Publications by authors named "P S Ebert"
Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplotype-collapsed assembly. Here, we present Graphasing, a workflow which synthesizes the global phase signal of Strand-seq with assembly graph topology to produce chromosome-scale de novo haplotypes for diploid genomes.
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- * It achieves a high level of completeness, closing 92% of previous assembly gaps and fully assembling complex regions, including 1,852 complex structural variants and 1,246 human centromeres.
- * The findings lead to significant improvements in genotyping accuracy and enable the detection of over 26,000 structural variants per sample, enhancing the potential for future disease association research.
Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess mutations (DNMs) and recombination. From this family, we estimate an average of 192 DNMs per generation, including 75.5 single-nucleotide variants (SNVs), 7.
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- A study evaluated the effectiveness of open-source large language models (LLMs) in extracting clinical data from unstructured mechanical thrombectomy reports for ischemic stroke patients.
- Three models (Mixtral, Qwen, BioMistral) were tested using data from two institutions, showing varying performance in precision and recall for clinical data categories.
- The findings suggest that LLMs, especially when combined with a human-in-the-loop approach, can significantly improve the efficiency and accuracy of clinical data extraction, with time savings of around 65.6% per case.
The electron optical phase contrast probed by electron holography at n-n GaN doping steps is found to exhibit a giant enhancement, in sharp contrast to the always smaller than expected phase contrast reported for p-n junctions. We unravel the physical origin of the giant enhancement by combining off-axis electron holography data with self-consistent electrostatic potential calculations. The predominant contribution to the phase contrast is shown to arise from the doping dependent screening length of the surface Fermi-level pinning, which is induced by FIB-implanted carbon point defects below the outer amorphous shell.
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