Genome Biology | Volume 3 Issue 7

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 3 Issue 7
	Comment
	Comment No place like Ome Gregory A Petsko Genome Biology 2002, 3:comment1010-comment1010.2 (26 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Of the two components of the word genome, 'ome' is the more interesting.
	Review
	Protein family review MAP kinase phosphatases Aspasia Theodosiou, Alan Ashworth Genome Biology 2002, 3:reviews3009-reviews3009.10 (26 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An emerging family of structurally distinct dual-specificity serine, threonine and tyrosine phosphatases that act on MAP kinases consists of ten members in mammals, and members have been found in animals, plants and yeast. Three subgroups have been identified that differ in exon structure, sequence and substrate specificity.
	Protein family review The 14-3-3s Robert J Ferl, Michael S Manak, Matthew F Reyes Genome Biology 2002, 3:reviews3010-reviews3010.7 (27 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The major native forms of 14-3-3s are homo- and hetero-dimers, the biological functions of which are to interact physically with specific client proteins and thereby effect a change in the client. As a result, 14-3-3s are involved in a vast array of processes such as the response to stress, cell-cycle control, and apoptosis, serving as adapters, activators, and repressors. There are currently 133 full-length sequences available.
	Minireview Oxidative stress responses - what have genome-scale studies taught us? John G Scandalios Genome Biology 2002, 3:reviews1019-reviews1019.6 (18 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Oxidative stress arises from an imbalance between generation and elimination of reactive oxygen species, often leading to cell death. Genomic tools are expanding our understanding of the antioxidant defenses aerobes have evolved and the recently discovered role(s) of reactive oxygen species in signaling.
	Minireview Principles of microbial alchemy: insights from the Streptomyces coelicolor genome sequence Charles J Thompson, Doris Fink, Liem D Nguyen Genome Biology 2002, 3:reviews1020-reviews1020.4 (26 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The availability of the recently completed Streptomyces coelicolor genome sequence provides a link between the folklore of antibiotics and other bioactive compounds to underlying biochemical, molecular genetic and evolutionary principles.
	Opinion Categorization of humans in biomedical research: genes, race and disease Neil Risch, Esteban Burchard, Elad Ziv, Hua Tang Genome Biology 2002, 3:comment2007-comment2007.12 (1 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A debate has arisen regarding the validity of racial/ethnic categories for biomedical and genetic research. An epidemiologic perspective on the issue of human categorization in biomedical and genetic research strongly supports the continued use of self-identified race and ethnicity.
	Report
	Paper report Sid knocks them out John C Rockett Genome Biology 2002, 3:reports0034 (24 June 2002) Abstract \| Full text \| Editor’s summary A putative transmembrane protein is required for systemic RNAi in Caenorhabditis elegans
	Paper report Cleaning up E. coli Wim D'Haeze Genome Biology 2002, 3:reports0039 (24 June 2002) Abstract \| Full text \| Editor’s summary A new method of creating large genomic deletions has been used to make a 'clean', stable bacterial genome
	Paper report Vegetarian adaptation Diane P Genereux Genome Biology 2002, 3:reports0033 (28 June 2002) Abstract \| Full text
	Paper report Rice genome revealed I: the indica sequence Jean-Nicolas Volff Genome Biology 2002, 3:reports0035 (28 June 2002) Abstract \| Full text \| Editor’s summary Together with the japonica rice genome sequence, this publicly available draft sequence of the indica rice genome should boost the genetic improvement of rice and other cereal crops
	Paper report Rice genome revealed II: the japonica sequence Jean-Nicolas Volff Genome Biology 2002, 3:reports0036 (28 June 2002) Abstract \| Full text \| Editor’s summary Together with the draft sequence of the indica rice genome, the draft sequence of the japonica rice genome should advance understanding of this important crop plant
	Paper report Genomic analysis of invasive streptococcus Wim D'Haeze Genome Biology 2002, 3:reports0037 (28 June 2002) Abstract \| Full text \| Editor’s summary The genome sequence of a Streptococcus group A strain that causes rheumatic fever has been determined
	Paper report A hyperthermophilic methanogen sequenced Wim D'Haeze Genome Biology 2002, 3:reports0038 (28 June 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of Methanopyrus kandleri will enhance our understanding of how methanogens live in extreme environmental conditions
	Meeting report Towards understanding neural survival, differentiation and death Karen Bailey, Andrew Gibbons Genome Biology 2002, 3:reports4018-reports4018.3 (14 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the 14th Biennial Meeting of the International Society for Developmental Neuroscience, Sydney, Australia, 31 January to 4 February 2002.
	Meeting report The salmon genome (and other issues in bioinformatics) Lena EF Milchert, David A Liberles, Arne Elofsson Genome Biology 2002, 3:reports4022-reports4022.4 (24 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the fourth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), Bioinformatics 2002, Bergen, Norway, 4-7 April 2002.
	Meeting report Trends in genomic 'evo-devo' Chun-che Chang, Charles E Cook Genome Biology 2002, 3:reports4019-reports4019.2 (27 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Meeting report Evolution of developmental mechanisms David EK Ferrier, Sebastian M Shimeld Genome Biology 2002, 3:reports4020-reports4020.3 (27 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint Spring meeting of the British Society of Developmental Biology and the Genetics Society, York, UK, 20-23 March 2002.
	Meeting report Drosophila melanogaster, two years into the post-genomic era Brian Oliver Genome Biology 2002, 3:reports4021-reports4021.2 (27 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 43rd Drosophila Research Conference held in San Diego, USA, 10-14 April 2002.
	Deposited research article Unraveling lipid metabolism with microarrays: Effects of arachidonate and docosahexaenoate acid on murine hepatic and hippocampal gene expression Alvin Berger, David M Mutch, J Bruce German, Matthew-Alan Roberts Genome Biology 2002, 3:preprint0004-preprint0004.53 (23 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The functions, actions, and regulation of polyunsaturated fatty acids (PUFAs) are beginning to be unraveled. Mice were fed diets rich in either arachidonic acid, docosahexaenoic acid, or both. Liver and hippocampus tissue were then analyzed through a combined gene expression-, lipid-, and behavioral- profiling strategy. Novel hippocampal PUFA-molecular targets suggest that PUFA transcriptionally regulated genes with roles in appetite and learning.
	Deposited research article Observation of intermittency in gene expression on cDNA microarrays Leif E Peterson, Kwong Lau Genome Biology 2002, 3:preprint0005-preprint0005.6 (29 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scaled factorial moments were used to search for intermittency in the log expression ratios for thousands of genes spotted on DNA microarrays. Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides additional insight into moderately expressed genes.
	Research news Modified primers Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020701-01 (1 July 2002) Abstract \| Full text \| Editor’s summary A new technique for preparing fluorescent cDNA probes will allow microarray analysis of smaller RNA samples.
	Research news Targeting human transgenes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020702-01 (2 July 2002) Abstract \| Full text \| Editor’s summary Adeno-associated virus vectors can be used for efficient transgene insertion into targeted loci in human cells.
	Research news Mutations in mental retardation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020703-01 (3 July 2002) Abstract \| Full text \| Editor’s summary Mutations in the gene encoding a receptor for angiotensin II are found in patients with X-linked mental retardation.
	Research news Dictyostelium chromosome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020704-01 (4 July 2002) Abstract \| Full text \| Editor’s summary Sequencing of the largest chromosome of the slime mold Dictyostelium reveals a very high gene density
	Research news Getting rid of nonsense Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020705-01 (5 July 2002) Abstract \| Full text \| Editor’s summary Translation signals regulate alternative mRNA splicing to eliminate harmful nonsense mutations.
	Research news MYC requirement Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020708-01 (8 July 2002) Abstract \| Full text \| Editor’s summary Constant expression of the MYC oncogene is required to maintain tumorigenesis.
	Research news RNAi in adult mice Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020709-01 (9 July 2002) Abstract \| Full text \| Editor’s summary RNA interference has been used to silence gene expression in living mice.
	Research news Tethering elements Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020710-01 (10 July 2002) Abstract \| Full text \| Editor’s summary Experiments in Drosophila provide evidence for promoter-proximal tethering elements that regulate interaction with distant enhancers.
	Research news T-cell switch Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020711-01 (11 July 2002) Abstract \| Full text \| Editor’s summary Chromatin remodelling complexes regulate the development of different T-lymphocyte lineages.
	Research news Genome SCORE Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020712-01 (12 July 2002) Abstract \| Full text \| Editor’s summary A computer algorithm can find transcriptional enhancers by searching for clusters of binding sites in the genome.
	Research news ADAM gene linked to asthma Tudor Toma Genome Biology 2002, 3:spotlight-20020715-01 (15 July 2002) Abstract \| Full text \| Editor’s summary Specific mutations in the ADAM33 gene are associated with asthma and bronchial hyperresponsiveness.
	Research news DOG patrol Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020715-02 (15 July 2002) Abstract \| Full text \| Editor’s summary A helicase protein, named DOG-1, is important for maintaining the stability of guanine-rich tracts of DNA.
	Research news Making ant wings Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020716-01 (16 July 2002) Abstract \| Full text \| Editor’s summary Gene expression patterns reveal features of the gene network governing wing development in ants.
	Research news Adenocarcinoma survival Tudor Toma Genome Biology 2002, 3:spotlight-20020717-01 (17 July 2002) Abstract \| Full text \| Editor’s summary Gene expression profiles can be used to predict patient survival in early-stage lung adenocarcinomas.
	Research news Death by PARP Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020717-02 (17 July 2002) Abstract \| Full text \| Editor’s summary The nuclear enzyme poly(ADP-ribose) polymerase-1 (PARP-1) kills cells by inducing translocation of a mitochondrial suicide protein.
	Research news Viral hit-and-run Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020718-01 (18 July 2002) Abstract \| Full text \| Editor’s summary Experiments with mutant adenoviruses reveal how viral oncoproteins target the cellular DNA-repair machinery to induce 'hit-and-run' transformation.
	Research news Malaria's many guises Tudor Toma Genome Biology 2002, 3:spotlight-20020719-01 (19 July 2002) Abstract \| Full text \| Editor’s summary Plasmodium falciparum is a genetically diverse and complex organism with mechanisms to evade host immunity and other antimalarial efforts.
	Research news Gene Genie Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020719-02 (19 July 2002) Abstract \| Full text \| Editor’s summary SAGE Genie provides new tools for exploring human gene-expression data.
	Research news Methylcytosine and mutation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020722-01 (22 July 2002) Abstract \| Full text \| Editor’s summary A methyl-CpG-binding protein protects against CpG mutability and can prevent tumor formation in mice.
	Research news Turning off a transgene Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020723-01 (23 July 2002) Abstract \| Full text \| Editor’s summary Studies of transgenic rice plants provide insights into the role of methylation in gene silencing.
	Research news Disease genes in yeast Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020724-01 (24 July 2002) Abstract \| Full text \| Editor’s summary Screening the yeast deletion collection for mutants with altered growth characteristics identifies a large number of genes linked to mitochondrial function and perhaps to human mitochondrial diseases.
	Research news Transfection using lasers Tudor Toma Genome Biology 2002, 3:spotlight-20020725-01 (25 July 2002) Abstract \| Full text \| Editor’s summary A variety of mammalian cells can be efficiently transfected with DNA using treatment with a femtosecond pulse laser.
	Research news Deletion bank Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020725-02 (25 July 2002) Abstract \| Full text \| Editor’s summary Yeast researchers have created a collection of mutants in which each gene has been systematically deleted.
	Research news Power to the pufferfish Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020726-01 (26 July 2002) Abstract \| Full text \| Editor’s summary The genome sequence of the pufferfish, Fugu rubripes, demonstrates the effectiveness of studying compact vertebrate genomes.
	Research news Nematode immunity Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020729-01 (29 July 2002) Abstract \| Full text \| Editor’s summary Genetic analysis reveals a pathway involved in innate immunity that is conserved from worms to man.
	Research news Genome to Life grants awarded Eugene Russo Genome Biology 2002, 3:spotlight-20020730-01 (30 July 2002) Abstract \| Full text \| Editor’s summary US Department of Energy gives $103 million for study of microbial systems biology and bugs that could help environment.
	Research news Keeping innate immunity at bay Michaela Torkar Genome Biology 2002, 3:spotlight-20020731-01 (31 July 2002) Abstract \| Full text \| Editor’s summary The mammalian kinase IRAK-M is a negative regulator of Toll-like receptor signaling and controls potentially harmful inflammatory immune reactions.
	Research
	Research Transcriptional programs activated by exposure of human prostate cancer cells to androgen Samuel E DePrimo, Maximilian Diehn, Joel B Nelson, Robert E Reiter, John Matese, Mike Fero, Robert Tibshirani, Patrick O Brown, James D Brooks Genome Biology 2002, 3:research0032-research0032.12 (14 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DNA microarrays were used to examine the temporal program of gene expression following treatment of a human prostate cancer cell line with androgen. Significant changes in levels of transcripts of more than 500 genes were observed; most were not previously known to be regulated by androgens.
	Research Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis Reinhard Hoffmann, Thomas Seidl, Martin Dugas Genome Biology 2002, 3:research0033-research0033.11 (14 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A number of procedures for normalization and detection of differentially expressed genes have been proposed. Four different normalization methods and all possible combinations with three different statistical algorithms have been used for detection of differentially expressed genes on a dataset. The number of genes detected as differentially expressed differs by a factor of about three.
	Research Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman Genome Biology 2002, 3:research0034-research0034.11 (18 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Using real-time reverse transcription PCR ten housekeeping genes from different abundance and functional classes in various human tissues were evaluated. The conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested.
	Research Gene-expression profiling of the response of peripheral blood mononuclear cells and melanoma metastases to systemic IL-2 administration Monica C Panelli, Ena Wang, Giao Phan, Markus Puhlmann, Lance Miller, Galen A Ohnmacht, Harvey G Klein, Francesco M Marincola Genome Biology 2002, 3:research0035-research0035.17 (25 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Early changes in transcriptional profiles of circulating mononuclear cells were compared with those occurring within the microenvironment of melanoma metastases following systemic IL-2 administration. The results suggest that the immediate effects of IL-2 administration on the tumor microenvironment is transcriptional activation of genes predominantly associated with monocyte cell function.
	Research A prediction-based resampling method for estimating the number of clusters in a dataset Sandrine Dudoit, Jane Fridlyand Genome Biology 2002, 3:research0036-research0036.21 (25 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. One aspect of this clustering problem is estimating the number of clusters in a dataset. A new prediction-based resampling method, Clest, was developed to address this problem.
	Research Normalization and analysis of DNA microarray data by self-consistency and local regression Thomas B Kepler, Lynn Crosby, Kevin T Morgan Genome Biology 2002, 3:research0037-research0037.12 (28 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A robust semi-parametric normalization technique has been developed, based on the assumption that the large majority of genes will not have their relative expression levels changed from one treatment group to the next, and on the assumption that departures of the response from linearity are small and slowly varying. The method was tested using data simulated under various error models and it performs well.
	Software CLUSFAVOR 5.0: hierarchical cluster and principal-component analysis of microarray-based transcriptional profiles Leif E Peterson Genome Biology 2002, 3:software0002-software0002.8 (24 June 2002) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary CLUSFAVOR (CLUSter and Factor Analysis with Varimax Orthogonal Rotation) 5.0 standardizes input data; sorts data according to gene-specific coefficient of variation, standard deviation, average and total expression, and Shannon entropy; performs hierarchical cluster analysis using nearest-neighbor, unweighted pair-group method using arithmetic averages (UPGMA), or furthest-neighbor joining methods, and Euclidean, correlation, or jack-knife distances; and performs principal-component analysis.

	Volume 3 Issue 7
	Comment
	Comment No place like Ome Gregory A Petsko Genome Biology 2002, 3:comment1010-comment1010.2 (26 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Of the two components of the word genome, 'ome' is the more interesting.
	Review
	Protein family review MAP kinase phosphatases Aspasia Theodosiou, Alan Ashworth Genome Biology 2002, 3:reviews3009-reviews3009.10 (26 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An emerging family of structurally distinct dual-specificity serine, threonine and tyrosine phosphatases that act on MAP kinases consists of ten members in mammals, and members have been found in animals, plants and yeast. Three subgroups have been identified that differ in exon structure, sequence and substrate specificity.
	Protein family review The 14-3-3s Robert J Ferl, Michael S Manak, Matthew F Reyes Genome Biology 2002, 3:reviews3010-reviews3010.7 (27 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The major native forms of 14-3-3s are homo- and hetero-dimers, the biological functions of which are to interact physically with specific client proteins and thereby effect a change in the client. As a result, 14-3-3s are involved in a vast array of processes such as the response to stress, cell-cycle control, and apoptosis, serving as adapters, activators, and repressors. There are currently 133 full-length sequences available.
	Minireview Oxidative stress responses - what have genome-scale studies taught us? John G Scandalios Genome Biology 2002, 3:reviews1019-reviews1019.6 (18 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Oxidative stress arises from an imbalance between generation and elimination of reactive oxygen species, often leading to cell death. Genomic tools are expanding our understanding of the antioxidant defenses aerobes have evolved and the recently discovered role(s) of reactive oxygen species in signaling.
	Minireview Principles of microbial alchemy: insights from the Streptomyces coelicolor genome sequence Charles J Thompson, Doris Fink, Liem D Nguyen Genome Biology 2002, 3:reviews1020-reviews1020.4 (26 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The availability of the recently completed Streptomyces coelicolor genome sequence provides a link between the folklore of antibiotics and other bioactive compounds to underlying biochemical, molecular genetic and evolutionary principles.
	Opinion Categorization of humans in biomedical research: genes, race and disease Neil Risch, Esteban Burchard, Elad Ziv, Hua Tang Genome Biology 2002, 3:comment2007-comment2007.12 (1 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A debate has arisen regarding the validity of racial/ethnic categories for biomedical and genetic research. An epidemiologic perspective on the issue of human categorization in biomedical and genetic research strongly supports the continued use of self-identified race and ethnicity.
	Report
	Paper report Sid knocks them out John C Rockett Genome Biology 2002, 3:reports0034 (24 June 2002) Abstract \| Full text \| Editor’s summary A putative transmembrane protein is required for systemic RNAi in Caenorhabditis elegans
	Paper report Cleaning up E. coli Wim D'Haeze Genome Biology 2002, 3:reports0039 (24 June 2002) Abstract \| Full text \| Editor’s summary A new method of creating large genomic deletions has been used to make a 'clean', stable bacterial genome
	Paper report Vegetarian adaptation Diane P Genereux Genome Biology 2002, 3:reports0033 (28 June 2002) Abstract \| Full text
	Paper report Rice genome revealed I: the indica sequence Jean-Nicolas Volff Genome Biology 2002, 3:reports0035 (28 June 2002) Abstract \| Full text \| Editor’s summary Together with the japonica rice genome sequence, this publicly available draft sequence of the indica rice genome should boost the genetic improvement of rice and other cereal crops
	Paper report Rice genome revealed II: the japonica sequence Jean-Nicolas Volff Genome Biology 2002, 3:reports0036 (28 June 2002) Abstract \| Full text \| Editor’s summary Together with the draft sequence of the indica rice genome, the draft sequence of the japonica rice genome should advance understanding of this important crop plant
	Paper report Genomic analysis of invasive streptococcus Wim D'Haeze Genome Biology 2002, 3:reports0037 (28 June 2002) Abstract \| Full text \| Editor’s summary The genome sequence of a Streptococcus group A strain that causes rheumatic fever has been determined
	Paper report A hyperthermophilic methanogen sequenced Wim D'Haeze Genome Biology 2002, 3:reports0038 (28 June 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of Methanopyrus kandleri will enhance our understanding of how methanogens live in extreme environmental conditions
	Meeting report Towards understanding neural survival, differentiation and death Karen Bailey, Andrew Gibbons Genome Biology 2002, 3:reports4018-reports4018.3 (14 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the 14th Biennial Meeting of the International Society for Developmental Neuroscience, Sydney, Australia, 31 January to 4 February 2002.
	Meeting report The salmon genome (and other issues in bioinformatics) Lena EF Milchert, David A Liberles, Arne Elofsson Genome Biology 2002, 3:reports4022-reports4022.4 (24 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the fourth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), Bioinformatics 2002, Bergen, Norway, 4-7 April 2002.
	Meeting report Trends in genomic 'evo-devo' Chun-che Chang, Charles E Cook Genome Biology 2002, 3:reports4019-reports4019.2 (27 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Meeting report Evolution of developmental mechanisms David EK Ferrier, Sebastian M Shimeld Genome Biology 2002, 3:reports4020-reports4020.3 (27 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint Spring meeting of the British Society of Developmental Biology and the Genetics Society, York, UK, 20-23 March 2002.
	Meeting report Drosophila melanogaster, two years into the post-genomic era Brian Oliver Genome Biology 2002, 3:reports4021-reports4021.2 (27 June 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 43rd Drosophila Research Conference held in San Diego, USA, 10-14 April 2002.
	Deposited research article Unraveling lipid metabolism with microarrays: Effects of arachidonate and docosahexaenoate acid on murine hepatic and hippocampal gene expression Alvin Berger, David M Mutch, J Bruce German, Matthew-Alan Roberts Genome Biology 2002, 3:preprint0004-preprint0004.53 (23 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The functions, actions, and regulation of polyunsaturated fatty acids (PUFAs) are beginning to be unraveled. Mice were fed diets rich in either arachidonic acid, docosahexaenoic acid, or both. Liver and hippocampus tissue were then analyzed through a combined gene expression-, lipid-, and behavioral- profiling strategy. Novel hippocampal PUFA-molecular targets suggest that PUFA transcriptionally regulated genes with roles in appetite and learning.
	Deposited research article Observation of intermittency in gene expression on cDNA microarrays Leif E Peterson, Kwong Lau Genome Biology 2002, 3:preprint0005-preprint0005.6 (29 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scaled factorial moments were used to search for intermittency in the log expression ratios for thousands of genes spotted on DNA microarrays. Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides additional insight into moderately expressed genes.
	Research news Modified primers Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020701-01 (1 July 2002) Abstract \| Full text \| Editor’s summary A new technique for preparing fluorescent cDNA probes will allow microarray analysis of smaller RNA samples.
	Research news Targeting human transgenes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020702-01 (2 July 2002) Abstract \| Full text \| Editor’s summary Adeno-associated virus vectors can be used for efficient transgene insertion into targeted loci in human cells.
	Research news Mutations in mental retardation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020703-01 (3 July 2002) Abstract \| Full text \| Editor’s summary Mutations in the gene encoding a receptor for angiotensin II are found in patients with X-linked mental retardation.
	Research news Dictyostelium chromosome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020704-01 (4 July 2002) Abstract \| Full text \| Editor’s summary Sequencing of the largest chromosome of the slime mold Dictyostelium reveals a very high gene density
	Research news Getting rid of nonsense Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020705-01 (5 July 2002) Abstract \| Full text \| Editor’s summary Translation signals regulate alternative mRNA splicing to eliminate harmful nonsense mutations.
	Research news MYC requirement Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020708-01 (8 July 2002) Abstract \| Full text \| Editor’s summary Constant expression of the MYC oncogene is required to maintain tumorigenesis.
	Research news RNAi in adult mice Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020709-01 (9 July 2002) Abstract \| Full text \| Editor’s summary RNA interference has been used to silence gene expression in living mice.
	Research news Tethering elements Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020710-01 (10 July 2002) Abstract \| Full text \| Editor’s summary Experiments in Drosophila provide evidence for promoter-proximal tethering elements that regulate interaction with distant enhancers.
	Research news T-cell switch Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020711-01 (11 July 2002) Abstract \| Full text \| Editor’s summary Chromatin remodelling complexes regulate the development of different T-lymphocyte lineages.
	Research news Genome SCORE Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020712-01 (12 July 2002) Abstract \| Full text \| Editor’s summary A computer algorithm can find transcriptional enhancers by searching for clusters of binding sites in the genome.
	Research news ADAM gene linked to asthma Tudor Toma Genome Biology 2002, 3:spotlight-20020715-01 (15 July 2002) Abstract \| Full text \| Editor’s summary Specific mutations in the ADAM33 gene are associated with asthma and bronchial hyperresponsiveness.
	Research news DOG patrol Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020715-02 (15 July 2002) Abstract \| Full text \| Editor’s summary A helicase protein, named DOG-1, is important for maintaining the stability of guanine-rich tracts of DNA.
	Research news Making ant wings Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020716-01 (16 July 2002) Abstract \| Full text \| Editor’s summary Gene expression patterns reveal features of the gene network governing wing development in ants.
	Research news Adenocarcinoma survival Tudor Toma Genome Biology 2002, 3:spotlight-20020717-01 (17 July 2002) Abstract \| Full text \| Editor’s summary Gene expression profiles can be used to predict patient survival in early-stage lung adenocarcinomas.
	Research news Death by PARP Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020717-02 (17 July 2002) Abstract \| Full text \| Editor’s summary The nuclear enzyme poly(ADP-ribose) polymerase-1 (PARP-1) kills cells by inducing translocation of a mitochondrial suicide protein.
	Research news Viral hit-and-run Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020718-01 (18 July 2002) Abstract \| Full text \| Editor’s summary Experiments with mutant adenoviruses reveal how viral oncoproteins target the cellular DNA-repair machinery to induce 'hit-and-run' transformation.
	Research news Malaria's many guises Tudor Toma Genome Biology 2002, 3:spotlight-20020719-01 (19 July 2002) Abstract \| Full text \| Editor’s summary Plasmodium falciparum is a genetically diverse and complex organism with mechanisms to evade host immunity and other antimalarial efforts.
	Research news Gene Genie Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020719-02 (19 July 2002) Abstract \| Full text \| Editor’s summary SAGE Genie provides new tools for exploring human gene-expression data.
	Research news Methylcytosine and mutation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020722-01 (22 July 2002) Abstract \| Full text \| Editor’s summary A methyl-CpG-binding protein protects against CpG mutability and can prevent tumor formation in mice.
	Research news Turning off a transgene Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020723-01 (23 July 2002) Abstract \| Full text \| Editor’s summary Studies of transgenic rice plants provide insights into the role of methylation in gene silencing.
	Research news Disease genes in yeast Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020724-01 (24 July 2002) Abstract \| Full text \| Editor’s summary Screening the yeast deletion collection for mutants with altered growth characteristics identifies a large number of genes linked to mitochondrial function and perhaps to human mitochondrial diseases.
	Research news Transfection using lasers Tudor Toma Genome Biology 2002, 3:spotlight-20020725-01 (25 July 2002) Abstract \| Full text \| Editor’s summary A variety of mammalian cells can be efficiently transfected with DNA using treatment with a femtosecond pulse laser.
	Research news Deletion bank Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020725-02 (25 July 2002) Abstract \| Full text \| Editor’s summary Yeast researchers have created a collection of mutants in which each gene has been systematically deleted.
	Research news Power to the pufferfish Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020726-01 (26 July 2002) Abstract \| Full text \| Editor’s summary The genome sequence of the pufferfish, Fugu rubripes, demonstrates the effectiveness of studying compact vertebrate genomes.
	Research news Nematode immunity Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020729-01 (29 July 2002) Abstract \| Full text \| Editor’s summary Genetic analysis reveals a pathway involved in innate immunity that is conserved from worms to man.
	Research news Genome to Life grants awarded Eugene Russo Genome Biology 2002, 3:spotlight-20020730-01 (30 July 2002) Abstract \| Full text \| Editor’s summary US Department of Energy gives $103 million for study of microbial systems biology and bugs that could help environment.
	Research news Keeping innate immunity at bay Michaela Torkar Genome Biology 2002, 3:spotlight-20020731-01 (31 July 2002) Abstract \| Full text \| Editor’s summary The mammalian kinase IRAK-M is a negative regulator of Toll-like receptor signaling and controls potentially harmful inflammatory immune reactions.
	Research
	Research Transcriptional programs activated by exposure of human prostate cancer cells to androgen Samuel E DePrimo, Maximilian Diehn, Joel B Nelson, Robert E Reiter, John Matese, Mike Fero, Robert Tibshirani, Patrick O Brown, James D Brooks Genome Biology 2002, 3:research0032-research0032.12 (14 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DNA microarrays were used to examine the temporal program of gene expression following treatment of a human prostate cancer cell line with androgen. Significant changes in levels of transcripts of more than 500 genes were observed; most were not previously known to be regulated by androgens.
	Research Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis Reinhard Hoffmann, Thomas Seidl, Martin Dugas Genome Biology 2002, 3:research0033-research0033.11 (14 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A number of procedures for normalization and detection of differentially expressed genes have been proposed. Four different normalization methods and all possible combinations with three different statistical algorithms have been used for detection of differentially expressed genes on a dataset. The number of genes detected as differentially expressed differs by a factor of about three.
	Research Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman Genome Biology 2002, 3:research0034-research0034.11 (18 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Using real-time reverse transcription PCR ten housekeeping genes from different abundance and functional classes in various human tissues were evaluated. The conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested.
	Research Gene-expression profiling of the response of peripheral blood mononuclear cells and melanoma metastases to systemic IL-2 administration Monica C Panelli, Ena Wang, Giao Phan, Markus Puhlmann, Lance Miller, Galen A Ohnmacht, Harvey G Klein, Francesco M Marincola Genome Biology 2002, 3:research0035-research0035.17 (25 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Early changes in transcriptional profiles of circulating mononuclear cells were compared with those occurring within the microenvironment of melanoma metastases following systemic IL-2 administration. The results suggest that the immediate effects of IL-2 administration on the tumor microenvironment is transcriptional activation of genes predominantly associated with monocyte cell function.
	Research A prediction-based resampling method for estimating the number of clusters in a dataset Sandrine Dudoit, Jane Fridlyand Genome Biology 2002, 3:research0036-research0036.21 (25 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. One aspect of this clustering problem is estimating the number of clusters in a dataset. A new prediction-based resampling method, Clest, was developed to address this problem.
	Research Normalization and analysis of DNA microarray data by self-consistency and local regression Thomas B Kepler, Lynn Crosby, Kevin T Morgan Genome Biology 2002, 3:research0037-research0037.12 (28 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A robust semi-parametric normalization technique has been developed, based on the assumption that the large majority of genes will not have their relative expression levels changed from one treatment group to the next, and on the assumption that departures of the response from linearity are small and slowly varying. The method was tested using data simulated under various error models and it performs well.
	Software CLUSFAVOR 5.0: hierarchical cluster and principal-component analysis of microarray-based transcriptional profiles Leif E Peterson Genome Biology 2002, 3:software0002-software0002.8 (24 June 2002) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary CLUSFAVOR (CLUSter and Factor Analysis with Varimax Orthogonal Rotation) 5.0 standardizes input data; sorts data according to gene-specific coefficient of variation, standard deviation, average and total expression, and Shannon entropy; performs hierarchical cluster analysis using nearest-neighbor, unweighted pair-group method using arithmetic averages (UPGMA), or furthest-neighbor joining methods, and Euclidean, correlation, or jack-knife distances; and performs principal-component analysis.

Explore Genome Biology

Articles

Volume 3 Issue 7

Comment

Review

Report

Research