Citation Impact
Citing Papers
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif
2001 StandoutNobel
Diversity and Complexity in DNA Recognition by Transcription Factors
2009 Science
Direct Response to Notch Activation: Signaling Crosstalk and Incoherent Logic
2009
Cooperative assembly of higher-order Notch complexes functions as a switch to induce transcription
2007
Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting
2003 Science
Notch2, but not Notch1, is required for proximal fate acquisition in the mammalian nephron
2007
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
2012 StandoutScienceNobel
DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity
2018 StandoutNobel
Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage
2022 StandoutNobel
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
2006
A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors
2009
Organization of the Drosophila Circadian Control Circuit
2008
Circadian- and Light-Dependent Regulation of Resting Membrane Potential and Spontaneous Action Potential Firing of Drosophila Circadian Pacemaker Neurons
2007
HIV-1 rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA
1991 StandoutNobel
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
1998
Score Distributions for Simultaneous Matching to Multiple Motifs
1997
A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993
1993
The Neuropeptide PDF Acts Directly on Evening Pacemaker Neurons to Regulate Multiple Features of Circadian Behavior
2009
Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase
1988 Standout
Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro
2011
MicroRNAs
2004 Standout
A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock
2007
C2H2 zinc finger proteins greatly expand the human regulatory lexicon
2015
Nas transgenic mouse line allows visualization of Notch pathway activity in vivo
2006
Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets
2000
MEME SUITE: tools for motif discovery and searching
2009 Standout
Adaptive Evolution in Zinc Finger Transcription Factors
2009
Oxytrichatelomeric nucleoprotein complexes reconstituted with synthetic DNA
1989 StandoutNobel
Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
2007
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
1999 Standout
Efficient genome editing in zebrafish using a CRISPR-Cas system
2013 Standout
Search for the optimal sequence of the ribosome binding site by random oligonucleotide-directed mutagenesis
1988
PairWise and SearchWise: Finding the Optimal Alignment in a Simultaneous Comparison of a Protein Profile against All DNA Translation Frames
1996
Vasoactive intestinal peptide and the mammalian circadian system
2007
Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
2004
VRILLE Feeds Back to Control Circadian Transcription of Clock in the Drosophila Circadian Oscillator
2003
A G Protein-Coupled Receptor, groom-of-PDF, Is Required for PDF Neuron Action in Circadian Behavior
2005
The Drosophila Circadian Network Is a Seasonal Timer
2007 StandoutNobel
A survey of multiple sequence comparison methods
1992
Discovering Sequence Motifs
2007
motifStack for the analysis of transcription factor binding site evolution
2018
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
2016
In vitro evolution suggests multiple origins for the hammerhead ribozyme
2001 StandoutNatureNobel
The Neuropeptide Pigment-Dispersing Factor Adjusts Period and Phase ofDrosophila's Clock
2009
The Human Transcription Factors
2018 Standout
Structures of CSL, Notch and Mastermind proteins: piecing together an active transcription complex
2006
Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component
2007 StandoutNobel
Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner
2012
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
2010
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
1993 StandoutNobel
DNA-Binding Specificities of Human Transcription Factors
2013
Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex
2007
Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes
2007
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
2015
Discovering Sequence Motifs with Arbitrary Insertions and Deletions
2008
Structure of an unusually stable RNA hairpin
1991
Multiple alignment using simulated annealing: branch point definition in human mRNA splicing
1992
A role for CK2 in the Drosophila circadian oscillator
2003
The role of enhancers in cancer
2016
Notch signalling: a simple pathway becomes complex
2006 Standout
PDF Receptor Signaling in Drosophila Contributes to Both Circadian and Geotactic Behaviors
2005
Modulation of Notch Signaling by Antibodies Specific for the Extracellular Negative Regulatory Region of NOTCH3
2008
The Genetics of Transcription Factor DNA Binding Variation
2016
Sequencing and comparison of yeast species to identify genes and regulatory elements
2003 Nature
Widespread Receptivity to Neuropeptide PDF throughout the Neuronal Circadian Clock Network of Drosophila Revealed by Real-Time Cyclic AMP Imaging
2008
Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins
2011
CRISPR-Cas systems for editing, regulating and targeting genomes
2014 Standout
Vasoactive intestinal polypeptide mediates circadian rhythmicity and synchrony in mammalian clock neurons
2005
HIV-1 regulator of virion expression (Rev) protein binds to an RNA stem-loop structure located within the Rev response element region
1990
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions
2014
Novel reactions of RNAase P with a tRNA-like structure in turnip yellow mosaic virus RNA
1988 StandoutNobel
PDFR and CRY Signaling Converge in a Subset of Clock Neurons to Modulate the Amplitude and Phase of Circadian Behavior in Drosophila
2011
Light-Mediated TIM Degradation within Drosophila Pacemaker Neurons (s-LNvs) Is Neither Necessary nor Sufficient for Delay Zone Phase Shifts
2010 StandoutNobel
Transcriptional regulatory code of a eukaryotic genome
2004 StandoutNature
Molecular and Statistical Tools for Circadian Transcript Profiling
2005
A Role for Blind DN2 Clock Neurons in Temperature Entrainment of the Drosophila Larval Brain
2009
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
1997 Standout
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
1994 Standout
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
1990
Th17 and Regulatory T Cells in Mediating and Restraining Inflammation
2010
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
2001 Nature
Control of TH17/Treg Balance by Hypoxia-Inducible Factor 1
2011 StandoutNobel
Quantifying similarity between motifs
2007
Transcription factors: from enhancer binding to developmental control
2012 Standout
Control of Daily Transcript Oscillations in Drosophila by Light and the Circadian Clock
2006
Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling
2009
Different gene regulation strategies revealed by analysis of binding motifs
2009
Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
2011
Using substitution probabilities to improve position-specific scoring matrices
1996
The secondary structure and sequence optimization of an RNA ligase ribozyme
1995
Circadian Remodeling of Neuronal Circuits Involved in Rhythmic Behavior
2008
Absence of a simple code: how transcription factors read the genome
2014
Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same
2010
Dissecting differential gene expression within the circadian neuronal circuit of Drosophila
2009 StandoutNobel
The Canonical Notch Signaling Pathway: Unfolding the Activation Mechanism
2009 Standout
An algorithm for finding protein–DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments
2002
Light Activates Output from Evening Neurons and Inhibits Output from Morning Neurons in the Drosophila Circadian Clock
2007
Reevaluation ofDrosophila melanogaster's neuronal circadian pacemakers reveals new neuronal classes
2006
A Subset of Dorsal Neurons Modulates Circadian Behavior and Light Responses in Drosophila
2007
Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences
1995 StandoutScienceNobel
Associating transcription factor-binding site motifs with target GO terms and target genes
2008
Adult-Specific Electrical Silencing of Pacemaker Neurons Uncouples Molecular Clock from Circadian Outputs
2011
The Transcription Factor Mef2 Links the Drosophila Core Clock to Fas2, Neuronal Morphology, and Circadian Behavior
2013 StandoutNobel
Drosophila GPCR Han Is a Receptor for the Circadian Clock Neuropeptide PDF
2005
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
2002
Peptidergic clock neurons in Drosophila: Ion transport peptide and short neuropeptide F in subsets of dorsal and ventral lateral neurons
2009
Quantitative Dissection of the Notch:CSL Interaction: Insights into the Notch-mediated Transcriptional Switch
2006
Applied bioinformatics for the identification of regulatory elements
2004
A core transcriptional network for early mesoderm development in Drosophila melanogaster
2007
An RNA motif that binds ATP
1993 StandoutNatureNobel
Evaluation of methods for modeling transcription factor sequence specificity
2013
A workbench for multiple alignment construction and analysis
1991
Sequence logos: a new way to display consensus sequences
1990 Standout
Autogenous translational operator recognized by bacteriophage T4 DNA polymerase
1990
Fluorescent indicators for Ca2+based on green fluorescent proteins and calmodulin
1997 StandoutNatureNobel
Vectors for selective expression of cloned DNAs by T7 RNA polymerase
1987
Diverse Targets of the Transcription Factor STAT3 Contribute to T Cell Pathogenicity and Homeostasis
2010
Solution structure of an informationally complex high-affinity RNA aptamer to GTP
2006 StandoutNobel
Genetics and molecular biology of rhythms in Drosophila and other insects
2003 StandoutNobel
A flexible motif search technique based on generalized profiles
1996
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
1997 Standout
Large Ventral Lateral Neurons Modulate Arousal and Sleep in Drosophila
2008
Development and morphology of the clock‐gene‐expressing lateral neurons of Drosophila melanogaster
2006
The Transcription Factor Mef2 Is Required for Normal Circadian Behavior in Drosophila
2010
PDF and cAMP enhance PER stability in Drosophila clock neurons
2014 StandoutNobel
Hidden Markov models of biological primary sequence information.
1994 StandoutNobel
Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product
1987 Standout
Active site and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis.
1985 StandoutNobel
Computer methods to locate signals in nucleic acid sequences
1984
Use of intrinsic binding energy for catalysis by an RNA enzyme
1997
Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.
1994
Isolation of high-affinity GTP aptamers from partially structured RNA libraries
2002 StandoutNobel
Impact of cytosine methylation on DNA binding specificities of human transcription factors
2017 Science
Mutation of the mouse klotho gene leads to a syndrome resembling ageing.
1997 Standout
RNA-peptide fusions for the in vitro selection of peptides and proteins
1997 StandoutNobel
Developmentally regulated alternative splicing generates a complex array of Drosophila para sodium channel isoforms
1994
Ca2+ binding and conformational change in two series of point mutations to the individual Ca(2+)-binding sites of calmodulin.
1992
Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment
1993 Science
Self-cleaving catalytic RNA.
1993
Green Fluorescent Protein as a Marker for Gene Expression
1994 StandoutScienceNobel
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution
2015
Schistosome Satellite DNA Encodes Active Hammerhead Ribozymes
1998
ADrosophilaCalcium Channel α1 Subunit Gene Maps to a Genetic Locus Associated with Behavioral and Visual Defects
1996 StandoutNobel
Function and Evolution of C2H2 Zinc Finger Arrays
2011
Functional information and the emergence of biocomplexity
2007 StandoutNobel
Aptamers Selected for Higher-Affinity Binding Are Not More Specific for the Target Ligand
2006 StandoutNobel
Surprising gene expression patterns within and between PDF-containing circadian neurons in Drosophila
2010 StandoutNobel
Harmonics of Circadian Gene Transcription in Mammals
2009
Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops".
1990
Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase
1990 StandoutScience
The new frontier of genome engineering with CRISPR-Cas9
2014 StandoutScienceNobel
The molecular logic of Notch signaling – a structural and biochemical perspective
2008
Massively parallel measurements of molecular interaction kinetics on a microfluidic platform
2012
Improved predictions of secondary structures for RNA.
1989
Structural Motifs in RNA
1999
Reprogramming homing endonuclease specificity through computational design and directed evolution
2013 StandoutNobel
Mapping the consequence of Notch1 proteolysis in vivo with NIP-CRE
2007
Structural analysis of the interaction between the human immunodeficiency virus Rev protein and the Rev response element.
1991
A Catalytic RNA and Its Gene from Salmonella typhimurium
1985 StandoutScienceNobel
Neutral evolution of mutational robustness
1999
Transcription Regulation within the Circadian Clock: The E-box and Beyond
2004
Structural diversity of self-cleaving ribozymes
2000
Fast and accurate short read alignment with Burrows–Wheeler transform
2009 Standout
Informational Complexity and Functional Activity of RNA Structures
2004 StandoutNobel
A resetting signal between Drosophila pacemakers synchronizes morning and evening activity
2005 StandoutNatureNobel
Amino acid substitution matrices from an information theoretic perspective
1991
Human immunodeficiency virus rev protein recognizes a target sequence in rev-responsive element RNA within the context of RNA secondary structure
1990
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
1994 Standout
Sequence complexity in Darwinian evolution
2002
Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements
1983
A survey of multiple sequence comparison methods
1992
Recognition of protein coding regions in DNA sequences
1982
The gut microbiota as an environmental factor that regulates fat storage
2004 Standout
RNA pseudoknots
1994
Repeated sequences and open reading frames in the 3' flanking region of the gene for the RNA subunit of Escherichia coli ribonuclease P.
1983 StandoutNobel
Drosophila CLOCK Is Constitutively Expressed in Circadian Oscillator and Non-Oscillator Cells
2006
Arginine-Mediated RNA Recognition: the Arginine Fork
1991 Science
Selection of DNA binding sites by regulatory proteins
1987
RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase.
1992
Analysis of functional neuronal connectivity in theDrosophilabrain
2012
Newt satellite 2 transcripts self-cleave by using an extended hammerhead structure.
1991
Information theory in molecular biology
2004
Complete sequence of the bithorax complex of Drosophila.
1995 StandoutNobel
The telomerase RNA pseudoknot is critical for the stable assembly of a catalytically active ribonucleoprotein
1999 StandoutNobel
The bacteriophage T4 dexA gene: Sequence and analysis of a gene conditionally required for DNA replication
1987
Structure and function of telomeres
1991 StandoutNatureNobel
DNA polymerase of bacteriophage T4 is an autogenous translational repressor.
1988
Differentiation of Effector CD4 T Cell Populations
2010 Standout
A comprehensive set of sequence analysis programs for the VAX
1984 StandoutNobel
Works of Gary D. Stormo being referenced
Protein-mediated Translational Repression
1983
Quantitative analysis of the relationship between nucleotide sequence and functional activity
1986
Exploring the DNA-recognition potential of homeodomains
2012
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
2003
The AP-1 transcription factor Batf controls TH17 differentiation
2009 Nature
Target Selectivity of Vertebrate Notch Proteins
2005
Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites
2008
Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA
1988
Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods
1992
Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
2013
Sequence requirements of the hammerhead RNA self-cleavage reaction
1990
An optimized two-finger archive for ZFN-mediated gene targeting
2012
enoLOGOS: a versatile web tool for energy normalized sequence logos
2005
Identification of consensus patterns in unaligned DNA sequences known to be functionally related
1990
Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments
1992
Is there a code for protein–DNA recognition? Probab(ilistical)ly…
2002
DNA binding sites: representation and discovery
2000
Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique
1989
Computer Methods for Analyzing Sequence Recognition of Nucleic Acids
1988
An improved predictive recognition model for Cys2-His2 zinc finger proteins
2014
Identification of Protein Coding Regions In Genomic DNA
1995
Determining the specificity of protein–DNA interactions
2010
Inferring Binding Energies from Selected Binding Sites
2009
Making connections between novel transcription factors and their DNA motifs
2005
Quantitative specificity of the Mnt repressor
1997
Innate Host Defense Requires TFEB-Mediated Transcription of Cytoprotective and Antimicrobial Genes
2014
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
1999
The Neuropeptide Pigment-Dispersing Factor Coordinates Pacemaker Interactions in theDrosophilaCircadian System
2004
Splicing signals inDrosophila: intron size, information content, and consensus sequences
1992
[13] Consensus patterns in DNA
1990
Five promoters integrate control of the cob/pdu regulon in Salmonella typhimurium
1995
ANN-SPEC: A METHOD FOR DISCOVERING TRANSCRIPTION FACTOR BINDING SITES WITH IMPROVED SPECIFICITY
1999
Characterization of translational initiation sites inE. coli
1982
The bacteriophage T4regAgene: primary sequence of a translational repressor
1984
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors
2008
Spec-seq: determining protein-DNA-binding specificity by sequencing
2014
Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions
2012
Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites inE. coli
1982
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation
1982
An improved map of conserved regulatory sites for <it>Saccharomyces cerevisiae</it>
2006
Translationsl regulation of expression of the bacteriophage T4 lysozyme gene
1986
Translational Initiation in Prokaryotes
1981
Delila system tools
1984
Influence of the period -dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster
2002
Conserved Motifs and Prediction of Regulatory Modules inCaenorhabditis elegans
2012
RNA binding site of R17 coat protein
1987
Autoregulation of gene expression
1982
CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes.
1988
Identifying protein-binding sites from unaligned DNA fragments.
1989
Modeling the specificity of protein‐DNA interactions
2013
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Richard Durbin , Sean R. Eddy , Anders Krogh , Graeme Mitchison
2000
Information content of binding sites on nucleotide sequences
1986