A Model of Elegance

Walhout, Albertha J.M.; Endoh, Hideki; Thierry‐Mieg, Nicolas; Wong, Wendy; Vidal, Marc

doi:10.1086/302078

Cited by 21 publications

(21 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…With the great advances in genome sequencing leading to prediction of tens of thousands of novel genes, new opportunities emerged to study biology as molecular networks (Walhout et al 1998). It soon became clear that new types of resources were needed, such as cloned ORFeomes, to support the automated production and subsequent analysis of a nearly full proteome, under many conditions and in many different functional assays (Walhout et al 1998;Vidal 2001).…”

Section: Discussionmentioning

confidence: 99%

“…It soon became clear that new types of resources were needed, such as cloned ORFeomes, to support the automated production and subsequent analysis of a nearly full proteome, under many conditions and in many different functional assays (Walhout et al 1998;Vidal 2001). This, in turn, created new needs for efficiency and compatibility in DNA cloning, in addition to that for adaptability.…”

Section: Discussionmentioning

confidence: 99%

“…The C. elegans interactome project (Walhout et al 1998) nicely illustrates the concepts outlined above. The Y2H-based map will eventually require the production of at least 38,000 proteins in yeast cells, because at least two hybrid proteins need to be made for each of the 19,000 predicted gene products, excluding splice variants (The C. elegans Sequencing Consortium 1998).…”

Section: The Example Of C Elegansmentioning

confidence: 96%

See 2 more Smart Citations

ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List

Brasch¹,

Hartley²,

Vidal³

2004

Genome Res.

Self Cite

View full text Add to dashboard Cite

Together with metabolites, proteins and RNAs form complex biological systems through highly intricate networks of physical and functional interactions. Large-scale studies aimed at a molecular understanding of the structure, function, and dynamics of proteins and RNAs in the context of cellular networks require novel approaches and technologies. This Special Issue of Genome Research features strategies for the high-throughput construction and manipulation of complete sets of protein-encoding open reading frames (ORFeome), gene promoters (promoterome), and noncoding RNAs, as predicted from genome and transcriptome sequences. Here we discuss the use of a recombinational cloning system that allows efficiency, adaptability, and compatibility in the generation of ORFeome, promoterome, and other resources.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: The Example Of C Elegansmentioning

confidence: 96%

See 1 more Smart Citation

ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List

Brasch¹,

Hartley²,

Vidal³

2004

Genome Res.

Self Cite

View full text Add to dashboard Cite

show abstract

“…C. elegans is the first multi-cellular organism whose genome has been completely sequenced [5], as well as being a choice model organism for many functional genomics projects, from cDNA microarrays [9] to systematic knock-outs [10] and protein-protein interaction mapping. It is also a convenient model organism for classical genetic studies [24].…”

Section: The Biological Problem: Protein-protein Interactionsmentioning

confidence: 99%

InterDB, a Prediction-Oriented Protein Interaction Database for C. elegans

Thierry‐Mieg¹,

Trilling²

2001

Computational Biology

Self Cite

View full text Add to dashboard Cite

Abstract. Protein-protein interactions are critical to many biological processes, extending from the formation of cellular macromolecular structures and enzymatic complexes to the regulation of signal transduction pathways. With the availability of complete genome sequences, several groups have begun large-scale identification and characterization of such interactions, relying mostly on high-throughput two-hybrid systems. We collaborate with one such group, led by Marc Vidal, whose aim is the construction of a protein-protein interaction map for C. elegans. In this paper we first describe WISTdb, a database designed to store the interaction data generated in Marc Vidal's laboratory. We then describe InterDB, a multi-organism prediction-oriented database of protein-protein interactions. We finally discuss our current approaches, based on inductive logic programming and on a data mining technique, for extracting predictive rules from the collected data. The Biological Problem: Protein-Protein InteractionsProtein-protein interactions are critical to many biological processes, extending from the formation of cellular macromolecular structures and enzymatic complexes to the regulation of signal transduction pathways.With the availability of complete genome sequences, several groups have begun large-scale identification and characterization of such interactions [11], [22], [25]. These groups rely mostly on high-throughput two-hybrid systems [23]. Although such approaches significantly increase the rate at which interaction data is produced, they will require several years to produce full interaction maps for modest-sized organisms, whereas the "working draft" of the human genome has been available since June 2000. It is therefore enticing and promising to develop computational methods that could predict protein-protein interactions, be it in a rough and approximate manner. Ideally, the data produced by those highthroughput projects could suffice to develop prediction algorithms that could then be applied to genome sequence as fast as it is being released. More reasonably, the high-throughput projects themselves could benefit from predictions to speed up the discovery of interesting protein-protein interactions (see part 4).In this paper we concentrate on a preliminary step to study protein-protein interactions in Caenorhabditis elegans. C. elegans is the first multi-cellular organism whose genome has been completely sequenced [5], as well as being a choice

show abstract

“…In addition, data emerging from any single omic approach can only provide crude indications of gene or protein function. It has been proposed that these limitations can be overcome by integrating data obtained from two or more distinct approaches [19,23]. Such integration should not only improve functional annotations but also help to formulate biological hypotheses (Fig.…”

mentioning

confidence: 99%