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

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0 O: k& M; a1 A- y& b7 [% {$ w. RBioinformatics for Omics Data  G/ [9 N3 a. Y! Z9 r, N0 w8 z/ _

4 K% l% ^2 }5 l- HMethods and Protocols
$ W( x6 a( \+ d. g( |( ?; s3 YSeries: Methods in Molecular Biology, Vol. 719" n" W, H3 K. B7 f# ~
Mayer, Bernd (Ed.)/ [3 U4 T- O) i
2011, XII, 584p. 90 illus., 2 illus. in color.
+ `5 B9 P8 q  }4 P, W- F' PA product of Humana Press* J& n; t, ~' o1 p) y: b+ S

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Part I Omics Bioi nformatics Fundamentals
5 ]4 U/ F" Z# @% T$ \! |1 d" M9 h% ^1 Omics Technologies, Data and Bioinformatics Principles . .         3& ?1 L# s, E9 c) E
Maria V. Schneider and Sandra Orchard6 M/ m( _4 o) z8 K/ p5 c" ?
2 Data Standards for Omics Data: The Basis of Data Sharing and Reuse . . . . .         31
& R% D/ `+ ?2 X8 _Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson,
0 O2 ?4 K. g( F& y& i& y: WJohn Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone,9 T( O7 f% {. M7 n3 q
Christian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor,
! o7 I, v6 q& Pand Catherine A. Ball
- Q- v# ^. |! p8 p7 d: ~3 Omics Data Management and Annotation . . . . . . . . . . . . . . . . . . . . . .         716 V) _( }* U; v& Z9 q8 G* ~: E
Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran,' g$ i* P- k' ]5 u
and Doron Lancet
$ `5 A" q" B0 p- {8 c) R+ ?4 Data and Knowledge Management in Cross-Omics Research Projects . . . . .         971 h+ X% v) L- P+ i& V
Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de: t2 ]( K( v; I  H
Abreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas
8 m. L9 _6 I1 L" b5 Statistical Analysis Principles for Omics Data . . . . .         1137 G$ R& s" R) L4 q7 W/ N1 x
Daniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze1 W; W' D% d; C6 y
6 Statistical Methods and Models for Bridging Omics Data Levels . . . . . .         133
* R5 x+ u$ Z4 [  f9 n* [, X* t+ s, nSimon Rogers2 K8 R! F& V' x
7 Analysis of Time Course Omics Datasets . . . . . .         1532 ?& |7 F9 X' U9 x9 q/ e  ]7 S
Martin G. Grigorov
1 o: V; |# p9 @3 d) K8 The Use and Abuse of -Omes . . . . . . . .         173; `, w1 D5 n9 u% q+ G2 `
Sonja J. Prohaska and Peter F. Stadler7 f4 `8 M8 W; N8 x& I! m
Part II Omics Data and Analysis Tracks
. W1 m! X( z& J& E6 C9 Computational Analysis of High Throughput Sequencing Data . . . . . . . . . . . . . .         199
; l' Q' C( }, _Steve Hoffmann
# @* H' }9 [) M9 }9 ?, q10 Analysis of Single Nucleotide Polymorphisms in Case–Control Studies . . . . .         219
& L" F$ H3 H2 ]" _' f+ NYonghong Li, Dov Shiffman, and Rainer Oberbauer
, A! g) l$ p, {$ x11 Bioinformatics for Copy Number Variation Data . . . . . . . . . . . . . . . . . . . . . . . .         235
' k+ i) r, V# z* U4 tMelissa Warden, Roger Pique-Regi, Antonio Ortega,& R' E, k6 A/ y5 J! g
and Shahab Asgharzadeh/ W8 V$ @. Q9 L3 e  P2 ]
12 Processing ChIP-Chip Data: From the Scanner to the Browser . . . . . . . .         251
' O/ Z. o9 R- ?" }) s) H9 oPierre Cauchy, Touati Benoukraf, and Pierre Ferrier
) X- S6 N# I1 s  O# E$ a6 d13 Insights Into Global Mechanisms and Disease by Gene Expression Profiling . . .         269
% O& J& [  K; s, C! fFátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo,
) U4 _5 v: o$ U4 o4 F+ {Zlatko Trajanoski, and Hubert Hackl
, ~; b, \! l) z& ^14 Bioinformatics for RNomics . . . .         299! [/ V. X3 [# r1 o7 b2 f" y
Kristin Reiche, Katharina Schutt, Kerstin Boll,+ J( q, @  T3 [# \  d
Friedemann Horn, and Jörg Hackermüller: l% x2 w+ T# D+ }4 a$ ~
15 Bioinformatics for Qualitative and Quantitative Proteomics . . . . . . . . . . . . . . . .         331. e6 ?9 H. G, [% o; n
Chris Bielow, Clemens Gröpl, Oliver Kohlbacher, and Knut Reinert9 Z; p* a  }: r
16 Bioinformatics for Mass Spectrometry-Based Metabolomics . . . . . . . . . . . . . . . . .         3512 H6 \1 k" V) c7 |6 _
David P. Enot, Bernd Haas, and Klaus M. Weinberger. H9 Y5 E$ M: k/ |0 q" N. E
Part III A pp lied Omics Bioi nformatics) E- _" Q6 p) {
17 Computational Analysis Workflows for Omics Data Interpretation . .         3798 Q8 e8 i' A0 T- x3 V, c9 u
Irmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler,
' }! b- ]" b1 _; T/ y# ?7 qRaul Fechete, Arno Lukas, and Paul Perco7 g2 F1 P+ i& j  r$ C
18 Integration, Warehousing, and Analysis Strategies of Omics Data . . . . . . . . . . . . . 399
( F* z- _4 ?9 LSrinubabu Gedela7 _  o+ i. t, x. _. m
19 Integrating Omics Data for Signaling Pathways, Interactome Reconstruction,
5 ?; U; [4 @9 m' t( Qand Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .         415: f& j; }. u$ o8 \, }0 ?( @0 @
Paolo Tieri, Alberto de la Fuente, Alberto Termanini,8 ~+ j4 z8 i) \9 t( M
and Claudio Franceschi
7 @/ a4 I* N# t) v  t20 Network Inference from Time-Dependent Omics Data . . . . . . . . . . . . . . . . . .         435
( `& j' X$ g' z5 }% w# q8 J( e( u3 XPaola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia
( d3 [1 H  Z% A8 l0 o2 q4 q8 e21 Omics and Literature Mining . . . . . . . . . . . .         457
9 _4 H' d. j3 J2 P; ~- P, b+ x2 I; YVinod Kumar
" z2 s9 _( U3 Y5 n, x6 u22 Omics–Bioinformatics in the Context of Clinical Data . . . . . . . . . . . . . . . . . . .         479
/ K$ ^0 U: X+ Q; J$ B2 G( F: CGert Mayer, Georg Heinze, Harald Mischak, Merel E. Hellemons,
# ?. b4 _; @" r! j3 cHiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zeeuw,
6 d, p' p9 c# e& AMartin Haiduk, Peter Rossing, and Rainer Oberbauer
. o3 h: v1 P! t/ ?- a" \5 \: g. A23 Omics-Based Identification of Pathophysiological Processes . . . . . . . . . . . . . . . . .         499; g  O5 w. R4 u& `8 T) H
Hiroshi Tanaka and Soichi Ogishima
3 m' @# c. h8 T& U8 _1 B/ M24 Data Mining Methods in Omics-Based Biomarker Discovery . . . . . . . . . . . . . . . .         511
: t9 p. I: b" LFan Zhang and Jake Y. Chen
) w  h8 c: g& Z& ]. k25 Integrated Bioinformatics Analysis for Cancer Target Identification . . . . . . . . . . .         527
- d1 m5 D' H5 N6 F# O) h8 H3 UYongliang Yang, S. James Adelstein, and Amin I. Kassis
2 E) Y. k3 e% o. ]" B1 D' R  C# I26 Omics-Based Molecular Target and Biomarker Identification . . . . . . . . . . . . . . .         547
6 S; Y3 d  P  m3 N4 QZgang–Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung,
1 a- w) ^) p5 [2 o" wAnatoly Dritschilo, Anna T. Riegel, and Anton Wellstein
; `3 L" d0 R" }- lIndex . . . . . . . . 573
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