PLoS Computational Biology

A General Definition and Nomenclature for Alternative Splicing Events

micha — Tue, 12 Aug 2008 06:53:19 -0700

Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora of different transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify the different types of reflected splicing variation.

PLoS Computational Biology

Small Regulatory RNAs May Sharpen Spatial Expression Patterns

apryl — Tue, 29 Apr 2008 13:56:47 -0700

The precise establishment of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low spatial expression domains requires a genetic mechanism that exhibits sensitivity, yet is robust to fluctuations, a demand that may not be easily achieved by morphogens alone. Recently, it has been demonstrated that small RNAs (and, in particular, microRNAs) play many roles in embryonic development. Whereas some RNAs are essential for embryogenesis, others are limited to fine-tuning a predetermined gene expression pattern.

PLoS Computational Biology

Ten Simple Rules for Good Presentations

Phil — Thu, 27 Sep 2007 17:27:38 -0700

Professor Philip Bourne, Editor-in-Chief of Public Library of Science (PLoS) Computational Biology, talks about the ten basic principles of making good presentations.

Senior Sequence Class of 2009-2010

Ten Simple Rules for Getting Grants

Phil — Mon, 24 Sep 2007 16:33:30 -0700

This piece follows an earlier Editorial, “Ten Simple Rules for Getting Published” [1], which has generated significant interest, is well read, and continues to generate a variety of positive comments. That Editorial was aimed at students in the early stages of a life of scientific paper writing.

Senior Sequence Class of 2009-2010

The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis

dzhang — Mon, 17 Sep 2007 15:12:38 -0700

Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists as tetramers associated with the proline-rich attachment domain (PRAD) of either collagen-like Q subunit (ColQ) or proline-rich membrane-anchoring protein. Crystallographic studies have revealed that different tetramer forms may be present, and it is not clear whether one or both are relevant under physiological conditions.

Structural Bioinformatics

Ten Simple Rules for Getting Published

Phil — Fri, 24 Aug 2007 16:51:06 -0700

Professor Philip Bourne, Editor-in-Chief of Public Library of Science (PLoS) Computational Biology, talks about the Ten Simple Rules for Getting Published.

CYBERBRIDGE

Wiggle—Predicting Functionally Flexible Regions from Primary Sequence

jgu — Thu, 19 Jul 2007 16:42:49 -0700

The Wiggle series are support vector machine–based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship between protein sequence and flexibility.

Structural Bioinformatics

Structural Evolution of the Protein Kinase–Like Superfamily

escheeff — Thu, 19 Jul 2007 10:11:23 -0700

The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all three superkingdoms of life. We used a carefully constructed structural alignment of selected kinases as the basis for a study of the structural evolution of the protein kinase–like superfamily. The comparison of structures revealed a “universal core” domain consisting only of regions required for ATP binding and the phosphotransfer reaction.

Structural Bioinformatics