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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2 g5 q' O2 G. d) h& S1 OMethods and Protocols3 _8 Y) h" l5 O4 ?
Series: Methods in Molecular Biology, Vol. 719
; F  C& l0 f  Z+ F1 Q% vMayer, Bernd (Ed.)
3 K) T: z; {$ K; i9 f; R2011, XII, 584p. 90 illus., 2 illus. in color.
5 ^' X1 H6 y: i! [A product of Humana Press; }0 K) P4 j+ b& {

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Part I Omics Bioi nformatics Fundamentals+ X% O. D9 k3 ~4 u$ u( P! k
1 Omics Technologies, Data and Bioinformatics Principles . .         3" X: f) p. n. O( W) ?3 r9 d' Y
Maria V. Schneider and Sandra Orchard1 T3 A# v. M; V* G* s# I
2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         317 m" e/ M/ y3 z0 u
Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,
# C6 v; I- e1 r4 G  c7 E. X9 R- f7 KJohn Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,
4 N% {; [* @! |5 }4 X( z. I* IChristian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,% x: ]2 T( f: Z. D( D  B1 Z  v
and Catherine A. Ball
0 }  K; T# R4 O( f3 M) R5 L* ^3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         71: V+ `' Y9 N: L; K
Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,. B) ?3 b( h6 Q) N1 k
and Doron Lancet$ ]8 U, n8 n6 x% o- I
4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         97
# x) G$ I& z- B9 ?# C8 PMartin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de: T! K% e6 Y9 ~4 d2 l7 L" r
Abreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas! O0 ]7 ]7 @* M5 ?2 n7 Z  S, T
5 Statistical Analysis Principles for Omics Data . . . . .         113' V- K5 W' x7 t/ u; {  R4 g3 f( j9 P
Daniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze2 B$ n5 n4 W. e; }( B! q
6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         133
: }( j  L' [5 V# f( ?( J# NSimon Rogers" \/ k  I0 m4 ?( w" P1 k
7 Analysis of Time Course Omics Datasets . . . . . .         153
, W( v, d. k7 B# f- Y' M1 |* P7 w/ PMartin G. Grigorov! ^1 M- D% q1 P6 s8 P' _
8 The Use and Abuse of -Omes . . . . . . . .         173
3 j1 n4 {# q; }. a: gSonja J. Prohaska and Peter F. Stadler
& D! S9 }' s- F' VPart II Omics Data and Analysis Tracks
$ x! ?3 C4 C0 g4 f' G0 e9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199$ y1 {1 r+ T5 o: C- A* N& x
Steve Hoffmann0 x: Y  D2 M% l* N
10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         219
: f, K% W" p; d. B; @Yonghong Li, Dov Shiffman, and Rainer Oberbauer- D; S7 c$ H) q) @0 ^2 d
11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235
3 }; V$ o; B) k, KMelissa Warden, Roger Pique-Regi, Antonio Ortega,! {9 F3 z- o4 U. I! G  s# r; v* @0 T, X
and Shahab Asgharzadeh5 j$ ^1 g8 B7 F
12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251
6 \. D, k  |1 z3 ^6 k4 \Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier
3 i  b2 o# F( A) D3 s13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269
& [, K9 h8 C* E; hFátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,
( ]- L2 E. o* i7 c5 w$ dZlatko Trajanoski, and Hubert Hackl
$ d" W; P& m2 x# }$ l: e14 Bioinformatics for RNomics . . . .         2997 A+ R3 s1 P  u/ d
Kristin Reiche, Katharina Schutt, Kerstin Boll,7 `1 x+ w9 x( {1 [. j; E* l1 k/ q
Friedemann Horn, and Jörg Hackermüller6 D+ q$ O6 j- @6 b1 v' _" @  {
15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331
/ d: K* s2 x  l! yChris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert. A' [7 _* e" `. m/ @7 H1 ^  M7 e
16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         351  F; ~. g2 n0 B
David P. Enot, Bernd Haas, and Klaus M. Weinberger
6 P7 r! p, H3 n# s/ d* F6 s9 MPart III A pp lied Omics Bioi nformatics
+ Y5 ~6 T' @/ M% }. V- r# a' e17 Computational Analysis Workflows for Omics Data Interpretation . .         379, O1 \9 t/ T1 r, X
Irmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,2 f8 q( y: X+ k7 \  y" |, [
Raul Fechete, Arno Lukas, and Paul Perco
/ W) K1 ]1 x  b/ r1 @  F8 ?18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399' h. _3 I5 Z2 v4 ~3 z5 w
Srinubabu Gedela
, [# f) x( M, c/ g6 _. U% ]19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,
; H- k3 _$ s" Zand Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         415' S8 W2 f2 N; F/ K# y6 b
Paolo Tieri, Alberto de la Fuente, Alberto Termanini,
# s7 o! S& t) Eand Claudio Franceschi
1 j  t' c# h" \& u20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         4354 T2 Q- [' ~& L! J, s
Paola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia
5 o. y! O9 I; A) ~+ h6 y21 Omics and Literature Mining . . . . . . . . . . . .         457/ s+ u# t: z* Y# L1 A: U" y
Vinod Kumar( I7 E% p, b& r" ^- [$ t" ^8 f
22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479
$ _4 x8 }2 p, i4 _1 d9 U; aGert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,
7 n) X5 A$ `+ m9 zHiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,
0 U: d, I- w0 m0 I6 s( D: H+ mMartin Haiduk, Peter Rossing, and Rainer Oberbauer5 B' e9 M) e: i$ W4 k
23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         499
8 ]( v. h5 h. yHiroshi Tanaka and Soichi Ogishima3 [, ^$ d% y( y3 I: }1 ^8 T* D" X
24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         5115 H& h- i7 B" m" D9 x( N* m
Fan Zhang and Jake Y. Chen  \1 u* r% v4 @7 D+ t
25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         5279 r; R! A' G! R
Yongliang Yang, S. James Adelstein, and Amin I. Kassis; x3 X3 Z+ {, m( B2 V% V8 |4 r
26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         547" S/ i" O! y7 a4 G! z& ~+ |
Zgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,% U. q; r- O1 m( z/ M% {9 A
Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein
+ L% l: l" Y/ E" @- @- O8 ~Index . . . . . . . . 573" _( G; w  h5 t/ ]2 \
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