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Steven L. Salzberg
Johns Hopkins University
395Publications
118H-index
135kCitations
Publications 395
Newest
2019 in Nature GeneticsIF: 27.13
Rachel M. Sherman1
Estimated H-index: 1
(Johns Hopkins University),
Juliet Forman (Harvey Mudd College)+ 43 AuthorsVictor E. Ortega8
Estimated H-index: 8
(Wake Forest University)
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...
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2019 in Nature GeneticsIF: 27.13
Rachel M. Sherman1
Estimated H-index: 1
(Johns Hopkins University),
Juliet Forman (Harvey Mudd College)+ 43 AuthorsVictor E. Ortega8
Estimated H-index: 8
(Wake Forest University)
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.
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2018 in Genome BiologyIF: 13.21
Mihaela Pertea30
Estimated H-index: 30
(Johns Hopkins University),
Alaina Shumate2
Estimated H-index: 2
(Johns Hopkins University)
+ 6 AuthorsSteven L. Salzberg118
Estimated H-index: 118
We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains 42,611 genes, of which 20,352 are potentially protein-coding and 22,259 are noncoding, and a total of 323,258 transcripts. These include 224 novel protein-coding genes and 116,156 novel transcripts. We detected over 30 million additional transcripts at more than 650,000 genomic loci, nearl...
2 Citations Source Cite
2018 in New PhytologistIF: 7.43
Amanda R. De La Torre5
Estimated H-index: 5
(University of California, Davis),
Daniela Puiu13
Estimated H-index: 13
(Johns Hopkins University)
+ 4 AuthorsDavid B. Neale38
Estimated H-index: 38
(University of California, Davis)
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2018 in Nature CommunicationsIF: 12.35
Seyedeh M. Zekavat9
Estimated H-index: 9
(Yale University),
Sanni Ruotsalainen2
Estimated H-index: 2
(University of Helsinki)
+ 339 AuthorsJesse M. Engreitz17
Estimated H-index: 17
(Broad Institute)
Lipoprotein(a), Lp(a), is a modified low-density lipoprotein particle that contains apolipoprotein(a), encoded by LPA, and is a highly heritable, causal risk factor for cardiovascular diseases that varies in concentrations across ancestries. Here, we use deep-coverage whole genome sequencing in 8392 individuals of European and African ancestry to discover and interpret both single-nucleotide variants and copy number (CN) variation associated with Lp(a). We observe that genetic determinants betwe...
2 Citations Download PDF Cite
Guillaume Marçais14
Estimated H-index: 14
(University of Maryland, College Park),
Arthur L. Delcher21
Estimated H-index: 21
(Johns Hopkins University)
+ 3 AuthorsAleksey V. Zimin25
Estimated H-index: 25
(University of Maryland, College Park)
The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major release of MUMmer version 3 in 2004, it has been applied to many types of problems including aligning whole genome sequences, aligning reads to a reference genome, and comparing different assemblies of the same genome. Despite its broad utility, MUMmer3 has limitations that can make it difficult to use for large genomes and for the very l...
22 Citations Source Cite
2018 in bioRxiv
Jennifer Lu5
Estimated H-index: 5
(Johns Hopkins University),
Steven L. Salzberg118
Estimated H-index: 118
(Johns Hopkins University)
Metagenomic sequencing of patient samples is a very promising method for the diagnosis of human infections. Sequencing has the ability to capture all the DNA or RNA from pathogenic organisms in a human sample. However, complete and accurate characterization of the sequence, including identification of any pathogens, depends on the availability and quality of genomes for comparison. Thousands of genomes are now available, and as these numbers grow, the power of metagenomic sequencing for diagnosi...
1 Citations Download PDF Cite
2018 in Genome BiologyIF: 13.21
Florian P. Breitwieser6
Estimated H-index: 6
(Johns Hopkins University),
Dannon Baker7
Estimated H-index: 7
(Johns Hopkins University),
Steven L. Salzberg118
Estimated H-index: 118
(Johns Hopkins University)
False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in ...
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2018 in bioRxiv
Daehwan Kim1
Estimated H-index: 1
(University of Texas Southwestern Medical Center),
Joseph M. Paggi4
Estimated H-index: 4
(Stanford University),
Steven L. Salzberg118
Estimated H-index: 118
(Johns Hopkins University School of Medicine)
Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses of human genomes. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT-genotype, for representing and searching an expanded model of the human reference genome, in which a comprehensive catalogue of known genomic variants and haplotypes is incor...
3 Citations Download PDF Cite
Kristian Stevens14
Estimated H-index: 14
,
Keith Woeste15
Estimated H-index: 15
(Purdue University)
+ 11 AuthorsAbhaya M. Dandekar40
Estimated H-index: 40
(University of California, Davis)
Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia : Juglans sigillata (also from section Dioscaryon ), Juglans nigra , Juglans microcarpa , Juglans hindsii (from section Rhysocaryon ), Juglans cathayensis (from section Cardiocaryon ), and the closely related Pterocarya stenoptera . While these are ‘draft’...
1 Citations Download PDF Cite
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