Scheme of Examination There will be three papers: Papers 1, 2, and 3, all of which must be taken. Papers 1 and 2 will be composite papers to be taken in one sitting. PAPER 1: This will consist of fifty multiple-choice objective questions drawn from Section A of the syllabus (the sec...
Gene expression inference with deep learning[github][paper] This deals with a specific prediction task, namely to predict the expression of specified target genes from a panel of about 1,000 pre-selected “landmark genes”. As the authors explain, gene expression levels are often highly correlate...
Tight junction genes specifically mark epicardium To follow transcriptional changes accompanying regeneration and discover specific markers of the salamander epicardium, we performed scRNA-seq on 2,386 live cells collected from sham-operated and regenerating hearts at 7, 14 and 28 d.p.ci. (Fig.3a...
d, Fluorescence microscopy images of 40 µM AR-AD droplets (WT* and mutants) at 1 M NaCl. Scale bar, 10 μm. e, Scheme of the phase diagram of the AR AD and of how Tc measurements at different solution conditions allow the phase separation capacity of the mutants to be ranked...
c Performance of SpaDo when using cell type annotation from original paper or Seurat v4 with different value of parameter “Resolution” on osmFISH, seqFISH, and STARmap datasets. R resolution. d Performance of SpaDo when using different spot deconvolution methods. e Performance of SpaDo when ...
plotHypercube.motifsMotif plot of feature acquisition probabilities at discrete orderingsfeaturenames=c("") (set of feature names),label.size=3 (size of feature labels),label.scheme="full" (feature labels every timestep, or more sparsely) ...
In this paper, we describe in detail the NetAct platform, extensive benchmark tests for TF-target databases, TF activity inference, network construction, and two examples of applications to model GRNs with time series gene expression data.
Identifying network architecture from observed neural activities is crucial in neuroscience studies. A key requirement is knowledge of the statistical input-output relation of single neurons in vivo. By utilizing an exact analytical solution of the spike
After a 15-s incubation, the grid was blotted for 4 s at 4 °C, 100% humidity, using Whatman grade-595 filter paper, then plunged into liquid ethane using a Vitrobot Mark IV system (Thermo Fisher Scientific). A single grid was imaged for data collection using a Talos Arctica ...
paper [102], simulators such as SymSim [103] and Splatter [68] do not preserve real genes, and Sergio [104] requires an additional input of a gene regulatory network and cannot preserve the observed gene-gene correlations in real data. We note that we do not aim to benchmark simulators...