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Many different statistical methods have been developed to deal with two groupcomparison microarray experiments. Most often, a substantial number of genes may be selected or not, depending on which method was a...
The Kuki-Chin-Mizo population comprising traditionally endogamous tribal groups residing in the state of Mizoram, India claim their descent from the ten lost tribes of Israel that were exiled by the Assyrians....
Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli.
The Janus kinase (Jak) family is one of ten recognized families of non-receptor tyrosine kinases. Mammals have four members of this family, Jak1, Jak2, Jak3 and Tyrosine kinase 2 (Tyk2). Birds, fish and insect...
We describe a computationally efficient statistical framework for estimating networks of coexpressed genes. This framework exploits first-order conditional independence relationships among gene-expression meas...
We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding-site evolution, on whic...
Can sequence segments coding for subcellular targeting or for posttranslational modifications occur in proteins that are not substrates in either of these processes? Although considerable effort has been inves...
The long-standing question of how genes acquire introns has provoked much debate. A recent study makes considerable progress by identifying numerous recently gained introns in nematodes - although it remains d...
A total of 74 small nuclear RNA (snRNA) genes and 395 genes encoding splicing-related proteins were identified in the Arabidopsis genome by sequence comparison and motif searches, including the previously elusive...
Arsenic is a nonmutagenic carcinogen affecting millions of people. The cellular impact of this metalloid in Saccharomyces cerevisiae was determined by profiling global gene expression and sensitivity phenotypes. ...
We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally rela...
Maps depicting binary interactions between proteins can be powerful starting points for understanding biological systems. A proven technology for generating such maps is high-throughput yeast two-hybrid screen...
A report on the Cold Spring Harbor Laboratory meeting 'Translational Control', Cold Spring Harbor, USA, 7-12 September 2004.
An evolutionary hypothesis suggested by studies of the genome of the tiger pufferfish Takifugu rubripes has now been confirmed by comparison with the genome of a close relative, the spotted green pufferfish Tetra...
A selection of evaluations from Faculty of 1000 covering phage receptor-binding proteins; genetic diversity in Toxoplasma; ribosome biogenesis and cell size; gene regulation by retrotransposons; manipulation of t...
A report on the 2004 meeting on Mouse Molecular Genetics, Cold Spring Harbor, USA, 1-5 September 2004.
A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004.
Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and hi...
We introduce a conceptually novel method for intracellular fluxome profiling from unsupervised statistical analysis of stable isotope labeling. Without a priori knowledge on the metabolic system, we identified ch...
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase catalyzes the conversion of HMG-CoA to mevalonate, a four-electron oxidoreduction that is the rate-limiting step in the synthesis of cholest...
Gene-expression profiling of endothelial cells infected with Kaposi's sarcoma-associated herpesvirus has led to a greater understanding of the histogenesis of Kaposi's sarcoma and cellular reprogramming events...
Recent research on mouse models has taken us closer to deciphering the molecular clock mechanism that defines an individual's 'body time'. How feasible will it be to create a molecular timetable that allows de...
Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number o...
By applying a graph-based algorithm to yeast protein-interaction networks we have extracted modular structures and show that they can be validated using information from the phylogenetic conservation of the ne...
The chromosome of Escherichia coli is maintained in a negatively supercoiled state, and supercoiling levels are affected by growth phase and a variety of environmental stimuli. In turn, supercoiling influences lo...
Carbon and nitrogen are two signals that influence plant growth and development. It is known that carbon- and nitrogen-signaling pathways influence one another to affect gene expression, but little is known ab...
A report on the 2nd Conference of the Consortium for Post-Genome Science (CPGS) 'Genomes to Systems', Manchester, UK, 1-3 September 2004.
A report on the 43rd annual meeting of the Society of Nematologists (SON), Estes Park, USA, 7-11 August 2004.
The plant hormones auxin and brassinosteroid promote cell expansion by regulating gene expression. In addition to independent transcriptional responses generated by the two signals, recent microarray analyses ...
Human centromere regions are characterized by the presence of alpha-satellite DNA, replication late in S phase and a heterochromatic appearance. Recent models propose that the centromere is organized into cons...
Although genes on the chromosome are organized in a fixed order, the spatial correlations in transcription have not been systematically evaluated. We used a combination of genomic and signal processing techniq...
The haploid male gametophyte generation of flowering plants consists of two- or three-celled pollen grains. This functional specialization is thought to be a key factor in the evolutionary success of flowering...
The Related Article to this article has been published in Nature Protocols 2016 11:nprot.2016.107
A report on the 6th EMBL Transcription Meeting, Heidelberg, Germany, 28 August-1 September 2004.
We present a novel graphical Gaussian modeling approach for reverse engineering of genetic regulatory networks with many genes and few observations. When applying our approach to infer a gene network for isopr...
A selection of evaluations from Faculty of 1000 covering fruit ripening comparative genomics; gene co-regulation during evolution; histone acetylation during plant development; microRNA gene identification; ChIP-...
Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or draft-quality ...
The apicomplexan parasite Cryptosporidium parvum is an emerging pathogen capable of causing illness in humans and other animals and death in immunocompromised individuals. No effective treatment is available and ...
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