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290 Tikhmyanova et al.25. Petermann, R., Mossier, B. M., Aryee, D. N., and Kovar, H. (1998) A recombinationbased method to rapidly assess specificity of two-hybrid clones in yeast.Nucleic Acids Res. 26, 2252, 2253.26. Stanyon, C. A., Limjindaporn, T., and Finley, R. L., Jr. (2003) Simultaneouscloning of open reading frames into several different expression vectors.Biotechniques 35, 520–522, 524–526.27. Hartley, J. L., Temple, G. F., and Brasch, M. A. (2000) DNA cloning using invitro site-specific recombination. Genome Res. 10, 1788–1795.
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Gene Function Analysis
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METHODS IN MOLECULAR BIOLOGYGene Fu
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PrefaceThis volume of Methods in Mo
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Prefaceixcolleagues demonstrate how
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xiiContentsPART III EXPERIMENTAL ME
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ICOMPUTATIONAL METHODS I
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4 BidautTable 1Input File Format Us
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6 BidautTable 2Folder Layout to Use
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8 Bidaut• alphaA: this is the num
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10 Bidautcomputing the maximum corr
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12 BidautFig. 3. The complete Clutr
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Table 3Some Identified Patterns (5,
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16 BidautFig. 4. This is a comparis
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18 BidautReferences1. Hughes, T. R.
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20 Kirov et al.way to associate gen
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22 Kirov et al.based on a study ass
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24 Kirov et al.1. Retrieve the gene
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26Fig. 1. Functional associations f
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28 Kirov et al.Fig. 2. Pathway anal
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30 Kirov et al.3. Gene symbols usag
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32 Kirov et al.9. OBO_Team, Open Bi
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3Estimating Gene Function With Leas
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Estimating Gene Function With LS-NM
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50 Gonye et al.activity and problem
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52 Gonye et al.Currently, PAINT can
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54 Gonye et al.dynamic nature of th
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Prediction Using PAINT 57represente
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Prediction Using PAINT 59In PAINT,
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Prediction Using PAINT 6114. On the
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Prediction Using PAINT 634.2. Size
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65Fig. 4. Localization of enrichmen
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Prediction Using PAINT 673. Okubo,
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5Prediction of Intrinsic Disorder a
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Prediction of ID and Its Use in Fun
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Table 1Summary of the Web Servers O
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IICOMPUTATIONAL METHODS II
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94 Crabtree et al.genomes, which is
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96 Crabtree et al.Fig. 2. Sybil pro
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98 Crabtree et al.Fig. 3. Computing
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100 Crabtree et al.3.1.5.1. FILTER
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102 Crabtree et al.3. For the sake
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104 Crabtree et al.Fig. 5. Best bid
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106 Crabtree et al.17. Some cluster
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108 Crabtree et al.19. Chado—The
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110 Dateproducts prevents the under
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112 DateDetails of these tasks are
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114 DateThis step creates additiona
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116 Date>hsapiens|gi|20093443 >hsap
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118 DateBLAST score from the match
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Table 1A Sample of Results From Pro
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122 DateFig. 1. A network of functi
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124 Datedescribed by Verjovsky Marc
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126 Dateor contracts put forth by t
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8Bioinformatics Tools for Modeling
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Modeling Transcription Factor Targe
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VISTA Program to search for TFBSs H
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Ac 0 0 0 1 0 1 0 1 0 1 1 0 0 0 0 0
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154 Osborne et al.are included in t
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156 Osborne et al.Fig. 2. Flowchart
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158 Osborne et al.UMLS source abbre
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160 Osborne et al.Fig. 3. Querying
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162 Osborne et al.3.4.2. Installati
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164 Osborne et al.amount of filteri
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166 Osborne et al.public class MMTx
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168 Osborne et al.Fig. 4. Input tes
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10Statistical Methods for Identifyi
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Identifying Differentially Expresse
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11Gene Function Analysis Using the
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Gene Function Analysis Using the Ch
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12Design and Application of a shRNA
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Design and Application of a shRNA 2
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224 Cheng and Chang1. IntroductionR
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226 Cheng and ChangFig. 1. Structur
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228 Cheng and ChangFig. 2. Sequence
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230 Cheng and Chang3. Handheld ultr
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232 Cheng and ChangFig. 4. Sequence
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234 Cheng and ChangFig. 5. Experime
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236 Cheng and Chang3.4. Functional
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238 Cheng and Chang3.4.4. Fixation
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240 Cheng and Chang16. Player, M. R
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14Selection of Recombinant Antibodi
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Selection of Recombinant Antibodies
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258 Tikhmyanova et al.functionally
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260 Tikhmyanova et al.partner was f
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262 Tikhmyanova et al.5. pGLS22-Ras
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Page 544: 266 Tikhmyanova et al.Fig. 3. Polyl
Page 548: 268 Tikhmyanova et al.To minimize t
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Page 556: 272 Tikhmyanova et al.3.3.1. Transf
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Page 564: 276 Tikhmyanova et al.the frozen ma
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Page 572: Table 3Suggested PCR Reactions and
Page 576: 282 Tikhmyanova et al.15. Prepare a
Page 580: 284 Tikhmyanova et al.6. Assay of m
Page 584: 286 Tikhmyanova et al.of tubes. Fin
Page 588: 288 Tikhmyanova et al.the polylinke
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Dual Bait-Compatible Bacterial Two-
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318 Thibodeau-Beganny and Joungbeen
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320 Thibodeau-Beganny and JoungFig.
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324 Thibodeau-Beganny and JoungTypi
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328 Thibodeau-Beganny and JoungPCR
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330 Thibodeau-Beganny and Joung16-1
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332 Thibodeau-Beganny and Joung2. P
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334 Thibodeau-Beganny and Joung11.
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336 IndexKknockin (gene knockin) 19
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