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Genetics for Immunology

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Ryo Yamada

on 19 January 2017

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Transcript of Genetics for Immunology


Genetics
for
Immune System

Ryo Yamada
Statistical Genetics
Kyoto Univ
2016/11/11 @ Yokohama, RIKEN
Genetics
Heterogeneous
多様
Stochastic
確率的
Discrete
離散的
Population/Swarm
集団/群衆
Immune System
Heterogeneous
多様
Stochastic
確率的
Discrete
離散的
Population/Swarm
集団/群衆
組合せか順列か
組み合わせなら、self-avoiding path
軌道重視なら、「ぶつかって」すり抜ける~ソリトン、波~か
順列なら
「歴史はべき乗則でつくられる」
群衆知
Slime mold is clever enough to find the shortest route in the labyrinth.
Its strategy is being investigated as a new model of parallel computing system.


Food

DNA molecules
4 letters, {A,T,G,C}
L=3 x 109 in length (Homo sapience)

Sequence variations
4L; L=1,2,…

Biological space is a part of physico-chemical space.

Environmental fluctuations change width of pathways in biological space

Recombination is three-term relation.
But graph is for two-term relation.
A more informational tool is necessary.

Graph distance between sequences is No. mutations.
Recombination’s distance?

Letters are changed : Mutation
Combination of letters are changed : Recombination

制限のあるランダム・ウォーク
Restricted random walk
Self-avoiding walk
くりこみ群
Renormalization group analysis
巨視と微視を大雑把に分ける
Grossly discriminate macro and micro phenomena
二重結合・1重結合の交互酔歩でSelf-avoiding path
探索
スイッチで切り替える
遺伝子発現状態

ほとんどすべての人で同じ走行の部分とそうでない部分と
構造上の分岐:ものの分岐

機能上の分岐:ことの分岐
単純なルール
枝分かれ
L-system
http://demonstrations.wolfram.com/GrowthModelForTheBlueGreenAlgaAnabaenaCatenula/
嗅覚遺伝子の配列多様化にL-system
鳥の囀りも?
> songs2
[[1]]
[1] "ピ"

[[2]]
[1] "ピピチ"

[[3]]
[1] "ピピチピピチチピ "

[[4]]
[1] "ピピチピピチチピ ピピチピピチチピ チピ ピピチ "

[[5]]
[1] "ピピチピピチチピ ピピチピピチチピ チピ ピピチ ピピチピピチチピ ピピチピピチチピ チピ ピピチ チピ ピピチ ピピチピピチチピ "
Epigenetic modifications
Next Generation Seq
Network
Transcripts,Proteins
Factors shared by
multiple disease phenotypes
Diseases and
their phenoypes
DNS seq
Genetic heterogeneity
vs.
All other heterogeneity
Phenotype heterogeneity
線形代数
Rectangle ~ Matrix
長方形~行列
個体の時空間
両親

機能的体細胞変異
体細胞モザイク
生殖細胞系列
受精卵
Phenotype(s)
When?
Where?
{0,1}
Phenotype of Individual
個体のフェノタイプ
Cancer's
pathological
type
癌の組織型
Cancer's
Transcriptome
癌トランスクリプトーム
Periph. Blood
Transcriptome
末梢血
トランスクリプトーム
https://scientificbsides.wordpress.com/2014/06/09/inferring-tumour-evolution-2-comparison-to-classical-phylogenetics/
Cancer Phylogeny 癌系統樹
https://scientificbsides.wordpress.com/2014/06/09/inferring-tumour-evolution-2-comparison-to-classical-phylogenetics/
Analogy of evolutional genetics
進化遺伝学のアナロジー
Periph. Blood
a biomarker conc.
末梢血
バイオマーカー濃度
Quantitative
量的
Stochastic process
確率過程
Discrete
離散的
http://slideplayer.com/slide/4897898/
https://blog.uvm.edu/cgoodnig/page/9/
Evolution Genetics
Population Genetics
進化遺伝学
集団遺伝学

Thermodynamics with some discreteness
熱力学に
若干の離散性

Extinction is due to discreteness
絶滅は離散性があってこそ
http://nptel.ac.in/courses/105103026/module5/lec40/5.html
Smooth
滑らか
Almost ZERO but NOT ZERO
ほぼゼロだがゼロではない
Genetic drift
Extinction of allele
Intra-species genetic heterogeneity
遺伝的浮動
アレルの「絶滅」
種内遺伝的多様性
Finiteness of population size
Discreteness
集団サイズの有限性
離散性
Population studies
http://blogs.discovermagazine.com/gnxp/2011/02/health-care-costs-and-ancestry/
Heterogeneity
We care space
空間はどうか
Spaces for Immune Cells
https://en.wikipedia.org/wiki/Genealogical_DNA_test
http://www.open.edu/openlearnworks/mod/oucontent/view.php?id=105&extra=thumbnail_idm17613792
Wikimedia commons
Events in the human world
http://www.thepeoplesvoice.org/TPV3/Voices.php/2013/09/06/target-is-still-iran-clear-cutting-the-m
http://rnspeak.com/medical-and-surgical-nursing/systemic-lupus-erythematosus-sle/
Events in the immune world
Genetic Epidemiology
遺伝疫学

Genotype, Genome
Phenotype
Multi-layered
Single (Immune) Cell Studies
Single Cell-
-Genome
-Epigenome
-Transcriptome
...
Single Cell
Individual Phenotype
Individual phenotype
個人フェノタイプ
Disease
Hight,Weight
...
-Epigenome
-Transcriptome
...
Shape
Motion
Population genetics
集団遺伝学

CREST
1-cell analysis
M. Ishii (Osaka-Univ)
H. Matsuda (Osaka-Univ)
K. Mimura (Hiroshima City Univ)
http://journal.frontiersin.org/article/10.3389/fpsyt.2011.00017/full
{0,1}
N
Information Decomposition on Structured Space
M. Sugiyama
Combination
Discrete data structure
CREST (K. Tsuda Univ. of Tokyo)
Discrete Data Structure Statistics
離散データ構造統計学
Switchs of Expression
Topological approach
位相的アプローチ
Geometry
幾何
CREST 研究員募集中です
You have an access to the slides today @ our facebook site.
NGS
Network
Disease phenotypes
Subtypes
DNA
Epigenomic changes
Variants
Summary...
Full transcript