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Publications

SEQAHEAD - COST Action BM1006: Next Generation Sequencing Data Analysis Network. Teresa Attwood, Erik Bongcam-Rudloff, Andreas Gisel. EMBnet. Journal 17.1, August 2012, pp 7-9. link

Articles that acknowledge COST Action BM1006 SeqAhead from May 2013 to March 2014 Peer review
  1. Nassa, Giovanni, et al. “Post-transcriptional regulation of human breast cancer cell proteome by unliganded Estrogen Receptor beta via microRNAs.” Molecular & Cellular Proteomics (2014): mcp-M113.
  2. Sifrim, Alejandro, et al. “eXtasy: variant prioritization by genomic data fusion.” Nature methods 10.11 (2013): 1083-1084.
  3. Gomez-Cabrero, David, et al. “Data integration in the era of omics: current and future challenges.” BMC Systems Biology 8.Suppl 2 (2014): I1.
  4. M Masseroli, et al “Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information”, BMC Bioinformatics,15; 1; 1-15 (2014)
  5. Schumacher, André, et al. “SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.” Bioinformatics 30.1 (2014): 119-120.
  6. De Filippo, Maria Rosaria, et al. “Lack of pathogenic mutations in six patients with MMPSI.” Epilepsy research (2013).
  7. Reverter, Ferran, Esteban Vegas, and Josep M. Oller. “Kernel-PCA data integration with enhanced interpretability.” BMC Systems Biology 8.Suppl 2 (2014): S6.
  8. Menche, Jörg, et al. “A diVIsive Shuffling Approach (VIStA) for gene expression analysis to identify subtypes in Chronic Obstructive Pulmonary Disease.” BMC Systems Biology 8.Suppl 2 (2014): S8.
  9. Fischer, Christoph, et al. “Complete mitochondrial DNA sequences of the threadfin cichlid (Petrochromis trewavasae) and the blunthead cichlid (Tropheus moorii) and patterns of mitochondrial genome evolution in cichlid fishes.” PloS one 8.6 (2013): e67048.
  10. Regierer, Babette, et al. “ICT needs and challenges for Big Data in the Life Sciences. A workshop report-SeqAhead/ISBE Workshop in Pula, Sardinia, Italy, 6 June 2013.” EMBnet. journal 19.1 (2013): pp-31.
  11. Via, Allegra, et al. “Best practices in bioinformatics training for life scientists.” Briefings in bioinformatics 14.5 (2013): 528-537.
  12. Conesa, Ana, and Erik Bongcam-Rudloff. “‘Next NGS Challenge–Data Processing and Integration’Conference–Conference report.” EMBnet. journal 19.1 (2013): pp-14.
  13. Scarpato, Margherita, et al. “AnaLysis of Expression on human chromosome 21, ALEHSA21: a pilot integrated web resource.” Database: the journal of biological databases and curation 2014 (2014).
  14. Attwood, Teresa K. “EMBnet, the Global Bioinformatics Network, in 2013: A Silver Anniversary.” EMBnet. journal 19.1 (2013): pp-16.
  15. Kienesberger, Sabine, et al. “Comparative Genome Analysis of Campylobacter fetus Subspecies Revealed Horizontally Acquired Genetic Elements Important for Virulence and Niche Specificity.” PloS one 9.1 (2014): e85491.
  16. Bongcam-Rudloff, Erik, et al. “The Next NGS Challenge Conference: Data Processing and Integration.” EMBnet. journal 19.A (2013): p-3.
  17. Strazzullo, Maria, et al. “Global Transcriptome Profiles of Italian Mediterranean Buffalo Embryos with Normal and Retarded Growth.” PloS one 9.2 (2014): e90027.
  18. Claesen, Marc, et al. “Fast Prediction with SVM Models Containing RBF Kernels.” arXiv preprint arXiv:1403.0736 (2014).
  19. Thomas, Minta, Anneleen Daemen, and Bart De Moor. “Maximum likelihood estimation of GEVD: Applications in Bioinformatics.” Age (years) 100 (2014): 31-88.
  20. Claesen, Marc, et al. “A Robust Ensemble Approach to Learn From Positive and Unlabeled Data Using SVM Base Models.” arXiv preprint arXiv:1402.3144 (2014).
  21. Zakeri, Pooya, et al. “Protein Fold Recognition Using Geometric Kernel Data Fusion.” Bioinformatics (2014): btu118.
  22. Valverde, José R., and Rafael P. Mellado. “Analysis of Metagenomic Data Containing High Biodiversity Levels.” PloS one 8.3 (2013): e58118.
  23. Watson-Haigh, Nathan S., et al. “Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.” Briefings in bioinformatics 14.5 (2013): 563-574.
  24. Tsiliki, Georgia, Konstantinos Tsaramirsis, and Sophia Kossida. “Integrated analysis of diverse genomic data.” EMBnet. journal 19.A (2013): pp-92.
  25. GOBLET Consortium. “The Global Organisation for Bioinformatics Learning, Education & Training (GOBLET).” EMBnet. journal 19.1 (2013): pp-10.
  26. Giurato, Giorgio, et al. “iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.” BMC bioinformatics 14.1 (2013): 362.
  27. Bellitto, Thomas, et al. “Next Generation Cluster Editing.” arXiv preprint arXiv:1310.3353 (2013).
  28. Costa, Valerio, et al. “RNA-Seq and human complex diseases: recent accomplishments and future perspectives.” European Journal of Human Genetics 21.2 (2013): 134-142.
  29. Momcilovic, Svetislav, Nuno Roma, and Leonel Sousa. “Exploiting task and data parallelism for advanced video coding on hybrid CPU+ GPU platforms.” Journal of Real-Time Image Processing (2013): 1-17.
  30. Lampa, Samuel, et al. “Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.” GigaScience 2.1 (2013):9.
  31. Moschopoulos, Charalampos, Jeroen Breckpot, and Yves Moreau. “An ontology describing congenital heart defects data.” EMBnet. journal 19.B (2013): pp-76.
  32. Vlachakis, Dimitrios, et al. “Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit.” Bioinformatics 29.1 (2013): 126-128.
  33. Claesen, Marc, et al. “EnsembleSVM: A Library for Ensemble Learning Using Support Vector Machines.” Journal of Machine Learning Research accepted (2013).
  34. Moschopoulos, Charalampos, et al. “A genetic algorithm for pancreatic cancer diagnosis.” Engineering Applications of Neural Networks. Springer Berlin Heidelberg, 2013. 222-230.
  35. Popovic, Dusan, et al. “A Hybrid Approach to Feature Ranking for Microarray Data Classification.” Engineering Applications of Neural Networks. Springer Berlin Heidelberg, 2013. 241-248.
  36. Mertzanidou, A., et al. “Microarray analysis reveals abnormal chromosomal complements in over 70% of 14 normally developing human embryos.” Human Reproduction 28.1 (2013): 256-264.
  37. Sablok, Gaurav, et al. “isomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets.” FEBS letters 587.16 (2013): 2629-2634.
  38. Popovic, Dusan, et al. “Department of Electrical Engineering (ES AT), STADIUS-iMinds Future Health Department, KU Leuven Leuven, Belgium.” Bioinformatics and Biomedicine (BIBM), 2013 IEEE International Conference on. IEEE, 2013.
  39. Allhoff, Manuel, et al. “Discovering motifs that induce sequencing errors.” BMC bioinformatics 14.Suppl 5 (2013): S1.
  40. Van der Aa, Niels, et al. “Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains.” Nucleic acids research 41.6 (2013): e66-e66.
  41. Darbo, Elodie, et al. “Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis.” BMC genomics 14.1 (2013): 226.
Other Publications
  1. Coimbra, Miguel. “MetaGen-FRAME.” (2013). Master thesis
 
Last modified: 2014/04/28 22:04 by Andreas Gisel
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