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Specificity, synergy, and mechanisms of splice-modifying drugs

Two small-molecule drugs, risdiplam and branaplam, have been developed for treating spinal muscular atrophy. Here the authors develop quantitative modeling methods for the sequence-specific and concentration-dependent effects of these and other splice-modifying drugs.

Yuma Ishigami
Mandy S. Wong
Justin B. Kinney
ResearchOpen Access29 Feb 2024
Nature Communications

Volume: 15, P: 1-13
Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models

The intersection of genomics and deep learning shows promise for real impact on healthcare and biological research, but the lack of interpretability in terms of biological mechanisms is limiting utility and further development. As a potential solution, Koo et al. present SQUID, an interpretability framework built using domain-specific genomic surrogate models.

Evan E. Seitz
David M. McCandlish
Peter K. Koo
Research21 Jun 2024
Nature Machine Intelligence

Volume: 6, P: 701-713
Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization

CRISPR/Cas9-based genome editing enables specific deletion of target genes. Here, Senturket al. develop an inducible editing system by fusing a conditional destabilization domain to Cas9 and demonstrate temporal control of gene editing in response to a synthetic ligand.

Serif Senturk
Nitin H. Shirole
Raffaella Sordella
ResearchOpen Access22 Feb 2017
Nature Communications

Volume: 8, P: 1-10
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

An improved understanding of enhancers in mammalian genomes could facilitate the design of new regulatory elements. Melnikov et al. synthesize thousands of ~90 nt enhancer variants, assay their activity in human cells and use the data to rationally optimize synthetic enhancers.

Alexandre Melnikov
Anand Murugan
Tarjei S Mikkelsen
Research26 Feb 2012
Nature Biotechnology

Volume: 30, P: 271-277
Cell diversity and network dynamics in photosensitive human brain organoids

Long-term cultures of human brain organoids display a high degree of cellular diversity, mature spontaneous neuronal networks and are sensitive to light.

Giorgia Quadrato
Tuan Nguyen
Paola Arlotta
Research26 Apr 2017
Nature

Volume: 545, P: 48-53
Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices

The influence of X chromosome genetic variation on blood lipids and coronary heart disease (CHD) is not well understood. Here, the authors analyse X chromosome sequencing data across 65,322 multi-ancestry individuals, identifying associations of the Xq23 locus with lipid changes and reduced risk of CHD and diabetes mellitus.

Pradeep Natarajan
Akhil Pampana
Gina M. Peloso
ResearchOpen Access12 Apr 2021
Nature Communications

Volume: 12, P: 1-14
Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

Cancer drug targets are identified by CRISPR-based screens that knock out functional protein domains.

Junwei Shi
Eric Wang
Christopher R Vakoc
Research11 May 2015
Nature Biotechnology

Volume: 33, P: 661-667
Evaluation of methods for modeling transcription factor sequence specificity

The most comprehensive analysis to date of models of transcription-factor binding specificity reveals the best methods for predicting in vivo binding from in vitro data.

Matthew T Weirauch
Atina Cote
Timothy R Hughes
Research27 Jan 2013
Nature Biotechnology

Volume: 31, P: 126-134

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Specificity, synergy, and mechanisms of splice-modifying drugs

Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models

Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization

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

Cell diversity and network dynamics in photosensitive human brain organoids

Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

Evaluation of methods for modeling transcription factor sequence specificity

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