Survey of Computations in Biological problems

tastelesscowcreekBiotechnology

Oct 4, 2013 (3 years and 8 months ago)

66 views

Components of a Cell (Eukaryotes)

Picture from
on
-
line biology book,

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html

~70% water

4% small molecules

15
-
20% proteins

2
-
7% DNA/RNA

4
-
7% membrane

Biological databases


Data explosion


-

96 new 83 updates
of well established databases in
2011


-

exponential growth of the quantity, complexity and
diversity of biological
data

Protein Data Bank (www.pdb.org)


-

An example of a neuron database

How to minimize the
representation?




Earlier individual research oriented databases vs. large
scale industrial like databases



Biological databases




Primary Databases :


-

nucleic acid sequences including whole genomes


-

amino acid sequences of proteins


-

protein and nucleic acid structures


-

small molecule crystal structures


-

protein functions


-

expression of genes


-

networks: of metabolic pathways, of gene and protein
interactions, of control cascades


-

publications




Specialized Databases



Computations in Proteomics


Introduction

to MS



Newer Techniques


Mass spectrometry (MS)


-

large scale of study of proteins


-

anytime, any cells





Determination of the content in a complex of
proteins


Determination of protein
-
protein interactions



Computations in Proteomics


Enright et al., Nature 402 p86
-
90



Protein
-
protein interactions


-

Use genomic sequences


fusion event detection through computation





Modeling
gene regulatory network


-

nodes: genes/proteins


-

edges: biological events


-

inputs: proteins (eg. transcription factors)


-

outputs: gene expression




Microarry Data



Microarray

technology


Microarray gene expression databases


(
eg
.
GEO

GSE17913), interested in co
-
expression of genes, relationship of genes,


system biology
, pathways



PubMed

literature databases



Extract the knowledge from literatures, text mining

Literature Data

Computations in 3D images


Imaging techniques


-

Magnetic Resonance Images (MRI)


good tissue contrast,
tumor detection, 2003 Nobel Price (
Paul
Lauterbur
,
Sir Peter
Mansfield
)



-

CT


-

Electron tomography (
eg
.
portal proteins
)




3D Volumetric data


-

pattern recognition
, registration, classification, image
retrieval, image data mining



Helix Tracer

Helix
,
density map

Helix
,
true structure

Protein 1BM1

Del Palu, A., He. J., Pontelli, E., Lu, Y. “Identification of

-
helices from Low Resolution Protein Density Map”
Proceedings of
Computational Systems Bioinformatics (CSB) 2006
, p89
-
98, Stanford University, Aug. 2006.