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What does it mean to be a bioinformatician?

Sharing experience of working in the field of bioinformatics.

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What does it mean to be a bioinformatician?

  1. 1. BIIT Inside Bioinformatics Dmytro Fishman
  2. 2. Com puter Land Science
  3. 3. Com puter Software Engineering MSc Land Science
  4. 4. Com puter Software Engineering MSc Science Land Algorithms canyon City of Data Mining Software Development area Other Stuff Wastelands
  5. 5. Pure Math Endless Ocean The Dark Forest of Biology Statistics Sea Economics World Let it be chemistry here Com puter Science Land Algorithms canyon City of Data Mining Software Development area Other Stuff Wastelands
  6. 6. Algorithms canyon Pure Math Endless Ocean Statistics Sea Economics World Let it be chemistry here Com puter Science Land The Dark Forest of Biology City of Data Mining Software Development area Other Stuff Wastelands
  7. 7. Pure Math Endless Ocean Statistics Sea Economics World Let it be chemistry here Com puter Science Land The Dark Forest of Biology Algorithms canyon City of Data Mining Software Development area Other Stuff Wastelands
  8. 8. Pure Math Endless Ocean Statistics Sea Economics World Let it be chemistry here Com puter Science Land The Dark Forest of Biology Algorithms canyon City of Data Mining Software Development area Other Stuff Wastelands
  9. 9. Pure Math Endless Ocean Statistics Sea Economics World Let it be chemistry here Com puter Science Land The Dark Forest of Biology Algorithms canyon City of Data Mining Software Development area Other Stuff Wastelands DIMA’S INTERESTS LAND
  10. 10. WELCOME TO DIMA’S INTERESTS LAND
  11. 11. WELCOME TO DIMA’S INTERESTS LAND AUTOIMMUNITY FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS MEDICAL IMAGING
  12. 12. WELCOME TO DIMA’S INTERESTS LAND AUTOIMMUNITY FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS MEDICAL IMAGING
  13. 13. AUTOIMMUNITY
  14. 14. Sample
  15. 15. ProtoarraySample
  16. 16. ProtoarraySample
  17. 17. ProtoarraySample Protein1 ProteinN Protein2 Patients Healthy
  18. 18. AUTOIMMUNITY AIRE-Deficient Patients Harbor Unique High-Affinity Disease-Ameliorating Autoantibodies (Meyer et al. 2016) The Serological Autoimmunome of AIRE- deficiency is Large and Comprises Two Distinct Subgroups Dmytro Fishman1, Kai Kisand2, Christina Hertel3, Mike Rothe3, Anu Remm2, Maire Pihlap2, Priit Adler1, Hedi Peterson1, Jaak Vilo1, Aleksandr Peet4, Antonella Meloni5, Katarina Trebusak Podkrajsek6, Tadej Battelino6, Øyvind Bruserud7, Annette SB Wolff7, Eystein S Husebye7, Nicolas Kluger8, Kai Krohn8, Annamari Ranki8, Adrian Hayday9, Pärt Peterson2
  19. 19. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS MEDICAL IMAGING AUTOIMMUNITY
  20. 20. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS MEDICAL IMAGING AUTOIMMUNITY
  21. 21. …AACCTGTTACAAACCG… ON OFF FUNCTIONAL GENOMICS
  22. 22. …AACCTGTTACAAACCG… ON OFF FUNCTIONAL GENOMICS
  23. 23. …AACCTGTTACAAACCG… ON OFF FUNCTIONAL GENOMICS
  24. 24. …AACCTGTTACAAACCG… …AGCCTGTTACAAACCG… ON OFF ON OFF FUNCTIONAL GENOMICS
  25. 25. …AACCTGTTACAAACCG… …AGCCTGTTACAAACCG… ON OFF ON OFF FUNCTIONAL GENOMICS
  26. 26. …AACCTGTTACAAACCG… …AGCCTGTTACAAACCG… ON OFF ON OFF FUNCTIONAL GENOMICS
  27. 27. Input Sequence A A A G C C T …AACCTGTTACAAACCG… …AGCCTGTTACAAACCG… ON OFF ON OFF FUNCTIONAL GENOMICS
  28. 28. Input Sequence A A A G C C T A C T G Convolution Convolution Layer #1 Convolution Layer #2 FC Layer Deep learning for computational biology Angermueller et al. Predicted Output …AACCTGTTACAAACCG… …AGCCTGTTACAAACCG… ON OFF ON OFF 87% 13% FUNCTIONAL GENOMICS
  29. 29. A/G? In collaboration with Kaur Alasoo (kauralasoo@gmail.com) & Yurii Toma (yurii.toma@gmail.com) FUNCTIONAL GENOMICS
  30. 30. Genome Geenivaramu
  31. 31. Genome Geenivaramu
  32. 32. Genome Geenivaramu
  33. 33. Genome Geenivaramu
  34. 34. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS A/G? MEDICAL IMAGING AUTOIMMUNITY
  35. 35. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL IMAGINGMEDICAL SIGNAL TEACHING AND GIVING TALKS A/G? AUTOIMMUNITY
  36. 36. MEDICAL IMAGING
  37. 37. Disease Stage Prediction Diabetic Retinopathy Sources of images are: kaggle.com and nature.com MEDICAL IMAGING
  38. 38. Heart Volume Prediction Heart Failure Sources of images are: kaggle.com and nature.com Disease Stage Prediction Diabetic Retinopathy MEDICAL IMAGING
  39. 39. Cell Segmentation Heart Volume Prediction Heart Failure Disease Stage Prediction Diabetic Retinopathy MEDICAL IMAGING
  40. 40. Cell Segmentation Heart Volume Prediction Heart Failure Disease Stage Prediction Diabetic Retinopathy Dmytro Fishman, Ardi Tampuu, William Jones, Elizabeth Bell, Ilya Kuzovkin, Tanel Pärnamaa, Leopold Parts, Jaak Vilo, Raul Vicente Mari-Liis Allikivi, Elena Sügis, Dmytro Fishman Anna Leontjeva, Ilya Kuzovkin, Dmytro Fishman MEDICAL IMAGING
  41. 41. ???
  42. 42. 0 1
  43. 43. 0 1
  44. 44. 0 1
  45. 45. 0 1
  46. 46. 0 1 90%
  47. 47. 0 1 Dermatologist-level classification of skin cancer with deep neural networks (Esteva et al., 2017) 90% VS 14%
  48. 48. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS A/G? MEDICAL IMAGING AUTOIMMUNITY
  49. 49. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS A/G? MEDICAL IMAGING AUTOIMMUNITY
  50. 50. MEDICAL SIGNAL
  51. 51. MEDICAL SIGNAL
  52. 52. Neuroimaging MEDICAL SIGNAL
  53. 53. Neuroimaging EEG Signal MEDICAL SIGNAL
  54. 54. Neuroimaging EEG Signal Fourier Transform Data MEDICAL SIGNAL
  55. 55. Neuroimaging EEG Signal Data MEDICAL SIGNAL
  56. 56. Neuroimaging EEG Signal Data Machine Learning MEDICAL SIGNAL
  57. 57. MEDICAL SIGNAL Neuroimaging EEG Signal Data Machine Learning
  58. 58. MEDICAL SIGNAL Neuroimaging EEG Signal Data Machine Learning Anna Leontjeva, Ilya Kuzovkin, Dmytro Fishman https://github.com/kuz/BrainActivity3D
  59. 59. Cardiogram Data Machine Learning P( ) = .92 Cardiograph
  60. 60. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS A/G? MEDICAL IMAGINGMEDICAL SIGNAL AUTOIMMUNITY
  61. 61. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS A/G? MEDICAL IMAGINGMEDICAL SIGNAL AUTOIMMUNITY
  62. 62. AI
  63. 63. AI Elena Sügis Anna Ufliand
  64. 64. AI Elena Sügis Anna Ufliand
  65. 65. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL SIGNAL TEACHING AND GIVING TALKS A/G? MEDICAL IMAGINGMEDICAL SIGNAL AUTOIMMUNITY
  66. 66. WELCOME TO DIMA’S INTERESTS LAND FUNCTIONAL GENOMICS MEDICAL IMAGING TEACHING AND GIVING TALKS MEDICAL SIGNAL A/G? AUTOIMMUNITY
  67. 67. BIIT dmytro@ut.ee

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