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Ivan Adzhubei
Harvard University
24Publications
15H-index
12.1kCitations
Publications 24
Newest
Published in Genetics in Medicine 8.68
Christopher A. Cassa18
Estimated H-index: 18
(Harvard University),
Daniel M. Jordan12
Estimated H-index: 12
(ISMMS: Icahn School of Medicine at Mount Sinai)
+ -3 AuthorsShamil R. Sunyaev64
Estimated H-index: 64
(Harvard University)
Over 150,000 variants have been reported to cause Mendelian disease in the medical literature. It is still difficult to leverage this knowledge base in clinical practice, as many reports lack strong statistical evidence or may include false associations. Clinical laboratories assess whether these variants (along with newly observed variants that are adjacent to these published ones) underlie clinical disorders. We investigated whether citation data—including journal impact factor and the number ...
Published on Apr 1, 2017in Developmental Biology 2.94
Virginia Savova13
Estimated H-index: 13
(Harvard University),
Esther J. Pearl5
Estimated H-index: 5
(MBL: Marine Biological Laboratory)
+ 4 AuthorsLeonid Peshkin29
Estimated H-index: 29
(Harvard University)
Abstract We characterize the genetic diversity of Xenopus laevis strains using RNA-seq data and allele-specific analysis. This data provides a catalogue of coding variation, which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). Fu...
Published on Feb 1, 2015in Nature Genetics 25.45
Ron Do36
Estimated H-index: 36
,
Daniel J. Balick7
Estimated H-index: 7
+ 3 AuthorsDavid Reich107
Estimated H-index: 107
David Reich, Shamil Sunyaev and colleagues report an analysis of the per-genome accumulation of nonsynonymous substitutions across diverse pairs of human populations. They find no evidence for a higher load of deleterious mutations in non-Africans than in West Africans and show that the observed patterns are not likely to reflect changes in natural selection.
Ron Do36
Estimated H-index: 36
,
Daniel J. Balick7
Estimated H-index: 7
+ -3 AuthorsDavid Reich107
Estimated H-index: 107
Non-African populations have experienced major bottlenecks in the time since their split from West Africans, which has led to the hypothesis that natural selection to remove weakly deleterious mutations may have been less effective in non-Africans. To directly test this hypothesis, we measure the per-genome accumulation of deleterious mutations across diverse humans. We fail to detect any significant differences, but find that archaic Denisovans accumulated non-synonymous mutations at a higher r...
Published on Jan 1, 2013in Current protocols in human genetics
Ivan Adzhubei15
Estimated H-index: 15
(Brigham and Women's Hospital),
Daniel M. Jordan12
Estimated H-index: 12
(Harvard University),
Shamil R. Sunyaev64
Estimated H-index: 64
(Brigham and Women's Hospital)
PolyPhen-2 (Polymorphism Phenotyping v2), available as software and via a Web server, predicts the possible impact of amino acid substitutions on the stability and function of human proteins using structural and comparative evolutionary considerations. It performs functional annotation of single-nucleotide polymorphisms (SNPs), maps coding SNPs to gene transcripts, extracts protein sequence annotations and structural attributes, and builds conservation profiles. It then estimates the probability...
Published on Aug 1, 2012in Genome Research 9.94
Ignaty Leshchiner18
Estimated H-index: 18
(Harvard University),
Kristen Alexa7
Estimated H-index: 7
(Harvard University)
+ 14 AuthorsMaija Garnaas11
Estimated H-index: 11
(Harvard University)
Genetic mapping of mutations in model systems has facilitated the identification of genes contributing to fundamental biological processes including human diseases. However, this approach has historically required the prior characterization of informative markers. Here we report a fast and cost-effective method for genetic mapping using next-generation sequencing that combines single nucleotide polymorphism discovery, mutation localization, and potential identification of causal sequence variant...
Published on Apr 1, 2010in Nature Methods 28.47
Ivan Adzhubei15
Estimated H-index: 15
(Harvard University),
Steffen Schmidt27
Estimated H-index: 27
(MPG: Max Planck Society)
+ 5 AuthorsShamil R. Sunyaev64
Estimated H-index: 64
(Harvard University)
To the Editor: Applications of rapidly advancing sequencing technologies exacerbate the need to interpret individual sequence variants. Sequencing of phenotyped clinical subjects will soon become a method of choice in studies of the genetic causes of Mendelian and complex diseases. New exon capture techniques will direct sequencing efforts towards the most informative and easily interpretable protein-coding fraction of the genome. Thus, the demand for computational predictions of the impact of p...
Published on Apr 1, 2009in Nature Genetics 25.45
John A. Stamatoyannopoulos71
Estimated H-index: 71
(UW: University of Washington),
Ivan Adzhubei15
Estimated H-index: 15
(Harvard University)
+ 3 AuthorsShamil R. Sunyaev64
Estimated H-index: 64
(Harvard University)
Eukaryotic DNA replication is highly stratified, with different genomic regions shown to replicate at characteristic times during S phase. Here we observe that mutation rate, as reflected in recent evolutionary divergence and human nucleotide diversity, is markedly increased in later-replicating regions of the human genome. All classes of substitutions are affected, suggesting a generalized mechanism involving replication time-dependent DNA damage. This correlation between mutation rate and regi...
Published on Dec 10, 2008in PLOS Genetics 5.22
Steffen Schmidt27
Estimated H-index: 27
,
Anna Gerasimova2
Estimated H-index: 2
+ 3 AuthorsShamil R. Sunyaev64
Estimated H-index: 64
The fourth author's name was spelled incorrectly. The correct name is: Ivan A. Adzhubei. The correct citation is: Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Kondrashov AS, et al. (2008) Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection. PLoS Genet 4(11): e1000281. doi:10.1371/journal.pgen.1000281
Published on Nov 28, 2008in PLOS Genetics 5.22
Steffen Schmidt27
Estimated H-index: 27
(MPG: Max Planck Society),
Anna Gerasimova2
Estimated H-index: 2
(UM: University of Michigan)
+ 3 AuthorsShamil R. Sunyaev64
Estimated H-index: 64
(Brigham and Women's Hospital)
Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be prese...
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