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

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/ L& W! n% Q$ @2 EBioinformatics for Omics Data
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' h" Y% t* J* g- w' L- \Methods and Protocols: v- h: {2 e7 L3 i
Series: Methods in Molecular Biology, Vol. 719
" }; I# {* N& W/ r6 lMayer, Bernd (Ed.)5 |3 b, ]! ]2 `
2011, XII, 584p. 90 illus., 2 illus. in color.7 W2 `. s3 J& R' [% D0 \: a
A product of Humana Press
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Part I Omics Bioi nformatics Fundamentals
0 R" u5 s+ H% {1 Omics Technologies, Data and Bioinformatics Principles . .         3
0 N3 ?: l& F  O( g! V; t, l$ rMaria V. Schneider and Sandra Orchard! K" x9 p( m2 a9 ~; i! y
2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         313 @* o/ ]' M0 f. ?% ?. ~7 x
Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,
2 b; `$ {4 C0 u" J& `/ A5 r( Y: A* r7 ]John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,# L& }+ f! a7 P( [* p
Christian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,' Q5 e5 g, h. X0 n3 i* A
and Catherine A. Ball
/ w- R& B& D; l$ b* q- m3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         71
- c4 f5 W  x5 z2 n; n. n# b. |. @- OArye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,
; f3 A5 v& }. i9 H4 ~and Doron Lancet4 `2 a$ ]/ l/ g2 b2 q, _
4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97# r0 G* v& H# L3 k, ?
Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de/ f: ?, v; F" _
Abreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas" q4 W  |6 r+ j0 g5 [* d1 e- O/ K$ b2 x0 r! |
5 Statistical Analysis Principles for Omics Data . . . . .         113
- i& ~/ X1 G( V; CDaniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze
. g- s* y7 ^/ P9 T6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         133& j9 d+ A2 m$ R6 b- Z
Simon Rogers7 ?5 e2 F8 h6 r  @7 ^4 d, m+ b
7 Analysis of Time Course Omics Datasets . . . . . .         153
+ O+ x+ v) d2 D3 @3 XMartin G. Grigorov
) V& C: N9 K) E1 W* \4 I8 The Use and Abuse of -Omes . . . . . . . .         1731 z7 W: |+ k1 _* w; d1 h
Sonja J. Prohaska and Peter F. Stadler* |7 v- q/ o6 N* u8 g! Y
Part II Omics Data and Analysis Tracks# U4 q5 S4 @' ]- |8 @
9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199  Z! G1 m5 ?# o& }+ A' g' G
Steve Hoffmann
; g! t0 l9 ~  p7 x10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         2196 g3 E+ c6 t9 f9 ~! a  H
Yonghong Li, Dov Shiffman, and Rainer Oberbauer  o- F5 g# z- q, k) V
11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235/ o7 n$ b5 ^! a/ x/ g* i
Melissa Warden, Roger Pique-Regi, Antonio Ortega,
( n$ v- ?5 R) }: z* \and Shahab Asgharzadeh, f7 v" H0 v" I2 |1 s
12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251
5 s+ I8 r  k, E; i) q: Q6 t4 zPierre Cauchy, Touati Benoukraf, and Pierre Ferrier
8 a6 Q3 ~- C+ w13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269
8 b0 j" I# w' x* KFátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,( \# i: Q) A  n  Y$ c5 T% D
Zlatko Trajanoski, and Hubert Hackl
1 k! R6 O! ~, P1 v, i14 Bioinformatics for RNomics . . . .         299
7 a) G! U6 x+ D1 v8 J" V. GKristin Reiche, Katharina Schutt, Kerstin Boll,  z0 t& G9 |; B
Friedemann Horn, and Jörg Hackermüller
# ]' Q% Q7 X7 c2 Y2 W15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331
  {9 f8 T5 S/ ?/ Q* e6 |  FChris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert
$ Y/ {8 B! ?" ]; A) C' `16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         351
  O  \. O" Y4 h; _7 w- |. E* DDavid P. Enot, Bernd Haas, and Klaus M. Weinberger  k" S8 Y' u! V+ z, }
Part III A pp lied Omics Bioi nformatics
2 S5 B" M) b# L5 _% l: I; K17 Computational Analysis Workflows for Omics Data Interpretation . .         379
' S( l: h" T( i/ J6 GIrmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,
" n* r8 I# N1 s, dRaul Fechete, Arno Lukas, and Paul Perco# ^9 `# I8 w+ Y9 p0 n  E
18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399, S$ k8 g9 g, H+ K% k6 i' m
Srinubabu Gedela  F/ T  D8 M6 F- r5 m
19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,
5 q* L, ~9 V6 Y9 Fand Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         415, ^1 b# ~) ~1 |- t$ h
Paolo Tieri, Alberto de la Fuente, Alberto Termanini,
( F) ?6 R, _* G( x# x- W6 Uand Claudio Franceschi1 l% I, m+ G2 X
20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435. E8 f' e* F/ B( q9 q
Paola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia
- i5 }, S) S( w& ~21 Omics and Literature Mining . . . . . . . . . . . .         457
% p6 o* i% G. w& rVinod Kumar, G3 C" `  x4 b/ A4 ~( [! V5 \
22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479
: i7 j, ?8 w; O( k* qGert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,
7 A6 Z4 y. N. n! |8 @Hiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,) [: z5 X6 D$ X2 o6 J
Martin Haiduk, Peter Rossing, and Rainer Oberbauer
* p8 v. T6 B  M( M( _! q2 g% W23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         499
$ c1 |2 J; t9 V1 f3 x. W: kHiroshi Tanaka and Soichi Ogishima
7 ^- K) P% Y% s24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         511
- H' W6 P% L4 e  v, s  Q$ `Fan Zhang and Jake Y. Chen
6 ?$ M, V( k4 x1 p- ~25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         527
. j+ i4 C+ C  e7 dYongliang Yang, S. James Adelstein, and Amin I. Kassis
8 `7 E0 z. ]3 P8 @; `! _9 ]26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         547
0 f/ R# d# u  Q. M- L6 `9 J4 lZgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,
- j: \" |) K- K$ R- O; `Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein
' X7 ?! l2 {9 UIndex . . . . . . . . 573
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