BT504 : Genomics and Proteomics

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Course Info

Course Category

Molecular Biology

Course Level

Undergraduate

Credit Hours

3

Pre-requisites

N/A

Instructor

Dr. Jamil Ahmed, Dr. Muhammad Nauman Aftab, Dr. Waseem Hiader
PhD, Post docs
Miscellaneous

Course Contents

1. study of omics 2. genomics, proteomics and metabolomics 3. structure of RNA 4. DNA transcription 5. protein translation 6. introduction to genomics 7. anatomy and organization of genome 8. gene anatomy 9. prokaryotic gene and eukaryotic gene 10. prokaryotic and eukaryotic gene expression 11. gene families and gene clusters 12. types of proteins and families 13. genome informatics 14. prokaryotic genome 15. eukaryotic genome 16. epichromosomal elements (Ees) 17. genome repeats 18. transposable elements (Tes) 19. eukaryotic gene structure 20. comparative genomics 21. functional genomics 22. structural genomics 23. concepts of comparative genomics 24. population genomics 25. metagenomics 26. why sequence genomes 27. genome characterization- techniques used 28. genome analysis steps 29. benefits of genome analysis 30. size of genomes-genes 31. viral genomes 32. bacterial genomes 33. yeast genome 34. mitochondrial genome 35. genomes comparison 36. comparing distantly and closely related species 37. genome mapping 38. genetic mapping of genomes 39. physical mapping of genomes 40. cytogentic mapping 41. FISH mapping 42. restriction mapping of genomes 43. radiation hybrid mapping of genomes 44. clone contigs mapping of genomes 45. generating sequence of genomes 46. human genome project 47. human genome project- hierarchical shotgun sequencing 48. human genome project- whole genome sequencing 49. charactersitics of our genomes (A) 50. charactersitics of human genome (B) 51. genome browser_ UCSC 52. genome browser_ Ensemble 53. HGP- ethical and legal issues 54. genome annotations- protein coding genes 55. genome annotations- transcription factors 56. arabidopsis genome 57. mouse genome 58. comparison of human and mouse genomes 59. mapping of disease genes 60. microarrays 61. types of microarray 62. microarrays formats- some errors 63. microarrays- procedure 64. microarray chips 65. microarray applications 66. types of RNA and RNomics 67. non coding DNA 68. non coding RNA 69. miRNA 70. biogenesis of miRNA 71. functions of miRNA 72. mode of action miRNA 73. non coding RNA and X chromosome silencing 74. RNA induced silencing complex 75. dicer and drosha 76. siRNA 77. design of siRNA 78. Applications of siRNA 79. transcriptome 80. sequencing techniques 81. automated sequencing 82. shot gun sequencing 83. next generation sequencing 84. NGS platforms 85. 454-Pyrosequencing 86. Illumina sequencing 87. Ion semiconductor 88. 3rd GenSequencing 89. helicos 90. Pacbiosequencing 91. Oxford nanopore 92. comparison of NGS methods 93. defining genes 94. finding genes 95. gene prediction 96. gene prediction in prokaryotes 97. gene prediction in eukaryotes 98. GO functional analysis 99. gene network 100. ORF prediction 101. ORF finders 102. TSS prediction 103. splice sites prediction 104. exon prediction 105. genome assembly 106. genome assembly overview 107. genome assembly planning 108. effect of repeats 109. related species assembled 110. greedy graph algo 111. ALLPATHS-LG 112. lander waterman curve 113. assembly pipeline 1 114. assembly pipeline 2 115. quality of assembled genome 116. graphs 117. OLC 118. DBG 119. DBG example 120. assembly issues 121. introduction to proteomics 122. comparative proteomics 123. between proteome comparison 124. proteomics types and techniques 125. characteristics of human proteome 126. why proteomics 127. importance of proteins 128. chemical composition of proteins 129. primary structure of proteins 130. secondary structure of proteins 131. alpha helix 132. b-pleated sheets 133. tertiary structure of proteins 134. quaternary structure of proteins 135. life and death of a protein 136. proteins as modular structures 137. proteins and families 138. overview of analytical proteomics 139. extracting proteins from biological samples 140. protein separations before digestion 141. one dimentional SDS-PAGE 142. two dimentional SDS-PAGE 143. problems of 2D SDS-PAGE 144. isoelectric focusing 145. high performance liquid chromatography 146. protein separations after digestion 147. tandem LC approaches for peptide analysis 148. capillary electrophoresis (CE)