Genome Biology | Volume 2 Issue 8

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	Volume 2 Issue 8
	Comment
	Comment Design by necessity Gregory A Petsko Genome Biology 2001, 2:comment1010-comment1010.3 (1 August 2001) Full text \| PDF \| PubMed \| Editor’s summary Necessity is the only designer we need to explain the world that genomics has shown to us.
	Review
	Protein family review The Smads Liliana Attisano, Si Tuen Lee-Hoeflich Genome Biology 2001, 2:reviews3010-reviews3010.8 (2 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Smads transmit signals to the nucleus from the transforming growth factor-β receptors. Regulatory Smads bind DNA in association with partner proteins and thereby regulate target genes. Other Smads aid this function, whereas inhibitory Smads antagonize it.
	Minireview Interorganellar crosstalk: new perspectives on signaling from the chloroplast to the nucleus Emma C Brown, Aravind Somanchi, Stephen P Mayfield Genome Biology 2001, 2:reviews1021-reviews1021.4 (30 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chlorophyll precursors, photosynthetic electron transport, and sugars have all been shown to be involved in signaling from the chloroplast to the nucleus, suggesting the presence of multiple signaling pathways of coordination between these two cellular compartments.
	Minireview Nucleomorph genomes: much ado about practically nothing Paul R Gilson Genome Biology 2001, 2:reviews1022-reviews1022.5 (30 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The DNA sequence of one of the smallest eukaryotic genomes has recently been finished - that of the reduced nucleus, or nucleomorph, of an algal endosymbiont that resides within a cryptomonad host cell. Its sequence promises insights into chloroplast acquisition, the constraints on genome size and the basic workings of eukaryotic cells.
	Minireview The genome of Mycobacterium leprae: a minimal mycobacterial gene set Varalakshmi D Vissa, Patrick J Brennan Genome Biology 2001, 2:reviews1023-reviews1023.8 (3 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the recently sequenced genome of the leprosy-causing pathogen Mycobacterium leprae with other mycobacterial genomes reveals a drastic gene reduction and decay in M. leprae affecting many metabolic areas, exemplified by the retention of a minimal set of genes required for cell-wall biosynthesis.
	Opinion Complex genetic diseases: controversy over the Croesus code Alan F Wright, Nicholas D Hastie Genome Biology 2001, 2:comment2007-comment2007.8 (1 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The polarization of views on how best to exploit new information from the Human Genome Project for medicine reflects our ignorance of the genetic architecture underlying common diseases: are susceptibility alleles common or rare, neutral or deleterious, few or many? Single-nucleotide polymorphism (SNP) technology is almost in place to dissect such diseases and to create a personalized medicine, but success is critically dependent on the biology and "Nature to be commanded must be obeyed" (Francis Bacon, 1620, Novum Organum).
	Report
	Web report Transgenic and targeted mouse mutation database Steven G Gray Genome Biology 2001, 2:reports2005 (20 July 2001) Abstract \| Full text
	Web report COPEing with cytokines Steven G Gray Genome Biology 2001, 2:reports2006 (27 July 2001) Abstract \| Full text \| Editor’s summary COPE is the electronic updated version of the Dictionary of Cytokines (Wiley; New York:1994) and represents a comprehensive online reference guide to the field of cytokine research.
	Web report Modeling RNA secondary structure Steven G Gray Genome Biology 2001, 2:reports2007 (27 July 2001) Abstract \| Full text \| Editor’s summary The mfold server has a simple interface that allows any researcher to analyze a submitted RNA sequence for various secondary structures using up-to-date algorithms and free-energy rules.
	Web report An anatomical view of gene expression Vasudeva Ginjala Genome Biology 2001, 2:reports2008 (27 July 2001) Abstract \| Full text
	Web report Gene imprinting gateway Vasudeva Ginjala Genome Biology 2001, 2:reports2009 (27 July 2001) Abstract \| Full text
	Paper report Xist comparative genomics Cathy Holding Genome Biology 2001, 2:reports0021 (10 July 2001) Abstract \| Full text \| Editor’s summary The primary sequence of Xist seems not to be important for Xist to function in X-chromosome inactivation.
	Paper report Tumor proteomics Steven G Gray Genome Biology 2001, 2:reports0022 (20 July 2001) Abstract \| Full text \| Editor’s summary A novel protein upregulated in certain cancers has been identified and characterized using an integrated proteomics, genomics, bioinformatics and standard molecular biology approach.
	Paper report Y-chromosome multicopy genes S Subramanian Genome Biology 2001, 2:reports0023 (20 July 2001) Abstract \| Full text
	Paper report Real-time flagellar gene expression Rachel Brem Genome Biology 2001, 2:reports0024 (8 August 2001) Abstract \| Full text
	Paper report Selection for reproduction S Subramanian Genome Biology 2001, 2:reports0025 (8 August 2001) Abstract \| Full text
	Paper report Resolving gene transfer issues Reiner Veitia Genome Biology 2001, 2:reports0026 (8 August 2001) Abstract \| Full text
	Paper report Further resolution of gene transfer issues Reiner Veitia Genome Biology 2001, 2:reports0027 (8 August 2001) Abstract \| Full text
	Meeting report More biology from the sequence Martin S Taylor Genome Biology 2001, 2:reports4018-reports4018.5 (31 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor meeting on Genome Sequencing and Biology, Cold Spring Harbor, NY, USA, 9-13 May 2001.
	Meeting report Towards a virtual Arabidopsis plant Benedikt Kost Genome Biology 2001, 2:reports4019-reports4019.4 (31 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Royal Society Discussion Meeting "The plant cell: between genome and plant", London, 13-14 June 2001.
	Deposited research article The genetic structure of recombinant inbred mice: High-resolution consensus maps for complex trait analysis Robert W Williams, Jing Gu, Shuhua Qi, Lu Lu Genome Biology 2001, 2:preprint0007-preprint0007.44 (18 July 2001) Abstract \| Full text \| PDF \| Editor’s summary The density of typed microsatellite markers has been increased 2- to 5-fold in each of several major recombinant inbred sets of mice and consensus RI maps that integrate genotypes of approximately 1600 microsatellite loci assembled.
	Research news The genome of Sinorhizobium meliloti David Bruce Genome Biology 2001, 2:spotlight-20010801-01 (1 August 2001) Abstract \| Full text \| Editor’s summary The sequencing of the genome of the bacterium involved in the rhizhobial symbiosis with alfalfa may help improve crop yields.
	Research news Putting the sea into cancer therapy Tudor Toma Genome Biology 2001, 2:spotlight-20010806-01 (6 August 2001) Abstract \| Full text \| Editor’s summary Tampering with the nucleotide excision DNA repair mechanism creates lethal breaks in the DNA and can kill cancerous cells.
	Research news Myotonic expansion Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010806-03 (6 August 2001) Abstract \| Full text \| Editor’s summary A huge expansion of intronic CCTG repeats causes Myotonic Dystrophy Type 2.
	Research news Perfect murder Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010806-02 (6 August 2001) Abstract \| Full text \| Editor’s summary A technique called "delitto perfetto" (perfect murder) can efficiently generate site-directed mutations in vivo.
	Research news Ink and Arf Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010807-02 (7 August 2001) Abstract \| Full text \| Editor’s summary The two proteins encodes by the Ink4a-Arf locus play different roles in senescence depending on the cell type.
	Research news Two-hybrid assay in plants Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010807-01 (7 August 2001) Abstract \| Full text \| Editor’s summary An in vivo protein-fragment complementation assay can monitor protein-protein interactions in living plant cells.
	Research news Lipocalin killer Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010808-01 (8 August 2001) Abstract \| Full text \| Editor’s summary Transcriptional regulation of a secreted lipocalin protein induces lymphocyte apoptosis upon removal of interleukin 3.
	Research news Sporozoite transcriptome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010809-01 (9 August 2001) Abstract \| Full text \| Editor’s summary ESTs have been generated on a large scale from the Plasmodium sporozoite stage.
	Research news Argonaute2 Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010810-02 (10 August 2001) Abstract \| Full text \| Editor’s summary Argonaute2, a component of the nuclease complex that carries out gene-silencing during RNAi, has been biochemically purified.
	Research news Structure of a DNA-damage repair protein David Bruce Genome Biology 2001, 2:spotlight-20010810-01 (10 August 2001) Abstract \| Full text \| Editor’s summary The Ku heterodimer forms a cradle in which broken DNA strands rest whilst being repaired.
	Research news A new mechanism for hypertension Jason Roach Genome Biology 2001, 2:spotlight-20010813-02 (13 August 2001) Abstract \| Full text \| Editor’s summary A newly identified metabolic pathway controlling blood pressure in humans could help design drugs to treat hypertension.
	Research news DNA/DNA microarrays Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010813-03 (13 August 2001) Abstract \| Full text \| Editor’s summary Microbial genomic hybridization on bacterial DNA microarrays offers a tool for comparing closely related organisms.
	Research news Space adds new dimension to cancer research Simon Frantz Genome Biology 2001, 2:spotlight-20010813-01 (13 August 2001) Abstract \| Full text \| Editor’s summary Culturing cells in the reduced gravity conditions of the International Space Station could help refine cancer treatment regimes.
	Research news Heterochromatin boundaries Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010814-01 (14 August 2001) Abstract \| Full text \| Editor’s summary The boundaries of functional chromatin domains are defined by site-specific methylation patterns of histone H3.
	Research news Transcriptional switch Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010815-01 (15 August 2001) Abstract \| Full text \| Editor’s summary Ordered acetylation of the HMGI(Y) protein controls enhanceosome stability and switches on gene expression.
	Research news A pathway to therapeutic destruction Tudor Toma Genome Biology 2001, 2:spotlight-20010816-01 (16 August 2001) Abstract \| Full text \| Editor’s summary Pancreatic cancer cells have an intact proapoptotic pathway activated by interferon gamma via caspase-1 dependent mechanisms.
	Research news Brainy stem cells Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010816-02 (16 August 2001) Abstract \| Full text \| Editor’s summary Stem cells purified from mouse brains can generate neural and non-neural cells in vitro and in vivo.
	Research news Proof of trans-splicing Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010817-01 (17 August 2001) Abstract \| Full text \| Editor’s summary Analysis of transgenic flies provides further evidence for trans-splicing within the Drosophila mod(mdg4) locus.
	Research news Making sense of antisense Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010820-01 (20 August 2001) Abstract \| Full text \| Editor’s summary DNA microarray analysis has been used to define gene-expression profiles following treatment with antisense oligonucleotides.
	Research news Tumor suppression by FEZ Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010821-01 (21 August 2001) Abstract \| Full text \| Editor’s summary The FEZ1 protein regulates mitosis and tumor cell proliferation.
	Research news Absolute BlyS Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010822-01 (22 August 2001) Abstract \| Full text \| Editor’s summary Insights into the function of the B-lymphocyte cytokine BAFF/BlyS and its receptors have come from mutant mice.
	Research news Prostate markers Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010823-01 (23 August 2001) Abstract \| Full text \| Editor’s summary Microarray analysis defines a prognostic expression profile signature for prostate cancer.
	Research news Agrobacterium goes live on the web Tudor Toma Genome Biology 2001, 2:spotlight-20010824-01 (24 August 2001) Abstract \| Full text \| Editor’s summary The entire Agrobacterium tumefaciens genome is now freely available on the web.
	Research news African elephants Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010824-02 (24 August 2001) Abstract \| Full text \| Editor’s summary Genetic analysis of free-ranging elephants suggests that there, in fact, are two species of African elephant.
	Research news Consequences of patrilocality Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010828-01 (28 August 2001) Abstract \| Full text \| Editor’s summary Female migrations explain population differences in the diversity of Y chromosomes compared to mitochondrial DNA.
	Research news Hazards of aging Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010828-02 (28 August 2001) Abstract \| Full text \| Editor’s summary Careful analysis confirms that damaged DNA accumulates as mice grow older.
	Research news Regulating p53 Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010829-01 (29 August 2001) Abstract \| Full text \| Editor’s summary Knockout mice highlight the importance of MDM4 in regulating the activity of the p53 tumor suppressor.
	Research news Not much in common Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010830-01 (30 August 2001) Abstract \| Full text \| Editor’s summary A comparison of the Celera and Ensembl transcriptomes examines how many predicted genes they have in common.
	Research news Viral killer Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010831-01 (31 August 2001) Abstract \| Full text \| Editor’s summary The adeno-associated virus (AAV) genome causes death of tumor cells in the absence of functional p53.
	Research
	Research The Adaptive Evolution Database (TAED) David A Liberles, David R Schreiber, Sridhar Govindarajan, Stephen G Chamberlin, Steven A Benner Genome Biology 2001, 2:research0028-research0028.6 (24 July 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In the Adaptive Evolution Database (TAED), potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotide substitution rates (K_A/K_S values). Evolutionary trees and reconstructed ancestral sequences were extracted from the Master Catalog for every subtree containing proteins from the Chordata only or the Embryophyta only. An unexpectedly large number of families were found to have at least one branch with high K_A/K_S values. TAED is a raw resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study.
	Research Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes Jodi M Maglich, Ann Sluder, Xiaojun Guan, Yunling Shi, David D McKee, Kevin Carrick, Kim Kamdar, Timothy M Willson, John T Moore Genome Biology 2001, 2:research0029-research0029.7 (24 July 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using the nearly completed human genome sequence, in silico and experimental approaches have been combined to define the complete human nuclear receptor set. Two novel NR pseudogenes have been identified and there are fewer than 50 functional human nuclear receptors, fewer than in C. elegans but more than in Drosophila.
	Research The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa David H Calhoun, Carol A Bonner, Wei Gu, Gary Xie, Roy A Jensen Genome Biology 2001, 2:research0030-research0030.16 (27 July 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Among the monofunctional AroQ chorismate mutase proteins, that from Erwinia herbicola was previously shown to be located in the periplasmic compartment. The gene coding for the AroQ protein from Salmonella typhimurium, and the AroQ protein from S. typhimurium and Pseudomonas aeruginosa have now been shown to be periplasmic. In addition, a so-far novel aromatic aminotransferase was shown to be present in the periplasm of P. aeruginosa.
	Research Cluster-Rasch models for microarray gene expression data Hongzhe Li, Fangxin Hong Genome Biology 2001, 2:research0031-research0031.13 (31 July 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two formulations of the Rasch statistical models can be used to study gene expression profiles in relation to phenotype. Datasets of acute leukemia classifications and of cancer cell lines were used to illustrate the methods. For tumor classification, the results were comparable to those previously obtained. For the cancer cell lines dataset, four clusters of genes related to drug response were found.
	Research A clustering method for repeat analysis in DNA sequences Natalia Volfovsky, Brian J Haas, Steven L Salzberg Genome Biology 2001, 2:research0027-research0027.11 (1 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational system for analysis of the repetitive structure of complete and partial genomic sequences is described.
	Research Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application Cheng Li, Wing Hung Wong Genome Biology 2001, 2:research0032-research0032.11 (3 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A model-based analysis of oligonucleotide expression arrays developed previously uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes. Probe-sensitivity indexes are stable across tissue types and the MBEI method is able to extend the reliable detection limit of expression to a lower mRNA concentration. Reliability indexes can be assigned for genes in a specific cluster of interest in hierarchical clustering by resampling clustering trees. A software dChip implementing many of these analysis methods is made available.
	Software AFM 4.0: a toolbox for DNA microarray analysis Bobby-Joe Breitkreutz, Paul Jorgensen, Ashton Breitkreutz, Mike Tyers Genome Biology 2001, 2:software0001-software0001.3 (6 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We have developed a series of programs, collectively packaged as Array File Maker 4.0 (AFM), that manipulate and manage DNA microarray data. AFM 4.0 is simple to use, applicable to any organism or microarray, and operates within the familiar confines of Microsoft Excel. Given a database of expression ratios, AFM 4.0 generates input files for clustering, helps prepare colored figures and Venn diagrams, and can uncover aneuploidy in yeast microarray data. AFM 4.0 should be especially useful to laboratories that do not have access to specialized commercial or in-house software.
	Correspondence
	Correspondence Lessons to be learned from studying Vibrio cholerae in model systems Keya Chaudhuri Genome Biology 2001, 2:interactions1003-interactions1003.2 (31 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles, by Gary K Schoolnik and Fitnat H Yildiz, Genome Biology 2000 1:reviews1016.1-1016.3.
	Correspondence Orthologs and paralogs - we need to get it right Roy A Jensen Genome Biology 2001, 2:interactions1002-interactions1002.3 (3 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Homologuephobia, by Gregory A Petsko, Genome Biology 2001 2:comment1002.1-1002.2, to An apology for orthologs - or brave new memes by Eugene V Koonin, Genome Biology 2001, 2:comment1005.1-1005.2, and to Can sequence determine function? by John A Gerlt and Patricia C Babbitt, Genome Biology 2000, 1:reviews0005.1-0005.10.

	Volume 2 Issue 8
	Comment
	Comment Design by necessity Gregory A Petsko Genome Biology 2001, 2:comment1010-comment1010.3 (1 August 2001) Full text \| PDF \| PubMed \| Editor’s summary Necessity is the only designer we need to explain the world that genomics has shown to us.
	Review
	Protein family review The Smads Liliana Attisano, Si Tuen Lee-Hoeflich Genome Biology 2001, 2:reviews3010-reviews3010.8 (2 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Smads transmit signals to the nucleus from the transforming growth factor-β receptors. Regulatory Smads bind DNA in association with partner proteins and thereby regulate target genes. Other Smads aid this function, whereas inhibitory Smads antagonize it.
	Minireview Interorganellar crosstalk: new perspectives on signaling from the chloroplast to the nucleus Emma C Brown, Aravind Somanchi, Stephen P Mayfield Genome Biology 2001, 2:reviews1021-reviews1021.4 (30 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chlorophyll precursors, photosynthetic electron transport, and sugars have all been shown to be involved in signaling from the chloroplast to the nucleus, suggesting the presence of multiple signaling pathways of coordination between these two cellular compartments.
	Minireview Nucleomorph genomes: much ado about practically nothing Paul R Gilson Genome Biology 2001, 2:reviews1022-reviews1022.5 (30 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The DNA sequence of one of the smallest eukaryotic genomes has recently been finished - that of the reduced nucleus, or nucleomorph, of an algal endosymbiont that resides within a cryptomonad host cell. Its sequence promises insights into chloroplast acquisition, the constraints on genome size and the basic workings of eukaryotic cells.
	Minireview The genome of Mycobacterium leprae: a minimal mycobacterial gene set Varalakshmi D Vissa, Patrick J Brennan Genome Biology 2001, 2:reviews1023-reviews1023.8 (3 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the recently sequenced genome of the leprosy-causing pathogen Mycobacterium leprae with other mycobacterial genomes reveals a drastic gene reduction and decay in M. leprae affecting many metabolic areas, exemplified by the retention of a minimal set of genes required for cell-wall biosynthesis.
	Opinion Complex genetic diseases: controversy over the Croesus code Alan F Wright, Nicholas D Hastie Genome Biology 2001, 2:comment2007-comment2007.8 (1 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The polarization of views on how best to exploit new information from the Human Genome Project for medicine reflects our ignorance of the genetic architecture underlying common diseases: are susceptibility alleles common or rare, neutral or deleterious, few or many? Single-nucleotide polymorphism (SNP) technology is almost in place to dissect such diseases and to create a personalized medicine, but success is critically dependent on the biology and "Nature to be commanded must be obeyed" (Francis Bacon, 1620, Novum Organum).
	Report
	Web report Transgenic and targeted mouse mutation database Steven G Gray Genome Biology 2001, 2:reports2005 (20 July 2001) Abstract \| Full text
	Web report COPEing with cytokines Steven G Gray Genome Biology 2001, 2:reports2006 (27 July 2001) Abstract \| Full text \| Editor’s summary COPE is the electronic updated version of the Dictionary of Cytokines (Wiley; New York:1994) and represents a comprehensive online reference guide to the field of cytokine research.
	Web report Modeling RNA secondary structure Steven G Gray Genome Biology 2001, 2:reports2007 (27 July 2001) Abstract \| Full text \| Editor’s summary The mfold server has a simple interface that allows any researcher to analyze a submitted RNA sequence for various secondary structures using up-to-date algorithms and free-energy rules.
	Web report An anatomical view of gene expression Vasudeva Ginjala Genome Biology 2001, 2:reports2008 (27 July 2001) Abstract \| Full text
	Web report Gene imprinting gateway Vasudeva Ginjala Genome Biology 2001, 2:reports2009 (27 July 2001) Abstract \| Full text
	Paper report Xist comparative genomics Cathy Holding Genome Biology 2001, 2:reports0021 (10 July 2001) Abstract \| Full text \| Editor’s summary The primary sequence of Xist seems not to be important for Xist to function in X-chromosome inactivation.
	Paper report Tumor proteomics Steven G Gray Genome Biology 2001, 2:reports0022 (20 July 2001) Abstract \| Full text \| Editor’s summary A novel protein upregulated in certain cancers has been identified and characterized using an integrated proteomics, genomics, bioinformatics and standard molecular biology approach.
	Paper report Y-chromosome multicopy genes S Subramanian Genome Biology 2001, 2:reports0023 (20 July 2001) Abstract \| Full text
	Paper report Real-time flagellar gene expression Rachel Brem Genome Biology 2001, 2:reports0024 (8 August 2001) Abstract \| Full text
	Paper report Selection for reproduction S Subramanian Genome Biology 2001, 2:reports0025 (8 August 2001) Abstract \| Full text
	Paper report Resolving gene transfer issues Reiner Veitia Genome Biology 2001, 2:reports0026 (8 August 2001) Abstract \| Full text
	Paper report Further resolution of gene transfer issues Reiner Veitia Genome Biology 2001, 2:reports0027 (8 August 2001) Abstract \| Full text
	Meeting report More biology from the sequence Martin S Taylor Genome Biology 2001, 2:reports4018-reports4018.5 (31 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor meeting on Genome Sequencing and Biology, Cold Spring Harbor, NY, USA, 9-13 May 2001.
	Meeting report Towards a virtual Arabidopsis plant Benedikt Kost Genome Biology 2001, 2:reports4019-reports4019.4 (31 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Royal Society Discussion Meeting "The plant cell: between genome and plant", London, 13-14 June 2001.
	Deposited research article The genetic structure of recombinant inbred mice: High-resolution consensus maps for complex trait analysis Robert W Williams, Jing Gu, Shuhua Qi, Lu Lu Genome Biology 2001, 2:preprint0007-preprint0007.44 (18 July 2001) Abstract \| Full text \| PDF \| Editor’s summary The density of typed microsatellite markers has been increased 2- to 5-fold in each of several major recombinant inbred sets of mice and consensus RI maps that integrate genotypes of approximately 1600 microsatellite loci assembled.
	Research news The genome of Sinorhizobium meliloti David Bruce Genome Biology 2001, 2:spotlight-20010801-01 (1 August 2001) Abstract \| Full text \| Editor’s summary The sequencing of the genome of the bacterium involved in the rhizhobial symbiosis with alfalfa may help improve crop yields.
	Research news Putting the sea into cancer therapy Tudor Toma Genome Biology 2001, 2:spotlight-20010806-01 (6 August 2001) Abstract \| Full text \| Editor’s summary Tampering with the nucleotide excision DNA repair mechanism creates lethal breaks in the DNA and can kill cancerous cells.
	Research news Myotonic expansion Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010806-03 (6 August 2001) Abstract \| Full text \| Editor’s summary A huge expansion of intronic CCTG repeats causes Myotonic Dystrophy Type 2.
	Research news Perfect murder Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010806-02 (6 August 2001) Abstract \| Full text \| Editor’s summary A technique called "delitto perfetto" (perfect murder) can efficiently generate site-directed mutations in vivo.
	Research news Ink and Arf Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010807-02 (7 August 2001) Abstract \| Full text \| Editor’s summary The two proteins encodes by the Ink4a-Arf locus play different roles in senescence depending on the cell type.
	Research news Two-hybrid assay in plants Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010807-01 (7 August 2001) Abstract \| Full text \| Editor’s summary An in vivo protein-fragment complementation assay can monitor protein-protein interactions in living plant cells.
	Research news Lipocalin killer Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010808-01 (8 August 2001) Abstract \| Full text \| Editor’s summary Transcriptional regulation of a secreted lipocalin protein induces lymphocyte apoptosis upon removal of interleukin 3.
	Research news Sporozoite transcriptome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010809-01 (9 August 2001) Abstract \| Full text \| Editor’s summary ESTs have been generated on a large scale from the Plasmodium sporozoite stage.
	Research news Argonaute2 Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010810-02 (10 August 2001) Abstract \| Full text \| Editor’s summary Argonaute2, a component of the nuclease complex that carries out gene-silencing during RNAi, has been biochemically purified.
	Research news Structure of a DNA-damage repair protein David Bruce Genome Biology 2001, 2:spotlight-20010810-01 (10 August 2001) Abstract \| Full text \| Editor’s summary The Ku heterodimer forms a cradle in which broken DNA strands rest whilst being repaired.
	Research news A new mechanism for hypertension Jason Roach Genome Biology 2001, 2:spotlight-20010813-02 (13 August 2001) Abstract \| Full text \| Editor’s summary A newly identified metabolic pathway controlling blood pressure in humans could help design drugs to treat hypertension.
	Research news DNA/DNA microarrays Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010813-03 (13 August 2001) Abstract \| Full text \| Editor’s summary Microbial genomic hybridization on bacterial DNA microarrays offers a tool for comparing closely related organisms.
	Research news Space adds new dimension to cancer research Simon Frantz Genome Biology 2001, 2:spotlight-20010813-01 (13 August 2001) Abstract \| Full text \| Editor’s summary Culturing cells in the reduced gravity conditions of the International Space Station could help refine cancer treatment regimes.
	Research news Heterochromatin boundaries Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010814-01 (14 August 2001) Abstract \| Full text \| Editor’s summary The boundaries of functional chromatin domains are defined by site-specific methylation patterns of histone H3.
	Research news Transcriptional switch Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010815-01 (15 August 2001) Abstract \| Full text \| Editor’s summary Ordered acetylation of the HMGI(Y) protein controls enhanceosome stability and switches on gene expression.
	Research news A pathway to therapeutic destruction Tudor Toma Genome Biology 2001, 2:spotlight-20010816-01 (16 August 2001) Abstract \| Full text \| Editor’s summary Pancreatic cancer cells have an intact proapoptotic pathway activated by interferon gamma via caspase-1 dependent mechanisms.
	Research news Brainy stem cells Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010816-02 (16 August 2001) Abstract \| Full text \| Editor’s summary Stem cells purified from mouse brains can generate neural and non-neural cells in vitro and in vivo.
	Research news Proof of trans-splicing Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010817-01 (17 August 2001) Abstract \| Full text \| Editor’s summary Analysis of transgenic flies provides further evidence for trans-splicing within the Drosophila mod(mdg4) locus.
	Research news Making sense of antisense Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010820-01 (20 August 2001) Abstract \| Full text \| Editor’s summary DNA microarray analysis has been used to define gene-expression profiles following treatment with antisense oligonucleotides.
	Research news Tumor suppression by FEZ Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010821-01 (21 August 2001) Abstract \| Full text \| Editor’s summary The FEZ1 protein regulates mitosis and tumor cell proliferation.
	Research news Absolute BlyS Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010822-01 (22 August 2001) Abstract \| Full text \| Editor’s summary Insights into the function of the B-lymphocyte cytokine BAFF/BlyS and its receptors have come from mutant mice.
	Research news Prostate markers Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010823-01 (23 August 2001) Abstract \| Full text \| Editor’s summary Microarray analysis defines a prognostic expression profile signature for prostate cancer.
	Research news Agrobacterium goes live on the web Tudor Toma Genome Biology 2001, 2:spotlight-20010824-01 (24 August 2001) Abstract \| Full text \| Editor’s summary The entire Agrobacterium tumefaciens genome is now freely available on the web.
	Research news African elephants Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010824-02 (24 August 2001) Abstract \| Full text \| Editor’s summary Genetic analysis of free-ranging elephants suggests that there, in fact, are two species of African elephant.
	Research news Consequences of patrilocality Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010828-01 (28 August 2001) Abstract \| Full text \| Editor’s summary Female migrations explain population differences in the diversity of Y chromosomes compared to mitochondrial DNA.
	Research news Hazards of aging Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010828-02 (28 August 2001) Abstract \| Full text \| Editor’s summary Careful analysis confirms that damaged DNA accumulates as mice grow older.
	Research news Regulating p53 Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010829-01 (29 August 2001) Abstract \| Full text \| Editor’s summary Knockout mice highlight the importance of MDM4 in regulating the activity of the p53 tumor suppressor.
	Research news Not much in common Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010830-01 (30 August 2001) Abstract \| Full text \| Editor’s summary A comparison of the Celera and Ensembl transcriptomes examines how many predicted genes they have in common.
	Research news Viral killer Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010831-01 (31 August 2001) Abstract \| Full text \| Editor’s summary The adeno-associated virus (AAV) genome causes death of tumor cells in the absence of functional p53.
	Research
	Research The Adaptive Evolution Database (TAED) David A Liberles, David R Schreiber, Sridhar Govindarajan, Stephen G Chamberlin, Steven A Benner Genome Biology 2001, 2:research0028-research0028.6 (24 July 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In the Adaptive Evolution Database (TAED), potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotide substitution rates (K_A/K_S values). Evolutionary trees and reconstructed ancestral sequences were extracted from the Master Catalog for every subtree containing proteins from the Chordata only or the Embryophyta only. An unexpectedly large number of families were found to have at least one branch with high K_A/K_S values. TAED is a raw resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study.
	Research Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes Jodi M Maglich, Ann Sluder, Xiaojun Guan, Yunling Shi, David D McKee, Kevin Carrick, Kim Kamdar, Timothy M Willson, John T Moore Genome Biology 2001, 2:research0029-research0029.7 (24 July 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using the nearly completed human genome sequence, in silico and experimental approaches have been combined to define the complete human nuclear receptor set. Two novel NR pseudogenes have been identified and there are fewer than 50 functional human nuclear receptors, fewer than in C. elegans but more than in Drosophila.
	Research The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa David H Calhoun, Carol A Bonner, Wei Gu, Gary Xie, Roy A Jensen Genome Biology 2001, 2:research0030-research0030.16 (27 July 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Among the monofunctional AroQ chorismate mutase proteins, that from Erwinia herbicola was previously shown to be located in the periplasmic compartment. The gene coding for the AroQ protein from Salmonella typhimurium, and the AroQ protein from S. typhimurium and Pseudomonas aeruginosa have now been shown to be periplasmic. In addition, a so-far novel aromatic aminotransferase was shown to be present in the periplasm of P. aeruginosa.
	Research Cluster-Rasch models for microarray gene expression data Hongzhe Li, Fangxin Hong Genome Biology 2001, 2:research0031-research0031.13 (31 July 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two formulations of the Rasch statistical models can be used to study gene expression profiles in relation to phenotype. Datasets of acute leukemia classifications and of cancer cell lines were used to illustrate the methods. For tumor classification, the results were comparable to those previously obtained. For the cancer cell lines dataset, four clusters of genes related to drug response were found.
	Research A clustering method for repeat analysis in DNA sequences Natalia Volfovsky, Brian J Haas, Steven L Salzberg Genome Biology 2001, 2:research0027-research0027.11 (1 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational system for analysis of the repetitive structure of complete and partial genomic sequences is described.
	Research Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application Cheng Li, Wing Hung Wong Genome Biology 2001, 2:research0032-research0032.11 (3 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A model-based analysis of oligonucleotide expression arrays developed previously uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes. Probe-sensitivity indexes are stable across tissue types and the MBEI method is able to extend the reliable detection limit of expression to a lower mRNA concentration. Reliability indexes can be assigned for genes in a specific cluster of interest in hierarchical clustering by resampling clustering trees. A software dChip implementing many of these analysis methods is made available.
	Software AFM 4.0: a toolbox for DNA microarray analysis Bobby-Joe Breitkreutz, Paul Jorgensen, Ashton Breitkreutz, Mike Tyers Genome Biology 2001, 2:software0001-software0001.3 (6 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We have developed a series of programs, collectively packaged as Array File Maker 4.0 (AFM), that manipulate and manage DNA microarray data. AFM 4.0 is simple to use, applicable to any organism or microarray, and operates within the familiar confines of Microsoft Excel. Given a database of expression ratios, AFM 4.0 generates input files for clustering, helps prepare colored figures and Venn diagrams, and can uncover aneuploidy in yeast microarray data. AFM 4.0 should be especially useful to laboratories that do not have access to specialized commercial or in-house software.
	Correspondence
	Correspondence Lessons to be learned from studying Vibrio cholerae in model systems Keya Chaudhuri Genome Biology 2001, 2:interactions1003-interactions1003.2 (31 July 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles, by Gary K Schoolnik and Fitnat H Yildiz, Genome Biology 2000 1:reviews1016.1-1016.3.
	Correspondence Orthologs and paralogs - we need to get it right Roy A Jensen Genome Biology 2001, 2:interactions1002-interactions1002.3 (3 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Homologuephobia, by Gregory A Petsko, Genome Biology 2001 2:comment1002.1-1002.2, to An apology for orthologs - or brave new memes by Eugene V Koonin, Genome Biology 2001, 2:comment1005.1-1005.2, and to Can sequence determine function? by John A Gerlt and Patricia C Babbitt, Genome Biology 2000, 1:reviews0005.1-0005.10.

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