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AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/prot.340070105openalex-snapshot

An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences

inferredcites →https://doi.org/10.1007/10_2013_225openalex-snapshot

Advances in Aptamer Screening and Small Molecule Aptasensors

inferredcites →https://doi.org/10.1007/978-3-319-05269-4_9openalex-snapshot

AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application

inferredcites →https://doi.org/10.1007/bf00993379openalex-snapshot

Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization

inferredcites →https://doi.org/10.1007/bfb0054337openalex-snapshot

Spelling approximate repeated or common motifs using a suffix tree

inferredcites →https://doi.org/10.1016/j.aca.2005.09.069openalex-snapshot

Selection of aptamers by systematic evolution of ligands by exponential enrichment: Addressing the polymerase chain reaction issue

inferredcites →https://doi.org/10.1016/j.cell.2012.12.009openalex-snapshot

DNA-Binding Specificities of Human Transcription Factors

inferredcites →https://doi.org/10.1016/s0022-2836(02)00917-8openalex-snapshot

Probabilistic Code for DNA Recognition by Proteins of the EGR Family

inferredcites →https://doi.org/10.1021/ac5044187openalex-snapshot

Emulsion PCR Significantly Improves Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures-Based Aptamer Selection: Allowing for Efficient and Rapid Selection of Aptamer to Unmodified ABH2 Protein

inferredcites →https://doi.org/10.1021/bi400704dopenalex-snapshot

Development of RNA Aptamers Targeting Ebola Virus VP35

inferredcites →https://doi.org/10.1038/346818a0openalex-snapshot

In vitro selection of RNA molecules that bind specific ligands

inferredcites →https://doi.org/10.1038/mt.2012.18openalex-snapshot

Isolation and Optimization of Murine IL-10 Receptor Blocking Oligonucleotide Aptamers Using High-throughput Sequencing

inferredcites →https://doi.org/10.1038/mtna.2015.4openalex-snapshot

FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections

inferredcites →https://doi.org/10.1038/nbt.2486openalex-snapshot

Evaluation of methods for modeling transcription factor sequence specificity

inferredcites →https://doi.org/10.1038/nbt1053openalex-snapshot

Assessing computational tools for the discovery of transcription factor binding sites

inferredcites →https://doi.org/10.1038/nbt1098-939openalex-snapshot

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

inferredcites →https://doi.org/10.1038/nbt717openalex-snapshot

An algorithm for finding protein–DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments

inferredcites →https://doi.org/10.1073/pnas.1009331107openalex-snapshot

Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing

inferredcites →https://doi.org/10.1073/pnas.1503951112openalex-snapshot

Shapely DNA attracts the right partner

inferredcites →https://doi.org/10.1089/10665270252935566openalex-snapshot

A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes

inferredcites →https://doi.org/10.1093/bib/bbs016openalex-snapshot

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era

inferredcites →https://doi.org/10.1093/bioinformatics/17.suppl_1.s207openalex-snapshot

An algorithm for finding signals of unknown length in DNA sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btl223openalex-snapshot

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE

inferredcites →https://doi.org/10.1093/bioinformatics/btq488openalex-snapshot

Deep and wide digging for binding motifs in ChIP-Seq data

inferredcites →https://doi.org/10.1093/bioinformatics/btr261openalex-snapshot

DREME: motif discovery in transcription factor ChIP-seq data

inferredcites →https://doi.org/10.1093/bioinformatics/bts210openalex-snapshot

Identification of sequence–structure RNA binding motifs for SELEX-derived aptamers

inferredcites →https://doi.org/10.1093/bioinformatics/btv545openalex-snapshot

APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data

inferredcites →https://doi.org/10.1093/nar/29.5.1034openalex-snapshot

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond

inferredcites →https://doi.org/10.1093/nar/gkf578openalex-snapshot

Additivity in protein-DNA interactions: how good an approximation is it?

inferredcites →https://doi.org/10.1093/nar/gkf669openalex-snapshot

Discovery of novel transcription factor binding sites by statistical overrepresentation

inferredcites →https://doi.org/10.1093/nar/gkh465openalex-snapshot

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

inferredcites →https://doi.org/10.1093/nar/gkl544openalex-snapshot

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

inferredcites →https://doi.org/10.1093/nar/gkp1010openalex-snapshot

Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling

inferredcites →https://doi.org/10.1093/nar/gkr574openalex-snapshot

STEME: efficient EM to find motifs in large data sets

inferredcites →https://doi.org/10.1093/nar/gkt407openalex-snapshot

DRIMust: a web server for discovering rank imbalanced motifs using suffix trees

inferredcites →https://doi.org/10.1093/nar/gkv308openalex-snapshot

Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

inferredcites →https://doi.org/10.1101/003251openalex-snapshot

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps

inferredcites →https://doi.org/10.1101/022277openalex-snapshot

HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data

inferredcites →https://doi.org/10.1101/gr.076117.108openalex-snapshot

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

inferredcites →https://doi.org/10.1101/gr.100552.109openalex-snapshot

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

inferredcites →https://doi.org/10.1101/gr.5113606openalex-snapshot

Extensive low-affinity transcriptional interactions in the yeast genome

inferredcites →https://doi.org/10.1126/science.8211139openalex-snapshot

Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment

inferredcites →https://doi.org/10.1142/9789814447362_0014openalex-snapshot

BIOPROSPECTOR: DISCOVERING CONSERVED DNA MOTIFS IN UPSTREAM REGULATORY REGIONS OF CO-EXPRESSED GENES

inferredcites →https://doi.org/10.1142/s021972000500120xopenalex-snapshot

PROFILE-BASED STRING KERNELS FOR REMOTE HOMOLOGY DETECTION AND MOTIF EXTRACTION

inferredcites →https://doi.org/10.1186/1471-2105-5-170openalex-snapshot

PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences

inferredcites →https://doi.org/10.1186/1471-2105-8-s7-s21openalex-snapshot

A survey of DNA motif finding algorithms

inferredcites →https://doi.org/10.1371/journal.pcbi.1000590openalex-snapshot

Inferring Binding Energies from Selected Binding Sites

inferredcites →https://doi.org/10.1371/journal.pcbi.1000832openalex-snapshot

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

inferredcites →https://doi.org/10.1371/journal.pone.0019395openalex-snapshot

Acyclic Identification of Aptamers for Human alpha-Thrombin Using Over-Represented Libraries and Deep Sequencing

inferredcites →https://doi.org/10.1371/journal.pone.0031948openalex-snapshot

Aptamers as a Sensitive Tool to Detect Subtle Modifications in Therapeutic Proteins

inferredcites →https://doi.org/10.1371/journal.pone.0043836openalex-snapshot

Rapid Identification of Cell-Specific, Internalizing RNA Aptamers with Bioinformatics Analyses of a Cell-Based Aptamer Selection

inferredcites →https://doi.org/10.1371/journal.pone.0070476openalex-snapshot

Whole Cell-SELEX Aptamers for Highly Specific Fluorescence Molecular Imaging of Carcinomas In Vivo

inferredcites →https://doi.org/10.7150/thno.10202openalex-snapshot

Nucleic Acid Aptamer-Guided Cancer Therapeutics and Diagnostics: the Next Generation of Cancer Medicine

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/b978-0-323-50878-0.00008-2openalex-snapshot

Systematic Evolution of Ligands by Exponential Enrichment for Aptamer Selection

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