Bioinformatics

BYM1201 Introduction to Bioengineering

Alper Yılmaz
November 30th & December 4th 2020, YTU Bioengineering
About me

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Table of Contents
Bioinformatics in general
Next-Generation Sequencing (NGS)
Deep Learning / Machine Learning
Virtual Screening / Drug Discovery

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Bioinformatics / Computational Biology
combines biology, computer science, mathematics and statistics
analysis and interpretation of biological data
in vitro, in vivo, in silico
studies (not a complete list):
sequence analysis (from genes to whole genomes, mutations),
transcriptomics (gene expresssion), structural biology (3D), microscopy and
image analysis, network and systems biology, literature analysis
generates tools/softwares, databases
can be performed via web services or software running locally

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Too much data

As experimental devices advance, amount of data generated per experiment is

increasing by time.
Genome Browsers help understand data by overlaying results on genomic
coordinates
Experimental output or computation results can be viewed along with overlapping
gene region.

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BRCA1 gene location at UCSC Genome Browser 6 / 18
Next-Generation Sequencing

Sequencing more than 100 million short sequences simultaneously. Short

sequences can originate from genome or mRNA.

If genome: assemble the short sequences to discover new genome or compare

with known genome to identify mutations
If mRNA: convert to cDNA and then sequence it. Shows expression level of all
the genes

May be combined with various experimental techniques so that results with one
base-pair resolution is achieved. Please visit For All You Seq posters by Illumina for
DNA, RNA and single cell sequencing.
Recently, single-cell sequencing is used for very detailed analysis of samples. 7 / 18
In following slides, NGS is summarized:

Amplify DNA on glass slide

Sequence one nucleotide at a time with separate orescent color for each
nucleotide (A,G,T,C)
After each step, shine laser on samples and determine current nucleotide at that
sequencing step
When images are overlaid, the sequence of each sample (represented as dot) is
revealed.

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Metzker, M. Sequencing technologies — the next generation. Nat Rev Genet 11, 31–46 (2010). https://doi.org/10.1038/nrg2626 9 / 18
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Deep Learning
Deep learning is subset of machine learning (arti cial intelligence) where neural
networks are used to extract high-level information from raw input.
Compared to Machine Learning, there's little or no need to extract features
manually.

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Special layers, convolutional layers, can be used to process, classify or interpret
images. These layers can extract and utilize image features such as edges, corners,
borders in images.

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Various layers in Deep Learning

MLP: Multilayer Perceptron, traditional arti cial neural networks

CNN: Convolutional Neural Network, used for processing image or other 2D data
RNN: Recurrent Neural Network, used for processing sequential data (time
series, language, DNA sequence, etc.)
Combination of any

And can be applied to different elds of science. There are many studies using
Deep Learning in biological context.

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Chemoinformatics and drug discovery Here's an extensive list
Biomarker discovery online.
Proteomics
Metabolomics
Genomics
Variant calling
Gene expression
Predicting enhancers and regulatory regions
Non-coding RNA
Methylation
Single-cell applications
Systems biology
Neuroscience

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Virtual Screening

is a computational technique used in drug discovery to search libraries of small

molecules in order to identify those structures which are most likely to bind to a
drug target, typically a protein receptor or enzyme.

Due to advancements in computation (both hardware and software) number of

small molecules to screen can reach billions per screening.

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Saving time and cost
Test millions of chemicals
for binding to target
protein, virtually
Filter candidates for
chemical properties
(toxicity, activity, etc.)
Final candidate molecules
can be tested
experimentally

Surabhi, Surabhi & Singh, BK. (2018). COMPUTER AIDED DRUG DESIGN: AN OVERVIEW. Journal of Drug Delivery and Therapeutics. 8. 504-509.
10.22270/jddt.v8i5.1894. 17 / 18
Requirements

You don't need to know programming as much as a software developer (unless

you're interested in writing bioinformatics softwares). There are many web-based
services which assist in biological data preparation, analysis, manipulation.

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