microbiome.ch

Welcome to the Website of Martin Hartmann

Bacteria may not build cities or have interesting social lives, but they will be here when the sun explodes. This is their planet, and we are on it only because they allow us to be. Welcome to the Website of Martin Hartmann. They control our planet, but are invisible to our naked eye. There are millions of different kinds, but they remain a mystery to us. The truth is, we would not be here without our microbial friends. Nowadays, novel high-throughput sequencing platforms can sequence millions of gene co...

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Welcome to the Website of Martin Hartmann | microbiome.ch Reviews

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Bacteria may not build cities or have interesting social lives, but they will be here when the sun explodes. This is their planet, and we are on it only because they allow us to be. Welcome to the Website of Martin Hartmann. They control our planet, but are invisible to our naked eye. There are millions of different kinds, but they remain a mystery to us. The truth is, we would not be here without our microbial friends. Nowadays, novel high-throughput sequencing platforms can sequence millions of gene co...

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3 publications

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5 collaborations

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7 bill bryson

8 microbial ecology research

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Welcome to the Website of Martin Hartmann | microbiome.ch Reviews

https://microbiome.ch

Bacteria may not build cities or have interesting social lives, but they will be here when the sun explodes. This is their planet, and we are on it only because they allow us to be. Welcome to the Website of Martin Hartmann. They control our planet, but are invisible to our naked eye. There are millions of different kinds, but they remain a mystery to us. The truth is, we would not be here without our microbial friends. Nowadays, novel high-throughput sequencing platforms can sequence millions of gene co...

INTERNAL PAGES

microbiome.ch

1

Publications and Presentations (updated September 2016)

http://www.microbiome.ch/Publications.html

They kill good trees to put out bad newspapers. James G. Watt. In press / ADVANCE ONLINE. Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, Hartmann M. 2016) Microbial diversity in European alpine permafrost and active layers. FEMS Microbiology Ecology (doi:10.1093/femsec/fiw018). Rime T, Hartmann M. Frey B (2016). Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier. The ISME Journal 10: 1625-1641. Rime T, Hartmann M. Deslippe JR, Hartmann M.

2

Tools

http://www.microbiome.ch/Tools.html

Humans have now become the dominant force controlling the ecosystems of the world, . and we don't know what the implications are. Here you will find open-source software tools that facilitate high-throughput analysis of data sets derived from next-generation sequencing platforms to study diversity and structure of microbial communities. Most of these tools are based on Hidden Markov Models and the corresponding software HMMER. For more information please visit Sean Eddy’s Website. From the University of ...

3

Links

http://www.microbiome.ch/Links.html

There are a thousand ways to get a problem wrong - not all of them bad - and many ways to get a problem right - not all of them good. David J. Griffith. EMBL Nucleotide Sequence Database. DNA Data Bank of Japan. Silva rRNA Database Project. Ribosomal Database Project (RDP). UNITE Fungal ITS Database. Emerencia Fungal ITS Database. Long-Term Soil Productivity (LTSP) British Columbia. Earth Microbiome Project (EMP). International Barcode of Life. Tools from Marti Jane Anderson.

4

Collaborations

http://www.microbiome.ch/Collaborations.html

The environment is everything that isn’t me. William W. Mohn, University of British Columbia, Vancouver. Steven J. Hallam, University of British Columbia, Vancouver. Charles G. Howes, University of British Columbia, Vancouver. Suzanne W. Simard, University of British Columbia, Vancouver. Brett Finlay, University of British Columbia, Vancouver. Benjamin Willing, University of Alberta, Vancouver. Kessy Abarenkov, University of Tartu, Tartu. Richard Christen, University of Nice, Nice.

5

Teaching

http://www.microbiome.ch/Teaching.html

This is truly the age of bacteria as it was in the beginning, is now and ever shall be. Stephen J. Gould. 2015, October 20 7th Argonne Soil Metagenomics Meeting - Data Analysis Workshop. Location: The Hilton Lisle/Naperville, Naperville, Illinois. Organizers: Sarah O’Brien, Sarah Owens, Dionysios Antonopoulos, Folker Meyer, Darlyn Mishur, David Myrold. Lecturers: Folker Meyer, Andreas Wilke, Martin Hartmann. Location: Technical University of Braunschweig. Location: mBioinform, Copenhagen, Denmark. Descri...

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microbiology.se

Summary of 2010 - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/yearly/summary-of-2010

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. Paperwise, results have still not been satisfying, but hopefully this will change in 2011. However, two posters at two workshops have shown preliminary results from these projects. In both cases we expect to be able to finish interesting papers during the first half of 2011. On the social side, I have finished a new Lost Shadow album ( Phonocratic Records. Member of the Departme...

microbiology.se

Scripts - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/software/scripts

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. Here is a collection my smart shell and perl scripts. Feel free to download and use my solutions. All software distributed through this page is free for non-commercial use and copying. Blastgrep This utility allows you to grep for pattern matches but on query-basis in BLAST reports. So, if you would like to find all. Version 1.0.2). After download, move the files to a place wher...

microbiology.se

Summary of 2011 - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/yearly/summary-of-2011

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. And one tool that is soon to be publicly unveiled. And Erik Kristiansson, who I will be working with for the next four years. In publications, there is a lot in the pipeline, but the only thing I managed to squeeze out before the new year was the paper on the bioinformatics tool Metaxa. Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm ...

microbiology.se

GoBiG 2013 Schedule and News - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/gobig/gobig-2013/gobig-2013-schedule-and-news

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. GoBiG 2013 Schedule and News. I hope you have all had a nice Christmas and New Years holiday. Right before Christmas, we had a GoBiG meeting in student seminar form, but we also made some important decisions for GoBiG in 2013. The details for that is outlined below. 1 Schedule for the Spring 2013 GoBiG Meetings. Thursday, January 31 (Master of Article: Kemal Sanli). Having an op...

microbiology.se

Software - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/software

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. A software package for automated identification and classification of small subunit (SSU) rRNA sequences from archaea, bacteria, eukaryotes, chloroplasts and mitochondria in metagenomic and environmental sequencing data sets. A software tool for detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing.

microbiology.se

Megraft - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/software/megraft

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes. Published in Research in Microbiology. Volume 163, Issues 6 7 (2012), 407 412. Doi: 10.1016/j.resmic.2012.07.00. Download the Megraft package. Version 1.0.2). About 4 years ago.

microbiology.se

Metaxa FAQ - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/software/metaxa/metaxa-faq

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. This FAQ intends to answer some of the questions we have gotten about the Metaxa software package. Please look through this document before contacting me with a question. If the FAQ does not answer your question, you are very welcome to send an e-mail with the question to metaxa [at] microbiology [dot] se The FAQ can also be downloaded as a PDF here. Does Metaxa work on Windows?

microbiology.se

Metaxa - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/software/metaxa

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. Metaxa: A software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek Journal of Microbiology. Download the Metaxa package. Version 1.1.2). Updated for version 1.1.2! 16th December 2011 1...

microbiology.se

GoBiG 2013 - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/gobig/gobig-2013

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. Thursday, January 31 (Master of Article: Kemal Sanli). Wednesday, February 27 (MoA: José Sanchez). Tuesday, March 19 (MoA: Chandan Pal). Monday, April 22 (MoA: Francesco Gatto). Thursday, May 30 (MoA: Amir Feizi). Wednesday, June 19 (Spring Special Meeting). Thursday, September 26 (MoA: Johan Bengtsson-Palme). Wednesday, October 30 (MoA: Chandan Pal). Jonathan A. Eisen.

microbiology.se

TriMetAss - Microbiology, Metagenomics and Bioinformatics

http://microbiology.se/software/trimetass

Mobility of genes and microbes. Microbiology, Metagenomics and Bioinformatics. Johan Bengtsson-Palme, University of Gothenburg. TriMetAss The Trinity-based Iterative Metagenomics Assembler. Johan Bengtsson-Palme, 2013. If you use TriMetAss in your research, please cite the following paper. In which it is briefly described:. Frontiers in Microbiology, Volume 5, Issue 648 (2014). Doi: 10.3389/fmicb.2014.00648. Please report bugs to my: first name (dot) last name (at) microbiology (dot) se. About 2 years ago.

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microbiome-sequencing.org

MR DNA next generation sequencing

The Whole Picture: Total RNA Sequencing. It is well known that scientists have been interested in studying the transcriptome of organisms since the popularization of microarrays. However, a major drawback of transcriptome analysis utilizing microarray technology is the requirement that the target of interest must already be mapped. The introduction of Next Generation Sequencing (NGS) has been able to […]. Epigenetics via ChIP-Seq (Chromatin Immunoprecipitation Sequencing). Nowadays, Twitter is not merely...

microbiome-standards.org

Home

A detailed understanding of human-microbe symbiosis requires a precise characterization of human-associated microorganisms, the human microbiome. To progress towards this ambitious goal it is of utmost importance that the data generated in each of many large projects involved in human metagenome research be optimally comparable. The International Human Microbiome Standards (IHMS) project coordinated the development of standard operating procedures designed to optimize data quality and comparabili...Heika...

microbiome-summit.com

Microbiome Drug Development Summit

As the White House launches the National Microbiome Initiative, understanding the functionality and disease causation in the human microbiome is poised to enter the clinical mainstream. As such, the. Microbiome Drug Development Summit. Will enable you to translate effective microbiome-based therapies. From proof-of-concept, through the clinic to become scalable and commercially viable therapeutics. Utilizing the latest scientific and clinical case studies. T: 44 (0)20 3141 8700. Boston, MA, 02210. This w...

microbiome.at

AMICI | Austrian Microbiome Initiative

AMICI is an interdisciplinary microbiome research platform that links diverse Austrian scientific and medical societies. What is the microbiome? The human and animal body is home to billions of symbiotic microorganisms - the microbiota. AMICI aims to support, stimulate, network, and communicate microbiome research in Austria. 1st AMICI Symposium - February 23, 2017 - Vienna. Posted: 10. 1. 2017. The first AMICI Symposium will take place in Vienna, Austria. On February 23, 2017. Follow us on Twitter.

microbiome.biz

MR DNA next generation sequencing

Chromatin immunoprecipitation (ChIP) is a powerful method for investigating interactions between specific proteins, genomic DNA, and RNA. Recent advancement in Next Generation Sequencing (NGS) technique allows us to sequence the ChIP DNA with high resolution, enabling us to perform unbiased and genome-wide mapping of epigenetic changes. Scientists at MR DNA are proficient in ChIP-Seq using […]. Nowadays, Twitter is not merely a social-network. It has become a must-read source of real-time industry ne...

microbiome.ch

Welcome to the Website of Martin Hartmann

Bacteria may not build cities or have interesting social lives, but they will be here when the sun explodes. This is their planet, and we are on it only because they allow us to be. Welcome to the Website of Martin Hartmann. They control our planet, but are invisible to our naked eye. There are millions of different kinds, but they remain a mystery to us. The truth is, we would not be here without our microbial friends. Nowadays, novel high-throughput sequencing platforms can sequence millions of gene co...

microbiome.fhcrc.org

microbiome.me

MR DNA next generation sequencing

Chromatin immunoprecipitation (ChIP) is a powerful method for investigating interactions between specific proteins, genomic DNA, and RNA. Recent advancement in Next Generation Sequencing (NGS) technique allows us to sequence the ChIP DNA with high resolution, enabling us to perform unbiased and genome-wide mapping of epigenetic changes. Scientists at MR DNA are proficient in ChIP-Seq using […]. Nowadays, Twitter is not merely a social-network. It has become a must-read source of real-time industry ne...

microbiome.mit.edu

The Center for Microbiome Informatics and Therapeutics

Health & Ventures in the Microbiome Symposium. Request for Applications: Microbiome Innovation and Pilot Grants. Letter of Intent Due Date: November 15, 2016. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. November 6, 2016. October 19, 2016. Synthetic recombinase-based state machines in living cells. August 8, 2016. October 19, 2016. Underworlds at the Cambridge Science Festival. May 12, 2016. The Outer Frontier: The Human Skin Microbiome. April 4, 2016. February 29, 2016.

microbiome.net

Main Page - Microbiome.net

Getting your own Genome. Possible genomic diseases of you. Storing your genome in you PC. Viewing your genetics family. A brief guide to genomics from NHGRI. Interesting things in your Genome. Compare your genome with other peoples. The principle of universal genome. Genomics Major Paper Publication. Your writing contribution to Genomics. Daphnia Genomics Consortium (DGC). Rice Genome at BGI China. TigerGenome Project by PGI Korea. Retrieved from " http:/ Microbiome.net/index.php/Main Page.

microbiome.nl

MICROBIOME Corporate - Microbiome,

Microbiome is trendsetter op het gebied van innovatieve moleculaire microbiologische technieken. lees meer. Voor vragen of opmerkingen over onze producten, diensten of deze website. Lees meer. Microbiome in de media. Improving healthcare through innovation. U kunt hier direct de uitslag van uw thuistest opvragen ». Klik om naar de Microbiome Diagnostics website te gaan. Klik om naar de Microbiome Legionella-preventie website te gaan. Diabetesprijs voor slimme waarschuwpleister. Xtc blijft het populairst.