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

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Bioinformatics for Omics Data
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Methods and Protocols
, z! g/ r9 r. k6 [, o' xSeries: Methods in Molecular Biology, Vol. 719
$ u; x1 P5 V! r! z  PMayer, Bernd (Ed.)
: c( r7 }) h# l5 `" a  x2011, XII, 584p. 90 illus., 2 illus. in color.6 ~: n, C( X' v! ~0 j8 r( p/ Y
A product of Humana Press
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2 p! F5 t. r) z* S7 jPart I Omics Bioi nformatics Fundamentals' `( ?# ~+ z9 Q- C* e
1 Omics Technologies, Data and Bioinformatics Principles . .         3
  a' \# _! o6 |/ ^7 gMaria V. Schneider and Sandra Orchard7 T8 n- J+ f' Z# k4 G, p' y! T
2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         31
0 `( Q5 _6 p" \1 _. g3 QStephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,
& A( S6 x5 M& b4 K7 Q, yJohn Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,
* v; c) p# n1 K" qChristian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,
- N0 C2 V  b! v; K$ d6 Hand Catherine A. Ball
4 u- A  R' v3 f8 B3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         714 B6 k; k" M, B  {8 P' S$ E2 D
Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,
8 X7 S. F6 k7 h. ?and Doron Lancet! ~2 F4 I8 h4 f
4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97
7 e! I" g; A0 b3 }) X; S! xMartin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de, Z: m$ P8 Y/ f: F3 O5 x& S
Abreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas
6 X+ L, x- q$ R& I0 J5 Statistical Analysis Principles for Omics Data . . . . .         113! g0 H  H: b* B5 d* R5 U
Daniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze% O, u$ G' C  y1 c
6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         1335 @2 j# M. U0 V; q
Simon Rogers
4 n, H) |  l) t, w) k$ I! q. h3 S7 Analysis of Time Course Omics Datasets . . . . . .         153  h( T! f  h% {* w
Martin G. Grigorov( H. S( H9 b* l. J. {
8 The Use and Abuse of -Omes . . . . . . . .         173" F- f! c+ I5 ]# u% i4 _, y- z
Sonja J. Prohaska and Peter F. Stadler3 V+ L* c; @8 T2 O) v& U5 L& [" W6 P' E
Part II Omics Data and Analysis Tracks8 c# U  ]2 ~, n
9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199
3 ?5 R: ^" q: F  Z/ Q; A. LSteve Hoffmann, {8 D/ p0 q, x$ v" h/ o5 T
10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         2197 c% n8 J" J/ S% @+ B* \0 w
Yonghong Li, Dov Shiffman, and Rainer Oberbauer
5 W, Y/ E  h2 M- s11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235
) h1 }- R+ [% q1 E% d" c) MMelissa Warden, Roger Pique-Regi, Antonio Ortega,
4 B6 E4 Z% }! T7 z8 |0 k; _0 c$ s& Sand Shahab Asgharzadeh
7 r# h/ }9 M3 f! |0 N$ O3 \: ?12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251
5 ]& N# b" i( a7 r% IPierre Cauchy, Touati Benoukraf, and Pierre Ferrier6 c& H9 _, T4 u: D
13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269
3 G2 Q# K: r: U; v4 M4 ^Fátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,7 f: O8 I8 r+ G3 b/ w) I
Zlatko Trajanoski, and Hubert Hackl6 N% O2 a4 C9 F. A8 d! d' A) o1 `; g
14 Bioinformatics for RNomics . . . .         299" P  X4 D# u) K2 h) e$ C$ X( z
Kristin Reiche, Katharina Schutt, Kerstin Boll,
$ {" k, M+ I$ k3 z( t5 JFriedemann Horn, and Jörg Hackermüller6 \2 K; g1 J0 l( J
15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331' `! @6 H9 Y. j& t- e( E+ a
Chris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert: V8 w3 B5 R: ^3 U# B
16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         351
/ U2 @4 x& @; u3 yDavid P. Enot, Bernd Haas, and Klaus M. Weinberger: D: J: T' Z: p4 e: c8 n1 t
Part III A pp lied Omics Bioi nformatics
- o1 t4 W0 E+ E4 [17 Computational Analysis Workflows for Omics Data Interpretation . .         379* C: M* X# E4 \2 o1 w. ?/ q
Irmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,( V; b/ G1 [% Y# r0 q
Raul Fechete, Arno Lukas, and Paul Perco% f' _+ B1 V1 `
18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399
' I/ u- A5 L. }* b6 pSrinubabu Gedela
* E8 b/ I/ V. r; Z/ X# T7 ^" }19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,* ]6 B4 r7 g2 u( R6 O
and Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         415( n4 n& w4 D8 B  H  f5 _- y) p% C. w
Paolo Tieri, Alberto de la Fuente, Alberto Termanini,& O6 e+ m& ]; p
and Claudio Franceschi3 u5 O, t& n1 ~% _+ z+ x! e5 r+ [
20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435
! s; o; S7 s* F- HPaola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia
& V4 ?% O+ i, y" c( K, C) z! P+ n21 Omics and Literature Mining . . . . . . . . . . . .         457. a  o  |, i% p+ u! V* h
Vinod Kumar& P' F, W0 }8 z3 K
22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479+ k9 [4 c$ q1 _1 Y1 ?9 X% z1 {
Gert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,
. Z; M' l. S  jHiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,+ l9 @' Z5 U- u, f
Martin Haiduk, Peter Rossing, and Rainer Oberbauer4 `9 |9 M7 C6 h/ |% x5 u
23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         4995 j  P9 c. T1 c8 N4 A* h( {
Hiroshi Tanaka and Soichi Ogishima! P! P0 i$ J3 n
24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         511* q+ n9 b, h- Z; M
Fan Zhang and Jake Y. Chen0 c( ^( X' B6 U, g4 N$ P( H) v
25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         5270 H6 M* K4 ^2 C) a' D
Yongliang Yang, S. James Adelstein, and Amin I. Kassis! I6 _! U+ R4 H6 j) \  _" D6 j- g
26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         5475 D2 |; k) ^8 E% a- B! ~/ ?
Zgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,+ w0 y( P7 O3 H0 L% o
Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein
8 `; p  B# T+ [. R2 C9 ^' fIndex . . . . . . . . 573+ L: D" e: Z' \! N
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