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High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene...
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Optimal Alignment
When we align two sequences, we in fact propose an evolutionary history for them. A history, where we account for three kinds of events, mutation,...
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Kinesin-7 CENP-E mediates chromosome alignment and spindle assembly checkpoint in meiosis I
In eukaryotes, meiosis is the genetic basis for sexual reproduction, which is important for chromosome stability and species evolution. The defects...
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Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment
DIA is a mainstream method for quantitative proteomics, but consistent quantification across multiple LC-MS/MS instruments remains a bottleneck in...
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Protein remote homology detection and structural alignment using deep learning
Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence...
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Pairwise Alignment, Multiple Alignment, and BLAST
Quantitative comparison of sequences can be performed pairwise by aligning two sequences based on considerations of gaps representing insertions or...
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Alignment and integration of spatial transcriptomics data
Spatial transcriptomics (ST) measures mRNA expression across thousands of spots from a tissue slice while recording the two-dimensional (2D)...
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Sequence Alignment
New biological sequences do not emerge de novo in nature but rather are derived from pre-existing sequences. This foundational principle underlies...
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PAK2 is essential for chromosome alignment in metaphase I oocytes
As a highly conserved and ubiquitously expressed serine/threonine kinase, p21-activated kinase 2 (PAK2) participates in diverse biologic events....
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Alignment of spatial genomics data using deep Gaussian processes
Spatially resolved genomic technologies have allowed us to study the physical organization of cells and tissues, and promise an understanding of...
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Fast Alignment
We change into the directory for chapters, make the directory for this chapter, change into that, make the directory for this section, and change...
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Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq
BackgroundParent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between...
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How Often Does Filtering of Alignment Columns Improve the Phylogenetic Inference of Two-Domain Proteins?
AbstractProtein phylogeny is usually reconstructed basing on a multiple alignment of amino acid sequences. One of the problems of such alignments is...
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Practicalities of Cell Sorting
Cell sorting is a technique commonly used in academic and biotechnology laboratories in order to separate out cells or particles of interest from...
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LocARNA 2.0: Versatile Simultaneous Alignment and Folding of RNAs
Generating accurate alignments of non-coding RNA sequences is indispensable in the quest for understanding RNA function. Nevertheless, aligning RNAs...
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SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment
Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them....
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Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
Charting an organs’ biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to...
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Scale-free dynamics in the core-periphery topography and task alignment decline from conscious to unconscious states
Scale-free physiological processes are ubiquitous in the human organism. Resting-state functional MRI studies observed the loss of scale-free...
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Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data
Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms....
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Application of Single-Cell Sequencing on Stem Cell Research
The variation and heterogeneity within cells are the fundamental features of stem cells. Each tissue has a resident stem cell niche compartmentalized...