PDF电子书：Bioinformatics for Omics Data. Methods and Protocols (Humana Press, 2

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Bioinformatics for Omics Data6 T0 m3 j  B/ G, ~" i! V

0 @  L/ Q: ^  S& x; \( e' eMethods and Protocols
1 O' S# Z- w) ?" }Series: Methods in Molecular Biology, Vol. 719
- t) M' P2 W  J5 E0 A9 E9 e6 B  YMayer, Bernd (Ed.)5 C3 Q" v( [. f- B& @( @7 f. H, ~
2011, XII, 584p. 90 illus., 2 illus. in color.! \1 E. ~! X5 B, g! }& T* a4 U
A product of Humana Press) S, F& v2 n, A: w' i# h! c) U- e: a

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/ h+ }& U" ~  C; R/ ?2 ~5 pPart I Omics Bioi nformatics Fundamentals0 I& V* L6 z1 f2 r
1 Omics Technologies, Data and Bioinformatics Principles . .         3/ x: _0 N, R' c* u
Maria V. Schneider and Sandra Orchard
0 A. R2 m" r  \3 W3 o) i2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         31* X/ Z6 d; b  `9 N  \* ~# G
Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,8 k7 v; v. I* \2 t
John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,
, o9 l0 |/ J  a- w2 E+ U* eChristian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,7 P) P* X6 U- e. n) T8 C
and Catherine A. Ball3 Y# @5 D( G1 L' J' `7 N" Z
3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         714 f) b4 T( Z+ U2 ]: I; W
Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran," M2 j( Z4 q3 A1 g* t2 U2 N
and Doron Lancet' M  u4 M+ E1 J# w5 c5 D5 e
4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97& r* T) Y. N. ~( \% A' b
Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de
" o; P0 Z. C+ QAbreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas
/ l! O* |4 c/ r. {5 Statistical Analysis Principles for Omics Data . . . . .         1134 }% u8 Z) I& M/ t6 U1 L5 {4 y" I
Daniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze% [7 a; T% j2 L5 p; x4 Q$ E' |
6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         133. A/ F/ J% j3 [- i
Simon Rogers
+ o/ p) s. e8 n/ Z9 W) F2 @" C$ w7 Analysis of Time Course Omics Datasets . . . . . .         153
# K9 j* N( b. A2 e' lMartin G. Grigorov9 y  e8 T$ x& V8 R- r% X& g
8 The Use and Abuse of -Omes . . . . . . . .         173
9 C* C8 X- X, uSonja J. Prohaska and Peter F. Stadler7 l1 `2 j( e: Y+ ~, s$ O
Part II Omics Data and Analysis Tracks
' B- B4 `2 W0 V2 c% ?4 m; r9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199$ A; g5 h" B& r
Steve Hoffmann2 j# ^* c4 B8 @2 b
10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         219# _% l, W  M5 X% y& D
Yonghong Li, Dov Shiffman, and Rainer Oberbauer
# A3 ]! M$ p* j$ O  [11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235
# F+ {" V/ {8 Z9 Q3 J! ~8 n  [Melissa Warden, Roger Pique-Regi, Antonio Ortega,
4 p9 I5 B* Z  K/ vand Shahab Asgharzadeh7 w1 c5 s3 H9 c
12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251  }3 u+ U* q6 m0 _  U) B$ N; C7 `
Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier
4 |/ P( n3 M, k; G' d1 e, k1 U1 c13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         2698 [5 E. z0 P( `: ?, s
Fátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,- e# x+ ~1 @, S# i  G
Zlatko Trajanoski, and Hubert Hackl" J& T9 \- J& p1 c
14 Bioinformatics for RNomics . . . .         299: Z2 X; M% x9 ^4 B. i  L
Kristin Reiche, Katharina Schutt, Kerstin Boll,
/ N6 z$ u3 s, `$ y+ N+ v7 p8 SFriedemann Horn, and Jörg Hackermüller5 E, O$ S- @% W3 O9 N( t
15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331
' F9 r9 V7 N2 X) Y/ }Chris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert
* [, J! _& a7 o5 v$ q16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         351! w; }& ^! e0 i2 F7 @, e
David P. Enot, Bernd Haas, and Klaus M. Weinberger
8 q3 K( B) J, G  W' v! RPart III A pp lied Omics Bioi nformatics+ Z, d' F  W. }; X
17 Computational Analysis Workflows for Omics Data Interpretation . .         3798 G% ~. y- y5 E: V
Irmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,
* C& c9 ~! F" H( k$ A6 TRaul Fechete, Arno Lukas, and Paul Perco6 z# z0 v% Z" p& r9 O1 o9 X
18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399. g$ E) A9 K: [, O8 h3 `
Srinubabu Gedela
+ k9 c9 z( V& Q% t* t- i6 {19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,9 {$ n9 B/ z( y' s7 y) p% P
and Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         415
" Q: D) n1 t6 }* C. sPaolo Tieri, Alberto de la Fuente, Alberto Termanini,& `5 ^; U1 Y$ J! j! ^
and Claudio Franceschi- N4 c7 W7 X! F- S' T# W( r
20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435
: W" H2 u* r" s$ j! i# RPaola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia
+ _+ k- e  T9 I& q( l1 g) f21 Omics and Literature Mining . . . . . . . . . . . .         457& h5 J0 o% J' k% _$ R! G$ g% M
Vinod Kumar
. n6 ]5 f5 J1 n% F22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479
2 @3 f* C7 F( c& K* P' rGert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,
. v( Y4 w' H/ b8 ZHiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,1 Z  Y" |  D& c- H
Martin Haiduk, Peter Rossing, and Rainer Oberbauer, \3 T+ ~2 O2 N6 B
23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         4990 d* P9 b: N' D4 {1 ?2 E9 }4 ]
Hiroshi Tanaka and Soichi Ogishima" i1 r% A5 w3 s" N" S) s* F
24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         511' J4 w4 ~6 I3 O6 O; ^1 m
Fan Zhang and Jake Y. Chen# H, d- V4 x2 s1 f5 K) M
25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         527
. d$ b+ n+ F# x. X4 }2 F2 uYongliang Yang, S. James Adelstein, and Amin I. Kassis
' V& z# r$ q$ L' W: J26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         547
, P, B  U, `8 i& V, D6 Y, WZgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,2 ]6 ?2 [& r0 I2 r/ }
Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein/ ?& y8 N/ J. j& i/ H( m5 f' M
Index . . . . . . . . 573
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