The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
The recognition of the role of mathematics and computer science in modern biology has led to new terminology, as did chemistry with biochemistry, and physics with biophysics. We need to think only of bioinformatics, computational biology, and even system biology and genomics for example. These terms seem to strongly suggest that this is all rather new. Yet a short review of the work of those such...
Protein interactions and complexes are major components of biological systems. Recent genome-wide applications of tandem affinity purification (TAP) in yeast have increased significantly the available information on such interactions. From these experiments, protein complexes were predicted with different approaches first from the individual experiments only and later from their combination. The resulting...
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing (ESS) overcomes this hurdle by sequencing the DNA from the organisms present in a microbial community. The interpretation of this metagenomic data can be greatly facilitated...
Clusters of genes that evolved from single progenitors via repeated segmental duplications present significant challenges to the generation of a truly complete human genome sequence. Such clusters can confound both accurate sequence assembly and downstream computational analysis, yet they represent a hotbed of functional innovation, making them of extreme interest. We have developed an algorithm for...
Next Generation Sequencing (NGS) technologies are capable of reading millions of short DNA sequences both quickly and cheaply. While these technologies are already being used for resequencing individuals once a reference genome exists, it has not been shown if it is possible to use them for ab initio genome assembly. In this paper, we give a novel network flow-based algorithm that, by taking advantage...
DNA methylation plays an important role in gene regulation. In order to gain a better understanding of the rules governing this epigenetic modification, we have used microarray technology to map DNA methylation in the human genome. This analysis has helped decipher the DNA sequences involved in setting up the basic global methylation pattern in the early embryo and has revealed the full range of methylation...
The transcriptional regulatory sequences in metazoan genomes often consist of multiple cis-regulatory modules (CRMs). Each CRM contains locally enriched occurrences of binding sites (motifs) for a certain array of regulatory proteins, capable of integrating, amplifying or attenuating multiple regulatory signals via combinatorial interaction with these proteins. The architecture of CRM organizations...
Methods suggested for reconstructing regulatory networks can be divided into two sets based on how the activity level of transcription factors (TFs) is inferred. The first group of methods relies on the expression levels of TFs assuming that the activity of a TF is highly correlated with its mRNA abundance. The second treats the activity level as unobserved and infers it from the expression of the...
As an increasing number of eukaryotic genomes are being sequenced, comparative studies aimed at detecting regulatory elements in intergenic sequences are becoming more prevalent. Most comparative methods for transcription factor (TF) binding site discovery make use of global or local alignments of orthologous regulatory regions to assess whether a particular DNA site is conserved across related organisms,...
One component of the genomic program controlling the transcriptional regulation of genes are the locations and arrangement of transcription factors bound to the promoter and enhancer regions of a gene. Because the genomic locations of the functional binding sites of most transcription factors is not yet known, predicting them is of great importance. Unfortunately, it is well known that the low specificity...
About the Keynote Speaker. Professor Edison Liu graduated from Stanford University and its medical school. From 1987–96, he was professor of medicine, biochemistry and epidemiology at the University of North Carolina, and Director of its Specialized Program of Research Excellence in Breast Cancer. From 1996–2001, Prof Liu was the Division Director of Clinical Sciences (Intramural program)...
The development of high-resolution microscopy makes possible the high-throughput screening of cellular information, such as gene expression at single cell resolution. One of the critical enabling techniques yet to be developed is the automatic recognition or annotation of specific cells in a 3D image stack. In this paper, we present a novel graph-based algorithm, ARC, that determines cell identities...
We report on a new algorithm for combining the information from several mass spectra of the same peptide. The algorithm automatically learns peptide fragmentation patterns, so that it can handle spectra from any instrument and fragmentation technique. We demonstrate the utility of the algorithm, and the power of multiple spectra, by showing that combining pairs of spectra (one CID and one ETD) greatly...
We present in this paper a novel fragmentation event model for peptide identification by tandem mass spectrometry. Most current peptide identification techniques suffer from the inaccuracies in the predicted theoretical spectrum, which is due to insufficient understanding of the ion generation process, especially the b/y ratio puzzle. To overcome this difficulty, we propose a novel fragmentation...
The protein inference problem represents a major challenge in shotgun proteomics. Here we describe a novel Bayesian approach to address this challenge that incorporates the predicted peptide detectabilities as the prior probabilities of peptide identification. Our model removes some unrealistic assumptions used in previous approaches and provides a rigorious probabilistic solution to this problem...
While nonribosomal peptides (NRPs) are of tremendous pharmacological importance, there is currently no technology capable of high-throughput sequencing of NRPs. Difficulties in sequencing NRPs slow down the progress in elucidating the non-ribosomal genetic code and negatively affect various screening programs aimed at the discovery of natural compounds of medical importance. We propose to employ multi-stage...
Metabolic engineering allows purposeful modification of metabolic and cellular network towards achieving several goals including enhanced production of various bioproducts, production of novel products, and broadening the substrate utilization range. Traditional metabolic engineering has been performed by manipulating a handful of genes and pathways based on known literature information and our rational...
In this paper, we propose a pattern-based protein function annotation framework, employing protein interaction networks, to predict annotation functions of proteins. More specifically, we first detect patterns that appear in the neighborhood of proteins with a particular functionality, and then transfer annotations between two proteins only if they have similar annotation patterns. We show that, in...
We developed Græmlin 2.0, a new multiple network aligner with (1) a novel scoring function that can use arbitrary features of a multiple network alignment, such as protein deletions, protein duplications, protein mutations, and interaction losses; (2) a parameter learning algorithm that uses a training set of known network alignments to learn parameters for our scoring function and thereby adapt it...
Although many studies have been successful in the discovery of cooperating groups of genes, mapping these groups to phenotypes has proved a much more challenging task. In this paper, we present the first genome-wide mapping of gene coexpression modules onto the phenome. We annotated coexpression networks from 136 microarray datasets with phenotypes from the Unified Medical Language System (UMLS)....
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.