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Rachel M. Sherman
Johns Hopkins University
GenomeReference genomeDNA sequencingGeneticsBiology
10Publications
5H-index
139Citations
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Publications 9
Newest
#1Alaina Shumate (Johns Hopkins University)H-Index: 2
#2Aleksey V. Zimin (Johns Hopkins University)H-Index: 29
Last. Steven L. Salzberg (Johns Hopkins University)H-Index: 131
view all 10 authors...
Here we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 ...
2 CitationsSource
#1Rachel M. Sherman (Johns Hopkins University)H-Index: 5
#2Steven L. SalzbergH-Index: 131
Since the early days of the genome era, the scientific community has relied on a single ‘reference’ genome for each species, which is used as the basis for a wide range of genetic analyses, including studies of variation within and across species. As sequencing costs have dropped, thousands of new genomes have been sequenced, and scientists have come to realize that a single reference genome is inadequate for many purposes. By sampling a diverse set of individuals, one can begin to assemble a pa...
5 CitationsSource
#1Sai Chen (Illumina)H-Index: 6
#2Peter Krusche (Illumina)H-Index: 12
Last. Michael A. Eberle (Illumina)H-Index: 25
view all 11 authors...
Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations. We demonstrate the accuracy of Paragraph on whole-genome sequence data from three samples using long-read SV calls as the truth set, and then apply Paragraph at scale to a cohort of 100 short-read sequenced samples ...
6 CitationsSource
#1Sergey Aganezov (Johns Hopkins University)H-Index: 6
#2Sara Goodwin (CSHL: Cold Spring Harbor Laboratory)H-Index: 9
Last. Michael C. Schatz (Johns Hopkins University)H-Index: 60
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Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of disease progression. We performed whole genome sequencing of the SKBR3 breast cancer cell-line and patient-derived tumor and normal organoids from two breast cancer patients using 10X/Illumina, PacBio, and Oxford Nanopore sequencing. We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble ...
1 CitationsSource
#1Sai Chen (Illumina)H-Index: 6
#2Peter Krusche (Illumina)H-Index: 12
Last. Michael A. Eberle (Illumina)H-Index: 25
view all 11 authors...
Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations. We demonstrate the accuracy of Paragraph on whole-genome sequence data from three samples using long read SV calls as the truth set, and then apply Paragraph at scale to a cohort of 100 short-read sequenced samples ...
6 CitationsSource
#1Rachel M. Sherman (Johns Hopkins University)H-Index: 5
#2Juliet Forman (HMC: Harvey Mudd College)H-Index: 2
Last. Steven L. SalzbergH-Index: 131
view all 46 authors...
In the version of this article initially published, the statement “there are no pan-genomes for any other animal or plant species” was incorrect. The statement has been corrected to “there are no reported pan-genomes for any other animal species, to our knowledge.” We thank David Edwards for bringing this error to our attention. The error has been corrected in the HTML and PDF versions of the article.
2 CitationsSource
#1Rachel M. Sherman (Johns Hopkins University)H-Index: 5
#2Juliet Forman (HMC: Harvey Mudd College)H-Index: 2
Last. Steven L. SalzbergH-Index: 131
view all 46 authors...
We used a deeply sequenced dataset of 910 individuals, all of African descent, to construct a set of DNA sequences that is present in these individuals but missing from the reference human genome. We aligned 1.19 trillion reads from the 910 individuals to the reference genome (GRCh38), collected all reads that failed to align, and assembled these reads into contiguous sequences (contigs). We then compared all contigs to one another to identify a set of unique sequences representing regions of th...
75 CitationsSource
#1Victoria L. Sork (UCLA: University of California, Los Angeles)H-Index: 45
#2Sorel Fitz-Gibbon (UCLA: University of California, Los Angeles)H-Index: 28
Last. Steven L. SalzbergH-Index: 131
view all 10 authors...
Oak represents a valuable natural resource across Northern Hemisphere ecosystems, attracting a large research community studying its genetics, ecology, conservation, and management. Here we introduce a draft genome assembly of valley oak (Quercus lobata) using Illumina sequencing of adult leaf tissue of a tree found in an accessible, well-studied, natural southern California population. Our assembly includes a nuclear genome and a complete chloroplast genome, along with annotation of encoded gen...
39 CitationsSource
#1John G. D. CannonH-Index: 1
#1John G. D. Cannon (Carleton College)H-Index: 5
Last. Grace A. Newman (Carleton College)H-Index: 1
view all 4 authors...
The role of amino acid-RNA nucleobase interactions in the evolution of RNA translation and protein-mRNA autoregulation remains an open area of research. We describe the inference of pairwise amino acid-RNA nucleobase interaction preferences using structural data from known RNA-protein complexes. We observed significant matching between an amino acid’s nucleobase affinity and corresponding codon content in both the standard genetic code and mitochondrial variants. Furthermore, we showed that know...
1 CitationsSource
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