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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5 f' Z! B, H7 L  {$ f/ [. PMethods and Protocols& I+ E( d3 W) s
Series: Methods in Molecular Biology, Vol. 719
% `4 C. p3 l3 r6 u* J7 S8 b5 pMayer, Bernd (Ed.)7 L1 C* K. ^& K& H8 i& ?4 M
2011, XII, 584p. 90 illus., 2 illus. in color.9 i! Q1 q2 T  u# q+ G7 G, H9 l, h3 p
A product of Humana Press6 D4 V: O$ n2 v3 i3 |+ J4 T
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Part I Omics Bioi nformatics Fundamentals
, F( b' Y$ ]5 u4 T4 d" Q1 Omics Technologies, Data and Bioinformatics Principles . .         38 Y3 M9 d' ?4 f. w
Maria V. Schneider and Sandra Orchard
. h# |1 A) w& e  q% b0 y, Z0 _7 U2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         31
. j" k1 D+ f8 fStephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,
7 F9 ^9 N! J7 QJohn Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,% Y& f; q" Q5 t& w5 z5 F
Christian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,! T/ ~- S8 G! a  ?
and Catherine A. Ball4 Q1 S( V. f1 n6 l9 h% @( b
3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         71
7 z. G$ L  Y& j7 rArye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,
" G, Q5 g1 K2 B" ~" pand Doron Lancet( I- t- X% E* I) ~" i4 B* d3 }" h. V
4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97% _, i5 s6 \/ b# w$ }. f7 Z
Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de
" T1 B; F# k# b: pAbreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas
% Z5 L) L, _; g5 Statistical Analysis Principles for Omics Data . . . . .         113
4 G% [$ o8 e& MDaniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze4 ]' y% F# x9 \: l/ S+ l8 g
6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         1338 L: y/ Q0 q: C& Q( T9 I& c
Simon Rogers
, ^( }( q/ |. g: P' b& j' Y5 w% ~7 Analysis of Time Course Omics Datasets . . . . . .         153
8 e( }# [0 M2 s% @" N  JMartin G. Grigorov
. J8 F& p, b) a+ H/ l( G4 q8 The Use and Abuse of -Omes . . . . . . . .         173+ o0 {# y! V7 v8 I2 z
Sonja J. Prohaska and Peter F. Stadler
# W( ^3 d; k* Q; IPart II Omics Data and Analysis Tracks
7 h: R" R7 C4 Z; ?9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199
) G/ P& Z7 a0 j- F4 MSteve Hoffmann
, {* ~; I/ [! D5 o10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         219' }4 a) q) r( O" J
Yonghong Li, Dov Shiffman, and Rainer Oberbauer2 `. U) |$ J- h9 o0 K; \6 v
11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235
6 Z' y$ R1 b2 n; uMelissa Warden, Roger Pique-Regi, Antonio Ortega,+ s8 H- b9 Y+ r% c: V6 U) K
and Shahab Asgharzadeh
! a$ q( {; W" Q4 i/ E3 e12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251/ n# @  Y6 F' A, d! N
Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier2 V/ l7 v7 H& @8 Y# m( X
13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269$ m3 l9 a; n# @+ @$ a$ g6 K
Fátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,( w4 M( z. a$ w- X: x! @
Zlatko Trajanoski, and Hubert Hackl
$ a. {& o; E( h" N6 k4 c6 F6 Q8 K" G14 Bioinformatics for RNomics . . . .         2999 Y# N' R: s" G
Kristin Reiche, Katharina Schutt, Kerstin Boll,
8 B" }$ G& ]/ m7 s* dFriedemann Horn, and Jörg Hackermüller
0 D0 V" B4 K) |: g! y7 p5 c/ O* B! ?15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331
* U$ \5 v2 f% m0 ]# u0 O, KChris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert1 ?7 s! z* [. a9 v; A* K
16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         351  @9 v. J4 ?$ P7 B% y8 o* O; T- P
David P. Enot, Bernd Haas, and Klaus M. Weinberger0 Q% x9 ]" t5 q' d6 f  a3 ~9 u% x
Part III A pp lied Omics Bioi nformatics
" L* F( Z9 _# n; a17 Computational Analysis Workflows for Omics Data Interpretation . .         379
9 q* Q1 [. N' l' E. ?Irmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,7 V; `3 W2 q4 b8 B" n  `9 R
Raul Fechete, Arno Lukas, and Paul Perco# D% z' o6 h: Y) @. d/ j' ?, j
18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399
$ M9 u. j7 ]9 B9 ^Srinubabu Gedela
0 v) {+ W* C1 o5 E* @$ q- p19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,
( b' L: \- _' C5 B/ F8 Nand Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         415
5 t! U- B# ]% |) q* }/ J3 R# @Paolo Tieri, Alberto de la Fuente, Alberto Termanini,
8 I8 R& p5 j2 O% k+ P: s8 W" ?; r# land Claudio Franceschi
* C4 E9 y! g2 l. j6 P20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435& i% G2 Y% h, j) w6 X8 M
Paola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia1 f6 S8 U, @6 P- P  G$ P
21 Omics and Literature Mining . . . . . . . . . . . .         457
1 g5 b: R# A* _: Z+ h9 r# uVinod Kumar
  |& {% e! p( q$ M8 E22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479: a& c$ u5 Q; h( i6 L4 C8 Z- T1 D
Gert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,
, ^' I0 B- c7 K$ r0 t! gHiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,3 n' U: b6 {8 d# }
Martin Haiduk, Peter Rossing, and Rainer Oberbauer6 @1 j" @: q1 Q5 U' z6 Q
23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         499
7 ]: h  b2 A; r) {4 X' FHiroshi Tanaka and Soichi Ogishima1 ?& \" X, h6 e
24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         5112 Q' \" P' C+ q! z/ p! A# P
Fan Zhang and Jake Y. Chen  J! i3 N$ m% u- u  S0 L
25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         527! L& w. U3 b; Q0 e
Yongliang Yang, S. James Adelstein, and Amin I. Kassis
& M5 @. V2 Y1 Y4 @" B, y/ H% Y26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         547" \: Q4 O  D- c' ?/ V# x! o' @
Zgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,- c  e. c8 i7 _/ o) P
Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein
6 Q/ J$ n, u( ~Index . . . . . . . . 573
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