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Bioinformatics group AgroBioInstitute

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Bioinformatics group AgroBioInstitute

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  1. AACATACCTGCTTTATGCACTCAAGCAGAGAAGAAATCCACAAGTACTCACCAGCCTCCTGGTCTGCAGAGAAGACAGAATCAATATGAGCACAGCAGGAAAAGTAATCAAATGCAAAGCAGCTGTGCTATGGGAGTTAAAGAAACCCTTTTCCATTGAGGAGGTAGAGGTTGCACCTCCTAAGGCTCATGAAGTTCGCATTAAGATGGTGGCTGCAGGAATCTGTCGTTCAGATGAGCATGTGGTTAGTGGCAACCTGGTGACCCCCCTTCCTGTGATTTTAGGCCATGAGGCAGCCGGCATCGTGGAAAGTGTTGGAGAAGGGGTGACTACAGTCAAACCAGGTGATAAAGTCATCCCGCTCTTTACTCCTCAGTGTGGAAAATGCAGAATTTGTAAAAACCCAGAAAGCAACTACTGCTTGAAAAATGATCTAGGCAATCCTCGGGGGACCCTGCAGGATGGCACCAGGAGGTTCACCTGCAGCGGGAAGCCCATCCACCACTTCGTCGGCGTCAGCACCTTCTCCCAGTACACAGTGGTGGATGAGAATGCAGTGGCCAAAATTGATGCAGCCTCGCCCCTGGAGAAAGTCTGCCTCATTGGCTGTGGATTTTCGACTGGTTATGGGTCTGCAGTCAAAGTTGCCAAGGTCACCCCAGGGTCTACCTGTGCTGTGTTTGGCCTGGGAGGGGTCGGCCTATCTGTTGTTATGGGCTGTAAAGCAGCTGGAGCAGCCAGAATCATTGCTGTGGACATCAACAAGGACAAATTTGCAAAGGCTAAAGAGTTGGGTGCCACTGAATGCATCAACCCTCAAGACTACAAGAAACCCATTCAGGAAGTGCTAAAGGAAATGACTGATGGAGGTGTGGATTTTTCGTTTGAAGTCATCGGTCGGCTTGACACCATGATGGCTTCCCTGTTATGTTGTCATGAGGCATGTGGCACAAGTGTCATTGTAGGGGTACCTCCTGATTCCCAGAACCTCTCAATAAACCCTATGCTGCTACTGACTGGACGCACGTGGAAAGGAGCTATTTTTGGAGGCTTTAAGAGTAAAGAATCTGTCCCCAAACTTGTGGCTGACTTTATGGCTAAGAAGTTTTCACTGGATGCATTAATAACAAATATTTTACCTTTTGAAAAAATAAATGAAGGATTTGACCTGCTTCGCTCTGGAAAGAGTAAACATACCTGCTTTATGCACTCAAGCAGAGAAGAAATCCACAAGTACTCACCAGCCTCCTGGTCTGCAGAGAAGACAGAATCAATATGAGCACAGCAGGAAAAGTAATCAAATGCAAAGCAGCTGTGCTATGGGAGTTAAAGAAACCCTTTTCCATTGAGGAGGTAGAGGTTGCACCTCCTAAGGCTCATGAAGTTCGCATTAAGATGGTGGCTGCAGGAATCTGTCGTTCAGATGAGCATGTGGTTAGTGGCAACCTGGTGACCCCCCTTCCTGTGATTTTAGGCCATGAGGCAGCCGGCATCGTGGAAAGTGTTGGAGAAGGGGTGACTACAGTCAAACCAGGTGATAAAGTCATCCCGCTCTTTACTCCTCAGTGTGGAAAATGCAGAATTTGTAAAAACCCAGAAAGCAACTACTGCTTGAAAAATGATCTAGGCAATCCTCGGGGGACCCTGCAGGATGGCACCAGGAGGTTCACCTGCAGCGGGAAGCCCATCCACCACTTCGTCGGCGTCAGCACCTTCTCCCAGTACACAGTGGTGGATGAGAATGCAGTGGCCAAAATTGATGCAGCCTCGCCCCTGGAGAAAGTCTGCCTCATTGGCTGTGGATTTTCGACTGGTTATGGGTCTGCAGTCAAAGTTGCCAAGGTCACCCCAGGGTCTACCTGTGCTGTGTTTGGCCTGGGAGGGGTCGGCCTATCTGTTGTTATGGGCTGTAAAGCAGCTGGAGCAGCCAGAATCATTGCTGTGGACATCAACAAGGACAAATTTGCAAAGGCTAAAGAGTTGGGTGCCACTGAATGCATCAACCCTCAAGACTACAAGAAACCCATTCAGGAAGTGCTAAAGGAAATGACTGATGGAGGTGTGGATTTTTCGTTTGAAGTCATCGGTCGGCTTGACACCATGATGGCTTCCCTGTTATGTTGTCATGAGGCATGTGGCACAAGTGTCATTGTAGGGGTACCTCCTGATTCCCAGAACCTCTCAATAAACCCTATGCTGCTACTGACTGGACGCACGTGGAAAGGAGCTATTTTTGGAGGCTTTAAGAGTAAAGAATCTGTCCCCAAACTTGTGGCTGACTTTATGGCTAAGAAGTTTTCACTGGATGCATTAATAACAAATATTTTACCTTTTGAAAAAATAAATGAAGGATTTGACCTGCTTCGCTCTGGAAAGAGTA Bioinformatics group AgroBioInstitute

  2. Who’s in it? 2 Assoc. professors Dimitar Vassilev, PhD – Group leader, bioinformatics, statistics, quantitative genetics, genome research George Dimov, PhD – population genetics 4 PhD students Ivan Popov– prediction of protein structures, genome analysis, phylogenetics Irena Avdjieva – genome assembly and synteny Milko Krachunov (FMI co-supervision) – Error detection in NGS, metagenomics, bio-ontologies Valeria Simeonova (FMI co supervision) –soft computing, NGS data analysis Several MSc students

  3. Projects Financed by the Agricultural Academy Contemporary biotech approaches for the preservation of biodiversity and selection in plant and animal breeding 2009-2010. Prof. Rossitza Batchvarova Financed by the NSF and the Ministry of Education Youth and Science Center for sustainable development of plant and animal genomics(EXELLENCE IN BIOECONOMY) (CESBD); 2009-2012 prof. Atanas Atanassov Analysis of anti-microbial and anti-cancer bioactive products from marine organisms 2008-2011; Asoc. Prof.P. DolashkaIOCBAS Research of the molecular mechanisms of drought stress in grain cultures, 2008-2011; ABI College of Agronomy and Biotechnology, China Agricultural University, Beijing (CHINA)

  4. Projects Financed by the 7 Framework Programme, EU Genetic and physiology of wheat development to flowering: tools to breed for improved adaptation and yield potential (ADAPTAWHEAT) 2011-2015Project leader: Dr. Simon Griffiths John Ines Centre, Norwich, UK; ABI’ coordinator: Dr. Elena Todorovska Dr. Dimitar Vassilev, Prof. Atanas Atanassov Public Perception of Genetically modified Animals – Science, Utility and Society (PEGASUS);FP7 KBBE 2008 1,2009-2012; Project leader: Lynn Frever (DSS Wageningen University, The Netherlands); ABI’ coordinator: Prof. Atanas Atanassov, Dr. Georgi Dimov COSTAction ВМ1006: Next Generation Sequencing Data Analysis Network"2011-2015; MC member from ABI: Dr. Dimitar Vassilev COSTActionTD0801: Statistical challenges on the 1000€ genome sequences in plants (StatSeq) 2009-2013; MC member from ABI: Dr. Dimitar Vassilev COST Action BM 0702: European Kidney and Urine Proteomics“ (EuroKUP) WG4 Bioinformatics for protein analisys; 2008-2012; MC representative from ABI: Dr. Dimitar Vassilev

  5. Group publications 2010 • Georgieva, M., Stoilov L., Rancheva, E.,Todorovska, Vassilev D. (2010) Comparative analysis of data distribution patterns in plant commet assay. Biotechnology and Biotechnological Equipment 24(4):2142-214 • Vassilev D., Dimov, G., Popov I., Atanassov A. Bioinformatics research and perspectives in the AgroBioInstitute. Biotechnology and Biotechnological Equipment 24(4):2172-2176 • Vukovic V., Andonov, S., Vassilev, D., Trpkovski Z., Murdzeva A-M. (2010) Improved classification results for macedonian pork , In Proc: 9WCGALP, Leipzig, Germany pub. 846. • Petrov P., van Ophuizen E., Leunissen J., Krachounov M., Popov I., Vassilev D. (2010) AnatOntoMerger – a system for computer-aided merging of anatomical ontologies, In: Book of Abstarcts: Workshop of COST action BM0702 “European Kidney and Urine Proteomics” (EuroKUP), meeting, Cyprus, 6-7 November. • Popov I., Vassilev D. (2010) A semi-automated structural class independent method for the prediction of protein secondary structures. Biotechnology and Biotechnological Equipment 24(3): 2044-2048 • Todorovska E., Atanassov A., Vassilev D. (2010). From genetics to genomics in plants and animals. Acta Yugoslavia Genetika, vol. 42, no. 1, 177-194. • Василев Д. (2010) Биоинформатика – методи, приложения и перспективи за използването и в медицината, стр. 180-193, в «Медицинска Генетика и Геномика» под редакцията на проф. Драга Тончева. (Монография). • Popov I., Vassilev D., Attwood T. (2010) Building diagnostic fingerpints for important kidney membrane proteins: the aquaporins (STSM results). In: Book of Abstarcts: Workshop of COST action BM0702 “European Kidney and Urine Proteomics” (EuroKUP), Rotterdam, The Netherlands 20-21 March 2010. • Todorovska E., Kolev S., Ganeva G., Christov N., Vassilev D. (2010) Allele variation in loci for adaptive response and yield traits in Bulgarian wheat. In: Book of Abstarcts of 2nd International Symposium on Genomics of Plant Genetics Resources (GPGR), p.218 (P5.32), Bologna, Italy, 24-27 April 2010. • Popov I., Simeonova V., Vassilev, D. (2010) Estimation of sequencing error rates in the database sequences of the Oryza Sativa (japonica cultivar group) genome. 2nd workshop of EU COST action TD0801 Statistica challenges on the 1000€ genome sequences in plants (StatSEQ), Het Pand, Univ. of Ghent, Ghent, Belgium, May 20-21, 2010., p.34.

  6. Services and productsWeb basedinformation system for control of milk productivity and cattle selection – ISKRA – George Dimov, PhD Main modules: Data management, reports – current and summarized error checking and validation ISKRAincludes 12 regions >600 farms about 22% of milk giving cows Services and reports: Regional selection offices Breeding organizations Farmers – advice and management Development though 2011 Feeding and breeding advice market information breeding values reproduction management

  7. Group development Collaborative projects in 7FP, ЕUROSTARSand other financing tools Main topics: NGS data analysis Biological ontologies Modeling protein structures Information resources for agriculture production management Population and associative genome studies GMO detection and data analysis Software development

  8. Group collaborations In Bulgaria Faculty of Mathematics and Informatics, Faculty of Biology, Sofia University Joint Genomic Center Agricultural University, Plovdiv Thracian University, Stara Zagora Medical University, Sofia Abroad: - Wageningen University – The Netherlands - Roslin Institute – University of Edinburgh, Scotland, UK - John Innes Centre, BBSRC, Norwich, UK - INRA France - Agricultural University Athens - European Bioinformatics Institute and EMBL, - Max Plank Institutes - CAU, Китай - IBB, Poland

  9. Other group activities Bioinformatics seminars – informal meeting for discussion and collaboration With foreign Bioinformatics groups Co-supervision and consultations of MSc an PhD students Attendance and organization of International courses: - ICGEB Course in Bioinformatics, Trieste - 2011 October – 3 day course on Bioinformaticsin genomics and metabolomics with speakers fromEBI, EMBL, Hinxton

  10. Thank you for your attention! 10

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