Genome Biology | Volume 1 Issue 2

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	Volume 1 Issue 2
	Comment
	Comment Dog eat dogma Gregory A Petsko Genome Biology 2000, 1:comment1002-comment1002.2 (28 July 2000) Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary It is human nature to inflate one's ideas and contributions. It is also human nature to hang onto one's ideas long after they have outlived their usefulness, in much the same way that a parent will still support a child who has grown up to be a menace to society. Both traits are at work whenever a scientist makes sweeping statements.
	Review
	Review The sequence of human chromosome 21 and implications for research into Down syndrome Katheleen Gardiner, Muriel Davisson Genome Biology 2000, 1:reviews0002-reviews0002.9 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of the major mouse models of Down syndrome, suggest how the chromosome sequence may help in understanding the complex Down syndrome phenotype.
	Minireview What makes desiccation tolerable? Hans J Bohnert Genome Biology 2000, 1:reviews1010-reviews1010.4 (2 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comparison of drought tolerance in plants at extreme ends of the evolutionary spectrum is beginning to show the mechanisms involved.
	Minireview Adding injury to insult: pathogen detection and responses Edward E Farmer Genome Biology 2000, 1:reviews1012-reviews1012.3 (2 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genomic approaches to the study of the expression of plant genes induced in response to disease and attack are now showing that there is an intimate association between pathogen perception and general stress detection.
	Minireview From lymphocytes to sharks: V(D)J recombinase moves to the germline David B Roth Genome Biology 2000, 1:reviews1014-reviews1014.4 (2 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The antigen-receptor genes of vertebrates are rearranged by a specialized somatic recombination mechanism in developing lymphocytes - and, unexpectedly, also in the germline of cartilaginous fishes. The recombination system that carries out these DNA rearrangements may thus be a significant evolutionary force, perhaps not limited to rearrangements at antigen-receptor loci.
	Minireview Host-pathogen studies in the post-genomic era Paul Kellam Genome Biology 2000, 1:reviews1009-reviews1009.4 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several studies are starting to show the power of DNA microarrays to identify interactions between animal hosts and their pathogens, and have revealed interesting correlations between host responses to different infectious agents.
	Minireview Where does fission yeast sit on the tree of life? Matthias Sipiczki Genome Biology 2000, 1:reviews1011-reviews1011.4 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe are as different from each other as either is from animals: their ancestors separated about 420 to 330 million years ago. Now that S. pombe is poised to join the post-genome era, its evolutionary position should become much clearer.
	Minireview A molecular portrait of the response to unfolded proteins Ardythe A McCracken, Jeffrey L Brodsky Genome Biology 2000, 1:reviews1013-reviews1013.3 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using DNA microarrays, 381 genes have been found to be induced in response to unfolded proteins. The identity of the previously characterized 208 of these, and further experiments, have revealed new details on the scope of the unfolded protein response and its connection to the degradation of proteins at the endoplasmic reticulum.
	Minireview Variations on a theme: flower development and evolution Vivian F Irish Genome Biology 2000, 1:reviews1015-reviews1015.4 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study, comparing the maize SILKY1 gene to its well-characterized homolog APETALA3 from Arabidopsis, has provided some of the first evidence pointing to conservation of homeotic gene function between monocots and dicots.
	Opinion Genomics: what is realistically achievable? Ross Overbeek Genome Biology 2000, 1:comment2002-comment2002.3 (28 July 2000) Full text \| PDF \| PubMed \| Editor’s summary We now have a large and growing number of sequenced genomes. It is widely understood that this presents research opportunities and promises to change the way biology advances, but the magnitude and nature of the opportunities is, for the most part, poorly understood. In this short piece, I wish to examine the following two questions: First, how quickly will sequence data be produced? Second, what impact will this have on our understanding of the sequenced organisms?
	Report
	Web report The family way Colin Semple Genome Biology 2000, 1:reports2044 (20 June 2000) Abstract \| Full text
	Web report Cross-referencing genes from model organisms and humans Kathryn Evans Genome Biology 2000, 1:reports2045 (20 June 2000) Abstract \| Full text
	Web report MOLMOL: A free biomolecular graphics/analysis package Jarrod A Smith Genome Biology 2000, 1:reports2046 (20 June 2000) Abstract \| Full text \| Editor’s summary MOLMOL is a molecular graphics program designed for display and analysis of biological macromolecules, particularly protein or DNA structures determined by nuclear magnetic resonance spectroscopy.
	Web report Making alignments prettier Mar Albà Genome Biology 2000, 1:reports2047 (19 July 2000) Abstract \| Full text \| Editor’s summary BoxShade takes sequence alignments and creates an output file in which the alignment is displayed with identical or similar residues shaded in two different tones of gray.
	Web report Finding restriction sites Mar Albà Genome Biology 2000, 1:reports2048 (19 July 2000) Abstract \| Full text \| Editor’s summary Webcutter provides a free and easy-to-use interface for the analysis of restriction sites in any sequence.
	Paper report How many amino-acid sequences can fold to a given protein structure? Rachel Brem Genome Biology 2000, 1:reports0041 (11 May 2000) Abstract \| Full text \| Editor’s summary Information about the set of amino-acid sequences that will fold to a given target protein structure can be predicted without assuming complete knowledge of the possible conformational space they can occupy.
	Paper report Classifying lymphomas Jonathan B Weitzman Genome Biology 2000, 1:reports0042 (11 May 2000) Abstract \| Full text
	Paper report A census of yeast protein-protein interactions Mar Alba Genome Biology 2000, 1:reports0043 (11 May 2000) Abstract \| Full text \| Editor’s summary Genome-wide yeast two-hybrid screening has provided a census of protein-protein interactions in Saccharomyces cerevisiae.
	Paper report Making high fidelity expression libraries Rachel Brem Genome Biology 2000, 1:reports0044 (11 May 2000) Abstract \| Full text
	Paper report Gene expression following HIV-1 infection Paul Kellam Genome Biology 2000, 1:reports0045 (11 May 2000) Abstract \| Full text
	Paper report What makes a yeast nuclear pore? Elena Porro Genome Biology 2000, 1:reports0046 (20 June 2000) Abstract \| Full text
	Paper report Levels of synteny between rice and maize Todd Richmond Genome Biology 2000, 1:reports0047 (20 June 2000) Abstract \| Full text
	Paper report Global analysis of chloroplast proteins Todd Richmond Genome Biology 2000, 1:reports0048 (20 June 2000) Abstract \| Full text
	Paper report Using chloroplasts to produce drugs Todd Richmond Genome Biology 2000, 1:reports0049 (20 June 2000) Abstract \| Full text
	Paper report Archaeal snoRNAs Rachel Brem Genome Biology 2000, 1:reports0050 (20 June 2000) Abstract \| Full text
	Paper report DNA sequences associated with chromatin proteins Michaela Torkar Genome Biology 2000, 1:reports0051 (20 June 2000) Abstract \| Full text
	Paper report Fruit fly p53, cell death and the cell cycle Jonathan Weitzman Genome Biology 2000, 1:reports0052 (20 June 2000) Abstract \| Full text
	Paper report Fruit fly p53 and cell death Jonathan Weitzman Genome Biology 2000, 1:reports0053 (20 June 2000) Abstract \| Full text
	Paper report Paternal genomic imprinting in plants Seung Yon Rhee Genome Biology 2000, 1:reports0054 (19 July 2000) Abstract \| Full text \| Editor’s summary Expression of paternal alleles for 20 loci expressed during early seed development in Arabidopsis was undetectable during early embryo and endosperm development, suggesting the presence of imprinting of the paternal genome.
	Paper report Evolutionary origins of photosynthetic organisms Devaki Bhaya Genome Biology 2000, 1:reports0055 (19 July 2000) Abstract \| Full text
	Paper report Identifying structured regions in E. coli DNA Rachel Brem Genome Biology 2000, 1:reports0056 (19 July 2000) Abstract \| Full text
	Paper report Finding flavor genes Philippe Reymond Genome Biology 2000, 1:reports0057 (19 July 2000) Abstract \| Full text
	Paper report Chromosome 21 sequenced Jonathan B Weitzman Genome Biology 2000, 1:reports0058 (19 July 2000) Abstract \| Full text \| Editor’s summary The complete DNA sequence of human chromosome 21 is now available.
	Paper report Vaccinia protein-protein interactions Mar Albà Genome Biology 2000, 1:reports0059 (19 July 2000) Abstract \| Full text \| Editor’s summary The availability of the complete sequence of the vaccinia virus genome has enabled a comprehensive two-hybrid analysis in yeast of virus protein-protein interactions.
	Paper report Towards uncultured-microbe genomics James Cotton Genome Biology 2000, 1:reports0060 (19 July 2000) Abstract \| Full text
	Paper report Plant wound responses Thomas Eulgem Genome Biology 2000, 1:reports0061 (19 July 2000) Abstract \| Full text
	Paper report Plant-pathogen interactions Thomas Eulgem Genome Biology 2000, 1:reports0062 (19 July 2000) Abstract \| Full text
	Paper report Dendrite guidance Joe Hao Genome Biology 2000, 1:reports0063 (19 July 2000) Abstract \| Full text
	Meeting report Gene prediction: the end of the beginning Colin Semple Genome Biology 2000, 1:reports4012-reports4012.3 (28 July 2000) Abstract \| Full text \| PDF \| Editor’s summary A report from the conference entitled Genome Based Gene Structure Determination, Hinxton, UK, 1-2 June, 2000, organised by the European Bioinformatics Institute (EBI).
	Meeting report How many genes does it take to make a human being? Pablo D Rabinowicz, Erik Vollbrecht, Bruce May Genome Biology 2000, 1:reports4013-reports4013.3 (28 July 2000) Abstract \| Full text \| PDF \| Editor’s summary A meeting report from the 13th Annual Cold Spring Harbor meeting on Genome Sequencing and Biology, May 10-14, 2000. Cold Spring Harbor, New York
	Research news Dolly, version 3.0 William Wells Genome Biology 2000, 1:spotlight-20000704-02 (4 July 2000) Abstract \| Full text \| Editor’s summary Gene modification has been achieved in sheep by directed integration into the DNA of a fibroblast, followed by nuclear transfer to generate three adult clones.
	Research news Responding to metal William Wells Genome Biology 2000, 1:spotlight-20000704-01 (4 July 2000) Abstract \| Full text \| Editor’s summary The vast number of genes that are turned on in response to zinc deprivation can be narrowed down by looking for common promoter elements.
	Research news Earlier than immediate-early William Wells Genome Biology 2000, 1:spotlight-20000706-01 (6 July 2000) Abstract \| Full text \| Editor’s summary A DNA virus packs away some mRNAs so that translation can begin immediately after the virus infects cells.
	Research news Daylight robbery William Wells Genome Biology 2000, 1:spotlight-20000706-02 (6 July 2000) Abstract \| Full text \| Editor’s summary A marine ciliate can keep photosynthesizing because it steals organelles from ingested algae.
	Research news The big-tomato gene William Wells Genome Biology 2000, 1:spotlight-20000710-01 (10 July 2000) Abstract \| Full text \| Editor’s summary Fw2.2, the first gene shown to control quantitative variation in tomato size, encodes a protein with structural similarity to Ras.
	Research news Targets for forkhead William Wells Genome Biology 2000, 1:spotlight-20000710-02 (10 July 2000) Abstract \| Full text \| Editor’s summary Yeast forkhead proteins control transcription of clusters of cell cycle genes either directly (for G2/M genes) or indirectly (for M/G1 genes).
	Research news Beauty has its cost William Wells Genome Biology 2000, 1:spotlight-20000710-03 (10 July 2000) Abstract \| Full text \| Editor’s summary Male guppies that are sexually more attractive are also evolutionarily less fit.
	Research news A list of lists for yeast William Wells Genome Biology 2000, 1:spotlight-20000712-01 (12 July 2000) Abstract \| Full text \| Editor’s summary A compendium of expression profiles from mutant yeast strains allows function to be attributed to uncharacterized genes and leads to the identification of a drug target.
	Research news Hopping along DNA William Wells Genome Biology 2000, 1:spotlight-20000713-02 (13 July 2000) Abstract \| Full text \| Editor’s summary The rate at which electrons and holes move along DNA is sufficient to prevent strand-cleavage reactions, but too slow to make DNA a useful molecular wire.
	Research news Of ozone holes and Triffids William Wells Genome Biology 2000, 1:spotlight-20000713-01 (13 July 2000) Abstract \| Full text \| Editor’s summary Increases in ultraviolet-B irradiation, which occur when stratospheric ozone is compromised, can reduce the genomic stability of plants.
	Research news Sequence of a plant pathogen William Wells Genome Biology 2000, 1:spotlight-20000714-01 (14 July 2000) Abstract \| Full text \| Editor’s summary The first public sequence of a free-living plant pathogen gives clues to its strategies for survival and pathogenesis.
	Research news Simulated fly segmentation William Wells Genome Biology 2000, 1:spotlight-20000718-01 (18 July 2000) Abstract \| Full text \| Editor’s summary The simplest working model of fly segment polarity determination is a robust module insensitive to variation in parameters and initial conditions.
	Research news Mad meiosis William Wells Genome Biology 2000, 1:spotlight-20000718-02 (18 July 2000) Abstract \| Full text \| Editor’s summary The spindle checkpoint operates in meiosis to reduce errors in chromosome segregation.
	Research news Rice - the prequel William Wells Genome Biology 2000, 1:spotlight-20000719-01 (19 July 2000) Abstract \| Full text \| Editor’s summary Transposons in rice are fewer in number and more distributed than expected, so rice genome sequencers may have it easy after all.
	Research news A cell of few modes William Wells Genome Biology 2000, 1:spotlight-20000721-01 (21 July 2000) Abstract \| Full text \| Editor’s summary A mathematical re-analysis of microarray gene expression data reveals that the vast majority of expression patterns can be represented by just a few "characteristic modes."
	Research news Early globetrotters William Wells Genome Biology 2000, 1:spotlight-20000725-02 (25 July 2000) Abstract \| Full text \| Editor’s summary Was Polynesia colonized by people migrating from Taiwan or Melanesia? New data suggest that neither theory is correct, and that southeast Asia may have been the starting-off point.
	Research news Human knockouts? William Wells Genome Biology 2000, 1:spotlight-20000725-01 (25 July 2000) Abstract \| Full text \| Editor’s summary A group II intron can be selected to insert into virtually any DNA target site in human cells.
	Research news A baffling protein William Wells Genome Biology 2000, 1:spotlight-20000731-02 (31 July 2000) Abstract \| Full text \| Editor’s summary BAF, a cellular protein that prevents virus autointegration, may normally function in chromosome condensation.
	Research news Breast cancer linked to chromatin remodeling William Wells Genome Biology 2000, 1:spotlight-20000731-01 (31 July 2000) Abstract \| Full text \| Editor’s summary BRCA1's association with a chromatin-remodeling complex may explain the many effects of this breast-cancer-related protein.
	Research news The jaws of transcription William Wells Genome Biology 2000, 1:spotlight-20000803-02 (3 August 2000) Abstract \| Full text \| Editor’s summary An RNA polymerase crystal structure and crosslinking data are combined to give clues about how transcription works.
	Research news Sex is good William Wells Genome Biology 2000, 1:spotlight-20000803-01 (3 August 2000) Abstract \| Full text \| Editor’s summary The effect of deleterious mutations on small populations competing for food resources explains why having sex is a good idea.
	Research news The two chromosomes of cholera William Wells Genome Biology 2000, 1:spotlight-20000804-01 (4 August 2000) Abstract \| Full text \| Editor’s summary The complete sequence of Vibrio cholerae suggests that the bacterium's second chromosome may have started life as a megaplasmid.
	Research news Profiles of metastasis William Wells Genome Biology 2000, 1:spotlight-20000807-02 (7 August 2000) Abstract \| Full text \| Editor’s summary DNA microarray analysis of metastatic cells reveals a new player, and an expression profile characteristic of reduced motility and invasive ability.
	Research news Breeding a better vector William Wells Genome Biology 2000, 1:spotlight-20000807-01 (7 August 2000) Abstract \| Full text \| Editor’s summary Application of DNA shuffling to the gene for a retrovirus coat protein yields viruses that can infect new cell types.
	Research news Many mutant mice William Wells Genome Biology 2000, 1:spotlight-20000810-02 (10 August 2000) Abstract \| Full text \| Editor’s summary Two random mutagenesis projects have yielded a vast array of new mouse mutants.
	Research news A polymerase for sister chromatid cohesion William Wells Genome Biology 2000, 1:spotlight-20000810-01 (10 August 2000) Abstract \| Full text \| Editor’s summary A fourth essential DNA polymerase in budding yeast may provide the link between making sister chromatids and sticking them together.
	Research news Can't get there from here William Wells Genome Biology 2000, 1:spotlight-20000814-01 (14 August 2000) Abstract \| Full text \| Editor’s summary Two populations of an RNA virus, derived from a single ancestral phage, repeatedly evolve towards different fitness maxima.
	Research news Destruction before salvation William Wells Genome Biology 2000, 1:spotlight-20000814-02 (14 August 2000) Abstract \| Full text \| Editor’s summary Early in cancer development, low levels of telomerase lead to genome rearrangements, before telomerase reactivation saves the cells from self-destruction.
	Research news 2D gels are not enough William Wells Genome Biology 2000, 1:spotlight-20000817-01 (17 August 2000) Abstract \| Full text \| Editor’s summary A detailed analysis of 2D gels shows that this proteomics technology does not pick up most medium or low abundance proteins.
	Research news A sea urchin genome project William Wells Genome Biology 2000, 1:spotlight-20000817-02 (17 August 2000) Abstract \| Full text \| Editor’s summary The sea urchin genome project is off to a start with sequence from the ends of 76,020 BAC recombinants.
	Research news Of cloned pigs and PERV William Wells Genome Biology 2000, 1:spotlight-20000818-01 (18 August 2000) Abstract \| Full text \| Editor’s summary Nuclear microinjection has yielded the first pig clones, but the wisdom of using the clones as xenotransplant donors is in doubt based on transmission of a pig retrovirus to immunocompromised mice.
	Research news Xena: small cloned piglet William Wells Genome Biology 2000, 1:spotlight-20000818-02 (18 August 2000) Abstract \| Full text \| Editor’s summary Nuclear microinjection has been used to produce the first pig clone.
	Research news Many ways to make a breast tumor William Wells Genome Biology 2000, 1:spotlight-20000821-01 (21 August 2000) Abstract \| Full text \| Editor’s summary Array analysis of breast tumors from 42 different individuals shows that there are many ways that cells can embark on a tumorigenic path.
	Research news Arrays for replication William Wells Genome Biology 2000, 1:spotlight-20000821-02 (21 August 2000) Abstract \| Full text \| Editor’s summary DNA microarrays have been used to track replication in bacteria and uncover a role for topoisomerase IV.
	Research news Assembling the human genome - for free Andrew McLaughlin Genome Biology 2000, 1:spotlight-20000823-01 (23 August 2000) Abstract \| Full text \| Editor’s summary Entrepreneurs looking to exploit the data collected through the Human Genome Project are to face stiff competition from a project designed to allow researchers around the world to access analysed and annotated genome information free of charge.
	Research news Genes that provide tumors with blood William Wells Genome Biology 2000, 1:spotlight-20000824-01 (24 August 2000) Abstract \| Full text \| Editor’s summary Based on expression analysis, tumor angiogenesis is very similar to normal blood vessel growth. The few differences may be critical for developing therapies.
	Research news A dictionary for genomes William Wells Genome Biology 2000, 1:spotlight-20000830-03 (30 August 2000) Abstract \| Full text \| Editor’s summary Regulatory sites in promoters can be identified by building a dictionary of the most probable 'words.'
	Research news Engineering translocations Jonathan B Weitzman Genome Biology 2000, 1:spotlight-20000830-01 (30 August 2000) Abstract \| Full text \| Editor’s summary The Cre-lox system for targeted recombination has been used successfully to create designer chromosomal translocations in mice that resemble those found in human tumors.
	Research news Translocation in a carcinoma William Wells Genome Biology 2000, 1:spotlight-20000830-02 (30 August 2000) Abstract \| Full text \| Editor’s summary Oncogenic fusions are common in leukemias/lymphomas and sarcomas, but a Pax8-PPARy1 fusion has been detected in thyroid carcinomas.
	Research
	Research Exclusion of EDNRB and KIT as the basis for white spotting in Border Collies Danika Metallinos, Jasper Rine Genome Biology 2000, 1:research0004-research0004.4 (28 July 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary White spotting patterns in mammals can be caused by mutations in the genes encoding the endothelin B receptor and c-KIT, which are necessary for proper migration, differentiation or survival of the melanoblasts. An intercross was generated from a female Newfoundland and a male Border Collie and the white spotting phenotypes of the intercross progeny were evaluated. Although EDNRB and KIT have been implicated in white spotting in horses, pigs, cows, mice and rats, polymorphisms were indentified that excluded both these genes as the cause of white spotting pattern in Border Collies.
	Research 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy, Louis Staudt, Wing C Chan, David Botstein, Patrick Brown Genome Biology 2000, 1:research0003-research0003.21 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A statistical method called 'gene shaving' can be used to analyze data from large gene expression studies. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene expression measurements made on samples from patients with diffuse large B-cell lymphoma were analyzed using the gene shaving method. A small cluster of genes whose expression is highly predictive of survival was identified.

	Volume 1 Issue 2
	Comment
	Comment Dog eat dogma Gregory A Petsko Genome Biology 2000, 1:comment1002-comment1002.2 (28 July 2000) Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary It is human nature to inflate one's ideas and contributions. It is also human nature to hang onto one's ideas long after they have outlived their usefulness, in much the same way that a parent will still support a child who has grown up to be a menace to society. Both traits are at work whenever a scientist makes sweeping statements.
	Review
	Review The sequence of human chromosome 21 and implications for research into Down syndrome Katheleen Gardiner, Muriel Davisson Genome Biology 2000, 1:reviews0002-reviews0002.9 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of the major mouse models of Down syndrome, suggest how the chromosome sequence may help in understanding the complex Down syndrome phenotype.
	Minireview What makes desiccation tolerable? Hans J Bohnert Genome Biology 2000, 1:reviews1010-reviews1010.4 (2 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comparison of drought tolerance in plants at extreme ends of the evolutionary spectrum is beginning to show the mechanisms involved.
	Minireview Adding injury to insult: pathogen detection and responses Edward E Farmer Genome Biology 2000, 1:reviews1012-reviews1012.3 (2 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genomic approaches to the study of the expression of plant genes induced in response to disease and attack are now showing that there is an intimate association between pathogen perception and general stress detection.
	Minireview From lymphocytes to sharks: V(D)J recombinase moves to the germline David B Roth Genome Biology 2000, 1:reviews1014-reviews1014.4 (2 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The antigen-receptor genes of vertebrates are rearranged by a specialized somatic recombination mechanism in developing lymphocytes - and, unexpectedly, also in the germline of cartilaginous fishes. The recombination system that carries out these DNA rearrangements may thus be a significant evolutionary force, perhaps not limited to rearrangements at antigen-receptor loci.
	Minireview Host-pathogen studies in the post-genomic era Paul Kellam Genome Biology 2000, 1:reviews1009-reviews1009.4 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several studies are starting to show the power of DNA microarrays to identify interactions between animal hosts and their pathogens, and have revealed interesting correlations between host responses to different infectious agents.
	Minireview Where does fission yeast sit on the tree of life? Matthias Sipiczki Genome Biology 2000, 1:reviews1011-reviews1011.4 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe are as different from each other as either is from animals: their ancestors separated about 420 to 330 million years ago. Now that S. pombe is poised to join the post-genome era, its evolutionary position should become much clearer.
	Minireview A molecular portrait of the response to unfolded proteins Ardythe A McCracken, Jeffrey L Brodsky Genome Biology 2000, 1:reviews1013-reviews1013.3 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using DNA microarrays, 381 genes have been found to be induced in response to unfolded proteins. The identity of the previously characterized 208 of these, and further experiments, have revealed new details on the scope of the unfolded protein response and its connection to the degradation of proteins at the endoplasmic reticulum.
	Minireview Variations on a theme: flower development and evolution Vivian F Irish Genome Biology 2000, 1:reviews1015-reviews1015.4 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study, comparing the maize SILKY1 gene to its well-characterized homolog APETALA3 from Arabidopsis, has provided some of the first evidence pointing to conservation of homeotic gene function between monocots and dicots.
	Opinion Genomics: what is realistically achievable? Ross Overbeek Genome Biology 2000, 1:comment2002-comment2002.3 (28 July 2000) Full text \| PDF \| PubMed \| Editor’s summary We now have a large and growing number of sequenced genomes. It is widely understood that this presents research opportunities and promises to change the way biology advances, but the magnitude and nature of the opportunities is, for the most part, poorly understood. In this short piece, I wish to examine the following two questions: First, how quickly will sequence data be produced? Second, what impact will this have on our understanding of the sequenced organisms?
	Report
	Web report The family way Colin Semple Genome Biology 2000, 1:reports2044 (20 June 2000) Abstract \| Full text
	Web report Cross-referencing genes from model organisms and humans Kathryn Evans Genome Biology 2000, 1:reports2045 (20 June 2000) Abstract \| Full text
	Web report MOLMOL: A free biomolecular graphics/analysis package Jarrod A Smith Genome Biology 2000, 1:reports2046 (20 June 2000) Abstract \| Full text \| Editor’s summary MOLMOL is a molecular graphics program designed for display and analysis of biological macromolecules, particularly protein or DNA structures determined by nuclear magnetic resonance spectroscopy.
	Web report Making alignments prettier Mar Albà Genome Biology 2000, 1:reports2047 (19 July 2000) Abstract \| Full text \| Editor’s summary BoxShade takes sequence alignments and creates an output file in which the alignment is displayed with identical or similar residues shaded in two different tones of gray.
	Web report Finding restriction sites Mar Albà Genome Biology 2000, 1:reports2048 (19 July 2000) Abstract \| Full text \| Editor’s summary Webcutter provides a free and easy-to-use interface for the analysis of restriction sites in any sequence.
	Paper report How many amino-acid sequences can fold to a given protein structure? Rachel Brem Genome Biology 2000, 1:reports0041 (11 May 2000) Abstract \| Full text \| Editor’s summary Information about the set of amino-acid sequences that will fold to a given target protein structure can be predicted without assuming complete knowledge of the possible conformational space they can occupy.
	Paper report Classifying lymphomas Jonathan B Weitzman Genome Biology 2000, 1:reports0042 (11 May 2000) Abstract \| Full text
	Paper report A census of yeast protein-protein interactions Mar Alba Genome Biology 2000, 1:reports0043 (11 May 2000) Abstract \| Full text \| Editor’s summary Genome-wide yeast two-hybrid screening has provided a census of protein-protein interactions in Saccharomyces cerevisiae.
	Paper report Making high fidelity expression libraries Rachel Brem Genome Biology 2000, 1:reports0044 (11 May 2000) Abstract \| Full text
	Paper report Gene expression following HIV-1 infection Paul Kellam Genome Biology 2000, 1:reports0045 (11 May 2000) Abstract \| Full text
	Paper report What makes a yeast nuclear pore? Elena Porro Genome Biology 2000, 1:reports0046 (20 June 2000) Abstract \| Full text
	Paper report Levels of synteny between rice and maize Todd Richmond Genome Biology 2000, 1:reports0047 (20 June 2000) Abstract \| Full text
	Paper report Global analysis of chloroplast proteins Todd Richmond Genome Biology 2000, 1:reports0048 (20 June 2000) Abstract \| Full text
	Paper report Using chloroplasts to produce drugs Todd Richmond Genome Biology 2000, 1:reports0049 (20 June 2000) Abstract \| Full text
	Paper report Archaeal snoRNAs Rachel Brem Genome Biology 2000, 1:reports0050 (20 June 2000) Abstract \| Full text
	Paper report DNA sequences associated with chromatin proteins Michaela Torkar Genome Biology 2000, 1:reports0051 (20 June 2000) Abstract \| Full text
	Paper report Fruit fly p53, cell death and the cell cycle Jonathan Weitzman Genome Biology 2000, 1:reports0052 (20 June 2000) Abstract \| Full text
	Paper report Fruit fly p53 and cell death Jonathan Weitzman Genome Biology 2000, 1:reports0053 (20 June 2000) Abstract \| Full text
	Paper report Paternal genomic imprinting in plants Seung Yon Rhee Genome Biology 2000, 1:reports0054 (19 July 2000) Abstract \| Full text \| Editor’s summary Expression of paternal alleles for 20 loci expressed during early seed development in Arabidopsis was undetectable during early embryo and endosperm development, suggesting the presence of imprinting of the paternal genome.
	Paper report Evolutionary origins of photosynthetic organisms Devaki Bhaya Genome Biology 2000, 1:reports0055 (19 July 2000) Abstract \| Full text
	Paper report Identifying structured regions in E. coli DNA Rachel Brem Genome Biology 2000, 1:reports0056 (19 July 2000) Abstract \| Full text
	Paper report Finding flavor genes Philippe Reymond Genome Biology 2000, 1:reports0057 (19 July 2000) Abstract \| Full text
	Paper report Chromosome 21 sequenced Jonathan B Weitzman Genome Biology 2000, 1:reports0058 (19 July 2000) Abstract \| Full text \| Editor’s summary The complete DNA sequence of human chromosome 21 is now available.
	Paper report Vaccinia protein-protein interactions Mar Albà Genome Biology 2000, 1:reports0059 (19 July 2000) Abstract \| Full text \| Editor’s summary The availability of the complete sequence of the vaccinia virus genome has enabled a comprehensive two-hybrid analysis in yeast of virus protein-protein interactions.
	Paper report Towards uncultured-microbe genomics James Cotton Genome Biology 2000, 1:reports0060 (19 July 2000) Abstract \| Full text
	Paper report Plant wound responses Thomas Eulgem Genome Biology 2000, 1:reports0061 (19 July 2000) Abstract \| Full text
	Paper report Plant-pathogen interactions Thomas Eulgem Genome Biology 2000, 1:reports0062 (19 July 2000) Abstract \| Full text
	Paper report Dendrite guidance Joe Hao Genome Biology 2000, 1:reports0063 (19 July 2000) Abstract \| Full text
	Meeting report Gene prediction: the end of the beginning Colin Semple Genome Biology 2000, 1:reports4012-reports4012.3 (28 July 2000) Abstract \| Full text \| PDF \| Editor’s summary A report from the conference entitled Genome Based Gene Structure Determination, Hinxton, UK, 1-2 June, 2000, organised by the European Bioinformatics Institute (EBI).
	Meeting report How many genes does it take to make a human being? Pablo D Rabinowicz, Erik Vollbrecht, Bruce May Genome Biology 2000, 1:reports4013-reports4013.3 (28 July 2000) Abstract \| Full text \| PDF \| Editor’s summary A meeting report from the 13th Annual Cold Spring Harbor meeting on Genome Sequencing and Biology, May 10-14, 2000. Cold Spring Harbor, New York
	Research news Dolly, version 3.0 William Wells Genome Biology 2000, 1:spotlight-20000704-02 (4 July 2000) Abstract \| Full text \| Editor’s summary Gene modification has been achieved in sheep by directed integration into the DNA of a fibroblast, followed by nuclear transfer to generate three adult clones.
	Research news Responding to metal William Wells Genome Biology 2000, 1:spotlight-20000704-01 (4 July 2000) Abstract \| Full text \| Editor’s summary The vast number of genes that are turned on in response to zinc deprivation can be narrowed down by looking for common promoter elements.
	Research news Earlier than immediate-early William Wells Genome Biology 2000, 1:spotlight-20000706-01 (6 July 2000) Abstract \| Full text \| Editor’s summary A DNA virus packs away some mRNAs so that translation can begin immediately after the virus infects cells.
	Research news Daylight robbery William Wells Genome Biology 2000, 1:spotlight-20000706-02 (6 July 2000) Abstract \| Full text \| Editor’s summary A marine ciliate can keep photosynthesizing because it steals organelles from ingested algae.
	Research news The big-tomato gene William Wells Genome Biology 2000, 1:spotlight-20000710-01 (10 July 2000) Abstract \| Full text \| Editor’s summary Fw2.2, the first gene shown to control quantitative variation in tomato size, encodes a protein with structural similarity to Ras.
	Research news Targets for forkhead William Wells Genome Biology 2000, 1:spotlight-20000710-02 (10 July 2000) Abstract \| Full text \| Editor’s summary Yeast forkhead proteins control transcription of clusters of cell cycle genes either directly (for G2/M genes) or indirectly (for M/G1 genes).
	Research news Beauty has its cost William Wells Genome Biology 2000, 1:spotlight-20000710-03 (10 July 2000) Abstract \| Full text \| Editor’s summary Male guppies that are sexually more attractive are also evolutionarily less fit.
	Research news A list of lists for yeast William Wells Genome Biology 2000, 1:spotlight-20000712-01 (12 July 2000) Abstract \| Full text \| Editor’s summary A compendium of expression profiles from mutant yeast strains allows function to be attributed to uncharacterized genes and leads to the identification of a drug target.
	Research news Hopping along DNA William Wells Genome Biology 2000, 1:spotlight-20000713-02 (13 July 2000) Abstract \| Full text \| Editor’s summary The rate at which electrons and holes move along DNA is sufficient to prevent strand-cleavage reactions, but too slow to make DNA a useful molecular wire.
	Research news Of ozone holes and Triffids William Wells Genome Biology 2000, 1:spotlight-20000713-01 (13 July 2000) Abstract \| Full text \| Editor’s summary Increases in ultraviolet-B irradiation, which occur when stratospheric ozone is compromised, can reduce the genomic stability of plants.
	Research news Sequence of a plant pathogen William Wells Genome Biology 2000, 1:spotlight-20000714-01 (14 July 2000) Abstract \| Full text \| Editor’s summary The first public sequence of a free-living plant pathogen gives clues to its strategies for survival and pathogenesis.
	Research news Simulated fly segmentation William Wells Genome Biology 2000, 1:spotlight-20000718-01 (18 July 2000) Abstract \| Full text \| Editor’s summary The simplest working model of fly segment polarity determination is a robust module insensitive to variation in parameters and initial conditions.
	Research news Mad meiosis William Wells Genome Biology 2000, 1:spotlight-20000718-02 (18 July 2000) Abstract \| Full text \| Editor’s summary The spindle checkpoint operates in meiosis to reduce errors in chromosome segregation.
	Research news Rice - the prequel William Wells Genome Biology 2000, 1:spotlight-20000719-01 (19 July 2000) Abstract \| Full text \| Editor’s summary Transposons in rice are fewer in number and more distributed than expected, so rice genome sequencers may have it easy after all.
	Research news A cell of few modes William Wells Genome Biology 2000, 1:spotlight-20000721-01 (21 July 2000) Abstract \| Full text \| Editor’s summary A mathematical re-analysis of microarray gene expression data reveals that the vast majority of expression patterns can be represented by just a few "characteristic modes."
	Research news Early globetrotters William Wells Genome Biology 2000, 1:spotlight-20000725-02 (25 July 2000) Abstract \| Full text \| Editor’s summary Was Polynesia colonized by people migrating from Taiwan or Melanesia? New data suggest that neither theory is correct, and that southeast Asia may have been the starting-off point.
	Research news Human knockouts? William Wells Genome Biology 2000, 1:spotlight-20000725-01 (25 July 2000) Abstract \| Full text \| Editor’s summary A group II intron can be selected to insert into virtually any DNA target site in human cells.
	Research news A baffling protein William Wells Genome Biology 2000, 1:spotlight-20000731-02 (31 July 2000) Abstract \| Full text \| Editor’s summary BAF, a cellular protein that prevents virus autointegration, may normally function in chromosome condensation.
	Research news Breast cancer linked to chromatin remodeling William Wells Genome Biology 2000, 1:spotlight-20000731-01 (31 July 2000) Abstract \| Full text \| Editor’s summary BRCA1's association with a chromatin-remodeling complex may explain the many effects of this breast-cancer-related protein.
	Research news The jaws of transcription William Wells Genome Biology 2000, 1:spotlight-20000803-02 (3 August 2000) Abstract \| Full text \| Editor’s summary An RNA polymerase crystal structure and crosslinking data are combined to give clues about how transcription works.
	Research news Sex is good William Wells Genome Biology 2000, 1:spotlight-20000803-01 (3 August 2000) Abstract \| Full text \| Editor’s summary The effect of deleterious mutations on small populations competing for food resources explains why having sex is a good idea.
	Research news The two chromosomes of cholera William Wells Genome Biology 2000, 1:spotlight-20000804-01 (4 August 2000) Abstract \| Full text \| Editor’s summary The complete sequence of Vibrio cholerae suggests that the bacterium's second chromosome may have started life as a megaplasmid.
	Research news Profiles of metastasis William Wells Genome Biology 2000, 1:spotlight-20000807-02 (7 August 2000) Abstract \| Full text \| Editor’s summary DNA microarray analysis of metastatic cells reveals a new player, and an expression profile characteristic of reduced motility and invasive ability.
	Research news Breeding a better vector William Wells Genome Biology 2000, 1:spotlight-20000807-01 (7 August 2000) Abstract \| Full text \| Editor’s summary Application of DNA shuffling to the gene for a retrovirus coat protein yields viruses that can infect new cell types.
	Research news Many mutant mice William Wells Genome Biology 2000, 1:spotlight-20000810-02 (10 August 2000) Abstract \| Full text \| Editor’s summary Two random mutagenesis projects have yielded a vast array of new mouse mutants.
	Research news A polymerase for sister chromatid cohesion William Wells Genome Biology 2000, 1:spotlight-20000810-01 (10 August 2000) Abstract \| Full text \| Editor’s summary A fourth essential DNA polymerase in budding yeast may provide the link between making sister chromatids and sticking them together.
	Research news Can't get there from here William Wells Genome Biology 2000, 1:spotlight-20000814-01 (14 August 2000) Abstract \| Full text \| Editor’s summary Two populations of an RNA virus, derived from a single ancestral phage, repeatedly evolve towards different fitness maxima.
	Research news Destruction before salvation William Wells Genome Biology 2000, 1:spotlight-20000814-02 (14 August 2000) Abstract \| Full text \| Editor’s summary Early in cancer development, low levels of telomerase lead to genome rearrangements, before telomerase reactivation saves the cells from self-destruction.
	Research news 2D gels are not enough William Wells Genome Biology 2000, 1:spotlight-20000817-01 (17 August 2000) Abstract \| Full text \| Editor’s summary A detailed analysis of 2D gels shows that this proteomics technology does not pick up most medium or low abundance proteins.
	Research news A sea urchin genome project William Wells Genome Biology 2000, 1:spotlight-20000817-02 (17 August 2000) Abstract \| Full text \| Editor’s summary The sea urchin genome project is off to a start with sequence from the ends of 76,020 BAC recombinants.
	Research news Of cloned pigs and PERV William Wells Genome Biology 2000, 1:spotlight-20000818-01 (18 August 2000) Abstract \| Full text \| Editor’s summary Nuclear microinjection has yielded the first pig clones, but the wisdom of using the clones as xenotransplant donors is in doubt based on transmission of a pig retrovirus to immunocompromised mice.
	Research news Xena: small cloned piglet William Wells Genome Biology 2000, 1:spotlight-20000818-02 (18 August 2000) Abstract \| Full text \| Editor’s summary Nuclear microinjection has been used to produce the first pig clone.
	Research news Many ways to make a breast tumor William Wells Genome Biology 2000, 1:spotlight-20000821-01 (21 August 2000) Abstract \| Full text \| Editor’s summary Array analysis of breast tumors from 42 different individuals shows that there are many ways that cells can embark on a tumorigenic path.
	Research news Arrays for replication William Wells Genome Biology 2000, 1:spotlight-20000821-02 (21 August 2000) Abstract \| Full text \| Editor’s summary DNA microarrays have been used to track replication in bacteria and uncover a role for topoisomerase IV.
	Research news Assembling the human genome - for free Andrew McLaughlin Genome Biology 2000, 1:spotlight-20000823-01 (23 August 2000) Abstract \| Full text \| Editor’s summary Entrepreneurs looking to exploit the data collected through the Human Genome Project are to face stiff competition from a project designed to allow researchers around the world to access analysed and annotated genome information free of charge.
	Research news Genes that provide tumors with blood William Wells Genome Biology 2000, 1:spotlight-20000824-01 (24 August 2000) Abstract \| Full text \| Editor’s summary Based on expression analysis, tumor angiogenesis is very similar to normal blood vessel growth. The few differences may be critical for developing therapies.
	Research news A dictionary for genomes William Wells Genome Biology 2000, 1:spotlight-20000830-03 (30 August 2000) Abstract \| Full text \| Editor’s summary Regulatory sites in promoters can be identified by building a dictionary of the most probable 'words.'
	Research news Engineering translocations Jonathan B Weitzman Genome Biology 2000, 1:spotlight-20000830-01 (30 August 2000) Abstract \| Full text \| Editor’s summary The Cre-lox system for targeted recombination has been used successfully to create designer chromosomal translocations in mice that resemble those found in human tumors.
	Research news Translocation in a carcinoma William Wells Genome Biology 2000, 1:spotlight-20000830-02 (30 August 2000) Abstract \| Full text \| Editor’s summary Oncogenic fusions are common in leukemias/lymphomas and sarcomas, but a Pax8-PPARy1 fusion has been detected in thyroid carcinomas.
	Research
	Research Exclusion of EDNRB and KIT as the basis for white spotting in Border Collies Danika Metallinos, Jasper Rine Genome Biology 2000, 1:research0004-research0004.4 (28 July 2000) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary White spotting patterns in mammals can be caused by mutations in the genes encoding the endothelin B receptor and c-KIT, which are necessary for proper migration, differentiation or survival of the melanoblasts. An intercross was generated from a female Newfoundland and a male Border Collie and the white spotting phenotypes of the intercross progeny were evaluated. Although EDNRB and KIT have been implicated in white spotting in horses, pigs, cows, mice and rats, polymorphisms were indentified that excluded both these genes as the cause of white spotting pattern in Border Collies.
	Research 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy, Louis Staudt, Wing C Chan, David Botstein, Patrick Brown Genome Biology 2000, 1:research0003-research0003.21 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A statistical method called 'gene shaving' can be used to analyze data from large gene expression studies. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene expression measurements made on samples from patients with diffuse large B-cell lymphoma were analyzed using the gene shaving method. A small cluster of genes whose expression is highly predictive of survival was identified.

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