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Nature Biotechnology
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#1Song Chen (UCSD: University of California, San Diego)H-Index: 3
#2Blue B. Lake (UCSD: University of California, San Diego)H-Index: 13
Last.Kun Zhang (UCSD: University of California, San Diego)H-Index: 46
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Single-cell RNA sequencing can reveal the transcriptional state of cells, yet provides little insight into the upstream regulatory landscape associated with open or accessible chromatin regions. Joint profiling of accessible chromatin and RNA within the same cells would permit direct matching of transcriptional regulation to its outputs. Here, we describe droplet-based single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq), a method that can link a cell’s transcriptome...
#1Binbin Chen (Stanford University)H-Index: 2
#2Michael S. Khodadoust (Stanford University)H-Index: 12
Last.Maximilian Diehn (Stanford University)H-Index: 43
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Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer immunotherapies. Current computational methods trained on in vitro binding data are limited by insufficient training data and algorithmic constraints. Here we describe MARIA (major histocompatibility complex analysis with recurrent integrated architecture; https://maria.stanford.edu/ ), a multimodal recurrent neural network for predicting the likeli...
#1Julien Racle (Swiss Institute of Bioinformatics)H-Index: 12
#2Justine Michaux (Ludwig Institute for Cancer Research)H-Index: 1
Last.Camilla Jandus (Ludwig Institute for Cancer Research)H-Index: 20
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Predictions of epitopes presented by class II human leukocyte antigen molecules (HLA-II) have limited accuracy, restricting vaccine and therapy design. Here we combined unbiased mass spectrometry with a motif deconvolution algorithm to profile and analyze a total of 99,265 unique peptides eluted from HLA-II molecules. We then trained an epitope prediction algorithm with these data and improved prediction of pathogen and tumor-associated class II neoepitopes. HLA class II epitopes are accurately ...
#1William H. Lewis (WUR: Wageningen University and Research Centre)
#2Thijs J. G. Ettema (WUR: Wageningen University and Research Centre)H-Index: 32
The move is the latest in the investor’s shift toward supporting early-stage companies. The move is the latest in the investor’s shift toward supporting early-stage companies.
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