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& R4 p3 ]0 P. W, E! F7 e9 i
Series: Methods in Molecular Biology, Vol. 7198 R. H% d0 a4 Z/ A
Mayer, Bernd (Ed.)
! N0 H+ @8 N& z4 n; M' |2011, XII, 584p. 90 illus., 2 illus. in color.
8 B7 `' x. N; T; t' T- CA product of Humana Press! h$ c. A0 z" z* T& ~0 C, {% g6 i! v

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Part I Omics Bioi nformatics Fundamentals
/ y: r" C  w5 q: ]0 n0 s1 Omics Technologies, Data and Bioinformatics Principles . .         35 B- Q% e9 \" H4 {7 f$ h6 U& ]
Maria V. Schneider and Sandra Orchard5 c. z' L. R$ i- }( j
2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         310 Z3 Q4 b6 L$ h# }: E
Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,
+ t) }5 }) g5 N/ J6 n/ I$ aJohn Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,( k; K  y) Y+ c5 X8 h- S8 w! T
Christian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,
5 D8 m; Z: f) g* Z* Zand Catherine A. Ball+ j3 _; v( E/ B  A
3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         71. ^9 C- Z2 d+ o- V9 j
Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,) T  f' V- n: Y( `- ]' f
and Doron Lancet
$ M5 q( H' y. F! S% O* q' ?4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97
. `2 _/ r( T9 ?8 \Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de* ?: Q; m* K; w
Abreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas# |7 z# X% K3 [
5 Statistical Analysis Principles for Omics Data . . . . .         113
2 f2 M/ \. R# Z. VDaniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze
  T/ Q  Z, v# C8 X( z6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         133
8 \. r) C. a6 H6 ^Simon Rogers
! L. _. u& V$ L8 u% S. S8 u* P7 Analysis of Time Course Omics Datasets . . . . . .         153: ]2 M# [9 q7 |. A. w3 ~
Martin G. Grigorov
/ j# H$ S: }5 Z' A7 p8 The Use and Abuse of -Omes . . . . . . . .         173
0 J5 V( }6 S# [5 vSonja J. Prohaska and Peter F. Stadler7 I( d1 z8 n0 m" w7 }9 A% p4 y0 t& H& Y
Part II Omics Data and Analysis Tracks( c/ \  \3 s8 b- e' s( k
9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199
8 }, M) x- `0 J& I& M$ k* wSteve Hoffmann
5 N, |0 g; z7 n! k& v10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         219
5 m: y$ H5 v1 B7 VYonghong Li, Dov Shiffman, and Rainer Oberbauer( d4 F! ?5 {1 A2 G
11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235, q) y) `" v6 j
Melissa Warden, Roger Pique-Regi, Antonio Ortega,
; y: Z) P$ H# F; X8 B7 Rand Shahab Asgharzadeh# A2 r+ C1 j" Y# L/ a! U
12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251; [9 J* s( O( I9 O' w3 d
Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier0 P8 k( v: T7 |9 q" e
13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269
" c2 y' n0 }; h2 M+ e: Q' W% DFátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,
  I$ f, _0 ~( x2 _1 V* VZlatko Trajanoski, and Hubert Hackl
6 O$ t* N( z3 ?' U) Q/ ~14 Bioinformatics for RNomics . . . .         299
' L8 B1 {* R  u( y; GKristin Reiche, Katharina Schutt, Kerstin Boll,
9 l, D% d) z( l% |0 \: iFriedemann Horn, and Jörg Hackermüller% a: q0 ^6 R( @' p* _
15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331
  A2 ~* u" I9 L3 T- [# j! QChris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert3 n4 Z% l% ]% S" f7 T8 x
16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         351
) t# \* x4 y. h* ~David P. Enot, Bernd Haas, and Klaus M. Weinberger
8 A% H* y0 t4 A. w5 T0 tPart III A pp lied Omics Bioi nformatics
. ]$ t0 w0 L# }4 ~& w6 o17 Computational Analysis Workflows for Omics Data Interpretation . .         379
* z4 g( Y8 e% U9 sIrmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,1 f' {* s: f  {, b
Raul Fechete, Arno Lukas, and Paul Perco
/ ]& n  Q0 }) O9 D6 o/ E& v18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399
1 C& T  j. c. d* M3 J: c7 D  ^Srinubabu Gedela/ b$ x" s, D  O: p9 \
19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,# u! Q! Q& J! j8 D: }- H
and Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         415
  b! X# ]* f, C  _, NPaolo Tieri, Alberto de la Fuente, Alberto Termanini,- h' P9 m  z* t! [0 P
and Claudio Franceschi) Z# J  a. t* N% M' g4 z) V
20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435
  I* h1 m: d1 VPaola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia
. Q0 r$ e! L. q& D6 a21 Omics and Literature Mining . . . . . . . . . . . .         457) C0 K( }* h( V: n2 }
Vinod Kumar
! X: A4 q/ A1 a4 C) J( h5 _22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479
2 G" W; v2 Q$ Q6 ^: a2 VGert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,# |; y: E' l  m$ m
Hiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,
$ ^, |5 k/ B, m- N& S# S( N6 [% ^Martin Haiduk, Peter Rossing, and Rainer Oberbauer
# g- L# L' c6 N/ `/ H23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         499' ~/ X0 H2 z8 H7 l+ T
Hiroshi Tanaka and Soichi Ogishima
% A; _8 X' y9 [1 M, w$ v24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         511
8 _- D+ p" s- ?7 g1 {5 MFan Zhang and Jake Y. Chen/ U) L- Q3 P* X$ m  E: S
25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         527. Q" N! a5 D- H% @# M
Yongliang Yang, S. James Adelstein, and Amin I. Kassis+ N% C7 r+ S* H6 L- T- d3 U1 t, R& [: @
26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         547+ @: a7 X  v; n2 A" P1 ^
Zgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,( `0 l% n% p5 d1 x% A
Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein
  a  Z, O+ p, e/ d7 _; ?7 UIndex . . . . . . . . 5734 X$ H" A4 h7 f+ P$ v
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