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

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. T- E0 X6 {7 \8 k/ ?Bioinformatics for Omics Data( u' j8 c/ P/ v% r
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Methods and Protocols# R8 c1 H2 Y! e5 O6 X& W  ?
Series: Methods in Molecular Biology, Vol. 719, T( u! T0 H% i0 m
Mayer, Bernd (Ed.)
7 L" D: o( Y) ~5 \6 b2011, XII, 584p. 90 illus., 2 illus. in color.& n5 i8 |& z! B2 C. f! Q7 p
A product of Humana Press+ G/ t; j7 ]2 R$ w7 m7 g% H

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Part I Omics Bioi nformatics Fundamentals
4 q7 R& W$ Q  [  o1 Omics Technologies, Data and Bioinformatics Principles . .         3
& I3 r& ^- K5 L& t0 {Maria V. Schneider and Sandra Orchard
% m5 H% P3 B: [0 J8 t& }$ r2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         31
6 ?3 ~( O3 z1 m2 U# j5 hStephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,. F  e0 b" S+ |' I: h2 o8 S6 Z5 Z
John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,
0 _( K! r5 ]5 \, o" qChristian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,
7 w! R4 W" W  N# G( z5 Wand Catherine A. Ball
0 F8 C, @/ T% a1 x3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         718 a4 p' u. w7 v- \
Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,8 g" V. c2 ^6 f9 x" T; T$ B
and Doron Lancet6 s+ ^1 C# Y( i' X9 \$ h
4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97. |, x) s$ Y4 y+ k9 P0 y7 g
Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de
. Y8 U- e7 @- RAbreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas4 H! F4 L  @( w* }
5 Statistical Analysis Principles for Omics Data . . . . .         113! N8 @9 R9 B# u5 p: x
Daniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze1 O8 U% _5 Y" g+ \) S! c+ P
6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         133* v7 ~; m2 B# \# ~9 K/ Z
Simon Rogers
5 A1 i% j! w3 _7 ^, V7 Analysis of Time Course Omics Datasets . . . . . .         153
" b$ J) u* w& y; E* NMartin G. Grigorov9 O! e) M% z4 `' O0 Q; v
8 The Use and Abuse of -Omes . . . . . . . .         173
/ }. i: i, e7 n4 P- @4 S5 vSonja J. Prohaska and Peter F. Stadler8 ^; ^! [# a0 M6 j) O6 S
Part II Omics Data and Analysis Tracks0 N( n5 Q: @$ t' J6 s
9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199. a' a1 G! c, ?9 L, H* l6 x: O) x
Steve Hoffmann
* B8 r2 t. J# e) e8 Z* I, R2 Q10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         219- y9 t; O- A: \1 m6 c
Yonghong Li, Dov Shiffman, and Rainer Oberbauer4 b* f1 v1 {/ K$ W. g1 |6 h6 m
11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         2353 H6 l' B8 U2 [+ s+ c
Melissa Warden, Roger Pique-Regi, Antonio Ortega,
6 P0 d+ Z5 R+ D2 K! oand Shahab Asgharzadeh
! M: f9 z5 W% g" D0 Z, w9 O12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251$ v$ }6 Y/ i; l* y4 h
Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier( i& D; @$ }! ]) f' }) h; ~) }% O3 g
13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269; D  x. m- I2 J5 o
Fátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,
" W# m  Y- Q8 s# f4 a" z) W5 D  XZlatko Trajanoski, and Hubert Hackl; x' a: T" q2 b7 s1 P/ C
14 Bioinformatics for RNomics . . . .         299
7 j' G$ ?/ w: O1 \Kristin Reiche, Katharina Schutt, Kerstin Boll,
( V3 \: N+ ^7 m' P4 ]* DFriedemann Horn, and Jörg Hackermüller$ g  `5 l" x  i: j) V
15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331, J* |- Y, O, q5 h
Chris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert8 A& ^5 ^, @3 @
16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         351
& k* w" V- {& {# i& TDavid P. Enot, Bernd Haas, and Klaus M. Weinberger& u7 `; U4 ?/ Z% a& X5 l4 G( d
Part III A pp lied Omics Bioi nformatics" ~/ Z1 ?/ `6 C$ P+ h
17 Computational Analysis Workflows for Omics Data Interpretation . .         379
, ~4 A8 V* e5 r, z( [/ K" A9 _- e# NIrmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,
, v+ M" R: N6 b* O! c& c5 h  x9 qRaul Fechete, Arno Lukas, and Paul Perco7 G7 j! H0 t, U
18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399
& B' e; g) Z9 Q4 a4 _Srinubabu Gedela
  {" \( W' F- r19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,
* Z# m6 t- M/ B3 gand Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         4153 s- _" r3 X0 ^
Paolo Tieri, Alberto de la Fuente, Alberto Termanini,! k& q: O3 h; |' D
and Claudio Franceschi/ @( f( S) {! n7 q% ~2 f
20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435( W) c* j7 M( e. S- _
Paola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia
* j' a8 M0 x) b+ a" l21 Omics and Literature Mining . . . . . . . . . . . .         457
$ ], r8 U: l9 tVinod Kumar
7 |) Z$ @8 m2 X/ l/ c; p22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479; b3 m$ _# y" {( n
Gert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,0 [% s) T2 v( u! J
Hiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,
4 ~+ ^" D: u2 p9 j3 D+ \Martin Haiduk, Peter Rossing, and Rainer Oberbauer
  `7 t- K0 K2 a% z# U23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         499# p6 \% S- O4 B
Hiroshi Tanaka and Soichi Ogishima
# [" x4 \0 W; H. G7 M24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         511
3 E* F8 h. R% l7 H) h) B' cFan Zhang and Jake Y. Chen
0 w! R/ E5 T0 Y25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         527+ E, v- l0 C- [) E" M8 g
Yongliang Yang, S. James Adelstein, and Amin I. Kassis
8 @# z( T3 ]/ a5 z26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         5474 ^: q  F  \0 o- [
Zgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,
9 A& C1 @+ F) V. X" zAnatoly Dritschilo, Anna T. Riegel, and Anton Wellstein
7 o" ~1 w" \$ |5 QIndex . . . . . . . . 573& u1 g- u) m( L& v8 Q

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