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Amit Kumar Yadav, PhD
Drug Discovery Research Center (DDRC)
Translational Health Science and Technology
Institute (THSTI)
...
DISCLAIMER
•This is not a class. Notes aren't helpful,
discussions are !!!
•Most are conceptual analogies, not accurate
de...
WHAT IS BIO-INFORMATICS ?
WHAT IS COMPUTATIONAL BIOLOGY?
Biology
Chemistry
Mathematics
Computer
Science
Statistics
WHAT DOES A BIO-INFORMATICIAN DO ?
DNA
protei
n
mRNA
tRNA
NEW AGE BIOLOGY = SYSTEMS BIOLOGY !
CREATING THE MAP = SEQUENCING
THINGS !
FASTA FILE
SEQUENCE ALIGNMENT
SEQUENCE ALIGNMENT
DATABASE RESOURCES
BLAST SEARCH
DOMAIN AND STRUCTURE DATABASES
ASSEMBLING 3 BILLION PIECES !!!
DNA SEQUENCING
TRANSCRIPTOMICS (RNA-SEQ)
TRANSCRIPTOMICS (RNA-SEQ)
ONE GENOME…MANY PROTEOMES
Perhaps not…
they still have a
dynamic
“proteome” code
to break. They
cannot hit a
moving target
MILESTONES
SHOTGUN PROTEOMICS
SHOTGUN PROTEOMICS ALGORITHM
Intensity of
matching
peaks
Continuity of
y-ions & b-
ions
Neutral
losses &
Immonium
ions
Fra...
PROTEIN IDENTIFICATION?
Protein Assembler
SIMILAR PROTEOMES … DIFFERENT
PHENOTYPES ?
OK…I will
wait to see
if they can
break the
PTM code
biological processes are modular
!!!
How not to collaborate !
I’m the brain,
he’s the brawn
Bioinformatics
/
Computational
Lab
Cell/Molecular
Biology Lab
THANK YOU !
TAKE HOME MESSAGE
• Bioinformatics is NOT biology or informatics, its
both
• Genomics, transcriptomics, proteomics = large...
ACKNOWLEDGEMENTS
• Dr. Rekha Kumari
• Dr. Richa Misra
• ICGEB, DDRC, THSTI
• DBT-IYBA
Bioinformatics mh 3_nov_2015_aky_for_students
Bioinformatics mh 3_nov_2015_aky_for_students
Bioinformatics mh 3_nov_2015_aky_for_students
Bioinformatics mh 3_nov_2015_aky_for_students
Bioinformatics mh 3_nov_2015_aky_for_students
Bioinformatics mh 3_nov_2015_aky_for_students
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Bioinformatics mh 3_nov_2015_aky_for_students

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The hitchhiker's guide to bioinformatics

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Bioinformatics mh 3_nov_2015_aky_for_students

  1. 1. Amit Kumar Yadav, PhD Drug Discovery Research Center (DDRC) Translational Health Science and Technology Institute (THSTI) 3rd Nov 2015
  2. 2. DISCLAIMER •This is not a class. Notes aren't helpful, discussions are !!! •Most are conceptual analogies, not accurate details !!! •Focus is on understanding, not subject coverage !!!
  3. 3. WHAT IS BIO-INFORMATICS ? WHAT IS COMPUTATIONAL BIOLOGY? Biology Chemistry Mathematics Computer Science Statistics
  4. 4. WHAT DOES A BIO-INFORMATICIAN DO ?
  5. 5. DNA protei n mRNA tRNA
  6. 6. NEW AGE BIOLOGY = SYSTEMS BIOLOGY !
  7. 7. CREATING THE MAP = SEQUENCING THINGS !
  8. 8. FASTA FILE
  9. 9. SEQUENCE ALIGNMENT
  10. 10. SEQUENCE ALIGNMENT
  11. 11. DATABASE RESOURCES
  12. 12. BLAST SEARCH
  13. 13. DOMAIN AND STRUCTURE DATABASES
  14. 14. ASSEMBLING 3 BILLION PIECES !!!
  15. 15. DNA SEQUENCING
  16. 16. TRANSCRIPTOMICS (RNA-SEQ)
  17. 17. TRANSCRIPTOMICS (RNA-SEQ)
  18. 18. ONE GENOME…MANY PROTEOMES Perhaps not… they still have a dynamic “proteome” code to break. They cannot hit a moving target
  19. 19. MILESTONES
  20. 20. SHOTGUN PROTEOMICS
  21. 21. SHOTGUN PROTEOMICS ALGORITHM Intensity of matching peaks Continuity of y-ions & b- ions Neutral losses & Immonium ions Fragment mass error sensitive scoring
  22. 22. PROTEIN IDENTIFICATION? Protein Assembler
  23. 23. SIMILAR PROTEOMES … DIFFERENT PHENOTYPES ? OK…I will wait to see if they can break the PTM code
  24. 24. biological processes are modular !!!
  25. 25. How not to collaborate ! I’m the brain, he’s the brawn Bioinformatics / Computational Lab Cell/Molecular Biology Lab
  26. 26. THANK YOU !
  27. 27. TAKE HOME MESSAGE • Bioinformatics is NOT biology or informatics, its both • Genomics, transcriptomics, proteomics = large scale studies of biomolecules DNA, RNA and proteins • Systems biology = holistic views of biological phenomenon = mountains of data • Algorithm development, Automated analysis, Database development and Data management = data science
  28. 28. ACKNOWLEDGEMENTS • Dr. Rekha Kumari • Dr. Richa Misra • ICGEB, DDRC, THSTI • DBT-IYBA

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