ANSHUL KUNDAJE
Interested in Genomics, Machine Learning, Statistics, Big Data ... and Football (Soccer)
Last synced from Twitter 19m ago
Charting a tissue from single-cell transcriptomes
Massively multiplexed sequencing of RNA in individual cells is transforming basic and clinical life sciences. However, in standard experiments, tissues must first be dissociated. Thus, after sequencing, information about the spatial relationships...
How Democracies Die - Steven Levitsky
Is American democracy in danger? Levitsky asked this question in his 2018 New York Times bestseller How Democracies Die.
Prioritizing transcriptomic and epigenomic experiments by using an optimization strategy that leverages imputed data
Successful science often involves not only performing experiments well, but also choosing well among many possible experiments. In a hypothesis generation setting, choosing an experiment well means choosing an experiment whose results are...
ENCODE Data Submission Engineer in School of Medicine, Stanford, California, United States
The Stanford Center for Genomics and Personalized Medicine (SCGPM) has an excellent opportunity available for a motivated ENCODE Data Submission...
Linking transcriptome and chromatin accessibility in nanoliter droplets for single-cell sequencing
Linked profiling of transcriptome and chromatin accessibility from single cells can provide unprecedented insights into cellular status. Here we developed a droplet-based Single- Nucleus chromatin Accessibility and mRNA Expression sequencing...
DNA mismatches reveal widespread conformational penalties in protein-DNA recognition
Transcription-factor (TF) proteins recognize specific genomic sequences, despite an overwhelming excess of non-specific DNA, to regulate complex gene expression programs. While there have been significant advances in understanding how DNA sequence...
Guest post by Julien Mairal: A Kernel Point of View on Convolutional Neural Networks, part II
[latexpage] This is a continuation of Julien Mairal’s guest post on CNNs, see part I here. Stability to deformations of convolutional neural networks In their ICML paper Zhang et al. introduc…
Research finds that a new culprit can cause breast cancer to spread
Stanford Engineering Digital Magazine Article
Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules
Our vision of DNA transcription and splicing has changed dramatically with the introduction of short-read sequencing. These high-throughput sequencing technologies promised to unravel the complexity of any transcriptome. Generally gene expression...
A Deep Generative Model for Graph Layout
Different layouts can characterize different aspects of the same graph.
Finding a "good" layout of a graph is thus an important task for graph
visualization. In practice, users often visualize a graph in multiple layouts
by using different methods...
Tools for the analysis of single-cell chromatin data
A toolkit for the analysis, quality control, visualization, and exploration of single-cell chromatin data.
olgabot/awesome-advisors
Academic (Masters', PhD, Postdoc) advisors with explicitly stated expectations of themselves and their mentees - olgabot/awesome-advisors
DSE-MSU/R-transformer
Contribute to DSE-MSU/R-transformer development by creating an account on GitHub.
R-Transformer: Recurrent Neural Network Enhanced Transformer
Recurrent Neural Networks have long been the dominating choice for sequence
modeling. However, it severely suffers from two issues: impotent in capturing
very long-term dependencies and unable to parallelize the sequential
computation procedure....
An hourglass pattern of inter-embryo gene expression variability and of histone regulation in fly embryogenesis
Gene expression is in part a stochastic process, which is at odds with the need for precise expression levels in biological processes such as embryonic development. To study the tension between precision and stochasticity of gene expression during...