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A report on the Conference on Systems Biology of Mammalian Cells, Dresden, Germany, 22-24 May 2008.
A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.
A report of the 18th Annual Growth Factor and Signal Transduction Symposium, Ames, USA, 11-14 June 2009.
The S. rosetta...genome sequence refines the catalog of metazoan-specific genes while also extending the evolutionary history of certain gene families that are central to metazoan biology. Transcriptome data sugg...
The 19th Annual Advances in Genome Biology and Technology (AGBT) meeting came back to Marco Island, Florida, and was held in the renovated venue from 27 February to 2 March 2019. The meeting showed a variety o...
The flood of data from genome-wide analysis is transforming biology. We need to develop new, interdisciplinary approaches to convert these data into information about the components and structures of individua...
A report on the joint Spring meeting of the British Society of Developmental Biology and the Genetics Society, York, UK, 20-23 March 2002.
The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade a...
The Erratum to this article has been published in Genome Biology 2017 18:11
Development of the vertebrate head depends on the multipotency and migratory behavior of neural crest derivatives. This cell population is considered a vertebrate innovation and, accordingly, chordate ancestor...
Genes are created by a variety of evolutionary processes, some of which generate duplicate copies of an entire gene, while others rearrange pre-existing genetic elements or co-opt previously non-coding sequenc...
The phenomenon of functional site turnover has important implications for the study of regulatory region evolution, such as for promoter sequence alignments and transcription factor binding site (TFBS) identif...
We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating pu...
The rates of molecular evolution for protein-coding genes depend on the stringency of functional or structural constraints. The Ka/Ks ratio has been commonly used as an indicator of selective constraints and i...
The role that chromosomal rearrangements might have played in the speciation processes that have separated the lineages of humans and chimpanzees has recently come into the spotlight. To date, however, results...
Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated ...
A report on the meeting 'Developmental Basis of Evolutionary Change', University of Chicago, USA, 16-18 October 2003.
Studies describing intricate patterns of DNA methylation in nematode and ciliate are controversial due to the uncertainty of genomic evolutionary conservation of DNA methylation enzymes.
A report on the joint Spring meeting of the British Society of Developmental Biology and the Genetics Society, York, UK, 20-23 March 2002.
Divergence of the sequences of reproductive genes has been accelerated by positive selection.
The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and ev...
Phylogenomics of eukaryote supergroups suggest a highly complex last common ancestor of eukaryotes and a key role of mitochondrial endosymbiosis in the origin of eukaryotes.
The completion of rice genome sequencing has made rice and its wild relatives an attractive system for biological studies. Despite great efforts, phylogenetic relationships among genome types and species in th...
Cellular functions are accomplished by the concerted actions of functional modules. The mechanisms driving the emergence and evolution of these modules are still unclear. Here we investigate the evolutionary o...
The classic paradigm of heterotrimeric G-protein signaling describes a heptahelical, membrane-spanning G-protein coupled receptor that physically interacts with an intracellular Gα subunit of the G-protein het...
Two significant evolutionary processes are fundamentally not tree-like in nature - lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate suc...
Archaea comprise one of the three distinct domains of life (with bacteria and eukaryotes). With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes t...
The history of yeast Saccharomyces cerevisiae, aka brewer’s or baker’s yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, ye...
Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome...
Recent analyses of human pathogens have revealed that their evolutionary histories are congruent with the hypothesized pattern of ancient and modern human population migrations. Phylogenetic trees of strains o...
CONTRAST, a new gene-prediction algorithm that uses sophisticated machine-learning techniques, has pushed de novo prediction accuracy to new heights, and has significantly closed the gap between de novo and evide...
A report on the 68th Symposium on Quantitative Biology, The Genome of Homo Sapiens', Cold Spring Harbor, USA, 28 May-2 June 2003.
A report of the seventh annual meeting on Systems Biology: Global Regulation of Gene Expression, 23-27 March 2010, Cold Spring Harbor, USA.
Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality h...
Selenocysteine (Sec) is co-translationally inserted into protein in response to UGA codons. It occurs in oxidoreductase active sites and often is catalytically superior to cysteine (Cys). However, Sec is used ...
Most bacterial genes were acquired by horizontal gene transfer from other bacteria instead of being inherited by continuous vertical descent from an ancient ancestor. To understand how the regulation of these ...
The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular, although it is fraught with practical difficulties. But the exponential growth of relevant information and improv...
We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus...
Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently,...
The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes ...
Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited ... , this approach loses predictive power at longer evolutionary distances. Here we propose a...
The Author Correction to this article has been published in Genome Biology 2024 25:50
The application of whole-genome sequencing to the study of microbial evolution promises to reveal the complex functional networks of mutations that underlie adaptation. A recent study of parallel evolution in ...
The sequencing of the genome of a female rhesus macaque (Macaca mulatta) of Indian origin will provide us with biomedical and evolutionary insights into both humans and Old World monkeys.
Comparison of microRNA expression identified tissues present in the last common ancestor of Bilaterians and put evolution of microRNAs in the context of tissue evolution.
The recent sequencing of a large chunk of euchromatin from the human Y chromosome is a technical tour de force. It answers some evolutionary questions about this unusual chromosome while raising others.
Almost 20 % of all infectious human diseases are vector borne and, together, are responsible for over one million deaths per annum. Over the past decade, the decreasing costs of massively parallel sequencing t...
A report of the 2007 Cold Spring Harbor Laboratory/Wellcome Trust Conference on Functional Genomics and Systems Biology, Hinxton, UK, 10-13 October 2007.
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