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- Search Terms:ISSN: 1553734XAndISSN: 15537358AndVolume Number: 2AndIssue Number: 5AndStart Page: e48AndDate: 2006 Revise Search
- 1From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedOf the many important signaling events that take place on the surface of a mammalian cell, activation of signal transduction pathways via interactions of cell surface receptors is one of the most important. Evidence...
- 2From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedFold designability has been estimated by the number of families contained in that fold. Here, we show that among orthologous proteins, sequence divergence is higher for folds with greater numbers of families. Folds with...
- 3From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedDuring the course of evolution, new proteins are produced very largely as the result of gene duplication, divergence and, in many cases, combination. This means that proteins or protein domains belong to families or, in...
- 4From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedA fundamental problem in functional genomics is to determine the structure and dynamics of genetic networks based on expression data. We describe a new strategy for solving this problem and apply it to recently published...
- 5From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedWhile combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need...
- 6From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedAlternative polyadenylation sites produce transcript isoforms with 3' untranslated regions (UTRs) of different lengths. If a microRNA (miRNA) target is present in the UTR, then only those target-containing isoforms...
- 7From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-Reviewed
Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays.
Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on genotyping tumor and... - 8From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedAmple evidence has accumulated for the evolutionary importance of duplication events. However, little is known about the ensuing step-by-step divergence process and the selective conditions that allow it to progress....
- 9From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedLike shoelaces, the backbones of proteins may get entangled and form knots. However, only a few knots in native proteins have been identified so far. To more quantitatively assess the rarity of knots in proteins, we make...
- 10From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedThe number of complete, publicly available genome sequences is now greater than 200, and this number is expected to rapidly grow in the near future as metagenomic and environmental sequencing efforts escalate and the...
- 11From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedTranscription factors with a large number of target genes--transcription hub(s), or THub(s)--are usually crucial components of the regulatory system of a cell, and the different patterns through which they transfer the...
- 12From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedWe address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of...
- 13From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedAccording to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally....
- 14From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedIn PLoS Computational Biology, volume 2, issue 4: The abbreviation GB/SA had an incorrect definition in the Abstract, Introduction, and Abbreviations list. The correct definition of GB/SA is generalized-Born/surface...
- 15From: PLoS Computational Biology. (Vol. 2, Issue 5) Peer-ReviewedIn prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis. The...