ANSHUL KUNDAJE
Interested in Genomics, Machine Learning, Statistics, Big Data ... and Football (Soccer)
Last synced from Twitter 8m ago
Supporting Essential Open Source Software for Science
New grants fund 44 open source projects that accelerate biomedical research
Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis
Adenosine-to-inosine (A-to-I) RNA editing catalyzed by ADAR enzymes occurs in double-stranded RNAs (dsRNAs). How the RNA sequence and structure (i.e., the cis-regulation) determine the editing efficiency and specificity is poorly understood, despite...
Neutrinos Lead to Unexpected Discovery in Basic Math
Three physicists stumbled across an unexpected relationship between some of the most ubiquitous objects in math.
Mapping the perturbome network of cellular perturbations
Our understanding of the mechanisms of drug interactions remains limited. Here the authors introduce a framework to study how complex cellular perturbations induced by different drugs affect each other in morphological feature space.
In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants
mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose....
Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery
Activation of gene expression with chemical epigenetic modifiers
What Your Family History Can’t Tell You
Thanks to the National Human Genome Research Institute for supporting this episode. If you’re interested in learning more about the human genome and the late...
How many rare diseases are there?
A lack of robust knowledge of the number of rare diseases and the number of people affected by them limits the development of approaches to ameliorate the substantial cumulative burden of rare diseases. Here, we call for coordinated efforts to more...
Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses
Horizontal integration of summary statistics from different GWAS traits can be used to evaluate evidence for their shared genetic causality. One popular method to do this is a Bayesian method, coloc, which is attractive in requiring only GWAS...
Self-training with Noisy Student improves ImageNet classification
We present a simple self-training method that achieves 87.4% top-1 accuracy
on ImageNet, which is 1.0% better than the state-of-the-art model that requires
3.5B weakly labeled Instagram images. On robustness test sets, it improves
ImageNet-A top-1...
How to review a paper
A blog from the Raj Lab for systems biology
Hikvision Markets Uyghur Ethnicity Analytics, Now Covers Up
Hikvision has marketed an AI camera that automatically identifies Uyghurs, only covering it up days ago after IPVM questioned them on it.
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation
FreeHi-C takes Hi-C sequencing data as input and simulates reads with random mutations and indels from the interacting fragment pairs. FreeHi-C-simulated replicates are used for benchmarking Hi-C analysis methods and enable data augmentation for...
JASPAR RESTful API
A RESTful API to access the latest version of JASPAR database programmatically.
Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability
The conserved long noncoding RNA Chaserr is transcribed upstream of the chromatin remodeler Chd2. Here, using mouse genetics and high throughput assays, the authors show that Chaserr inhibits expression of Chd2 in cis and is required for postnatal...
MOFA+: a probabilistic framework for comprehensive integration of structured single-cell data
Technological advances have enabled the joint analysis of multiple molecular layers at single cell resolution. At the same time, increased experimental throughput has facilitated the study of larger numbers of experimental conditions. While methods...
The multiscale effects of polycomb mechanisms on 3D chromatin folding
(2019). The multiscale effects of polycomb mechanisms on 3D chromatin folding. Critical Reviews in Biochemistry and Molecular Biology. Ahead of Print.
Systematic bias assessment in solid tissue 10x scRNA-seq workflows
Single-cell and single-nucleus RNA sequencing have been widely adopted in studies of heterogeneous tissues to estimate their cellular composition and obtain transcriptional profiles of individual cells. However, the current fragmentary understanding...