Bioinformatics

Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction
Single nucleotide variants (SNVs) are prevalent genetic factors shaping individual trait profiles and disease susceptibility. The …
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Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction
BMP Signaling Interferes with Optic Chiasm Formation and Retinal Ganglion Cell Pathfinding in Zebrafish
Decussation of axonal tracts is an important hallmark of vertebrate neuroanatomy resulting in one brain hemisphere controlling the …
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Yap1b, a divergent Yap/Taz family member, cooperates with yap1 in survival and morphogenesis via common transcriptional targets
Yap1/Taz are well-known Hippo effectors triggering complex transcriptional programs controlling growth, survival, and cancer …
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Novel components of germline sex determination acting downstream of foxl3 in medaka
Germline sex determination is an essential process for the production of sexually dimorphic gametes. In medaka, Forkhead box L3 (foxl3) …
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TGFβ-facilitated optic fissure fusion and the role of bone morphogenetic protein antagonism
The optic fissure is a transient gap in the developing vertebrate eye, which must be closed as development proceeds. A persisting optic …
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Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications
Genome editing with the CRISPR–Cas9 system has enabled unprecedented efficacy for reverse genetics and gene correction approaches. …
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Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications
iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins
DNA adenine methyltransferase identification (DamID) has emerged as an alternative method to profile protein-DNA interactions; however, …
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iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins
Depletion of Key Meiotic Genes and Transcriptome-Wide Abiotic Stress Reprogramming Mark Early Preparatory Events Ahead of Apomeiotic Transition
Molecular dissection of apomixis – an asexual reproductive mode – is anticipated to solve the enigma of loss of meiotic sex, and to …
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MEPD: medaka expression pattern database, genes and more
The Medaka Expression Pattern Database (MEPD; http://mepd.cos.uni-heidelberg.de/) is designed as a repository of medaka expression data …
PDF DOI MEPD
Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle
Enhancers have been described to evolve by permutation without changing function. This has posed the problem of how to predict enhancer …
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