TY  - JOUR
A1  - Gupta, Shishir K.
A1  - Srivastava, Mugdha
A1  - Osmanoglu, Oezge
A1  - Dandekar, Thomas
T1  - Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs
JF  - Scientific Reports
N2  - Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6% of the entire C. floridanus proteome.
KW  - interaction map
KW  - drosophila
KW  - identification
KW  - evolutionary
KW  - reliability
KW  - annotation
KW  - database
KW  - target
KW  - cycle
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229406
VL  - 10
IS  - 1
ER  - 
TY  - JOUR
A1  - Wolf, Beat
A1  - Kuonen, Pierre
A1  - Dandekar, Thomas
A1  - Atlan, David
T1  - DNAseq workflow in a diagnostic context and an example of a user friendly implementation
JF  - BioMed Research International
N2  - Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.
KW  - next generation sequencing
KW  - genome browser
KW  - mutation
KW  - algorithm
KW  - database
KW  - format
KW  - discovery
KW  - exome
KW  - variants
KW  - alignment
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-144527
IS  - 403497
ER  - 
TY  - JOUR
A1  - Kunz, Meik
A1  - Liang, Chunguang
A1  - Nilla, Santosh
A1  - Cecil, Alexander
A1  - Dandekar, Thomas
T1  - The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development
JF  - Database
N2  - The drug-minded protein interaction database (DrumPID) has been designed to provide fast, tailored information on drugs and their protein networks including indications, protein targets and side-targets. Starting queries include compound, target and protein interactions and organism-specific protein families. Furthermore, drug name, chemical structures and their SMILES notation, affected proteins (potential drug targets), organisms as well as diseases can be queried including various combinations and refinement of searches. Drugs and protein interactions are analyzed in detail with reference to protein structures and catalytic domains, related compound structures as well as potential targets in other organisms. DrumPID considers drug functionality, compound similarity, target structure, interactome analysis and organismic range for a compound, useful for drug development, predicting drug side-effects and structure–activity relationships.
KW  - drug-minded protein
KW  - database
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147369
VL  - 2016
ER  -