Alberto Peretti
National Institutes of Health
GeneDeep sequencingIntrinsic immunityViral replicationGenomeViral loadPathologyEmbryonic stem cellCellTranslation (biology)MetagenomicsRefSeqMolecular biologyVirologyCytoplasmHuman viromePhylogenetic treeCapsidImmunologyImmunodeficiencySkin cancerHPV infectionViral metagenomicsEpidermodysplasia verruciformisDNA Tumor VirusFamily PolyomaviridaeOne shotCircular DNADNA sequencingENCODERNAComputational biologyMedicineEvolutionary biologyGenBankChromatinBiologyViral evolutionRibosomeZoology
25Publications
9H-index
416Citations
Publications 22
Newest
#1Luca MinatiH-Index: 20
Last. Massimiliano ClamerH-Index: 4
view all 16 authors...
A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here we present AHARIBO, a method for the dete...
Source
#1Luca MinatiH-Index: 20
Last. Massimiliano ClamerH-Index: 4
view all 16 authors...
Source
#1Gabriel J. StarrettH-Index: 21
#2Michael J. TiszaH-Index: 7
Last. Christopher B. BuckH-Index: 52
view all 7 authors...
4 CitationsSource
#1Gabriel J. StarrettH-Index: 21
#2Michael J. TiszaH-Index: 7
Last. Christopher B. BuckH-Index: 52
view all 7 authors...
Abstract Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA (dsDNA) viruses. This supports the inference that at least some polintons are viruses that remain capable of cell-to-cell ...
4 CitationsSource
#1Michael J. Tisza (NIH: National Institutes of Health)H-Index: 7
#2Diana V. Pastrana (NIH: National Institutes of Health)H-Index: 30
Last. Christopher B. Buck (NIH: National Institutes of Health)
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When scientists hunt for new DNA sequences, sometimes they get a lot more than they bargained for. Such is the case in metagenomic surveys, which analyze not just DNA of a particular organism, but all the DNA in an environment at large. A vexing problem with these surveys is the overwhelming number of DNA sequences detected that are so different from any known microbe that they cannot be classified using traditional approaches. However, some of these “known unknowns” are undoubtedly viral sequen...
59 CitationsSource
#1Michael J. Tisza (NIH: National Institutes of Health)H-Index: 7
#2Diana V. Pastrana (NIH: National Institutes of Health)H-Index: 30
Last. Christopher B. Buck (NIH: National Institutes of Health)H-Index: 52
view all 26 authors...
7 CitationsSource
#1Michael J. Tisza (NIH: National Institutes of Health)H-Index: 7
#2Diana V. Pastrana (NIH: National Institutes of Health)H-Index: 30
Last. Christopher B. BuckH-Index: 52
view all 24 authors...
Although it is suspected that there are millions of distinct viral species, fewer than 9,000 are catalogued in GenBank9s RefSeq database. We selectively enriched for and amplified the genomes of circular DNA viruses in over 70 animal samples, ranging from cultured soil nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2,500 circular genomes in a GenBank-compliant format. The new genomes belong to dozens of established and e...
8 CitationsSource
#1Diana V. PastranaH-Index: 30
#2Alberto PerettiH-Index: 9
Last. Christopher B. BuckH-Index: 52
view all 32 authors...
ABSTRACT Several immunodeficiencies are associated with high susceptibility to persistent and progressive human papillomavirus (HPV) infection leading to a wide range of cutaneous and mucosal lesions. However, the HPV types most commonly associated with such clinical manifestations in these patients have not been systematically defined. Here, we used virion enrichment, rolling circle amplification, and deep sequencing to identify circular DNA viruses present in skin swabs and/or wart biopsy samp...
36 CitationsSource
#1Alberto Peretti (NIH: National Institutes of Health)H-Index: 9
#2Eileen M. Geoghegan (NIH: National Institutes of Health)H-Index: 1
Last. Christopher B. Buck (NIH: National Institutes of Health)H-Index: 52
view all 23 authors...
Summary BK polyomavirus (BKV) frequently causes nephropathy (BKVN) in kidney transplant recipients (KTRs). BKV has also been implicated in the etiology of bladder and kidney cancers. We characterized BKV variants from two KTRs who developed BKVN followed by renal carcinoma. Both patients showed a swarm of BKV sequence variants encoding non-silent mutations in surface loops of the viral major capsid protein. The temporal appearance and disappearance of these mutations highlights the intra-patient...
31 CitationsSource
#1Diana V. PastranaH-Index: 30
Last. Christopher B. BuckH-Index: 2
view all 4 authors...