Comparative and Functional Genomics

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A system for identifying named entities in biomedical text: how results from two evaluations reflect on both the system and the evaluations
Comparative and Functional Genomics - Tập 6 Số 1‐2 - Trang 77-85 - 2005
Shipra Dingare, Malvina Nissim, Jenny Finkel, Christopher Manning, Claire Grover
Abstract We present a maximum entropy‐based system for identifying named entities (NEs) in biomedical abstracts and present its performance in the only two biomedical named entity recognition (NER) comparative evaluations that have been held to date, namely BioCreative and Coling BioNLP. Our system obtained an exact match F‐score of 83.2% in the BioCreative evaluation and 70.1% in the BioNLP evalu... hiện toàn bộ
#automatic named entity recognition #manual annotation of biomedical texts
Why chloroplasts and mitochondria contain genomes
Comparative and Functional Genomics - Tập 4 Số 1 - Trang 31-36 - 2003
John F. Allen
AbstractChloroplasts and mitochondria originated as bacterial symbionts. The larger, host cells acquired genetic information from their prokaryotic guests by lateral gene transfer. The prokaryotically‐derived genes of the eukaryotic cell nucleus now function to encode the great majority of chloroplast and mitochondrial proteins, as well as many proteins of the nucleus and cytosol. Genes are copied... hiện toàn bộ
Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P. taeda, P. sylvestris or Picea abies
Comparative and Functional Genomics - Tập 3 Số 4 - Trang 306-318 - 2002
Leonel van Zyl, Sara von Arnold, Peter V. Bozhkov, Yongzhong Chen, Ulrika Egertsdotter, John Mackay, Ronald R. Sederoff, Jing Shen, Любов Зелена, David H. Clapham
AbstractHybridization of labelled cDNA from various cell types with high‐density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The ... hiện toàn bộ
A survey of nucleotide cyclases in Actinobacteria: unique domain organization and expansion of the class III cyclase family in Mycobacterium tuberculosis
Comparative and Functional Genomics - Tập 5 Số 1 - Trang 17-38 - 2004
Avinash R. Shenoy, K. Sivakumar, A. Krupa, N. Srinivasan, Sandhya S. Visweswariah
AbstractCyclic nucleotides are well‐known second messengers involved in the regulation of important metabolic pathways or virulence factors. There are six different classes of nucleotide cyclases that can accomplish the task of generating cAMP, and four of these are restricted to the prokaryotes. The role of cAMP has been implicated in the virulence and regulation of secondary metabolites in the p... hiện toàn bộ
Protein Coding Gene Nucleotide Substitution Pattern in the Apicomplexan ProtozoaCryptosporidium parvumandCryptosporidium hominis
Comparative and Functional Genomics - Tập 2008 - Trang 1-6 - 2008
Guangtao Ge, Lenore Cowen, Grace Ndeezi, Giovanni Widmer
Cryptosporidium parvumandC. hominisare related protozoan pathogens which infect the intestinal epithelium of humans and other vertebrates. To explore the evolution of these parasites, and identify genes under positive selection, we performed a pairwise whole-genome comparison between all orthologous protein coding genes inC. parvumandC. hominis. Genome-wide calculation of the ratio of nonsynonymou... hiện toàn bộ
Alternative Mechanisms to Initiate Translation in Eukaryotic mRNAs
Comparative and Functional Genomics - Tập 2012 - Trang 1-12 - 2012
Encarnación Martínez‐Salas, David Piñeiro, Noemí Fernández
The composition of the cellular proteome is under the control of multiple processes, one of the most important being translation initiation. The majority of eukaryotic cellular mRNAs initiates translation by the cap-dependent or scanning mode of translation initiation, a mechanism that depends on the recognition of the m7G(5′)ppp(5′)N, known as the cap. However, mRNAs encoding proteins required fo... hiện toàn bộ
Regulation of Translation Initiation under Abiotic Stress Conditions in Plants: Is It a Conserved or Not so Conserved Process among Eukaryotes?
Comparative and Functional Genomics - Tập 2012 - Trang 1-8 - 2012
Alfonso Muñoz, M. Mar Castellano
For years, the study of gene expression regulation of plants in response to stress conditions has been focused mainly on the analysis of transcriptional changes. However, the knowledge on translational regulation is very scarce in these organisms, despite in plants, as in the rest of the eukaryotes, translational regulation has been proven to play a pivotal role in the response to different stress... hiện toàn bộ
Comparative Analysis of CpG Islands in Four Fish Genomes
Comparative and Functional Genomics - Tập 2008 - Trang 1-6 - 2008
Leng Han, Zhongming Zhao
There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are considered gene markers and involved in gene regulation. To date, there has been no genome-wide analysis of CGIs in the fish genome. We first evaluated the performance of three popular CGI identification algorithms in four fish genomes (tetraodon, stickleback, medaka, and zebrafis... hiện toàn bộ
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