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1 SELEX analysis identified GC-rich RNA sequences as a com
2 SELEX assays and footprinting data indicate that DEAF-1
3 SELEX coupled with SPR is expected to speed up the selec
4 SELEX directed against the RNA-binding face of the STNV
5 SELEX experiments with human Fox-1 revealed highly selec
6 SELEX of the combined H4a and H4b region in satC generat
7 SELEX selections for repeats 5 and 2 enriched for oligon
8 SELEX with a N30 RNA pool yielded an aptamer (B6) that b
9 SELEX, however, is an iterative process requiring multip
10 SELEX-generated RNA aptamers are proving to be highly ef
13 eviously published KLF motif identified by a SELEX experiment, but the new motif is consistent with m
15 sequence-randomized region was employed in a SELEX-type procedure to identify DNAs that bound strongl
18 ower and utility of SELEX and offer an AEGIS-SELEX that could possibly generate receptors, ligands, a
22 algorithm, originally implemented to analyze SELEX data; extends the applicability of AptaMotif to HT
23 us on the novel applications of aptamers and SELEX, as well as opportunities to develop molecular too
27 s (uPBMs), genomic context PBMs (gcPBMs) and SELEX-seq data, we demonstrate that incorporating DNA sh
32 ress this challenge, we have used cell-based SELEX (Systematic Evolution of Ligands by Exponential En
34 he aptamers were selected using a cell-based SELEX strategy in our laboratory for cancer cells that,
35 mer sequence was selected using a cell-based SELEX strategy in our laboratory for CCRF-CEM acute leuk
36 dily conjugated to magnetic beads, MMS-based SELEX provides a general platform for rapid generation o
38 re in vitro selected using a new single-bead SELEX approach, which was rapid and consumed only ca. 45
41 etry based in-vitro selection technique (BLI-SELEX) for fishing out specific aptamers against E. coli
42 on of an optimal binding sequence for BEN by SELEX (systematic evolution of ligands by exponential en
43 to unnatural-base DNA aptamers generated by SELEX using genetic alphabet expansion, without reducing
45 target 17beta-estradiol (E2) was isolated by SELEX with dissociation constant of 50 nM and tethered t
47 the preferred DNA binding sequence of Opa by SELEX and shown that it is necessary and sufficient to a
48 n designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential En
49 o-recognition elements which are produced by SELEX (systematic evolution of ligands by exponential en
53 the first report of aptamers isolated by CE-SELEX with higher affinity than those obtained for the s
54 ion of ligands by exponential enrichment (CE-SELEX) and had a dissociation constant (K(d)) of 112 nM.
55 ion of ligands by exponential enrichment (CE-SELEX) has previously been used to select aptamers for l
56 ion of ligands by exponential enrichment (CE-SELEX) is a powerful technique for isolating aptamers fo
58 sults also provided insight into why many CE-SELEX selections obtain pools with reduced affinities af
60 ucleotide pool through multiple rounds of CE-SELEX selection against the target recombinant human vas
61 For the first time, we have performed CE-SELEX selection for a small-molecule target, N-methyl me
63 was observed, supporting the premise that CE-SELEX selects a uniquely heterogeneous pool of high affi
65 steria spp. were selected using a whole-cell SELEX (Systematic Evolution of Ligands by EXponential en
67 t ovarian cancer previously obtained by cell-SELEX (SELEX = systematic evolution of ligands by expone
68 is challenge, aptamers were selected by cell-SELEX (Systematic Evolution of Ligands by EXponential en
71 identification of aptamers obtained by cell-SELEX can serve as a means to identify promising biomark
73 Here we screened the aptamer CH6 by cell-SELEX, specifically targeting both rat and human osteobl
74 selected a DNA aptamer against GCGR by cell-SELEX, which can specifically bind membrane protein of C
77 n of Ligands by Exponential Enrichment (Cell-SELEX) and development of sandwich type aptamer-based co
78 n of Ligands by Exponential Enrichment (Cell-SELEX) to identify glioblastoma TIC-specific nucleic aci
80 report a DNA aptamer probe evolved from cell-SELEX that can recognize thrombospondin-1 protein in hum
81 Thus, with the aptamer obtained from cell-SELEX, real-time modification of live-cell membrane prot
82 DNA aptamers (generated with a modified cell-SELEX procedure to display low-nanomolar affinity for th
83 ch served as target in eleven rounds of cell-SELEX with multiple subtractive counter-selections again
85 ells using a combined approach based on cell-SELEX, state-of-the-art applications of quantitative rea
87 new results (compared with our reported cell-SELEX methodology) in addition to the generation of apta
89 ucement); and the second result is that cell-SELEX can be used for adhesive cells and thus open the d
91 tact vaccinia virus were selected using cell-SELEX technique and integrated into impedimetric sensors
94 efficient method of affinity chromatography-SELEX followed by a quantitative binding (QuMFRA) assay
95 ned efficiently with affinity chromatography-SELEX, but those sequences alone provide a weight matrix
101 DNA aptamers selected using the conventional SELEX protocol, and their application in an ELISA assay
102 (Kd 14nM), screened by new in-situ developed SELEX method using phenylboronic acid on microtitre plat
105 on of ligands by exponential enrichment (egg-SELEX) and identified a panel of ssDNA aptamers specific
108 lution of ligands by exponential enrichment (SELEX) analysis, the enormous datasets generated in the
109 lution of ligands by exponential enrichment (SELEX) and NMR spectroscopy to demonstrate that the majo
111 lution of ligands by exponential enrichment (SELEX) approaches, the ability of NECEEM to select aptam
112 lution of ligands by exponential enrichment (SELEX) due to its small size and scarcity of reactive gr
113 lution of ligands by exponential enrichment (SELEX) exhibited dissociation constants in the nanomolar
115 lution of ligands by exponential enrichment (SELEX) in conjunction with high throughput sequencing wa
116 lution of ligands by exponential enrichment (SELEX) in vitro, which allows for sensitive detection of
117 lution of ligands by exponential enrichment (SELEX) is a screening technique that involves the progre
118 n of ligands through exponential enrichment (SELEX) is a well-established method for generating nucle
119 lution of Ligands by Exponential Enrichment (SELEX) method, which can generate a nucleic acid-based p
121 lution of Ligands by Exponential Enrichment (SELEX) methodology and the description of the first apta
122 lution of Ligands by EXponential Enrichment (SELEX) offers an iterative process to discover these apt
124 lution of ligands by exponential enrichment (SELEX) procedure, we have identified two consensus seque
125 lution of ligands by exponential enrichment (SELEX) process enables the isolation of aptamers from ra
126 lution of ligands by exponential enrichment (SELEX) process is used for the isolation of specific, hi
127 lution of ligands by exponential enrichment (SELEX) process to discover slow off-rate modified aptame
128 lution of Ligands by Exponential Enrichment (SELEX) protocol capable of selecting xeno-nucleic acid (
129 lution of ligands by exponential enrichment (SELEX) protocol identified a single, efficiently cleaved
130 lution of Ligands by EXponential Enrichment (SELEX) represents a state-of-the-art technology to isola
132 lution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-sel
134 lution of ligands by exponential enrichment (SELEX) to identify the preferred binding sequence of ETR
135 lution of ligands by exponential enrichment (SELEX) to isolate RNA aptamers against aminoglycoside an
136 lution of ligands by exponential enrichment (SELEX) to isolate RNA aptamers that bind the Caenorhabdi
137 uation of ligands by exponential enrichment (SELEX) to systematically identify additional DNA sequenc
139 lution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process,
140 lution of ligands by exponential enrichment (SELEX) was used to identify RNA sequences that bind Mbl
141 lution of ligands by exponential enrichment (SELEX)) are often labor-intensive and time-consuming.
142 lution of ligands by exponential enrichment (SELEX), we found a single 58-nt aptamer sequence that as
143 lution of ligands by exponential enrichment (SELEX), we have selected a group of RNA aptamers against
144 lution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specifi
145 lution of ligands by exponential enrichment (SELEX), we identified DNA sequences that bound to the HT
146 lution of ligands by exponential enrichment (SELEX), we identify DNA aptamers that bind specifically
157 ion of splicing and polyadenylation by ESRP, SELEX-Seq analysis was performed, coupling traditional S
159 itro RNA-binding site selection experiments (SELEX) identified distinct binding motif specificities f
160 of Ligands by Exponential Enrichment (FluMag-SELEX) method to isolate a urea specific DNA aptamer wit
163 regulatory motifs, substitute for functional SELEX in most cases, and provide insights about splicing
164 We have now carried out a refined functional SELEX screen for motifs that can act as ESEs in response
165 nstrate the feasibility of employing genomic SELEX to identify vertebrate transcription factor bindin
170 eloped novel in-silico methods to analyze HT-SELEX data and utilized them to study the emergence of p
173 parison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the
176 presence of motif-free sequences in late HT-SELEX rounds and their enrichment in weak binders allows
178 published motifs estimated using the same HT-SELEX data, we demonstrate that BEESEM provides signific
179 oinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial
180 roarrays (PBM) and high-throughput SELEX (HT-SELEX), have enabled rapid measurements of the specifici
181 coupled with high-throughput sequencing (HT-SELEX), creates billions of random sequences capable of
182 extends the applicability of AptaMotif to HT-SELEX data and introduces new functionalities, as the po
185 of 239 and 56 TFs extracted from in vitro HT-SELEX binding assays and in vivo ChIP-seq data, respecti
188 focusing in spiral microfluidic channels, I-SELEX enables stringent partitioning of cells (efficienc
191 This perspective covers recent advances in SELEX methodology for improving efficiency of the SELEX
192 This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzy
193 et concentration, on selection efficiency in SELEX and identify strategies to control these uncertain
197 eic acid libraries improves success rates in SELEX experiments and facilitates the identification of
198 Target immobilization plays a key role in SELEX and other ligand enrichment methods, particularly
200 e a variety of RNA binding assays, including SELEX, to characterize the interaction in vitro and a mo
201 (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propa
202 i-Mb aptamer was generated by five iterative SELEX (Systematic evolution of ligands by exponential en
205 t studies suggest that microfluidic SELEX (M-SELEX) technology can accelerate aptamer isolation by en
206 model to demonstrate the efficiency of the M-SELEX process, we describe here the isolation of DNA apt
207 on of ligands by exponential enrichment (MAI-SELEX), a technique designed for the efficient selection
210 tspot, we used an in vitro selection method (SELEX) that revealed an 18-bp consensus sequence for Atf
211 isting of a magnetic bead-based microfluidic SELEX chip and a competitive assay chip to automate the
213 Recent studies suggest that microfluidic SELEX (M-SELEX) technology can accelerate aptamer isolat
214 synthesized DNA oligonucleotides as in most SELEX studies, we utilized zebrafish genomic DNA to isol
215 the assignment of motifs to 200 TFs with no SELEX-derived motifs, roughly a 50% increase compared to
219 Our experimental results and analysis of SELEX publications spanning 13 years implicate the alkal
222 chieves the full microfluidic integration of SELEX, thereby enabling highly efficient isolation of ap
224 candidates were isolated in three rounds of SELEX within a total process time of approximately 10 ho
228 ion of aptamers in the first three rounds of SELEX, while SELEX with conventional PCR failed in a num
229 ep toward expanding the power and utility of SELEX and offer an AEGIS-SELEX that could possibly gener
233 onuclease single-strand recovery step in our SELEX to direct aptamers to the surface of erythrocytes
237 an experimental and computational platform, SELEX-seq, that can be used to determine the relative af
240 alized for the efficient and systematic post-SELEX development of aptamers for down-stream applicatio
241 containing sequences present early in the R1 SELEX process to identify novel anti-p65 RNA aptamers, t
243 e interactions, we have developed an RNA-RNA SELEX approach for mapping the sequences involved in int
247 ness in plants by in vivo genetic selection (SELEX) resulted in winning sequences that contain an H4a
250 an cancer previously obtained by cell-SELEX (SELEX = systematic evolution of ligands by exponential e
251 of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential en
253 followed by high-throughput DNA sequencing (SELEX-seq) on several floral MADS domain protein homo- a
254 igands by exponential enrichment sequencing (SELEX-seq), chromatin immunoprecipitation sequencing (Ch
256 ning the library using a structure-switching SELEX approach, a high affinity SA aptamer was identifie
257 y an in vitro selection process, also termed SELEX (Systematic Evolution of Ligands by EXponential en
258 terial system is, however, more limited than SELEX, and some eukaryotic factors may not express or fo
259 ressed on the surface of yeast, we show that SELEX can yield binding specificity motifs and identify
263 The mapped AtTopoIIA cleavage sites and the SELEX sites differed in their genomic distribution and a
264 nity were isolated from a RNA library by the SELEX (Systematic Evolution of Ligands by EXponential en
268 ides and selecting for slow off-rates in the SELEX procedure, we have evolved a special class of apta
269 This putative CsrA binding site matched the SELEX-derived binding site consensus sequence in 8 out o
270 methodology for improving efficiency of the SELEX procedure and enhancing affinity and specificity o
275 inding microarrays (PBM) and high-throughput SELEX (HT-SELEX), have enabled rapid measurements of the
281 h varying genome compositions and for tuning SELEX pools to optimize the chance of finding specific f
282 sponding yeast one-hybrid system and, unlike SELEX, it does not require purification of the TF(s).
286 ral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential en
290 terize its tripartite consensus sequence via SELEX (systematic evolution of ligands by exponential en
295 rs in the first three rounds of SELEX, while SELEX with conventional PCR failed in a number of attemp
296 ogy and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects o