Abstract:
:Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. The four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1-4 h or more to complete, depending on the processing time of the various software used.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Majumder EL,Billings EM,Benton HP,Martin RL,Palermo A,Guijas C,Rinschen MM,Domingo-Almenara X,Montenegro-Burke JR,Tagtow BA,Plumb RS,Siuzdak Gdoi
10.1038/s41596-020-00455-4subject
Has Abstractpub_date
2021-01-22 00:00:00eissn
1754-2189issn
1750-2799pii
10.1038/s41596-020-00455-4pub_type
杂志文章相关文献
Nature Protocols文献大全abstract::This protocol describes a simple but robust microfluidic assay combining three-dimensional (3D) and two-dimensional (2D) cell culture. The microfluidic platform comprises hydrogel-incorporating chambers between surface-accessible microchannels. By using this platform, well-defined biochemical and biophysical stimuli c...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.051
更新日期:2012-06-07 00:00:00
abstract::Reversible thiol oxidation of cysteine residues occurs in many intracellular catalytic and signaling processes. Here we describe an optimized protocol, which can be completed in ∼5 d, to unambiguously identify specific cysteine residues that are transiently and reversibly oxidized by comparing two complex biological s...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.065
更新日期:2014-05-01 00:00:00
abstract::This protocol details a subset of assays developed within the touchscreen platform to measure various aspects of executive function in rodents. Three main procedures are included: extinction, measuring the rate and extent of curtailing a response that was previously, but is no longer, associated with reward; reversal ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.123
更新日期:2013-10-01 00:00:00
abstract::Ex vivo perfusion systems offer a reliable, reproducible method for studying acute physiological responses of an organ to various environmental manipulations. Unlike in vitro culture systems, the cellular organization, compartmentalization and three-dimensional structure of ex vivo-perfused organs are maintained. Thes...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.144
更新日期:2013-01-01 00:00:00
abstract::Metabolic labeling of glycans with a bioorthogonal chemical reporter such as the azide enables their visualization in cells and organisms as well as the enrichment of specific glycoprotein types for proteomic analysis. This process involves two steps. Azido sugars are fed to cells or organisms and integrated by the gl...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.422
更新日期:2007-01-01 00:00:00
abstract::This protocol describes the efficient, generally applicable Ullmann coupling reaction of bromaminic acid with alkyl- or aryl-amines in phosphate buffer under microwave irradiation using elemental copper as a catalyst. The reaction leads to a number of biologically active compounds. As a prototypical example, the synth...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.63
更新日期:2010-05-01 00:00:00
abstract::The Golgi apparatus undergoes extensive disassembly during mitosis and reassembly in post-mitotic daughter cells. This process has been mimicked in vitro by treating Golgi membranes with mitotic and interphase cytosol. To determine the minimal machinery that controls the morphological change, we have developed a defin...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.38
更新日期:2010-04-01 00:00:00
abstract::Neurotransmitter release is triggered by membrane depolarization, Ca(2+) influx and Ca(2+) sensing by the release machinery, causing synaptic vesicle (SV) fusion with the plasma membrane. Interlinked is a complex membrane cycle in which vesicles are tethered to the release site, primed, fused and recycled. As many of ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.074
更新日期:2012-06-21 00:00:00
abstract::The accurate knowledge of receptor kinetics is crucial to our understanding of cell signal transduction in general and neural function in particular. The classical technique of probing membrane receptors on a millisecond scale involves placing a recording micropipette with a membrane patch in front of a double-barrel ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.075
更新日期:2013-01-01 00:00:00
abstract::Social recognition (SR) enables rodents to distinguish between familiar and novel conspecifics, largely through individual odor cues. SR tasks utilize the tendency for a male to sniff and interact with a novel individual more than a familiar individual. Many paradigms have been used to study the roles of the neuropept...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.141
更新日期:2009-01-01 00:00:00
abstract::The ability to isolate and analyze rare circulating tumor cells (CTCs) has the potential to further our understanding of cancer metastasis and enhance the care of cancer patients. In this protocol, we describe the procedure for isolating rare CTCs from blood samples by using tumor antigen-independent microfluidic CTC-...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.044
更新日期:2014-03-01 00:00:00
abstract::Here, we describe a robust protocol for the reverse transfection of cells on small interfering (siRNA) arrays, which, in combination with multi-channel immunofluorescence or time-lapse microscopy, is suitable for genome-wide RNA interference (RNAi) screens in intact human cells. The automatic production of 48 'transfe...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.483
更新日期:2007-01-01 00:00:00
abstract::This protocol describes the principles and methods used for the preparation of cryopreserved cell stocks. Following these procedures will ensure the availability of reproducible cultures for use within a single laboratory at different times and for different collaborating laboratories. Although the basic principle is ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.190
更新日期:2008-01-01 00:00:00
abstract::Several noncanonical initial nucleotides (NCINs) have been found to cap RNAs and possibly regulate RNA stability, transcription and translation. NAD+ is one of the NCINs that has recently been discovered to cap RNAs in a wide range of species. Identification of the NAD+-capped RNAs (NAD-RNAs) could help to unveil the ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-020-0363-z
更新日期:2020-09-01 00:00:00
abstract::Fast, high-resolution mapping of heterogeneous interfaces with a wide elastic modulus range is a major goal of atomic force microscopy (AFM). This goal becomes more challenging when the nanomechanical mapping involves biomolecules in their native environment. Over the years, several AFM-based methods have been develop...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-018-0070-1
更新日期:2018-12-01 00:00:00
abstract::This protocol describes a method for directing the expression of genes of interest into postmitotic neocortical neurons in vivo. Microinjection of a DNA plasmid-amphiphilic molecule mix into the neocortex followed by delivery of an ad hoc electric pulse protocol during the first few days of life in mice allows rapid, ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2015.001
更新日期:2015-01-01 00:00:00
abstract::Unlike humans, mouse bone marrow-derived mesenchymal stem cells (MSCs) cannot be easily harvested by adherence to plastic owing to the contamination of cultures by hematopoietic cells. The design of the protocol described here is based on the phenomenon that compact bones abound in MSCs and hematopoietic cells exist i...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.238
更新日期:2010-03-01 00:00:00
abstract::The small ubiquitin-like modifier (SUMO) is a protein modifier that is post-translationally coupled to thousands of lysines in more than a thousand proteins. An understanding of which lysines are modified by SUMO is critical in unraveling its function as a master regulator of all nuclear processes, as well as its invo...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2016.082
更新日期:2016-09-01 00:00:00
abstract::Mouse embryonic stem cells (mESCs) are key tools for genetic engineering, development of stem cell-based therapies and basic research on pluripotency and early lineage commitment. However, successful derivation of germline-competent embryonic stem cell lines has, until recently, been limited to a small number of inbre...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.030
更新日期:2014-03-01 00:00:00
abstract::Limbal stem cells (LSCs) have an important role in the maintenance of the corneal surface epithelium, and autologous cultured limbal epithelial cell transplantations have contributed substantially to the treatment of the visually disabling condition known as LSC deficiency. In this protocol, we describe a method of es...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.115
更新日期:2010-08-01 00:00:00
abstract::Surface- and matrix-bound signals modulate stem cell fate in vivo and in vitro. This protocol enables the immobilization of a wide range of biomolecules that contain primary amino groups to different types of solid carriers, including glass substrates and standard polystyrene well plates. We describe how thin polymer ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.70
更新日期:2010-06-01 00:00:00
abstract::A big challenge in proteomics is the identification of cell-type-specific proteomes in vivo. This protocol describes how to label, purify and identify cell-type-specific proteomes in living mice. To make this possible, we created a Cre-recombinase-inducible mouse line expressing a mutant methionyl-tRNA synthetase (L27...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-018-0106-6
更新日期:2019-02-01 00:00:00
abstract::Detailed biochemical analysis of unmanipulated germinal center (GC) B cells has not been achieved. Previously, we designed and used a simple, economical and new magnetic bead separation scheme for the purification of 'untouched' mature GC and non-GC B cells from the spleens of immunized mice and reported the first bio...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2011.344
更新日期:2011-06-09 00:00:00
abstract::Post-translational modifications alter protein structure, affecting activity, stability, localization and/or binding partners. Antibodies that specifically recognize post-translationally modified proteins have a number of uses including immunocytochemistry and immunoprecipitation of the modified protein to purify prot...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.017
更新日期:2014-02-01 00:00:00
abstract::The pig has emerged as an important large animal model in biomedical and pharmaceutical research. We describe a protocol for high-efficiency germline transgenesis and sustained transgene expression in pigs by using the Sleeping Beauty (SB) transposon system. The protocol is based on co-injection of a plasmid encoding ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.010
更新日期:2014-04-01 00:00:00
abstract::The development of single-molecule switching (SMS) fluorescence microscopy (also called single-molecule localization microscopy) over the last decade has enabled researchers to image cell biological structures at unprecedented resolution. Using two opposing objectives in a so-called 4Pi geometry doubles the available ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-020-00428-7
更新日期:2020-12-16 00:00:00
abstract::High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.333
更新日期:2006-01-01 00:00:00
abstract::Human embryonic stem (hES) cells are self-renewing, pluripotent cells that are valuable research tools and hold promise for use in regenerative medicine. Most hES cell lines are derived from cryopreserved human embryos that were created during in vitro fertilization (IVF) and are in excess of clinical need. Embryos th...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.60
更新日期:2008-01-01 00:00:00
abstract::Neurons in cortical sensory regions receive modality-specific information through synapses that are located on their dendrites. Recently, the use of two-photon microscopy combined with whole-cell recordings has helped to identify visually evoked dendritic calcium signals in mouse visual cortical neurons in vivo. The c...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.169
更新日期:2011-01-01 00:00:00
abstract::The pollen tube is an excellent single-cell model system for studying cellular processes in plant cell biology. This protocol describes a detailed step-by-step procedure with optimized conditions for introducing various fluorescent reporter proteins into lily, tobacco and Arabidopsis pollen grains by means of biolisti...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2011.309
更新日期:2011-04-01 00:00:00