Concepedia

Self-organization of mouse embryonic stem cells into reproducible pre-gastrulation embryo models via CRISPRa programming

Gerrald A. Lodewijk, Sayaka Kozuki, Clara Han, Benjamin R. Topacio, Seung‐Ho Lee, Lily Nixon, Abolfazl Zargari, Gavin Knight, Randolph S. Ashton, Lei S. Qi,

Cell stem cell · 2025 · 13 citations · 98 references

DOIFull text

Open access

Concepts

References

98

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin, Ignacio Arganda‐Carreras, Erwin Frise et al. · Nature Methods · 2012 · 70.9K citations

, , +9

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text

, , +13

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

, , +11

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Yang Liao, Gordon K. Smyth, Wei Shi · Bioinformatics · 2013 · 29.1K citations · Full text

, , +14

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim, Ben Langmead, Steven L. Salzberg · Nature Methods · 2015 · 26.1K citations · Full text

, , +3