, Meng-Chih Lin, Yi-Hsi Wang, Jien-Wei Liu, Hock-Liew Eng, Ping-Cherng Chiang, Ting-Shu Wu, Kuo-Chein Tsao, Chung-Guei Huang, Yin-Jing Tien…
    Citation: BMC Genomics 2005 6:132
  25. Serial Analysis of Gene Expression (SAGE) is a new technique that allows a detailed and profound quantitative and qualitative knowledge of gene expression profile, without previous knowledge of sequence of ana...

    Authors: Carlos Pérez-Plasencia, Gregory Riggins, Guelaguetza Vázquez-Ortiz, José Moreno, Hugo Arreola, Alfredo Hidalgo, Patricia Piña-Sanchez and Mauricio Salcedo
    Citation: BMC Genomics 2005 6:130
  26. A large number of animal and plant genomes have been completely sequenced over the last decade and are now publicly available. Although genomes can be rapidly sequenced, identifying protein-coding genes still ...

    Authors: Dário E Kalume, Suraj Peri, Raghunath Reddy, Jun Zhong, Mobolaji Okulate, Nirbhay Kumar and Akhilesh Pandey
    Citation: BMC Genomics 2005 6:128
  27. The trypanosomatids Leishmania major, Trypanosoma brucei and Trypanosoma cruzi cause some of the most debilitating diseases of humankind: cutaneous leishmaniasis, African sleeping sickness, and Chagas disease. Th...

    Authors: Marilyn Parsons, Elizabeth A Worthey, Pauline N Ward and Jeremy C Mottram
    Citation: BMC Genomics 2005 6:127
  28. We have developed and fabricated a salmonid microarray containing cDNAs representing 16,006 genes. The genes spotted on the array have been stringently selected from Atlantic salmon and rainbow trout expressed...

    Authors: Kristian R von Schalburg, Matthew L Rise, Glenn A Cooper, Gordon D Brown, A Ross Gibbs, Colleen C Nelson, William S Davidson and Ben F Koop
    Citation: BMC Genomics 2005 6:126
  29. The rTS gene (ENOSF1), first identified in Homo sapiens as a gene complementary to the thymidylate synthase (TYMS) mRNA, is known to encode two protein isoforms, rTSα and rTSβ. The rTSβ isoform appears to be an e...

    Authors: Ping Liang, Jayakumar R Nair, Lei Song, John J McGuire and Bruce J Dolnick
    Citation: BMC Genomics 2005 6:125
  30. The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation...

    Authors: Willem Albert Rensink, Yuandan Lee, Jia Liu, Stacy Iobst, Shu Ouyang and C Robin Buell
    Citation: BMC Genomics 2005 6:124
  31. Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly imp...

    Authors: Alexander Sczyrba, Michael Beckstette, Ali H Brivanlou, Robert Giegerich and Curtis R Altmann
    Citation: BMC Genomics 2005 6:123
  32. Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressu...

    Authors: Stefano Campanaro, Alessandro Vezzi, Nicola Vitulo, Federico M Lauro, Michela D'Angelo, Francesca Simonato, Alessandro Cestaro, Giorgio Malacrida, Giulio Bertoloni, Giorgio Valle and Douglas H Bartlett
    Citation: BMC Genomics 2005 6:122
  33. Corynebacterium glutamicum is a high-GC Gram-positive soil bacterium of great biotechnological importance for the production of amino acids. To facilitate the rational design of sulphur amino acid-producing strai...

    Authors: Christian Rückert, Daniel J Koch, Daniel A Rey, Andreas Albersmeier, Sascha Mormann, Alfred Pühler and Jörn Kalinowski
    Citation: BMC Genomics 2005 6:121
  34. In C. elegans, single nucleotide polymorphisms (SNPs) can function as silent genetic markers, with applications ranging from classical two- and three-factor mapping to measuring recombination across whole chromos...

    Authors: M Wayne Davis, Marc Hammarlund, Tracey Harrach, Patrick Hullett, Shawn Olsen and Erik M Jorgensen
    Citation: BMC Genomics 2005 6:118
  35. The human genome carries a high load of proviral-like sequences, called Human Endogenous Retroviruses (HERVs), which are the genomic traces of ancient infections by active retroviruses. These elements are in m...

    Authors: Nathalie de Parseval, Gora Diop, Sandra Blaise, François Helle, Alexandre Vasilescu, Fumihiko Matsuda and Thierry Heidmann
    Citation: BMC Genomics 2005 6:117
  36. Theoretical proteome analysis, generated by plotting theoretical isoelectric points (pI) against molecular masses of all proteins encoded by the genome show a multimodal distribution for pI. This multimodal di...

    Authors: Soumyadeep Nandi, Nipun Mehra, Andrew M Lynn and Alok Bhattacharya
    Citation: BMC Genomics 2005 6:116
  37. Pseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, encounters toxicity from phagocyte-derived reactive oxidants including hydrogen peroxide during active infection. P. aeruginosa responds wi...

    Authors: Wook Chang, David A Small, Freshteh Toghrol and William E Bentley
    Citation: BMC Genomics 2005 6:115
  38. The fibrinogen-like (FBG) domain, which consists of approximately 200 amino acid residues, has high sequence similarity to the C-terminal halves of fibrinogen β and γ chains. Fibrinogen-related proteins (FREPs...

    Authors: Xinguo Wang, Qin Zhao and Bruce M Christensen
    Citation: BMC Genomics 2005 6:114
  39. As a first step to explore the possible relationships existing between the effects of low oxygen pressure in the first trimester placenta and placental pathologies developing from mid-gestation, two subtracted...

    Authors: Daniel Vaiman, Françoise Mondon, Alexandra Garcès-Duran, Thérèse-Marie Mignot, Brigitte Robert, Régis Rebourcet, Hélène Jammes, Sonia T Chelbi, Frédérique Quetin, Geoffrey Marceau, Vincent Sapin, François Piumi, Jean-Louis Danan, Virginie Rigourd, Bruno Carbonne and Françoise Ferré
    Citation: BMC Genomics 2005 6:111
  40. We use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant categories, and enables the identification of genes...

    Authors: Juan Jose Lozano, Marta Soler, Raquel Bermudo, David Abia, Pedro L Fernandez, Timothy M Thomson and Angel R Ortiz
    Citation: BMC Genomics 2005 6:109

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