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

zsg

- v& L( |' T8 d5 l( S8 x( ^

) d$ a5 m; k7 T9 E; U# O; xBioinformatics for Omics Data: y: x" w6 U8 c2 q! G$ e9 r

: @6 V, d; e- Z6 {( {+ K7 sMethods and Protocols
' b& a8 m; l- ^3 R$ ]( kSeries: Methods in Molecular Biology, Vol. 719" [+ f7 s' U3 d' m% {+ J2 f( q) i
Mayer, Bernd (Ed.)7 I/ C& I6 z% A& I* K9 S
2011, XII, 584p. 90 illus., 2 illus. in color.
3 f5 L: C) H  FA product of Humana Press' x& n6 X: m5 Z' ]

3 L- i# O3 \% z; o( [' `. K% \# r4 Q
' ]3 O5 d; p5 R% u  Z9 QPart I Omics Bioi nformatics Fundamentals0 T% K2 Z+ `  d) D0 A
1 Omics Technologies, Data and Bioinformatics Principles . .         3' k, z) W* Z% N, |
Maria V. Schneider and Sandra Orchard) j* X4 a+ L4 W" `
2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         314 J  x  j1 _: E% t9 c
Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,6 y5 q, X! b" R8 x/ [" U
John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,% X/ Q4 H3 a2 k2 v( i7 |% w/ @
Christian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,! X' w2 k! L, T5 \
and Catherine A. Ball7 n+ b$ y" |  G
3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         71
! P3 X) {+ q7 B  s+ b7 iArye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,
5 c( w9 c0 N5 Aand Doron Lancet- U! \8 V+ X% l7 X% c6 }
4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97
! m/ f: M" `+ d6 t, _Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de
7 X% [8 A' e/ q& H: M+ s7 kAbreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas( U& e: j1 D2 k- z
5 Statistical Analysis Principles for Omics Data . . . . .         1134 f- k4 j# y4 W9 L2 j
Daniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze! X! c; E8 V# T3 V' i  z/ p, ?4 [
6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         133( [( _' |' }  ]. A- v* O' C
Simon Rogers
4 s, `9 e5 M4 v9 R7 q7 Analysis of Time Course Omics Datasets . . . . . .         153' C# P  T* A6 P) j
Martin G. Grigorov7 K( S9 A4 g5 p+ q6 @: Q
8 The Use and Abuse of -Omes . . . . . . . .         173
! F; i) x. W  {9 h3 H4 E* ASonja J. Prohaska and Peter F. Stadler
# F6 d1 ^! f2 |: l. ePart II Omics Data and Analysis Tracks
& P4 }# p. u6 ^& c/ T9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199
& I9 r; K7 Q) T6 ?Steve Hoffmann- a7 x& J. [  }( A' S
10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         219- Q8 S$ J  ?  U
Yonghong Li, Dov Shiffman, and Rainer Oberbauer
7 {( G# E, ]3 r11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235
2 b  \1 H1 g# N; o) s, q. ^$ oMelissa Warden, Roger Pique-Regi, Antonio Ortega," O' ^4 e* p) _. g! i$ }9 z0 Q
and Shahab Asgharzadeh6 `8 w" ?% t$ X( q' s1 _
12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         2518 ^! O8 s5 `$ D6 N4 ^$ ]
Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier, R5 e- X% r6 V+ A2 t7 n
13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269) k5 M9 {, k" w1 ^
Fátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,+ D2 A  Y3 I' ~1 l2 e" F+ ~
Zlatko Trajanoski, and Hubert Hackl# y5 N6 D; N0 f/ w, ^& c
14 Bioinformatics for RNomics . . . .         299* x$ G7 F8 _- I0 _
Kristin Reiche, Katharina Schutt, Kerstin Boll,0 K+ g' s" v( d
Friedemann Horn, and Jörg Hackermüller
  m+ H2 b  l( Z15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331, w% u4 s4 ~, T
Chris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert% t" t, @+ e# O- |
16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         351/ P. D% a9 E) E; I" a
David P. Enot, Bernd Haas, and Klaus M. Weinberger( J: C9 q) z+ i+ f0 Q
Part III A pp lied Omics Bioi nformatics( N* u& n( x+ X, q! @' b# Q) j3 ]
17 Computational Analysis Workflows for Omics Data Interpretation . .         379
  g* w* G4 w' |4 b8 q; z* GIrmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,
' q$ \# O/ i) b  r. ERaul Fechete, Arno Lukas, and Paul Perco" {; ?8 M% e+ O3 u2 Z
18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399: U, G8 W% t) ]: h" c6 ~4 [
Srinubabu Gedela7 @+ \& W* I9 O- Z! e
19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,0 e7 K+ B! B  S
and Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         415
6 x2 N. e: l' _( Q5 ]0 E/ ^  O. XPaolo Tieri, Alberto de la Fuente, Alberto Termanini,5 C* }8 _7 E  E" w
and Claudio Franceschi
+ q" B& \2 n" j: f4 H( Z  ]; K% {20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435
5 _& g% O& |, }Paola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia, X, e  r; U, z0 x8 l" D! p
21 Omics and Literature Mining . . . . . . . . . . . .         457
0 z/ m6 v! y: i3 J7 YVinod Kumar, f" b" Y' ]( d% w
22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479
5 Y  V, W/ k# V, S, B! SGert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,
4 P4 P. S6 P& U) L; S: j& ]Hiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,
$ U( T' K8 E$ [Martin Haiduk, Peter Rossing, and Rainer Oberbauer" X+ {' u( c$ ?* s& t/ |
23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         499& P$ Q) m: t5 w
Hiroshi Tanaka and Soichi Ogishima
3 E, O) U( {) P( _24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         511, [% d4 i, \" x( u, s/ z1 j
Fan Zhang and Jake Y. Chen
4 k/ c, W4 {9 C5 S25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         527) q  e9 ^% X7 \- S" k, h8 [: ^
Yongliang Yang, S. James Adelstein, and Amin I. Kassis0 M# R4 k$ {0 O! S; G6 z- n
26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         547
1 B. t$ x- ]  Q; H0 `1 yZgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,
' [3 f+ M7 K6 G; CAnatoly Dritschilo, Anna T. Riegel, and Anton Wellstein; w+ X  a6 E# @
Index . . . . . . . . 573: e! f0 ~- Q; `; R1 c) a/ |9 Z

8 x9 W& Z3 y# N' f' e

游客，如果你要查看本帖隐藏内容请回复