Computational Systems Biology Methods and Protocols.7z

Genome-wide association study (GWAS)............97–106,
394, 395, 397–399, 405
Gini correlation coefficient (GCC)....................... 11, 139
Glioblastoma (GBM)...........................................192, 356

H

Hidden Markov model (HMM) ........................196, 236,
243, 360, 401
High-throughput sequencing (HTS).........................2–4,
15, 30–42, 194, 404
Human Metabolites Database (HMDB)....................112,
113, 266, 279, 284

I

Ictidomys tridecemlineatus.............................................. 31
Integrated Clustering of Multidimensional
biomedical data (ICM)............................124, 125
Integrative analysis..............................................109–117,
119–127

K

K-nearest neighbor (kNN).................................249, 250,
252, 255, 258
Kyoto Encyclopedia of Genes and Genomes
(KEGG)...................................................9, 17, 24,
112, 113, 120, 150, 158, 177, 283, 284

L

Leave-one-out cross-validation (LOOCV).................215,
229, 230
Linear discriminant analysis (LDA).............................122,
123, 321, 346
Local lazy learning (LLL).............................................251
Local lazy regression (LLR).........................................251
Local tangent space alignment (LTSA) ..............122, 123
Long noncoding RNAs (lncRNAs)............................113,
206, 209–211, 213–215, 217, 218, 313
Long-range library capture hybridization
(LR-LCH) .................................32, 34, 38, 40, 42
Long-range polymerase chain reaction
(LR-PCR)..................................32, 33, 35, 36, 38

M

Machine learning.......................................... 86,111, 122,
183–194, 196–198, 211, 215, 224–228, 230,
231, 243, 247–259
Magnetic resonance (NMR)........................................197,
266, 272, 274, 275, 277–279, 281, 284
Matthew’s correlation coefficient (MCC)..................230,
242, 244
Messenger RNA (mRNA) .......................................15–17,
26, 45, 48, 109, 116–120, 123, 156, 172, 189,
191, 193, 210, 217, 312, 334, 353, 354, 402

MicroRNA (miRNA)......................................15, 45,113,

117–120, 123, 191, 205, 210, 213

Microscopic observation drug susceptibility

(MODS).............................................................377

Minimal residual disease (MRD)............................ 47, 68,

390, 398

Mitochondrial DNA (mtDNA).............................. 32, 33,

38, 313

Mitochondrial genome (mitogenome).........................32,

33, 35, 38–40, 314, 317, 319

Modified multiple annealing and looping-based

amplification cycles (MALBAC).......................334

Molecular Evolutionary Genetics Analysis

(MEGA)............................................................... 11

Mutated allele frequency (MAF)...................................72,

81, 91, 92, 102

Mutual information (MI)....................................139, 148

Mycobacterium tuberculosis(MTB).............................375,

377, 379, 380

N

Naive Bayes (NB)................................................185, 187,

191, 211, 252, 255, 258

Non-coding RNA (ncRNA)..........................................15,

205–211, 213–215, 217, 218, 313, 315

O

O-linkedN-acetylglucosamine

(O-GlcNAc)..............................................235–244

Online Mendelian Inheritance in Man

(OMIM)....................................................207, 208

Operational taxonomy units (OTUs)..........................194

P

Partial order optimum likelihood (POOL).................190

Phage lambda............................................................31, 42

Piwi-interacting RNA (piRNA)...........................205, 210

Post-bisulfite adaptor tagging (PBAT)........................333

Precision (PR).....................................................111, 125,

190, 196, 230, 231, 252, 312, 404

Precision-recall (PR).....................................................231

Principal component analysis (PCA)...........................116,

169, 171, 176, 178, 258, 282, 316, 320, 321,

324, 349, 352, 356

Protein-protein interactions (PPIs).............................113,

119, 155, 191

Pseudomonas fluorescens................................................... 30

Q

Quality control (QC)....................................................... 6,

15–17, 19, 70, 72, 73, 76, 77, 86, 87, 99, 102,

103, 107, 121, 277, 280, 282, 312, 314, 324,

335, 336, 339, 352, 359, 395

Quantitative PCR (qPCR)...................................333, 398

416
COMPUTATIONALSYSTEMSBIOLOGY:METHODS ANDPROTOCOLS
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