John Bryan
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View article: Single-cell and spatiotemporal profile of ovulation in the mouse ovary
Single-cell and spatiotemporal profile of ovulation in the mouse ovary Open
Ovulation is a spatiotemporally coordinated process that involves several tightly controlled events, including oocyte meiotic maturation, cumulus expansion, follicle wall rupture and repair, and ovarian stroma remodeling. To date, no studi…
View article: Accurate trajectory inference in time-series spatial transcriptomics with structurally-constrained optimal transport
Accurate trajectory inference in time-series spatial transcriptomics with structurally-constrained optimal transport Open
New experimental and computational methods use genetic or gene expression observations with single cell resolution to study the relationship between single-cell molecular profiles and developmental trajectories. Most tissues contain spatia…
View article: Single-cell and spatiotemporal profile of ovulation in the mouse ovary
Single-cell and spatiotemporal profile of ovulation in the mouse ovary Open
Summary Ovulation is a spatiotemporally coordinated process that involves several tightly controlled events, including oocyte meiotic maturation, cumulus expansion, follicle wall rupture and repair, and ovarian stroma remodeling. To date, …
View article: Optimization-based decoding of Imaging Spatial Transcriptomics data
Optimization-based decoding of Imaging Spatial Transcriptomics data Open
Motivation Imaging Spatial Transcriptomics techniques characterize gene expression in cells in their native context by imaging barcoded probes for mRNA with single molecule resolution. However, the need to acquire many rounds of high-magni…
View article: Optimization-Based Decoding of Imaging Spatial Transcriptomics Data
Optimization-Based Decoding of Imaging Spatial Transcriptomics Data Open
Motivation Imaging Spatial Transcriptomics (iST) techniques characterize gene expression in cells in their native context by imaging barcoded probes for mRNA with single molecule resolution. However, the need to acquire many rounds of high…
View article: Deep Unrolled Recovery in Sparse Biological Imaging
Deep Unrolled Recovery in Sparse Biological Imaging Open
Deep algorithm unrolling has emerged as a powerful model-based approach to develop deep architectures that combine the interpretability of iterative algorithms with the performance gains of supervised deep learning, especially in cases of …
View article: Key Elements for a Doctoral Annotated Bibliography
Key Elements for a Doctoral Annotated Bibliography Open
The purpose of this article is to present an overview of why annotated bibliographies are needed in higher education, especially in doctoral education programs. The necessity for emerging scholars to build an annotated bibliography is para…
View article: The highs and lows of English consort music: compass, range and register as a guide to instrumental character
The highs and lows of English consort music: compass, range and register as a guide to instrumental character Open
By analysing the ways in which Elizabethan and Jacobean composers used different combinations of range in individual parts of polyphonic pieces, and the overall compass of their works, we can gain insights into their expectations of the in…