it includes IUPAC consensus characters:
sub reverse_complement () {
my $new = $_[0];
$new =~ tr/acgtrymkbdhvACGTRYMKBDHV/tgcayrkmvhdbTGCAYRKMVHDB/;
$new = reverse ($new);
return ($new); }
Author Archives: Bas Dutilh
Invite people for the Journal Club
Step 1: Choose a paper. Have a different person choose the paper every week. Check the previous Journal Clubs here to see who chose one the longest time ago. Let new lab members join the club a few times so they can see what it is like before asking them to choose a paper themselves.
Step 2: Ask them to come up with papers that represent the Cutting Edge of Science. Think about:
– papers that present something new (e.g. a novel data set or approach)
– papers should preferentially be recent (so that we can use the new insights/data promptly)
– if the paper appeared in a lower-impact journal, this could avoid it having been noticed by competing groups 😉
– review papers are good to learn some background, but they usually do not represent the Cutting Edge of Science.
Step 3: Use the “Add content” link to post the paper on the Edwards Lab Site http://edwards.sdsu.edu/labsite/index.php/intranet/journal-club. Mention who chose the paper and when we are discussing it.
Step 4: Send out an email to the Edwards Lab mailing list telling them which paper to read and the date of the Journal Club. Attach a PDF of the paper. Also, tell everyone to really read the paper, or the Journal Club will lose its meaning.
Step 5: While reading, try to understand what the paper is about. If something is not clear, discuss it with the others.
Step 6: During the Journal Club discussion, remember the following points:
– Think about how we can use the information presented in the paper in our own research.
– Try to focus on positive things – trashing something is just too easy.
June 15th 2011: “Rapid pneumococcal evolution in response to clinical interventions”
Rob Edwards’ choice:
http://www.ncbi.nlm.nih.gov/pubmed/21273480 and http://www.ncbi.nlm.nih.gov/pubmed/21273474
Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD.
Rapid pneumococcal evolution in response to clinical interventions.
Science. 2011 Jan 28;331(6016):430-4.
Enright MC, Spratt BG. Genomics. The genomic view of bacterial diversification.
Science. 2011 Jan 28;331(6016):407-9.
June 8th 2011: “A window into third-generation sequencing”
Rob Schmieder’s choice:
http://www.ncbi.nlm.nih.gov/pubmed/20858600
Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing.
Hum Mol Genet. 2010 Oct 15;19(R2):R2Q27-40. Epub 2010 Sep 21. Review.
Converting FASTQ to FASTA and QUAL
Since I couldn’t find one readily available anywhere online, I wrote a small PERL script to split a FASTQ file into two files: a FASTA and a QUAL file. Click above to view more.
Robert Schmieder
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Location: GMCS 429 Phone: +1 619 594-3137 Email: rschmied@sciences.sdsu.edu |
Research
I started in the PhD program in Computational Sciences at SDSU in fall 2008. Since then, I have been working on the development of tools related to metagenomics (genomic analysis of all microorganisms present in a specific habitat) and environmental studies. The Computational Sciences program supports the collaboration between computer scientists and applied sciences, such as Biology. As part of the program, I worked in the laboratory of Dr. Forest Rohwer to extend my training in laboratory methods and now I apply this knowledge to my computational work, analyzing data sets and developing tools for their automatic analysis.
I implemented several programs for the analysis of microbial community samples for the ease of use by biologists, especially those performing specialized analyses in our collaborator’s labs. Additionally, I work on the analysis of metagenomic data from a wide variety of samples including mosquitoes, cystic fibrosis patients, and coral reefs.
Education
- PhD Student (since 2008), Computational Science Research Center, SDSU, San Diego, CA
- Master of Science in Bioinformatics and Genome Research, 2007 (Bielefeld University, Bielefeld, Germany)
- Bachelor of Science in Bioinformatics and Genome Research, 2005 (Bielefeld University, Bielefeld, Germany)
More details about my professional and educational background can be found here.
Publications
An up-to-date list of my publications can be found at Google Scholar (http://bit.ly/robpubl).
My publications in 100 words (Thanks to wordle.net)
Tools
Some of the tools I developed as part of my research:
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Awards
- BiCi Leonardo Melandri Program for Bertinoro Computational Biology 2012
- Inamori Fellowship, Fall 2011 and Spring 2012
- First Place in Lavine VentureStart Competition, 2011
- Travel Grant for International Human Microbiome Congress, 2011
- Instructionally Related Activities (IRA) Travel Grant, 2010
- Travel Grant for Human Microbiome Research Conference, 2010
- Merit Award for poster presentation at 7th annual ACSESS meeting, 2010
- CGU Fellowship – Math, Fall 2009 and Spring 2010
- Claremont Graduate University Travel Award for microbial community-profiling project on Curaçao, Netherlands Antilles, 2009
- California State University Program for Education and Research in Biotechnology (CSUPERB) Travel Grant Award, 2009
- Instructionally Related Activities (IRA) Travel Grant for ISMB/ECCB 2009
- Student Travel Grant at Metagenomics 2008
- German Academic Exchange Service (DAAD) Study Abroad Scholarship, 2007
Presentations
Oral:
- Bertinoro Computational Biology Meeting, Bertinoro, Italy, 2012
- TSRC Cystic Fibrosis Meeting, Telluride, CO, 2011
- Student Research Symposium (SRS), San Diego, CA, 2010
- Student Research Symposium (SRS), San Diego, CA, 2009
Workshop:
- Bioinformatics for metagenomics, Ensenada, Mexico, 2010
Poster:
- International Human Microbiome Congress (IHMC), Paris, France, 2012
- San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2012
- Student Research Symposium (SRS), San Diego, CA, 2012
- Advances in Genome Biology & Technology (AGBT), Marco Island, FL, 2012
- International Human Microbiome Congress (IHMC), Vancouver, Canada, 2011
- San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2011
- Student Research Symposium (SRS), San Diego, CA, 2011
- Microbiome Studies @ Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii, 2011
- Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO, 2010
- Human Microbiome Research Conference, St Louis, MO, 2010
- General meeting of the American Society for Microbiology (ASM), San Diego, CA, 2010
- San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2010
- Applied Computational Science and Engineering Student Support (ACSESS), San Diego, CA, 2010
- Metagenomics, Metadata, and Metaanalysis (M3), Sweden, 2009
- Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB), Sweden, 2009
- Applied Computational Science and Engineering Student Support (ACSESS), San Diego, CA, 2009
- San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2009
- 3rd Annual International Conference on Metagenomics, San Diego, CA, 2008
- International Coral Reef Symposium (ICRS), Fort Lauderdale, FL, 2008
- Student Research Symposium (SRS), San Diego, CA, 2008
- San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2008
- Applied Computational Science and Engineering Student Support (ACSESS), San Diego, CA, 2008