Bioinformatics group

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AACATACCTGCTTTATGCACTCAAGCAGAGAAGAAATCCACAAGTACTCA
CCAGCCTCCTGGTCTGCAGAGAAGACAGAATCAATATGAGCACAGCAGGA
AAAGTAATCAAATGCAAAGCAGCTGTGCTATGGGAGTTAAAGAAACCCTT
TTCCATTGAGGAGGTAGAGGTTGCACCTCCTAAGGCTCATGAAGTTCGCA
TTAAGATGGTGGCTGCAGGAATCTGTCGTTCAGATGAGCATGTGGTTAGT
GGCAACCTGGTGACCCCCCTTCCTGTGATTTTAGGCCATGAGGCAGCCGG
CATCGTGGAAAGTGTTGGAGAAGGGGTGACTACAGTCAAACCAGGTGATA
AAGTCATCCCGCTCTTTACTCCTCAGTGTGGAAAATGCAGAATTTGTAAA
AACCCAGAAAGCAACTACTGCTTGAAAAATGATCTAGGCAATCCTCGGGG
GACCCTGCAGGATGGCACCAGGAGGTTCACCTGCAGCGGGAAGCCCATCC
ACCACTTCGTCGGCGTCAGCACCTTCTCCCAGTACACAGTGGTGGATGAG
AATGCAGTGGCCAAAATTGATGCAGCCTCGCCCCTGGAGAAAGTCTGCCT
CATTGGCTGTGGATTTTCGACTGGTTATGGGTCTGCAGTCAAAGTTGCCA
AGGTCACCCCAGGGTCTACCTGTGCTGTGTTTGGCCTGGGAGGGGTCGGC
CTATCTGTTGTTATGGGCTGTAAAGCAGCTGGAGCAGCCAGAATCATTGC
TGTGGACATCAACAAGGACAAATTTGCAAAGGCTAAAGAGTTGGGTGCCA
CTGAATGCATCAACCCTCAAGACTACAAGAAACCCATTCAGGAAGTGCTA
AAGGAAATGACTGATGGAGGTGTGGATTTTTCGTTTGAAGTCATCGGTCG
GCTTGACACCATGATGGCTTCCCTGTTATGTTGTCATGAGGCATGTGGCA
CAAGTGTCATTGTAGGGGTACCTCCTGATTCCCAGAACCTCTCAATAAAC
CCTATGCTGCTACTGACTGGACGCACGTGGAAAGGAGCTATTTTTGGAGG
CTTTAAGAGTAAAGAATCTGTCCCCAAACTTGTGGCTGACTTTATGGCTA
AGAAGTTTTCACTGGATGCATTAATAACAAATATTTTACCTTTTGAAAAA
ATAAATGAAGGATTTGACCTGCTTCGCTCTGGAAAGAGTA
Bioinformatics group AgroBioInstitute
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Whos 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

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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. Dolashka IOC BAS
• Research of the molecular mechanisms of drought
  stress in grain cultures, 2008-2011 ABI College
  of Agronomy and Biotechnology, China Agricultural
  University, Beijing (CHINA)

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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) 2011-2015
  Project 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
• COST Action ??1006 Next Generation Sequencing
  Data Analysis Network" 2011-2015 MC member from
  ABI Dr. Dimitar Vassilev
• COST ActionTD0801 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

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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.
• ??????? ?. (2010) ?????????????? ??????,
  ?????????? ? ??????????? ?? ???????????? ? ?
  ??????????, ???. 180-193, ? ?????????? ????????
  ? ???????? ??? ?????????? ?? ????. ?????
  ???????. (??????????).
• 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.

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Services and productsWeb based information
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
• ISKRA includes 12 regions
• gt600 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

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Group development

• Collaborative projects in 7FP, ?UROSTARS and
  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

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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, ?????
• - IBB, Poland

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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 Bioinformatics
  in genomics and metabolomics with speakers from
  EBI, EMBL, Hinxton

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Thank you for your attention!
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