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266 Tikhmyanova et al.Fig. 3. Polylinkers of basic two-hybrid vectors. (A) pGLS23. (B) pMW103. (C) pJG4-5.Maps and sequences for these and additional vectors are available on the web athttp://www.fccc.edu/research/labs/golemis/InteractionTrapInWork.html. Only restrictionsites that are available for insertion of coding sequences are shown; those shown in boldtype are unique.11. Microfuge the cells for 20 s at 10,000–15,000g. Pour off the supernatant andresuspend the yeast in 0.5 mL of sterile water.12. Spread each transformation mixture on Glu/CM Ura − His − dropout plates, and keepat 30°C for 2 d to select for yeast colonies containing transformed plasmids (Note 5).3.2. Replica Technique/Gridding Yeast: Assessing Bait Activationof ReportersFor each transformation: pick and analyze at least six independent colonies fortheir transcriptional activation phenotype, using the auxotrophic and colorimetric
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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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Page 500: 14Selection of Recombinant Antibodi
Page 504: Selection of Recombinant Antibodies
Page 528: 258 Tikhmyanova et al.functionally
Page 532: 260 Tikhmyanova et al.partner was f
Page 536: 262 Tikhmyanova et al.5. pGLS22-Ras
Page 540: 264 Tikhmyanova et al.4. pYESTrp2 p
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16A Bacterial/Yeast Merged Two-Hybr
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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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