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  1. 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
    Content type: Research article Published on:

  2. 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
    Content type: Software Published on:

  3. 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
    Content type: Research article Published on:

  4. 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
    Content type: Research article Published on:

  5. 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
    Content type: Research article Published on:

  6. 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
    Content type: Research article Published on:

  7. 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
    Content type: Research article Published on:

  8. 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
    Content type: Research article Published on:

  9. 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
    Content type: Methodology article Published on:

  11. 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
    Content type: Research article Published on:

  12. 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
    Content type: Research article Published on:

  13. 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
    Content type: Software Published on:

  14. 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
    Content type: Research article Published on:

  15. 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
    Content type: Research article Published on:

  17. 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
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  20. 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
    Content type: Research article Published on:

  21. 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
    Content type: Methodology article Published on:

  22. 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
    Content type: Research article Published on:

  23. 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
    Content type: Research article Published on:

  24. 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
    Content type: Database Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Research article Published on:

  29. 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
    Content type: Methodology article Published on:

  30. 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
    Content type: Research article Published on:

  31. 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
    Content type: Research article Published on:

  32. 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
    Content type: Research article Published on:

  33. 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
    Content type: Research article Published on:

  36. 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
    Content type: Research article Published on:

  37. Variation in gene expression between two Drosophila melanogaster strains, as revealed by transcriptional profiling, seldom corresponded to variation in proximal promoter sequence for 34 genes analyzed. Two sets o...

    Authors: Rebecca Petersen Brown and Martin E Feder
    Citation: BMC Genomics 2005 6:110
    Content type: Research article Published on:

  38. 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
    Content type: Research article Published on:

  39. At least 18 replication-dependent histone H2a genes are distributed in 3 Hist gene clusters on different chromosomes of the mouse genome. In this analysis we designed specific PCR primers for each histone H2a tra...

    Authors: Hiromi Nishida, Takahiro Suzuki, Hiroki Ookawa, Yasuhiro Tomaru and Yoshihide Hayashizaki
    Citation: BMC Genomics 2005 6:108
    Content type: Research article Published on:

  40. Mobile genetic elements comprise a substantial fraction of vertebrate genomes. These genes are considered to be deleterious, and in vertebrates they are usually inactive. High throughput sequencing of salmonid...

    Authors: Aleksei Krasnov, Heikki Koskinen, Sergey Afanasyev and Hannu Mölsä
    Citation: BMC Genomics 2005 6:107
    Content type: Research article Published on:

  41. The cell-membrane G-protein coupled receptors (GPCRs) are one of the largest known superfamilies and are the main focus of intense pharmaceutical research due to their key role in cell physiology and disease. ...

    Authors: Raghu Prasad Rao Metpally and Ramanathan Sowdhamini
    Citation: BMC Genomics 2005 6:106
    Content type: Research article Published on:

  44. Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis belong to the genetically close-knit Bacillus cereus sensu lato group, a family of rod-shaped Gram-positive bacteria. pAW63 is the first conjugative ...

    Authors: Géraldine A Van der Auwera, Lars Andrup and Jacques Mahillon
    Citation: BMC Genomics 2005 6:103
    Content type: Research article Published on:

  46. DNA microarrays are widely used in gene expression analyses. To increase throughput and minimize costs without reducing gene expression data obtained, we investigated whether four mRNA samples can be analyzed ...

    Authors: Yvonne CM Staal, Marcel HM van Herwijnen, Frederik J van Schooten and Joost HM van Delft
    Citation: BMC Genomics 2005 6:101
    Content type: Methodology article Published on:

  47. To date, only a few transcription factors have been identified in the genome of the parasite Plasmodium falciparum, the causative agent of malaria. Moreover, no detailed molecular analysis of its basal transcript...

    Authors: Isabelle Callebaut, Karine Prat, Edwige Meurice, Jean-Paul Mornon and Stanislas Tomavo
    Citation: BMC Genomics 2005 6:100
    Content type: Research article Published on:

  48. Microarray studies of the same phenomenon in different labs often appear at variance because the published lists of regulated transcripts have disproportionately small intersections. We demonstrate that compar...

    Authors: Mayte Suárez-Fariñas, Scott Noggle, Michael Heke, Ali Hemmati-Brivanlou and Marcelo O Magnasco
    Citation: BMC Genomics 2005 6:99
    Content type: Methodology article Published on:

  49. Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is lethal. In contrast, dystrophin-deficient mdx mice recover due to effective regeneration of affected muscle tissue. To characteriz...

    Authors: R Turk, E Sterrenburg, EJ de Meijer, G-JB van Ommen, JT den Dunnen and PAC 't Hoen
    Citation: BMC Genomics 2005 6:98
    Content type: Research article Published on:

  50. Loss of chromosome 11q defines a subset of high-stage aggressive neuroblastomas. Deletions are typically large and mapping efforts have thus far not lead to a well defined consensus region, which hampers the i...

    Authors: Katleen De Preter, Jo Vandesompele, Björn Menten, Philippa Carr, Heike Fiegler, Anders Edsjö, Nigel P Carter, Nurten Yigit, Wim Waelput, Nadine Van Roy, Scott Bader, Sven Påhlman and Frank Speleman
    Citation: BMC Genomics 2005 6:97
    Content type: Research article Published on:

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BMC Genomics

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