lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction

(2019) Fumitaka Inoue et al.   Cell Stem Cell

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

(2019) Martin Kircher et al.   Nature Communications

Design tools for MPRA experiments

(2018) Andrew R Ghazi et al.   BIOINFORMATICS

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments

(2016) Ilias Georgakopoulos-Soares et al.   BIOINFORMATICS

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Multiplex pairwise assembly of array-derived DNA oligonucleotides

(2015) Jason C. Klein et al.   NUCLEIC ACIDS RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE