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Steven L. Salzberg
Johns Hopkins University
Publications 395
Published on Feb 20, 2019in Nature Communications 11.88
Michelle Daya8
Estimated H-index: 8
(University of Colorado Denver),
Nicholas Rafaels29
Estimated H-index: 29
(University of Colorado Denver)
+ 62 AuthorsGenevieve L. Wojcik9
Estimated H-index: 9
(Stanford University)
Asthma is a complex disease with striking disparities across racial and ethnic groups. Despite its relatively high burden, representation of individuals of African ancestry in asthma genome-wide association studies (GWAS) has been inadequate, and true associations in these underrepresented minority groups have been inconclusive. We report the results of a genome-wide meta-analysis from the Consortium on Asthma among African Ancestry Populations (CAAPA; 7009 asthma cases, 7645 controls). We find ...
Published on Dec 1, 2019in Genome Biology 14.03
Steven L. Salzberg120
Estimated H-index: 120
(Johns Hopkins University)
While the genome sequencing revolution has led to the sequencing and assembly of many thousands of new genomes, genome annotation still uses very nearly the same technology that we have used for the past two decades. The sheer number of genomes necessitates the use of fully automated procedures for annotation, but errors in annotation are just as prevalent as they were in the past, if not more so. How are we to solve this growing problem?
Published in Nature Biotechnology 31.86
Daehwan Kim7
Estimated H-index: 7
(UTSW: University of Texas Southwestern Medical Center),
Joseph M. Paggi6
Estimated H-index: 6
(Stanford University)
+ -3 AuthorsSteven L. Salzberg120
Estimated H-index: 120
(Johns Hopkins University)
The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index. We use HISAT2 to represent and search an expanded model of the human reference genome in which over 14.5 million genomic variants in combination with haplotypes are incorporated into the data structure use...
Published on Jul 8, 2019in bioRxiv
Sam Kovaka (Johns Hopkins University), Aleksey V. Zimin24
Estimated H-index: 24
(Johns Hopkins University)
+ 3 AuthorsMihaela Pertea31
Estimated H-index: 31
(Johns Hopkins University)
RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads. StringTie2 includes new computational methods to handle the high error rate of long-read sequencing technology, which previous assemblers could not tolerate. It...
Published on Jun 20, 2019in bioRxiv
Andrew Read2
Estimated H-index: 2
(Cornell University),
Matthew J. Moscou16
Estimated H-index: 16
(Norwich Research Park)
+ 7 AuthorsAdam J. Bogdanove36
Estimated H-index: 36
(Cornell University)
Background: Long-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes make up one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice var...
Published on Jan 1, 2019in eLife 7.55
Evan T. Saitta4
Estimated H-index: 4
(FMNH: Field Museum of Natural History),
Evan T. Saitta1
Estimated H-index: 1
+ 16 AuthorsBen J. Novak2
Estimated H-index: 2
The chances of establishing a real-world Jurassic Park are slim. During the fossilization process, biological tissues degrade over millions of years, with some types of molecules breaking down faster than others. However, traces of biological material have been found inside some fossils. While some researchers believe these could be the remains of ancient proteins, blood vessels, and cells, traditionally thought to be among the least stable components of bone, others think that they have more re...
Published on May 7, 2019in Genome Research 9.94
Florian P. Breitwieser18
Estimated H-index: 18
Mihaela Pertea31
Estimated H-index: 31
+ 1 AuthorsSteven L. Salzberg120
Estimated H-index: 120
Published on Mar 1, 2019in New Phytologist 7.30
Amanda R. De La Torre8
Estimated H-index: 8
(UC Davis: University of California, Davis),
Daniela Puiu15
Estimated H-index: 15
(Johns Hopkins University)
+ 4 AuthorsDavid B. Neale36
Estimated H-index: 36
(UC Davis: University of California, Davis)
Published on Feb 15, 2019in Bioinformatics 4.53
Richard Wilton3
Estimated H-index: 3
(Johns Hopkins University),
Sarah J. Wheelan28
Estimated H-index: 28
(Johns Hopkins University)
+ 1 AuthorsSteven L. Salzberg120
Estimated H-index: 120
Published on Feb 1, 2019in Nature Genetics 25.45
Rachel M. Sherman2
Estimated H-index: 2
(Johns Hopkins University),
Juliet Forman1
Estimated H-index: 1
(HMC: Harvey Mudd College)
+ 43 AuthorsVictor E. Ortega9
Estimated H-index: 9
(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.