kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

Network of epistatic interactions within a yeast snoRNA

(2016) O. Puchta et al.   SCIENCE

The fitness landscape of a tRNA gene

(2016) C. Li et al.   SCIENCE

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes

(2015) Wenwen Fang et al.   MOLECULAR CELL

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

(2013) Vincent C. Auyeung et al.   CELL

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

(2013) Vikram Pattanayak et al.   NATURE BIOTECHNOLOGY

pLogo: a probabilistic approach to visualizing sequence motifs

(2013) Joseph P O'Shea et al.   NATURE METHODS

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH