Experiences with workflows for automating data-intensive bioinformatics
Review article (Peer reviewed)
Erik Bongcam Rudloff
Department of Animal Breeding and Genetics
Faculty of Veterinary Medicine and Animal Sciences
Email: Erik.Bongcam@slu.se
Publications
2015
Genome-Guided Analysis of Physiological Capacities of Tepidanaerobacter acetatoxydans Provides Insights into Environmental Adaptations and Syntrophic Acetate Oxidation
Research article (Peer reviewed)
The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers
Research article (Peer reviewed)
2014
Capacity building and bioinformatics challenges
Report chapter
Genome Analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: A Rhizobacterium That Improves Plant Growth and Stress Management
Research article (Peer reviewed)
2014 Annual General Meeting – Executive Board Report
Other publication in scientific journal
eBioKit bioinformatics workshops in Dar es Salaam, Tanzania
Research article
Molecular Typing of Escherichia coli O157:H7 Isolates from Swedish Cattle and Human Cases: Population Dynamics and Virulence
Research article (Peer reviewed)
Studies of plant colonisation by closely related Bacillus amyloliquefaciens biocontrol agents using strain specific quantitative PCR assays
Research article (Peer reviewed)
Relationship between genome and epigenome - challenges and requirements for future research
Research article (Peer reviewed)
Data integration in the era of omics: current and future challenges
Other publication (Peer reviewed)
Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033
Research article (Peer reviewed)
Silencing Motifs in the Clr2 Protein from Fission Yeast, Schizosaccharomyces pombe
Research article (Peer reviewed)
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Review article (Peer reviewed)
2013
The next NGS Challenge Conference: Data processing and integration
Other publication
Viral Metagenomics – New applications for the broad-range detection of viromes in veterinary and public health settings
Other publication
Best practices in bioinformatics training for life scientists
Research article (Peer reviewed)
Camel Streptococcus agalactiae populations are associated with specific disease complexes and acquired the tetracycline resistance gene tetM via a Tn916-like element
Research article (Peer reviewed)
Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
Research article (Peer reviewed)
First genome sequence of a syntrophic acetate-oxidizing bacterium, Tepidanaerobacter acetatoxydans strain re1
Other publication in scientific journal
Genome sequence of Streptococcus agalactiae strain 09mas018883, isolated from a Swedish cow
Other publication in scientific journal (Peer reviewed)
Genome sequence of two pathogenic Streptococcus agalactiae isolates from the one-humped camel Camelus dromedarius
Other publication in scientific journal (Peer reviewed)
Next NGS Challenge – Data Processing and Integration’ Conference – Conference report
Other publication
2013 Annual General Meeting: Executive Board Report
Other publication
Workshop on laboratory protocol standards for the molecular methods database
Research article (Peer reviewed)
Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036
Other publication in scientific journal (Peer reviewed)
Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium
Other publication in scientific journal (Peer reviewed)
Metagenomics sample preparation and sequencing
Other publication
The bioinformatics of viral metagenomics
Other publication
Ion Torrent sequencing and pipeline assembly of the first genome sequence of a mesophilic syntrophic acetate oxidizing bacterium (SAOB)
Research article
Genome sequence of plant associated rhizobacterium Bacillus amyloliquefaciens strain UCMB5033
Research article
Rapid whole genome sequencing investigation of a familial outbreak of E. coli 0121:H19 with a sheep farm as the suspected source
Conference paper
Biobanking in emerging countries, a special issue on challenges and opportunities
Conference abstract
2012
Evaluation of selective sweeps for Brachycephaly in dogs and associated susceptibility loci for glioma
Other publication
COST Action BM 1006 (SeqAhead): MC BUSINESS MEETING AND SCIENTIFIC MEETING
Other publication (Peer reviewed)
Integration and analysis of multi-type high-throughput data for biomolecular knowledge discovery
Other publication
EMBnet at ISCB Latin America 2012 Conference on Bioinformatics
Other publication
The origin of the ‘Mycoplasma mycoides cluster’coincides with domestication of ruminants
Research article (Peer reviewed)
Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development
Research article (Peer reviewed)
Implementation of proteomic biomarkers: making it work
Research article (Peer reviewed)
2011
SEQscoring: a tool to facilitate the interpretation of data generated with next generation sequencing technologies
Research article
ISCB Africa ASBCB Conference on Bioinformatics and eBioKit Workshop
Research article
Report of the EMBnet AGM 2011 Workshop
Other publication
SEQAHEAD - COST Action BM1006: Next Generation Sequencing Data Analysis Network
Other publication
Contributions of the EMERALD project to assessing and improving microarray data quality
Research article (Peer reviewed)
The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships
Research article (Peer reviewed)
2010
EMBRACE Workshop – “Next Generation Sequencing II”
Research article
Recommendations for biomarker identification and qualification in clinical proteomics
Research article (Peer reviewed)
Comprehensive human urine standards for comparability and standardization in clinical proteome analysis
Research article (Peer reviewed)
A Community Standard Format for the Representation of Protein Affinity Reagents
Research article (Peer reviewed)