An Optimized Graph-Based Metagenomic Gene Classification Approach: Metagenomic Gene Analysis: 10.4018/978-1-7998-1204-3.ch059: Biological interaction mainly depends on the interactions of various genes and genomes. To identify actual meaning of interactions we have to find out the
While Metagenomics tells us which microbes are present and what genomic potential they have, Metatranscriptomics tells us about their activity: the genes that are highest expressed in a specific mircobial environement. Thus, Metatranscriptomics is the study of the function and activity of the complete set of transcripts (RNA-seq) from environmental samples ...
Microbial communities from cow rumen are known for their ability to degrade diverse plant polymers at high rates. In this work, we identified 15 hydrolases through an activity-centred metagenome analysis of a fibre-adherent microbial community from dairy cow rumen. Among them, 7 glycosyl hydrolases (GHs) and 1 feruloyl esterase were successfully cloned, expressed, purified and characterised. The most striking result was a protein of GH family 43 (GHF43), hereinafter designated as R_09-02, which had characteristics very distinct from the other proteins in this family with mono-functional β-xylosidase, α-xylanase, α-L-arabinase and α-L-arabinofuranosidase activities. R_09-02 is the first multifunctional enzyme to exhibit β-1,4 xylosidase, α-1,5 arabinofur(pyr)anosidase, β-1,4 lactase, α-1,6 raffinase, α-1,6 stachyase, β-galactosidase and α-1,4 glucosidase activities. The R_09-02 protein appears to originate from the chromosome of a member of Clostridia, a class of phylum Firmicutes, members of
Microbial communities from cow rumen are known for their ability to degrade diverse plant polymers at high rates. In this work, we identified 15 hydrolases through an activity-centred metagenome analysis of a fibre-adherent microbial community from dairy cow rumen. Among them, 7 glycosyl hydrolases (GHs) and 1 feruloyl esterase were successfully cloned, expressed, purified and characterised. The most striking result was a protein of GH family 43 (GHF43), hereinafter designated as R_09-02, which had characteristics very distinct from the other proteins in this family with mono-functional bxylosidase, a-xylanase, a-L-arabinase and a-L-arabinofuranosidase activities. R_09-02 is the first multifunctional enzyme to exhibit b-1,4 xylosidase, a-1,5 arabinofur(pyr)anosidase, b-1,4 lactase, a-1,6 raffinase, a-1,6 stachyase, b-galactosidase and a- 1,4 glucosidase activities. The R_09-02 protein appears to originate from the chromosome of a member of Clostridia, a class of phylum Firmicutes, members of ...
High-throughput meta-omic approaches over the last few years have facilitated researches on understanding of the unculturable majority of microorganisms on earth. Environmental and clinical microbiota samples are characterized in metagenomics, metatranscriptomics, metaproteomics and metabolomics levels. Metagenome reveals taxonomic composition and functional genes abundance. Metatranscriptome accompany with metaproteome further reflect the temporal fluctuation of gene expression. Metabolome identifies metabolites associated with phenotype and physiology as biomarkers. Previously, biologists focused on one or part of all types of meta-omic information, while the integration of metagenomics, metatranscriptomics, metaproteomics and metabolomics data has begun to gain attention for the purpose of systematically characterizing complex microbial communities [1]. Therefore, related bioinformatics tools for processing all types of meta-omics data is in urgent need.. Though the combination of meta-omics ...
Moving on, our next objective is to identify microbial protein coding genes and metabolic pathways. Here, the methods become much more challenging, and difficult to benchmark. I basically dont like the idea of assembling reads into contigs. This adds a lot of compute time, huge inconsistency among different samples (some will assemble better than others), and creates all kinds of bias for various species (high vs low GC genomes, repeats, etc.) and genes. Also, Im having a hard time coming up with a solid data analysis plan that meets all of our objectives. Bacteria are diverse. A specific enzyme that fulfills a metabolic function (for example in a MetaCyc pathway), could differ by 80% of its DNA sequence from one type of bacteria to another, but still do the job. Alternately, there are plenty of multi-gene families of enzymes in bacteria with paralogs that differ in DNA sequence by 20% or less within the genome of a single organism, but perform different metabolic functions. And of course ...
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Sinopsis: Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP) which has become a world-wide effort and the Global Ocean Sampling (GOS) surveys. The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to ...
Metagenomics is a new scientific field that involves the analysis of organismal DNA sequences obtained directly from an environmental sample, enabling studies of microorganisms that are not easily cultured in a laboratory [1]. Metagenomic studies, pioneered in the early 2000s [2], have recently increased in number and scope due to the emergence of next generation sequencing technologies. Due to the difficulty of assembling entire organisms from a metagenomic dataset [1], most analyses take a gene-centric view, treating the community as an aggregate and ignoring the exact assignment of genes to individual organisms. In fact, it can be argued that the environment is better characterized by its gene complement rather than by its taxonomic composition, given that similar biological functions can be performed by microbes of distinct taxonomic origins. Supporting this view is the observation that, while the taxonomic composition of the human gut microbiome varies significantly between people, the ...
Understanding emerging viruses is critical for disease monitoring and prediction; however, surveys of novel viruses are hindered by the lack of a universal assay for viruses. Viral metagenomics, consisting of viral particle purification and shotgun sequencing, is a powerful technique for discovering viruses in a wide variety of sample types. However, current protocols are not effective on tissue samples (e.g., lungs, livers and tumors), where they are hindered by the high amount of host nucleic acids which limits the percentage of sequences that originate from viruses. In this dissertation, a modified viral metagenomics protocol was developed and utilized to effectively purify viruses from tissues, enabling the sequencing of novel viruses from animals, plants, and insect vectors. Viral metagenomics performed directly on tissue samples enabled the discovery of novel vertebrate, plant, insect and bacterial viruses. From a sea turtle fibropapilloma, viral metagenomics revealed a novel tornovirus STTV1,
High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based amplicon sequencing: it is less susceptible to amplification biases, it captures only living organisms, and it enables a larger set of genes to be used for taxonomic identification. Using a model mock community comprising 17 fungal isolates, we evaluated whether metatranscriptomics can accurately identify fungal species and subspecies in mixed communities. Overall, 72.9% of the RNA transcripts were classified, from which the vast majority (99.5%) were correctly identified at the species level. Of the 15 species sequenced, 13 were retrieved and identified correctly. We also detected strain-level variation within the Cryptococcus species complexes: 99.3% of
In the ERC funded FuMe (Functional Metagenomics) project, we are trying to change this. We, therefore, characterize metagenomic proteins to learn about their function and to discover new biocatalysts. However, because metagenomic data is generated from environmental samples, we face several challenges: first and foremost, it is estimated that far more than 90% of the microbial species that are sequenced during a typical metagenomic data acquisition cannot be cultivated in the lab. But even if we were able to find the right conditions and convince all those species to grow, the experimental characterization of millions of proteins in the laboratory would still be an insurmountable task ...
Metagenomic profiling: microarray analysis of an environmetal genomic library. Vector systems allowing efficient autonomous or integrative gene cloning in Micromonospora sp. strain 40027
Metagenomic sequencing is an important tool that often uses next generation amplicon sequencing to target specific hypervariable regions of the microbial 16S rRNA gene. This is used to identify any relative abundance calculation of bacteria and archaea present in heterogeneous samples, such as soil, marine, or gut microbiome.. 16S MetaVx™ is a proprietary, patent-pending assay that improves upon current 16S metagenomics techniques with significant sensitivity and specificity. Compared side-by-side with the most commonly used 16S metagenomics assays, 16S MetaVx™ has the ability to detect more bacterial and archaeal genera with a lower limit of detection.. ...
Metagenomic sequencing is an important tool that often uses next generation amplicon sequencing to target specific hypervariable regions of the microbial 16S rRNA gene. This is used to identify any relative abundance calculation of bacteria and archaea present in heterogeneous samples, such as soil, marine, or gut microbiome.. 16S MetaVx™ is a proprietary, patent-pending assay that improves upon current 16S metagenomics techniques with significant sensitivity and specificity. Compared side-by-side with the most commonly used 16S metagenomics assays, 16S MetaVx™ has the ability to detect more bacterial and archaeal genera with a lower limit of detection.. ...
An Article in the June issue of Nature Methods uses simulated data sets to evaluate programs used for metagenomics data analysis. The author of a News & Views argues that although the results indicate existing programs do work, new algorithms are needed as well as model metagenomics systems for use as test beds.. ...
Trevor Charles provides expertise in the areas of bacteria genetics and functional genomics, environmental genomics and functional metagenomics. His group has successfully constructed cosmid metagenomic libraries from soil and activated sludge, and used phenotypic screening methods to isolate clones from these libraries encoding a number of different functions including PHA metabolism, P metabolism and quorum sensing, He will direct construction of metagenomic libraries and contribute to library screening activities and sequence and functional characterization of the isolated clones.. ...
In this study, we developed and validated a sample preparation protocol for unbiased amplification and high-throughput metagenomic sequencing of viruses in routine diagnostic use. In an unbiased metagenomic approach, prior knowledge of the virus sequence is not required. In principle, it can therefore detect any virus. However, sample processing needs to be optimized for recovery and amplification of viral genomes that might be present only in very small amounts in clinical samples. We optimized such a protocol using plasma samples spiked with different classes of viruses.. First, we tested filtration, extraction, and nuclease digestion procedures in order to find optimal conditions for virus enrichment and reduction of unwanted, non-viral reads. Filtration proved to be indispensable, as the number of virus reads after sequencing significantly increased. Additionally, sample pre-processing including a freeze thaw cycle showed the best enrichment (Fig. 1), and for best integration into the daily ...
Abstract:. Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with ,98.5% accuracy at coverages as low as 1Ã-. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples. ...
Several metagenomic projects have been accomplished or are in progress. However, in most cases, it is not feasible to generate complete genomic assemblies of species from the metagenomic sequencing of a complex environment. Only a few studies have reported the reconstruction of bacterial genomes from complex metagenomes. In this work, Binning-Assembly approach has been proposed and demonstrated for the reconstruction of bacterial and viral genomes from 72 human gut metagenomic datasets. A total 1156 bacterial genomes belonging to 219 bacterial families and, 279 viral genomes belonging to 84 viral families could be identified. More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes. Selected draft assembled genomes could be validated with 99.8% accuracy using their ORFs. The study provides useful information on the assembly expected for a species given its number of reads and abundance. This approach along with spiking was also ...
Dr. Huttenhowers research focuses on computational biology at the intersection of microbial community function and human health. The human body carries some four pounds of microbes, primarily in the gut, and understanding their biomolecular functions, their influences on human hosts, and the metabolic and functional roles of microbial communities generally is one of the key areas of study enabled by high-throughput sequencing. First, computational methods are needed to advance functional metagenomics. How can we understand what a microbial community is doing, what small molecule metabolites or signaling mechanisms its employing, and how its function relates to its organismal composition? Second, our understanding of the human microbiome and its relationship with public health remains limited. Pathogens have been examined by centuries of microbiology and epidemiology, but we know relatively little about the transmission or heritability of the normal commensal microbiota, its carriage of ...
The new innovative academic journal Metabarcoding and Metagenomics is launched to welcome novel papers on environmental DNA, metabarcoding and metagenomics from basic and applied aspects. Issued via ARPHA -- the first ever publishing platform to support manuscripts all the way from authoring to peer review to publication and dissemination -- the new journal is to host a wide range of research outcomes, including data, models, methods, workflows, software, perspectives, opinions, implementation strategies and conventional research articles.
The diverse and multiple aspects of metagenomics and the multiplicity of its potential applications. The new theoretical insights, the more recent applications, and the dynamically developing methods of data acquisition and analysis. Essential reading for all researchers wishing to broaden their knowledge of metagenomics and highly recommended for those new to the field.
Environmental Genomics Division National Environmental Engineering Research Institute (NEERI) Nagpur-440020 Applications are invited on plain paper for engagement as project assistant (level II) as per the following details 1 Prescribed education and qualification Project assistant level II- NET (LS) qualified M.Sc Biotechnology or MTech Biotechnology 2 Age Project assistant level II- 28 years (age relaxation for OBC/SC/ST as per GOI rules) 3 Job requirement The project will use comparative metagenomics to study the behavior of the microbial community in activated sludge and map the degradative pathways operating in the system. Gene quantification and stress response of bacteria will be studied and bioinspired proteinbased materials as pollutant scavengers will be developed. The applicants should have some basic knowledge of handing molecular biology tools. Preference will be given to students who have some experience in analyzing sequence data 4 Fixed remuneration Project assistant level II: Rs ...
Metagenomic technologies enable the study of microbial genetic material in human biomedical sample types such as stool, nasal, oral, urogenital, skin and bronchoalveolar lavage samples. In addition, environmental samples such as soil, water, air and biofilms can be also be analyzed. Metagenomic data can not only be used to examine healthy microbiomes and shed light on causes, effects, and future therapies for a variety of diseases, but it can also be useful to help understand the environments microbial biodiversity. QIAGEN provides next-generation sequencing technologies for metagenomics, as well as qPCR assays and arrays for verification of sequencing results and screening for specific bacterial species, virulence factor genes, and antibiotic resistance genes ...
Five cruises were conducted, two transects from coastal New England to the BATS site (R/V Endeavor cruise EN351 and R/V Oceanus cruise OC413) and three transects across the Florida Straits (R/V Walton Smith cruises WS0503, WS0518, WS0528) with characteristics as in Table 1. Samples were collected in surface and DCM waters using a Sea-Bird Niskin Rosette equipped with standard CTD and PAR detectors (see also below). For DNA extraction samples, 1 l of seawater was gravity filtered through 2 um pore size filters (GE Osmonics, Minnetonka, MN, USA) and then onto a 0.45 um pore size (2001) or 0.2 um pore size (2005) Supor filter (Pall Gelman, Ann Arbor, MI, USA) using vacuum. For FISH samples whole seawater (no size fractionation) was preserved with 1% paraformaldahyde (final concentration) for at least 1 h in the dark at 4°C. For each replicate, volumes of 180 ml or more of seawater were gently filtered onto a 25 mm, 0.2 um Anodisc filter (Whatman, Maidstone, England). The filters were then ...
The analysis of these vast amounts of data is complicated by the fact that reconstructing large genomic segments from metagenomic reads is a formidable computational challenge. Even for single organisms, the assembly of genome sequences from sequencing reads is a complex task, primarily due to ambiguities in the reconstruction that are caused by genomic repeats. In metagenomic data, additional challenges arise from the non-uniform representation of genomes in a sample as well as from the genomic variants between the sequences of closely related organisms. Despite advances in metagenomic assembly algorithms over the past years, the computational difficulty of the assembly process remains high and the quality of the resulting data fairly low. As a result, many analyses of metagenomic data are performed directly on unassembled reads, however the much shorter genomic context leads to lower accuracy.. Reference-guided, comparative assembly approaches have previously been used to assist the assembly ...
Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater and sediments were subjected to Hiseq Illumina sequencing (c.15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p
Metagenomics is the field of biology that endeavors to study microbial communities directly obtained from the environment. Metagenomics aims to decipher uncultured organisms to understand the diversity of microbes, their functions, co‐operation and evolution in environment. Metagenomic studies provided a snapshot of the genetic composition of the community at any given time. In contrast, metatranscriptomics enables researchers to investigate the actively transcribed messenger RNA from a community. It has been applied to environments as diverse as soil and sea water. The primary goals of these approaches are to characterize the organisms present in a sample and identify the activities that are occurring. The metagenome and metatranscriptome sequencing is performed on various platforms like Illumina HiSeq 2000, NextSeq500, MiSeq, & Roche GS FLX. Xcelris Genomics provides sequencing and bioinformatic analysis services for all types of metagenome/metatranscriptome samples with international ...
Description: The contribution of microbial processes to soil biogeochemistry, particularly the management of soil carbon and nitrogen, is arguably one of the most important knowledge gaps in terrestrial ecology. Discovery and characterization of these microbial processes using environmental samples is being pursued by means of multiple "omics" approaches including metagenomics, metatranscriptomics, and metaproteomics. Metagenomic sequencing, enhanced by the latest advances in DNA sequencing technologies, is enabling unprecedented illumination of microbial community composition in soils. The sequence data alone, though, provides only limited information on the metabolic potential of the microbes to mediate terrestrial biogeochemistry. Metatranscriptomes, when directly associated with metagenomic data, elucidate the genes that are actively transcribed by a community, and, therefore, allow prediction of active metabolism in response to spatial or temporal environmental gradients. It is ...
Metagenomics technologies enable genomic study of the collective microbial communities present in environmental, stool, oral, urogenital and other sample types. Metagenomic data can be used to examine the species present in natural or healthy microbiomes, quantify the abundance of virulent or antibiotic resistance genes, or shed light on the causes, effects and future therapies for a variety of diseases. ...
Watch this vide tutorial to learn about metagenomic assembly using DNASTARs SeqMan NGen. The analysis of human gut content is used as an example. Discover how to remove host DNA and identify matches with known bacterial species.
As different evolutionary strategies are required to cope with the unique set of challenges specific to each geographic site sampled, our results suggest how environmental pressures shaped these pathway differences. The detailed analysis of 3 case studies revealed particular pathway adaptations that provide numerous testable hypotheses for linking metabolic versatility to the environment.. Recently, Dinsdale et al. (7) demonstrated that functional differences can be used to discriminate among 9 qualitatively categorized, discrete ecosystems. However, as in genome wide association studies where methods using binned data have been supplemented by more sensitive methods that make use of continuous measurements (19), we have demonstrated the utility of a similar transition in microbial ecology by using comparative metagenomics. Our methods associate microbial community functions with quantitative, continuous features of the environment, allowing for an objective, data-driven framework to classify ...
www.MOLUNA.de Metagenomics of the Human Body [4176238] - The book brings a completely different perspective than available books by combining the information gained from the human genome with that derived from parallel metagenomic studies, and new results from investigating the effects of these microbes on the host immune system. Although there are a number of books that focus
The Microbial Metagenomic Trait Statistical Analysis workflow computes the multivariate statistics related to the metagenomic community traits outlined in Barberan et al. (2012) "Exploration of community traits as ecological markers in microbial metagenomes" (DOI: 10.1111/j.1365-294X.2011.05383.x). The traits included in the statistical analyses range from GC-content to functional diversity, and deliver a valuable set of ecological markers in order to discriminate between habitats or geographic locations. Furthermore, inter-trait relationships can be used as habitat descriptors or indicators of artifacts during sample processing. Overall, these metagenomics community traits approach, here combined in a single workflow, helps to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework.. ...
Abstract: Background: Gut microbiota and the host exist in a mutualistic relationship, with the functional composition of the microbiota strongly affecting the health and well-being of the host. Thus, it is important to develop a synthetic approach to study the host transcriptome and the microbiome simultaneously. Early microbial colonization in infants is critically important for directing neonatal intestinal and immune development, and is especially attractive for studying the development of human-commensal interactions. Here we report the results from a simultaneous study of the gut microbiome and host epithelial transcriptome of three-month-old exclusively breast- and formula-fed infants. Results: Variation in both host mRNA expression and the microbiome phylogenetic and functional profiles was observed between breast- and formula-fed infants. To examine the interdependent relationship between host epithelial cell gene expression and bacterial metagenomic-based profiles, the host ...
Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided ...
Analyze the human microbiome with experimental techniques including shotgun metagenomics, 16S rRNA metagenomics, or metatranscriptomics.
Metagenomics is the study of the microbial genomes isolated from communities found on our bodies or in our environment. By correctly determining the relation between human health and the human associated microbial communities, novel mechanisms of health and disease can be found, thus enabling the development of novel diagnostics and therapeutics. Due to the diversity of the microbial communities, strategies developed for aligning human genomes cannot be utilized, and genomes of the microbial species in the community must be assembled de novo. However, in order to obtain the best metagenomic assemblies, it is important to choose the proper assembler. Due to the rapidly evolving nature of metagenomics, new assemblers are constantly created, and the field has not yet agreed on a standardized process. Furthermore, the truth sets used to compare these methods are either too simple (computationally derived diverse communities) or complex (microbial communities of unknown composition), yielding results ...
Microbes play fundamental roles in all biology-associated processes on the planet. A powerful new tool in such studies is metagenomics wherein one uses high throughput DNA sequencing methods on DNA isolated directly from environmental samples. Metagenomics has the potential to revolutionize our understanding of the normally hidden yet incredibly important world of microorganisms. However this great potential comes with enormous challenges in the analysis of the sequence data, including (i) the fragmentary nature of sequence data, (ii) the sparse sampling of genomes, populations and communities, and (iii) the unknown phylogenetic diversity and ecological structure of the communities being sampled. We are now working on methodology for analysis of metagenomic data as part of a new collaborative project: Integrating Statistical Evolutionary, and Ecological Approaches to Metagenomics (iSEEM). The iSEEM Project, funded by the Gordon and Betty Moore Foundation, takes an integrated, interdisciplinary ...
in Microbiome (2015). Background Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent ... [more ▼]. Background Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge. Results We present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior ...
Bent Petersen is an Associate Professor at DTU Bioinformatics, Technical University of Denmark. Bent has years of experience within Bioinformatics, Computational biology, DNA Sequencing, NGS data analysis, metagenomics, protein structure prediction and Genome assembly of: Bacteria, insects, mammals, metagenomics samples, parasites and highly complex organisms. Currently he is working within the area of metagenomics using Next Generation Sequencing technologies. He has worked on many exciting projects spanning from Ancient horses to modern breeds, Extinct animals, Malaria parasites and metagenomics samples from exotic places.. My updated CV can be found here: https://docs.google.com/document/d/198DWctB_oWq6GeBX-f0unI9MjebIdry6wCJJE_ZPou0/edit?usp=sharing ...
This presentation will be demonstrating several different approaches to explore the diversity, function, and ecology of microbial communities.  In Metagenomics, the sequencing of DNA dir
This presentation will be demonstrating several different approaches to explore the diversity, function, and ecology of microbial communities.  In Metagenomics, the sequencing of DNA dir
Genomic analysis of gastrointestinal tract pathogens is key to understanding them and could potentially lead to the development of therapeutics against them. This collection of articles in Gut Pathogens aims to showcase the latest research in metagenomics of gut pathogens and microbiota published in this journal. If you would like your manuscript to be considered for this collection, please indicate so at the time of submission. ...
CompostBin is a DNA-composition-based binning algorithm for classifying metagenomic reads. Unlike previous methods that seek to bin assembled contigs and often require training on known reference genomes, CompostBin has the ability to accurately bin raw sequence reads without need for assembly or training. It applies principal component analysis to project the data into an informative…
Metagenomics is a new scientific field that combines molecular biology and genetics to identify the genomes of environmental microbes that cannot be cultured in the laboratory medium.
Metagenomics is so easy to understand, right? Scientists just go out and get DNA sequences from...stuff...in the environment. And then they answer lots of
Folker Meyer is a computational biologist at Argonne National Laboratory and a senior fellow at the Computation Institute at the University of Chicago. He is also associate division director of the Institute of Genomics and Systems Biology. He trained as a computer scientists and started to work with biologists early on in his career. It was that exposure to interesting biological problems that sparked his interest in building software systems to tackle biological problems, mostly in the field of genomics or post-genomics. In the past he has been best known for his leadership role in the development of the GenDB genome annotation system. He has also played an active role in the design and implementation of several high-performance computing platforms. His current work focuses on the analysis of shotgun metagenomics data sets and on the MG-RAST community resource for metagenomics. He also has an interest in microbial genomics and the analysis of complete microbial genomes and is a member of the ...