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Xiaolei Zhang
National Institutes of Health
7Publications
4H-index
40Citations
Publications 7
Newest
#1Roddy Walsh (NIH: National Institutes of Health)H-Index: 6
#2Francesco Mazzarotto (UniFI: University of Florence)H-Index: 6
Last.James S. Ware (Imperial College London)H-Index: 29
view all 28 authors...
Background International guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false-positive rate over test sensitivity and diagnostic yield. Genetic testing is also more likely informative in individuals with well-characterised variants from extensively studied European-ancestry populations. Inherited cardiomyopathies are relatively common Mendelian diseases that allow empirical calibration and asse...
5 CitationsSource
#1Nicola Whiffin (Broad Institute)H-Index: 18
#2Konrad J. Karczewski (Broad Institute)H-Index: 35
Last.James S. Ware (Broad Institute)H-Index: 29
view all 18 authors...
Upstream open reading frames (uORFs) are important tissue-specific cis-regulators of protein translation. Although isolated case reports have shown that variants that create or disrupt uORFs can cause disease, genetic sequencing approaches typically focus on protein-coding regions and ignore these variants. Here, we describe a systematic genome-wide study of variants that create and disrupt human uORFs, and explore their role in human disease using 15,708 whole genome sequences collected by the ...
4 CitationsSource
#1Massimo Maiolo (Swiss Institute of Bioinformatics)H-Index: 1
#2Xiaolei Zhang (NIH: National Institutes of Health)H-Index: 4
Last.Maria Anisimova (Swiss Institute of Bioinformatics)H-Index: 24
view all 4 authors...
Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny. Changes between homologous characters are typically modelled by a Markov substitution model. In contrast, the dynamics of indels are not modelled explicitly, because the computation of the marginal likelihood under such models has exponential time c...
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#1Nicola Whiffin (Imperial College London)H-Index: 18
#2Roddy Walsh (NIH: National Institutes of Health)H-Index: 6
Last.Stuart A. CookH-Index: 49
view all 22 authors...
Internationally adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier ( http://www.cardioclassifier.org ), a semiautomated decision-support tool for inherited cardiac conditions (ICCs). CardioClassifier integrates data retrieved from multiple sources with user-input case-specific information, through an interactive interface, to support variant interpretat...
16 CitationsSource
#1Nicola Whiffin (Imperial College London)H-Index: 18
#2Roddy Walsh (Imperial College London)H-Index: 6
Last.Stuart A. Cook (Imperial College London)H-Index: 49
view all 22 authors...
Purpose: Internationally-adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier (www.cardioclassifier.org), a semi-automated decision-support tool for inherited cardiac conditions (ICCs). Methods: CardioClassifier integrates data retrieved from multiple sources with user-input case-specific information, through an interactive interface, to support variant i...
2 CitationsSource
#1Xiaolei Zhang (NIH: National Institutes of Health)H-Index: 4
#2Eric Minikel (Broad Institute)H-Index: 12
Last.Ben Weisburd (Broad Institute)H-Index: 7
view all 6 authors...
This software repository provides a pipeline for converting raw ClinVar data files into analysis-friendly tab-delimited tables, and also provides these tables for the most recent ClinVar release. Separate tables are generated for genome builds GRCh37 and GRCh38 as well as for mono-allelic variants and complex multi-allelic variants. Additionally, the tables are augmented with allele frequencies from the ExAC and gnomAD datasets as these are often consulted when analyzing ClinVar variants. Overal...
13 CitationsSource
#1Massimo MaioloH-Index: 1
#2Xiaolei Zhang (NIH: National Institutes of Health)H-Index: 4
Last.Maria Anisimova (UZH: University of Zurich)
view all 4 authors...
Sequence alignment lies at the heart of many evolutionary and comparative genomics studies. However, the optimal alignment of multiple sequences is NP-hard, so that exact algorithms become impractical for more than a few sequences. Thus, state of the art alignment methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogenetic tree. Changes between homologous characters are typically modelled by a continuous-time Markov substitution model...
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