Author Archives: Robert

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2009

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ADAPTdb/ADAPT – A Framework for the Analysis of ARISA Data Sets

Robert Schmieder, Matthew Haynes, Elizabeth Dinsdale, Forest Rohwer, and Robert Edwards


Presented at: ISMB/ECCB and M3 2009
Download PDF file (812 KB)

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Deviation of amino acid utilization and correlation with G+C composition in bacterial genome

Sajia Akhter, Hochul K Lee, Barbara Bailey, Peter Salamon, Robert Edwards


Presented at: Applied Computational Science and Engineering Student Support (ACSESS) 2009
Download PDF file (1.6 MB)

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Assembler for SOLiD data: by Improving memory management of Velvet assembler

Sajia Akhter and Robert Edwards


Presented at: Rocky Mountain Bioinformatics Conference (Rocky) 2009
Download PDF file (1.0 MB)

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Phage Annotation Tools and Methods

Ramy K. Aziz, Bhakti Dwivedi, Joe Anderson, Bonnie Hurwitz, JP Massar, Mya Breitbart, Matthew Sullivan, Jeff Elhai and Robert A. Edwards


Presented at: Rocky Mountain Bioinformatics Conference (Rocky) 2009
Download PDF file (940 KB)

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2011

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Tools for Quality Control and Preprocessing of Metagenomic Datasets

Robert Schmieder, Yan Wei Lim and Robert Edwards


Presented at: Pacific Symposium on Biocomputing (PSB) 2011
Download PDF file (4.2 MB)

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FACIL: fast and accurate genetic code inference and logo

Bas E. Dutilh, Rasa Jurgelenaite, Radek Szklarczyk, Sacha A.F.T. van Hijum, Harry R. Harhangi, Markus Schmid, Bart de Wild, Kees-Jan Françoijs, Hendrik G. Stunnenberg, Marc Strous, Mike S.M. Jetten, Huub J.M. Op den Camp and Martijn A. Huynen


Presented at: SDMG All Day Meeting 2011
Download PDF file (3.6 MB)

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Genomic Comparison of Salmonella enterica Serovars Enteritidis and Dublin

D. Matthews, R. Schmieder, J. Busch, N. Cassman, M. Doherty, D. Green, B. Matolock, B. Heffernan, G. Olsen, L. Farris, D. Schiffeli, S. Maloy, E. Dinsdale, and R. Edwards


Presented at: ASM 2011
Download PDF file (561 KB)

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PhiSpy: A novel similarity-independent tool for predicting prophages in microbial genomes

Sajia Akhter, Ramy K Aziz, Robert A Edwards


Presented at: Evergreeen International Phage Biology Meeting
Download PDF file (1.5 MB)

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2012

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Tools for Detecting Macrolide Resistance in the Human Microbiome

Robert Schmieder, Yan Wei Lim, Anca Segall, Molly Schmid, and Robert Edwards


Presented at: Advances in Genome Biology & Technology (AGBT) 2012
Download PDF file (1.2 MB)

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Host prediction for viral metagenomes using oligonucleotide profiles

Michiyo Wellington-Oguri, Robert Schmieder, Barbara Bailey, Robert A. Edwards, and Bas E. Dutilh


Presented at: Student Research Symposium (SRS) 2012
Download PDF file (705 KB)

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Database Structure and Visualization Software for Microbial Physiology Data

Nicholas Turner, Haquio Liu, Jeremy Frank, and Robert Edwards


Presented at: Student Research Symposium (SRS) 2012
Download PDF file (176 KB)

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Tools for Fast Sequence Alignment

Sajia Akhter and Robert Edwards


Presented at: Student Research Symposium (SRS) 2012
Download PDF file (1.3 MB)

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2010

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Real-Time Metagenomics Analysis

Daniel A. Cuevas, Joshua A. Hoffman and Robert A. Edwards


Presented at: ASM 2010
Download PDF file (980 KB)

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Investigating the Frequency of Quinolone Resistance Genes in Environmental Samples

Sajia Akhter, Anca M. Segall, Molly Schmid and Robert A. Edwards


Presented at: ASM 2010
Download PDF file (1.5 MB)

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Identification of Macrolide Resistance Alleles in Environmental Metagenomes

Robert Schmieder, Anca Segall, Molly Schmid and Robert Edwards


Presented at: ASM 2010
Download PDF file (2.7 MB)

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Fast Identification and Removal of Sequence Contaminations from Genomic and Metagenomic Datasets

Robert Schmieder and Robert Edwards


Presented at: Human Microbiome Meeting 2010
Download PDF file (1.2 MB)

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PHANTOME: Phage Annotation Tools and Methods

Ramy K. Aziz, Brad Hull, Bhakti Dwivedi, Joe Anderson, Bonnie Hurwitz, JP Massar, Matthew Sullivan, Jeff Elhai, Mya Breitbart, Ross Overbeek and Robert A. Edwards


Presented at: Institut Pasteur Virus of Microbes meeting 2010
Download PDF file (808 KB)

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Phages Without Borders: Distribution of Phage Nucleic Acids in 310 Metagenomes

Ramy K. Aziz, Mya Breitbart and Robert A. Edwards


Presented at: ASM 2010
Download PDF file (1.9 MB)

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Phage Annotation Tools and Methods

Ramy K. Aziz, Bhakti Dwivedi, Joe Anderson, Bonnie Hurwitz, Brad Hull, JP Massar, Mya Breitbart, Matthew Sullivan, Jeff Elhai and Robert A. Edwards


Presented at: ASM 2010
Download PDF file (924 KB)

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Predicting Phage Preferences: Lytic vs. Lysogenic Lifestyle from Genomes

Katelyn McNair, Rob Edwards and Barbara Bailey


Presented at: CSHL meeting 2010
Download PDF file (269 KB)

Automated analysis of ARISA data using ADAPT system – White Paper

This white paper was written by Robert in 2008 while working on different community profiling projets that combined microbiolgy and computer science.

The white paper describes a computational system consisting of the database ADAPTdb and the program ADAPT for the analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) data sets. ARISA is a method for analyzing the composition of microbial communities that is both faster and cheaper than other community profiling techniques. In an application example, we describe the use of the tool for an unpublished data set and compare the results to work previously published using different analysis methods. Although there have been many papers until 2008 that used ARISA to analyze community samples, there were none that described computational approaches that allow the automatic analysis of the raw data sets. We have taken the manual process, automated it, and developed a web-based program for the automatic analysis, including taxonomic classifications, as well as autotrophic/heterotrophic and pathogenic/non-pathogenic comparisons.

This paper was submitted to BMC Bioinformatics and reviewed, but it was never published because of the comments that reviewer #2 made.

If this software is published in BMC Bioinformatics, this software will likely be used by many colleagues who will not look carefully at how ARISA works and doesn’t work. As a result, many analyses of microbial diversity will be highly flawed. Eventually, the community will learn the inaccuracy provided by the program but not before lots of scarce resources are spent and many meaningless papers are published.

That’s a pretty harsh criticism of their fellow microbial ecologists, who are apparently too stupid to understand their work and analyze their data.

Frankly, whoever wrote that review should be ashamed of themselves. Given comments like that there was no incentive for us to carry on making software that would mislead people, and so we never bothered.  The journal was not interested in publishing the paper, and we are not interested in helping people that are idiots.

Here are the complete reviews and the paper so you can decided for yourself. If you use ARISA, please cite this paper as:

Schmieder, R., Haynes, M., Dinsdale, E., Rohwer, F., and Edwards, R.A. Automated analysis of ARISA data using ADAPT system. 2009. http://edwards.sdsu.edu/research/adapt/

The ADAPT paper (1.4 MB).

reviewer #1 comments

Reviewer #2 comments

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