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

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- v$ ~6 R3 v8 j; LBioinformatics for Omics Data2 I: g4 g# a# p! ?  U
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Methods and Protocols
/ `. a, Q* B: Q3 pSeries: Methods in Molecular Biology, Vol. 719
+ [9 q0 r! ^0 s8 T8 {1 A* QMayer, Bernd (Ed.)
& t) ]3 J" X" N. I' \! }% V2011, XII, 584p. 90 illus., 2 illus. in color.) F) b) M, V" S
A product of Humana Press- b! c0 _2 x% l2 ^& R; S/ B

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Part I Omics Bioi nformatics Fundamentals
9 j& |5 n' v$ q- X& G7 w" w) o1 Omics Technologies, Data and Bioinformatics Principles . .         3  L% F' ]2 _  h' W% `, c2 q0 W
Maria V. Schneider and Sandra Orchard
! A; j& k9 o& ^6 R2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         318 {3 m, ~, D* T6 P/ f7 A
Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,7 G" C* H, m& P8 o! I0 p! d
John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,1 A% S; j& J* R) `5 e" X
Christian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,
) E/ [2 F% F9 c6 b- E* }and Catherine A. Ball
' B- B4 g0 ~8 w( ^+ ?; X! [3 h3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         71
) C- \6 B( N' p" K) \9 sArye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,& h" B4 G% y, h7 N& [) b$ F8 \! F
and Doron Lancet) @; m/ l9 @* y' m' N5 }0 F
4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97
; A# I: t% ?( p, P/ g! \Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de
& K" S, z: A" }Abreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas
' T- _* ^- @6 M3 L: `5 u/ y: V6 \5 Statistical Analysis Principles for Omics Data . . . . .         1134 a' X' Y8 N0 P( q0 p
Daniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze
' `4 s5 Q: u$ I# ~* e# p6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         133
$ r( ^0 S* N1 lSimon Rogers( v) n  I% G, D
7 Analysis of Time Course Omics Datasets . . . . . .         1533 O( m% [: d$ c% ~
Martin G. Grigorov/ _* g1 {' K) r7 S2 D; P) Y. a5 G
8 The Use and Abuse of -Omes . . . . . . . .         173
1 Z" B, N# K9 j" f& O. mSonja J. Prohaska and Peter F. Stadler
2 v, q( {7 {2 y3 B9 G4 l) X/ M. JPart II Omics Data and Analysis Tracks
! V) G* e: B8 P  l1 A: {9 b9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199
7 `+ G+ `1 {7 \" n; d( qSteve Hoffmann
( P# }' r% D2 P' n' n! q10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         2195 a' @8 ]6 x3 Q: T
Yonghong Li, Dov Shiffman, and Rainer Oberbauer; s4 I+ `9 u  m  a
11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235* L0 e/ k$ Y. p  U8 Q
Melissa Warden, Roger Pique-Regi, Antonio Ortega,
. u; D+ T5 H) G; B0 J) E" a" Nand Shahab Asgharzadeh
+ [8 p( _* k; w; [1 [12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251
6 J: x  [& ^8 ~- C; ~Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier$ \+ S% i: S: a+ @# ]; I( l8 T
13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269
8 q8 l6 N. r' x* Q# qFátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,
2 ?! G, B) k- R3 D, eZlatko Trajanoski, and Hubert Hackl5 ~+ T8 c; I( R+ N+ r. G4 w
14 Bioinformatics for RNomics . . . .         299
  `- I* X  _' ?* F+ E" KKristin Reiche, Katharina Schutt, Kerstin Boll,
, y% b) r6 [4 n( Q, pFriedemann Horn, and Jörg Hackermüller
6 b0 O9 W7 D- c; U2 E15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331
- V& M7 G) P7 c& |  S' }4 a9 mChris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert
0 O1 \2 O3 T' P( t0 W16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         3511 H" e* a- h$ O. w6 H$ `, p( b
David P. Enot, Bernd Haas, and Klaus M. Weinberger5 t; W+ o/ W: D  L" C# k9 H
Part III A pp lied Omics Bioi nformatics
8 o8 s/ G4 s  p$ O  l( p9 [3 X17 Computational Analysis Workflows for Omics Data Interpretation . .         3795 Z+ c9 ^9 a1 J5 f" P
Irmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,7 {, }+ q- }3 u+ p
Raul Fechete, Arno Lukas, and Paul Perco
  t3 O& I& C7 g. C6 w18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399
. ^" \/ u' F1 C  k+ N, Z5 LSrinubabu Gedela
& H4 P  z' j7 [7 f. E( j19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,% r3 r- s5 t, U/ M0 N" K5 j
and Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         4152 O) H8 E7 F* j8 r
Paolo Tieri, Alberto de la Fuente, Alberto Termanini,
% A1 i. Z) I3 h- a; z/ q# i( P/ hand Claudio Franceschi9 X) c/ U) T% n* s, {" P" `
20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435* ^6 u0 r: [! P' \" l" W
Paola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia
* J" t, r. V+ C3 L8 S. \21 Omics and Literature Mining . . . . . . . . . . . .         457
" ~' z! x8 T, Q# _2 a9 eVinod Kumar
  v; f! r2 m- Z9 U( \, L22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479
" I4 F/ ?& B* j3 d! l) mGert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,5 P6 e6 m9 X, E: V, S) A- N9 C
Hiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,4 d) @* J! y* `0 r0 z& e
Martin Haiduk, Peter Rossing, and Rainer Oberbauer; X# I  }0 a7 t& \+ e
23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         499# s. A! c4 E6 |1 d. I
Hiroshi Tanaka and Soichi Ogishima# k! z* ]9 G9 c+ W  o4 }/ V
24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         511
0 H. d$ t5 l+ r1 y- z7 jFan Zhang and Jake Y. Chen
# a  K1 N1 H. k3 D  |. S0 P25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         527% c6 i# q& c. d: K
Yongliang Yang, S. James Adelstein, and Amin I. Kassis
) Q" Q$ Z' C7 E2 v/ L( j+ B" n26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         547/ D, b$ h0 m6 }0 [4 z
Zgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,$ x3 ^" F' M7 U: S# Q8 P
Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein
( Y& ]8 U' E# Y  _7 \  v1 zIndex . . . . . . . . 573
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