Author
Rob Knight
Other affiliations: Anschutz Medical Campus, University of Sydney, Veterans Health Administration ...read more
Bio: Rob Knight is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Microbiome & Gut flora. The author has an hindex of 201, co-authored 1061 publications receiving 253207 citations. Previous affiliations of Rob Knight include Anschutz Medical Campus & University of Sydney.
Topics: Microbiome, Gut flora, Medicine, Metagenomics, Biology
Papers published on a yearly basis
Papers
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University of New South Wales1, University of California, San Diego2, University of Auckland3, UPRRP College of Natural Sciences4, Wageningen University and Research Centre5, Shanghai Jiao Tong University6, National University of Ireland, Galway7, Victoria University of Wellington8, University of Notre Dame9, Paul Sabatier University10, University of Alabama11, Institut national de la recherche agronomique12, University of Haifa13, Australian Institute of Marine Science14, Tel Aviv University15, University of North Carolina at Wilmington16, University of Oldenburg17, University of British Columbia18, Stony Brook University19, University of Lisbon20, University of Maryland Center for Environmental Science21, King Abdullah University of Science and Technology22, Leibniz Institute of Marine Sciences23, University of Queensland24
TL;DR: A formula was incorrect upon initial publication that should instead be p-value = binomial cdf (T(v)-Kv(s), T(v), PNull (s), 1-PNull (s).
Abstract: The sponge microbiome project Lucas Moitinho-Silva et al. GigaScience, 6, 2017; doi: 10.1093/gigascience/gix077. A formula was incorrect upon initial publication. The formula p-value = binomial cdf (T(v)-Kv(s), T(v), PNull (s)) should instead be p-value = binomial cdf (T(v)-Kv(s), T(v), 1-PNull (s)). This has now been corrected.
3 citations
3 citations
TL;DR: It is determined that bacterial metabolism underpins fluoropyrimidine cytotoxicity, providing a paradigm for unraveling bacterial mechanisms in drug metabolism.
3 citations
TL;DR: Transient ischaemic attacks often have very similar, sometimes identical, characteristics, which implies that the same area of the brain is rendered ischaemia at each attack.
Abstract: Transient ischaemic attacks often have very similar, sometimes identical, characteristics. This implies that the same area of the brain is rendered ischaemic at each attack. The cause is usually an atherothrombo-embolism. To produce stereotypical episodes of ischaemia, such emboli must lodge in the same small artery each time. As the embolus starts from a point far from its eventual destination, how do many emboli reach the same artery?
The probable explanation is that currents and eddies in a major blood vessel are similar at different times. So, emboli released into the internal carotid artery at the same point, but at different times, might be expected to arrive at the same destination, or at least many might.
This suggestion is hard to test, but the picture is in some ways similar to what happens in a river or stream. This is how the concept of the …
3 citations
TL;DR: The basic behavioral and electrophysiological signatures of implicit ChoI are common to a wide range of ages, however, older subjects, despite showing a similar dynamic decision trajectory as younger adults, are slower, more prudent and finalize the decision making process before letting the information affect the peripheral motor system.
Abstract: Decision making often requires making arbitrary choices (‘picking’) between alternatives that make no difference to the agent, that are equally desirable, or when the potential rewards are unknown. Using event-related potentials we tested the effect of age on this common type of decision making. We compared two age groups: ages 18-25, and ages 41-67 on a masked-priming paradigm while recording EEG and EMG. Participants pressed a right or left button following either an instructive arrow cue or a neutral free-choice picking cue, both preceded by a masked arrow or neutral prime. The prime affected the behavior on the Instructed and the Free-choice picking conditions both in the younger and older groups. Moreover, electrophysiological ‘Change of Intention’ was observed via Lateralized Readiness Potential (LRP) in both age groups – the polarity of the LRP indicated first preparation to move the primed hand and then preparation to move the other hand. However, the older participants were more conservative in responding to the instructive cue, exhibiting a speed-accuracy trade-off, with slower response times, less errors in incongruent trials, and reduced probability of EMG activity in the non-responding hand. Additionally, ‘Change of Intention’ was observed in both age groups in slow RT trials with a neutral prime as a result of an endogenous early intention to respond in a direction opposite the eventual instructing arrow cue. We conclude that the basic behavioral and electrophysiological signatures of implicit change of intention are common to a wide range of ages. However, older subjects, despite showing a similar dynamic decision trajectory as younger adults, are slower, more prudent and finalize the decision making process before letting the information affect the peripheral motor system. In contrast, the flow of information in younger subjects occurs in parallel to the decision process.
3 citations
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TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Abstract: Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion of QIIME analyses presented in the main text; Sequencing of 16S rRNA gene amplicons; QIIME analysis notes; Expanded Figure 1 legend; Links to raw data and processed output from the runs with and without denoising.
28,911 citations
28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
18,940 citations
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
18,256 citations
University of Massachusetts Amherst1, University of Michigan2, University of New Mexico3, University of British Columbia4, Texas A&M University5, University of Minnesota6, University of Warwick7, Dalhousie University8, Colorado School of Mines9, University of Ljubljana10, Graz University of Technology11, Louisiana State University12
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Abstract: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
17,350 citations
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Abstract: Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification.
Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Availability: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch
Contact: [email protected]
Supplementary information:Supplementary data are available at Bioinformatics online.
17,301 citations