Peter Uetz

Peter Uetz
Virginia Commonwealth University | VCU · Center for Biological Data Science

PhD
Looking for collaborators in the areas of reptile biodiversity informatics

About

261
Publications
91,407
Reads
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14,941
Citations
Introduction
Peter Uetz currently works at the Center for Biological Data Science (formerly Center for the Study of Biological Complexity), Virginia Commonwealth University. Peter does research in Genetics, Bioinformatics, Microbiology, Molecular Biology, and Reptile Taxonomy. Current projects include 'Protein functions and protein-protein interactions in bacteria' and the Reptile Database.
Additional affiliations
September 2011 - present
Virginia Commonwealth University
Position
  • Professor (Associate)
January 2011 - September 2011
University of Delaware
Position
  • Professor
January 2006 - July 2010
J. Craig Venter Institute
Position
  • Professor (Associate)

Publications

Publications (261)
Conference Paper
Full-text available
Assessing and addressing biodiversity needs are of critical and time-sensitive importance, with the post-2020 Global Biodiversity Framework’s Global Taxonomy Initiative underscoring the need to build capacity in how we conceptualize biodiversity (Abrahamse et al. 2021). Species—as biological units—and their names are the backbone for the data integ...
Article
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Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional...
Chapter
Bei jedem biologischen Prozess spielen Protein-Protein-Wechselwirkungen eine wesentliche Rolle: DNA-Replikation, Transkription, Translation, Spleißen, Sekretion, Kontrolle des Zellzyklus oder Signaltransduktion können weitgehend anhand ihrer Proteininteraktionen beschrieben werden. Daher ist die Aufklärung dieser Abläufe vor allem eine Aufklärung d...
Article
Full-text available
We investigated to what extent European snakes can be identified by using their color, pattern and location. We coded these criteria for all 84 snake species of Europe, including European Russia, Ukraine, and Turkey as their eastern border. Brown and blotched snakes are most common, followed by dark (brown, black) and uniformly colored species. Som...
Article
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The Reptile Database (RDB) curates the literature and taxonomy for about 14,000 species and subspecies of reptiles (Uetz et al. 2021). Together with a few other databases, the RDB curates the literature for about 70,000 species of fish, amphibians, reptiles, birds and mammals. While it acts as a current name list for extant reptile taxa, including...
Article
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In 2020, the Reptile Database (RDB) and AmphibiaWeb (AW) celebrated their 25th and 20th anniversaries, respectively. Here, we briefly review their history and highlight the biodiversity informatics context in which AmphibiaWeb and the Reptile Database have grown for a quarter century. More specifically, we outline the similarities and differences o...
Article
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The secretive behavior and life history of snakes makes studying their biology, distribution, and the epidemiology of venomous snakebite challenging. One of the most useful, most versatile, and easiest to collect types of biological data are photographs, particularly those that are connected with geographic location and date-time metadata. Photos v...
Article
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YhcB, a poorly understood protein conserved across gamma-proteobacteria, contains a Domain of Unknown Function (DUF 1043) and an N-terminal transmembrane domain. Here we used an integrated approach including X-ray crystallography, genetics and molecular biology to investigate the function and structure of YhcB. The E. coli yhcB knock-out strain doe...
Article
Our knowledge of the conservation status of reptiles, the most diverse class of terrestrial vertebrates, has improved dramatically over the past decade, but still lags behind that of the other tetrapod groups. Here, we conduct the first comprehensive evaluation (~92% of the world's ~1714 described species) of the conservation 1 Joint senior authors...
Article
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Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions...
Preprint
Full-text available
YhcB, an uncharacterized protein conserved across gamma-proteobacteria, is composed predominantly of a single Domain of Unknown Function (DUF 1043) with an N-terminal transmembrane α-helix. Here, we show that E. coli YhcB is a conditionally essential protein that interacts with the proteins of the cell divisome (e.g., FtsI, FtsQ) and elongasome (e....
Article
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No central online repository exists for the collection of animal images; hence it remains unclear how extensively species have been illustrated in the published literature or online. Here we compiled a list of more than 8000 reptile species (out of 11,341) that have photos in one of six popular online repositories, namely iNaturalist (6,349 species...
Article
1935 gecko species (and 224 subspecies) were known in December 2019 in seven families and 124 genera. These nearly 2000 species were described by ~950 individuals of whom more than 100 described more than 10 gecko species each. Most gecko species were discovered during the past 40 years. The primary type specimens of all currently recognized geckos...
Article
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We compared the species names in the Reptile Database, a dedicated taxonomy database, with those in the NCBI taxonomy database, which provides the taxonomic backbone for the GenBank sequence database. About 67% of the known ~11,000 reptile species are represented with at least one DNA sequence and a binary species name in GenBank. However, a common...
Article
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We present information on primary type specimens for 13,282 species and subspecies of reptiles compiled in the Reptile Database, that is, holotypes, neotypes, lectotypes, and syntypes. These represent 99.4% of all 13,361 currently recognized taxa (11,050 species and 2311 subspecies). Type specimens of 653 taxa (4.9%) are either lost or not located,...
Article
Aim: Understanding the mechanisms determining species richness is a primary goal of biogeography. Richness patterns of subgroups within a taxon are usually assumed to be driven by similar processes. However, if richness of distinct ecological strategies respond differently to the same processes, inferences made for an entire taxon may be misleading...
Preprint
Full-text available
Research Infrastructures (RIs) are facilities, resources and services used by the scientific community to conduct research and foster innovation. LifeWatch ERIC has developed various virtual research environments, which include many virtual laboratories (vLabs) offering high computational capacity and comprehensive collaborative platforms that supp...
Preprint
Full-text available
Research Infrastructures (RIs) are facilities, resources and services used by the scientific community to conduct research and foster innovation. LifeWatch ERIC has developed various virtual research environments, which include many virtual laboratories (vLabs) offering high computational capacity and comprehensive collaborative platforms that supp...
Article
Full-text available
Folate derivatives are important cofactors for enzymes in several metabolic processes. Folate-related inhibition and resistance mechanisms in bacteria are potential targets for antimicrobial therapies and therefore a significant focus of current research. Here, we report that the activity of Escherichia coli poly-γ-glutamyl tetrahydrofolate/dihydro...
Article
Viruses infect their human hosts by a series of interactions between viral and host proteins, indicating that detailed knowledge of such virus-host interaction interfaces are critical for our understanding of viral infection mechanisms, disease etiology and the development of new drugs. In this review, we primarily survey human host-virus interacti...
Chapter
Two-hybrid methods remain among the most preferred choices for detecting protein–protein interactions (PPIs) and much of the PPI data in databases have been produced using yeast two-hybrid (Y2H) screens. The Y2H methods are extensively used to detect PPIs because of their scalability and accessibility. Several variants of Y2H methods have been deve...
Preprint
Full-text available
Research Infrastructures (RIs) are facilities, resources and services used by the scientific community to conduct research and foster innovation. LifeWatch ERIC has developed various virtual research environments, which include many virtual laboratories (vLabs) offering high computational capacity and comprehensive collaborative platforms that supp...
Article
Full-text available
Helicobacter pylori is a common pathogen that is estimated to infect half of the human population, causing several diseases such as duodenal ulcer. Despite one of the first pathogens to be sequenced, its proteome remains poorly characterised as about one third of its proteins have no functional annotation. Here, we integrate and analyze known prote...
Article
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By August 2017 an estimated 13,047 species and subspecies of extant reptiles have been described by a total of 6,454 papers and books which are listed in a supplementary file. For 1,052 species a total of 2,452 subspecies (excluding nominate subspecies) had been described by 2017, down from 1,295 species and 4,411 subspecies in 2009, due to the ele...
Article
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Bacterial cell envelope protein (CEP) complexes mediate a range of processes, including membrane assembly, antibiotic resistance and metabolic coordination. However, only limited characterization of relevant macromolecules has been reported to date. Here we present a proteomic survey of 1,347 CEPs encompassing 90% inner- and outer-membrane and peri...
Article
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p>In the version of this Article originally published, grant no. 2015/20215-7 for C.N. was omitted from the Acknowledgements section. This has now been corrected in all versions of the Article.</p
Article
Amino sugars are good sources of both ammonia and fructose-6-phosphate, produced by the glucosamine 6-phosphate deaminase, NagB. NagB is known to be allosterically regulated by N-acetylglucosamine 6-phosphate (GlcNAc-6P) and the phosphocarrier protein of the bacterial phosphotransferase system, HPr, in Escherichia coli. We provide evidence that Nan...
Article
Full-text available
Mycobacteriophage are viruses that infect mycobacteria. More than 1,400 mycobacteriophage genomes have been sequenced, coding for over one hundred thousand proteins of unknown functions. Here we investigate mycobacteriophage Giles-host protein-protein interactions (PPIs) using yeast two-hybrid screening (Y2H). A total of 25 reproducible PPIs were f...
Article
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Aim: Small geographic ranges make species especially prone to extinction from anthropogenic disturbances or natural stochastic events. We assemble and analyse a comprehensive dataset of all the world's lizard species and identify the species with the smallest ranges—those known only from their type localities. We compare them to wide-ranging specie...
Article
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The distributions of amphibians, birds and mammals have underpinned global and local conservation priorities, and have been fundamental to our understanding of the determinants of global biodiversity. In contrast, the global distributions of reptiles, representing a third of terrestrial vertebrate diversity, have been unavailable. This prevented th...
Article
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In this Article originally published, owing to a technical error, the author ‘Laurent Chirio’ was mistakenly designated as a corresponding author in the HTML version, the PDF was correct. This error has now been corrected in the HTML version. Further, in Supplementary Table 3, the authors misspelt the surname of ‘Danny Meirte’; this file has now be...
Article
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The family Tectiviridae comprises a group of tailless, icosahedral, membranecontaining bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well-characterized lytic viruses, the second one includes more variable temperate pha...
Article
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The functions of roughly a third of all proteins in Streptococcus pneumoniae , a significant human-pathogenic bacterium, are unknown. Using a yeast two-hybrid approach, we have determined more than 2,000 novel protein interactions in this organism. We augmented this network with meta-interactome data that we defined as the pool of all interactions...
Article
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The histidine-phosphorylatable phosphocarrier protein HPr, is an essential component of the sugar-transporting phosphotransferase system (PTS) in many bacteria. Recent interactome findings suggested that HPr interacts with several carbohydrate-metabolizing enzymes, but whether HPr plays a regulatory role was unclear. Here, we provide evidence that...
Article
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Background Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactome studies while several more h...
Article
Two-hybrid systems are one of the most popular, preferred, cost effective, and scalable in vivo genetic approaches for screening protein–protein interactions. A number of variants of yeast and bacterial two-hybrid systems exist, rendering them ideal for modern, flexible proteomics-driven studies. For mapping protein interactions at genome scales (t...
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The investigation of host-pathogen interaction interfaces and their constituent factors is crucial for our understanding of an organism's pathogenesis. Here, we explored the interactomes of HIV, hepatitis C virus, influenza A virus, human papillomavirus, herpes simplex virus, and vaccinia virus in a human host by analyzing the combined sets of viru...
Article
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Although an abundance of bacteriophages exists, little is known about interactions between their proteins and those of their bacterial hosts. Here, we experimentally determined the phage-host interactomes of the phages Dp-1 and Cp-1 and their underlying protein interaction network in the host Streptococcus pneumoniae. We compared our results to the...
Article
The human genome contains a large number of protein polymorphisms due to individual genome variation. How many of these polymorphisms lead to altered protein-protein interaction is unknown. We have developed a method to address this question. The intersection of the SKEMPI database (of affinity constants among interacting proteins) and CAPRI 4.0 do...
Article
Full-text available
Hepatitis E Virus (HEV) is an emerging virus causing epidemic acute hepatitis in developing countries as well as sporadic cases in industrialized countries. The life cycle of HEV is still poorly understood and the lack of efficient cell culture systems and animal models are the principal limitations for a detailed study of the viral replication cyc...
Article
AimAlthough most reptiles are oviparous, viviparity is a common mode of reproduction in squamates and has evolved multiple times in different lineages. We test two prevailing hypotheses regarding the biogeography of reptile reproductive modes to evaluate the selective forces driving the evolution of viviparity in snakes. The cold climate hypothesis...
Article
Full-text available
Mycobacteriophages are viruses that infect mycobacterial hosts and are prevalent in the environment. Nearly 700 mycobacteriophage genomes have been completely sequenced, revealing considerable diversity and genetic novelty. Here, we have determined the protein complement of mycobacteriophage Giles by mass spectrometry and mapped its genome-wide pro...
Article
Unlabelled: Helicobacter pylori (H. pylori) is a ε-proteobacterium that colonizes the stomach of about half of the world's population. Persistent infections have been associated with several gastric diseases. Mainly rod- or spiral shaped but also coccoid H. pylori forms have been isolated from mucus layer biopsies of patients. It is still being de...
Article
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Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays....
Article
Full-text available
Virtually all processes in living cells are dependent on protein-protein interactions (PPIs). Understanding PPI networks is thus essential for molecular biology and disease research. One powerful genetic system for mapping PPIs both at a small scale and in a high-throughput manner is the yeast two-hybrid (Y2H) screen. In Y2H screening, PPIs are det...
Article
Longevity is an important life-history trait, directly linked to the core attributes of fitness (reproduction and survival), yet large-scale comparative studies quantifying its implications for the ecology and life history of ectotherms are scarce. We tested the allometry of longevity in squamates and the tuatara, and determined how longevity is re...
Article
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Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 "gold standard" protein complexes identified by Ec...
Article
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Enterohemorrhagic E. coli (EHEC) manipulate their human host through at least 39 effector proteins which hijack host processes through direct protein-protein interactions (PPIs). To identify their protein targets in the host cells, we performed yeast two-hybrid screens, allowing us to find 48 high-confidence protein-protein interactions between 15...