Musset-Bilal F et al. (1994) Worm Breeder's Gazette "Characterization of the C. elegans Basement Membrane-Associated Protein SPARC"

Musset-Bilal F, Schwarzbauer JE, Ryan CS

[Worm Breeder's Gazette, 1994]

Characterization of the C. elegans Basement Membrane- Associated Frederique Musset-Bilal, Carol S. Ryan, and Jean E. Schwarzbauer Department of Molecular Biology, Princeton University, Princeton NJ 08544

Lejeune, Francois-Xavier et al. (2011) International Worm Meeting "The Biogemix knowledge base project: cross-species and network-based data integration for Huntington's disease research."

Vert, Jean-Philippe, Parmentier, Frederic, Lejeune, Francois-Xavier, Neri, Christian, Bicep, Cedric, Mesrob, Lilia

[International Worm Meeting, 2011]

The identification and validation of neuroprotective targets is of primary importance in research on neurodegenerative diseases such as Huntington's disease (HD). The development of genetically tractable models of disease and their use in genome-wide screens has generated a large amount of data in several species. A current challenge is the unbiased integration of these data sets in order to prioritize candidate target genes. The Biogemix knowledge base project has been developed with the European HD network (Euro-HD) to integrate 'omics' data from models of HD pathogenesis as available in several species (invertebrates, mammalian cells, mice, human samples). This project relies on the combination of network-based and cross-species procedures to unlock the biological information buried into disease data sets. The Biogemix procedure is a method that relies on the use of molecular networks for the unbiased integration of 'omics' data across different species. This method is particularly suited to the analysis of data sets for which the number of genes analyzed clearly exceeds the number of conditions tested. Single data sets are firstly processed with respect to a reference molecular network (for instance, use of MouseNet to analyze mouse data) to extract clusters (modules) that are made of highly interconnected genes, enriched in HD-relevant information and automatically annotated for their biological role and biomedical potential. In a second step, cross-species clusters (meta-modules) are calculated by balancing gene/protein connectivity with protein sequence similarities. In a third step, all of the Biogemix products are ranked according to topological and biological features of interest, which is part of a larger prioritisation system that uses several criteria to classify modules and genes of high interest. A user-friendly graphical interface and query system is being developed to allow the users to browse and select Biogemix information of interest. Further developments will aim at fine-tuning data analysis and information display in view of making the Biogemix knowledge base v 1.0 publically available on-line. Preliminary results will be shown to illustrate how the Biogemix system might be useful for basic research and disease research.

Kowalski T et al. (2015) PLoS One "Indexing Arbitrary-Length k-Mers in Sequencing Reads."

Grabowski S, Deorowicz S, Kowalski T

[PLoS One, 2015]

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating k-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments.

Martinelli SD et al. (1995) International C. elegans Meeting "ACEDB"

Durbin RM, Martinelli SD

[International C. elegans Meeting, 1995]

We hope to provide a demonstration of the current state of the ACeDB worm database on Unix workstations, and if possible Apple Macintosh, throughout the poster sessions. This will be based on the new version 4 release of the acedb software (Jean Thierry-Mieg, Richard Durbin and numerous others), which contains many new features for greater efficiency, more flexible printing, and display of new features.

Kelley S (2000) Brief Bioinform "Getting started with Acedb."

Kelley S

[Brief Bioinform, 2000]

Acedb is one of the more venerable pieces of Genomics software. Acedb was originally created in 1992 by Richard Durbin and Jean Thierry-Mieg to manage the data from the Caenorhabditis elegans mapping project and subsequently the C. elegans sequencing project. From beginnings as a C. elegans-specific tool, it has been continuously developed into a flexible suite of data management, display and scripting tools providing facilities for managing and annotation mapping information and DNA and peptide sequences.This paper gives a basic overview of the Acedb suite, and step-by-step guidance on how to download and install Acedb. It is intended to take an Acedb novice to stage where they can begin to experiment and explore the facilities that are available.

Edgley ML et al. (1995) International C. elegans Meeting "CYBERWORMS"

Collins D, Bryer J, Baillie DL, Edgley ML, Rose AM

[International C. elegans Meeting, 1995]

We are engaged in two projects to improve the alignment of the genetic and physical maps for C. elegans. The Genetic Toolkit project uses PCR to tie the endpoints of balanced deficiencies to the physical map; and the CGAT project uses microinjection of cloned cosmids from the worm sequencing project to generate transgenic arrays that are used to rescue mapped, balanced lethal mutations. Both projects are generating large amounts of genetic map information, which is being integrated into the CGC map (compiled by Jonathan Hodgkin) using the ACEDB program (Richard Durbin and Jean Thierry-Mieg). We also have established a World-Wide Web hypertext server to provide access to information generated by these projects. This Genetic Toolkit web site (http: genetic balancers and transgenic strains available from our laboratories. For stable transgenic strains, listed cosmids are linked to modified GenBank entries describing the sequence. This work is funded by the NIH National Center for Research Resources (NCRR) and the Canadian Genome Analysis and Technology Program (CGAT).

Consortium Wormbase et al. (2000) West Coast Worm Meeting "From ACeDB to a more complete and usable database"

Consortium Wormbase, Foltz NL, Schwarz EM, Sternberg PW

[West Coast Worm Meeting, 2000]

We briefly describe the current status and plans for WormBase, initially an extension of the existing ACeDB database with a new user interface. The WormBase consortium includes the team that developed ACeDB (Richard Durbin and colleagues at the Sanger Centre; Jean Thierry-Mieg and colleagues at Montpellier); Lincoln Stein and colleagues at Cold Spring Harbor, who developed the current web interface for WormBase; and John Spieth and colleagues at the Genome Sequencing Center at Washington University, who along with the Sanger Centre team, continue to annotate the genomic sequence. The Caltech group will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level, and gene interactions. Data will be extracted from the literature, as well as by community submission. We look forward to providing the C. elegans and broader research community easy access to vast quantities of high quality data on C. elegans. Also, we welcome your suggestions and criticism at any time. WormBase can be accessed at www.wormbase.org.

Consortium Wormbase (2000) Worm Breeder's Gazette "Update on the C. elegans database WormBase"

Consortium Wormbase

[Worm Breeder's Gazette, 2000]

WormBase (www.wormbase.org) is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. WormBase builds upon the existing ACeDB database of the C. elegans genome by providing curation from the literature, an expanded range of content and a user friendly web interface. The team that developed and maintained ACeDB (Richard Durbin, Jean Thierry-Mieg) remains an important part of WormBase. Lincoln Stein and colleagues at Cold Spring Harbor are leading the effort to develop the user interface, including visualization tools for the genome and genetic map. Teams at Sanger Centre (led by Richard Durbin) and the Genome Sequencing Center at Washington University, St. Louis (led by John Spieth) continue to curate the genomic sequence. Jean and Danielle Thierry-Mieg at NCBI spearhead importation of large-scale data sets from other projects. Paul Sternberg and colleagues at Caltech will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level; and gene interactions. Paul Sternberg assumes overall responsibility for WormBase, and is delighted to hear feedback of any sort. WormBase has recently received major funding from the National Human Genome Research Institute at the US National Institutes of Health, and also receives support from the National Library of Medicine/NCBI and the British Medical Research Council. WormBase is an expansion of existing efforts, and as such continues to need you help and feedback. Even with the increased scope and funding, all past contributors to ACeDB remain involved. The Caenorhabditis Genetics Center (Jonathan Hodgkin and Sylvia Martinelli) collaborate with WormBase to curate the genetic map and related topics. Ian Hope and colleagues continue to supply expression data to WormBase. Leon Avery will continue his superb website and serves as one advisor to WormBase. While the major means of access to WormBase is via the world wide web, downloadable versions of WormBase as well as the acedb software engine will continue to be available.

Kearn J et al. (2013) Invert Neurosci "Meeting report: 2012 Caenorhabditis elegans Neurobiology meeting, EMBL Advanced Training Centre, Germany."

Dalliere N, Dillon J, Kearn J

[Invert Neurosci, 2013]

Some of the finest minds in the field of Caenorhabditis elegans neurobiology were brought together from 14 June to 17 June 2012 in the small, quaint and picturesque German city of Heidelberg for the biannual C. elegans neurobiology conference. Held at the EMBL Advanced Training Centre and wonderfully organised by Diah Yulianti, Jean-Louis Bessereau, Gert Jansen and William Schafer, the meeting contained 62 verbal presentations and hundreds of posters that were displayed around the double-helical walkways that looped throughout the conference centre. Presentations on recent advances in microfluidics, cell ablation and targeted gene expression exemplified the strengths of C. elegans as a model organism, with these advances allowing detailed high-throughput analysis and study. Interesting behaviours that were previously poorly characterised were widely discussed, as were the advantages of C. elegans as a model for neurodevelopment and neurodegeneration and the investigation of neuropeptide function. The examples discussed in this meeting report seek to illustrate the breadth and depth of presentations given on these recurring topics.

Lynch, Allison et al. (2010) C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany "MAGI-1 modulates the function of the C. elegans cadherin-catenin complex during morphogenesis"

Hardin, Jeff, Lynch, Allison

[C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany, 2010]

In multicellular organisms, cell-cell junctions are involved in all aspects of tissue morphogenesis, including regulation of cell shape and movement. To establish junctions, cytoplasmic proteins that interact with the actin cytoskeleton must stabilize adhesion molecules. For example, catenins connect cadherins to the cytoskeleton and mutations in catenin proteins significantly impact morphogenesis. A previously isolated hypomorphic allele of the C. elegans ?-catenin homolog, hmp-1(fe4) , exhibits ~70% lethality and body shape defects (Pettitt, et al., 2003, JCB 162, 15-22). In continuing efforts to identify regulators of the cadherin-catenin complex, we conducted a genome-wide RNAi screen to identify genes whose loss of function enhances the hmp-1(fe4) phenotype. We uncovered MAGI-1, a vert ebrate tight junction protein known to interact with actin-binding proteins (Patrie, et al., 2002, JBC 277, 30183-90). We have shown C. elegans MAGI-1 genetically interacts with hmp-1 /?-catenin and hmp-2 /?-catenin, suggesting MAGI-1 may modulate cadherin-catenin function during morphogenesis. MAGI-1 localizes at the C. elegans apical junction, but is surprisingly basal to the cadherin-catenin complex. In addition, MAGI-1 junction localization is not dependent on ?-catenin, in contrast to what has been shown in tissue culture (Dobrosotskaya, et al., 2000, BBRC 270, 903-09). We are currently examining if MAGI-1 modulates actin dynamics during morphogenesis and we are characterizing proteins that potentially interact with MAGI-1 to further assess how MAGI-1 functions in a living organism.