Cbcb - User contributions [en]

Crime Analysis

2009-09-30T19:07:48Z

Boliu:

'''Analyzing Campus Crime and Incident Events Using Spotfire'''

Team members: '''Hyoungtae Cho''' and '''Bo Liu''', graduate students in Computer Science of UMCP

=Introduction=

Campus crimes occurred around College Park pose serious threats to the regular life of students, faculty and staff. How to prevent these incidents as much as possible? Are there any crime hot spots in terms of location or time? In order to try to answer these and other relevant questions, in this application project, we analyzed historical crime events data released by the Department of Public Safety at University of Maryland, College Park.

=Dataset Description=

All the crime events data from January 2005 to August 2009 are released by the Department of Public Safety at University of Maryland, College Park, and are downloaded from the Daily Crime and Incident Logs website (http://www.umpd.umd.edu/UMDPS-IncidentLogs.cfm). The raw data are stored in HTML pages, and we extracted and preprocessed them using PERL and PYTHON. Irrelevant events (e.g., traffic stop) are removed, and resulting in totally 4849 cases belonging to 13 categories (shown below).

=Findings=

==The Number of Property Destructions is Increasing==

To get an overview of the general trend of the occurrences of different events, we plot the counts of different events type by type across 5 years. One important thing we want to point out is that the 2009 data is not complete (only first eight months). For most types, the number of occurrences fluctuates, but the number of property destructions is steadily increasing from 2005 to 2008. This is a very interesting trend, but we could not find a reasonable explanation for this.

[[image:jbl_jhl_yearly_overview.jpg|900px]]

=Critique of Spotfire=
Pros:

1, Spotfire is really easy to use, and it only takes less than 10 minutes for us to get used to it. The data manipulation and chart creation are very interactive and convenient, which means it is extremely efficient for exploratory data analysis, because normally we do not know where the data trend or pattern is.

2, I like the filter panel most. In our case, most of the features of the crime events are discrete (e.g., location, date, type), so the sliding bar allows us to easily filter the features.

Cons:

1, Spotfire requires internet connection when logging in. When internet is not available, instead of reminding the user or giving warnings, it crashes.

2, When switch to another chart, the whole graph has to be build from scratch. For example, I built a bar chart by selecting some features that I am interested in. But I am not sure bar chart is the best way for visualization, then I decided to try line chart. After switch, the line chart was built using default data features instead of the ones I used in bar chart.

Crime Analysis

2009-09-30T18:26:21Z

Boliu:

Cbcb:Pop-Lab:Bo-Report

2009-09-30T17:35:40Z

Boliu:

== Research Log ==
* [[september 2009 | September 2009]]

== Metagenomic Date Sets ==
* [[Cbcb:Pop-Lab:Bo-Report:metagenomicsData| Metagenomic Datasets]]

== CMSC734 Application Project ==
* [[Crime Analysis| Analyzing Campus Crime and Incident Events Using Spotfire]] - Hyoungtae Cho & Bo Liu

September 2009

2009-09-17T23:54:59Z

Boliu: /* Some Interesting Visualizations from Class */

== September 17, 2009 (Thursday) ==
===Compute the Number of k-edge Subgraphs ===

The problem I'm working on is to calculate or estimate the number of n-edge subgraph in a larger graph, which can be used for Bonferroni correction for my multiple hypothesis testing problem. I've tried to google different keywords ("counting subgraph") in order to find previous methods, and most of the previous studies are kind of related with network motif finding. In brief, I could not find efficient algorithms or tools that can solve the problem I have. In graph motif finding, in order to find over- or under-represented motifs, generally two approaches are used: (1) Explicitly enumerate all n-edge subgraph, then count the frequencies, to see which motifs are abundant or depleted. This approaches is not applicable for large motif finding because of computation time. (2) Another approach I noticed is based on sampling (here is the paper [http://bioinformatics.oxfordjournals.org/cgi/reprint/bth163v1.pdf Kashtan N, Itzkovitz S, Milo R, Alon U: Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 2004, 20(11):1746-1758.]). Basically, they randomly sample some subgraphs and then estimate the subgraph concentrations. Hence, this method can only estimates the relative abundance of subgraphs, but not the frequencies. In addition, this method also only applies to motif detection of size less than 8 vertices.

My problem is a little bit simpler than the motif finding problem, because I'm not trying to find explicit motifs, but only the number of n-edge subgraphs. I tried two approaches (unfortunately, both failed): (1) Suppose the network has n edges, and we try to find the number of k-edge subgraphs. I randomly sample k edges (do not need to be connected), to see if they are connected with each other. If I sample 1000 times, and in 3 times the k edges are connected, then approximately 0.3% of all possible k edges are connected. Consequently, the total number of k-edge subgraph can be approximated by 0.3% X (n chooose k), where n choose k is the number of all possible combinations of k edges. However, the problem is n choose k is really huge, which means in order to get a good approximation, huge amount of samplings is needed. (2) Explicitly find all k-edge subgraph. Start from a node n1, expand to its neighbors n2, then expand to their (n1 and n2) neighbors until (k-1)th neighbor. This approach requires to keep track of all found subgraphs, because same k-edge subgraph could be found in different ways (multiple times). Again, this process is very expensive for large subgraphs (takes more than a hour for k=6).

=== Some Interesting Visualizations from Class===
1. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/want-to-be-rich-get-a-doctorate-de Want to be rich? Get a Doctorate Degree First!]

2. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/comparison-of-federal-contracts-pe/comments/28cf13cca26411deb146000255111976 VA, TX, and CA take in high percentage of federal contracts]

3. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/number-of-records-in-genbank-datab Spain Ranks Third Following US and China on Contributing GenBank Database]

4. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/women-obtaining-bachelors-degrees- Women Obtaining Bachelor's Degrees Outnumber Men Significantly]

5. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/medicare-benefits-wealthy-most Medicare Benefits Wealthy Most.]

6. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/what-is-the-most-common-female-nam What is the most common female name in US?]

7. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/1a403aaea2e411de857a000255111976/comments/489f598ea2e411de9e1f000255111976 Where are rich people?]

September 2009

2009-09-17T23:54:44Z

Boliu: /* Some Interesting Visualizations from Class */

== September 17, 2009 (Thursday) ==
===Compute the Number of k-edge Subgraphs ===

The problem I'm working on is to calculate or estimate the number of n-edge subgraph in a larger graph, which can be used for Bonferroni correction for my multiple hypothesis testing problem. I've tried to google different keywords ("counting subgraph") in order to find previous methods, and most of the previous studies are kind of related with network motif finding. In brief, I could not find efficient algorithms or tools that can solve the problem I have. In graph motif finding, in order to find over- or under-represented motifs, generally two approaches are used: (1) Explicitly enumerate all n-edge subgraph, then count the frequencies, to see which motifs are abundant or depleted. This approaches is not applicable for large motif finding because of computation time. (2) Another approach I noticed is based on sampling (here is the paper [http://bioinformatics.oxfordjournals.org/cgi/reprint/bth163v1.pdf Kashtan N, Itzkovitz S, Milo R, Alon U: Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 2004, 20(11):1746-1758.]). Basically, they randomly sample some subgraphs and then estimate the subgraph concentrations. Hence, this method can only estimates the relative abundance of subgraphs, but not the frequencies. In addition, this method also only applies to motif detection of size less than 8 vertices.

My problem is a little bit simpler than the motif finding problem, because I'm not trying to find explicit motifs, but only the number of n-edge subgraphs. I tried two approaches (unfortunately, both failed): (1) Suppose the network has n edges, and we try to find the number of k-edge subgraphs. I randomly sample k edges (do not need to be connected), to see if they are connected with each other. If I sample 1000 times, and in 3 times the k edges are connected, then approximately 0.3% of all possible k edges are connected. Consequently, the total number of k-edge subgraph can be approximated by 0.3% X (n chooose k), where n choose k is the number of all possible combinations of k edges. However, the problem is n choose k is really huge, which means in order to get a good approximation, huge amount of samplings is needed. (2) Explicitly find all k-edge subgraph. Start from a node n1, expand to its neighbors n2, then expand to their (n1 and n2) neighbors until (k-1)th neighbor. This approach requires to keep track of all found subgraphs, because same k-edge subgraph could be found in different ways (multiple times). Again, this process is very expensive for large subgraphs (takes more than a hour for k=6).

=== Some Interesting Visualizations from Class===
1. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/want-to-be-rich-get-a-doctorate-de Want to be rich? Get a Doctorate Degree First!]
2. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/comparison-of-federal-contracts-pe/comments/28cf13cca26411deb146000255111976 VA, TX, and CA take in high percentage of federal contracts]
3. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/number-of-records-in-genbank-datab Spain Ranks Third Following US and China on Contributing GenBank Database]
4. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/women-obtaining-bachelors-degrees- Women Obtaining Bachelor's Degrees Outnumber Men Significantly]
5. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/medicare-benefits-wealthy-most Medicare Benefits Wealthy Most.]
6. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/what-is-the-most-common-female-nam What is the most common female name in US?]
7. [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/1a403aaea2e411de857a000255111976/comments/489f598ea2e411de9e1f000255111976 Where are rich people?]

September 2009

2009-09-17T23:41:29Z

Boliu: /* Some Interesting Visualizations from Class */

== September 17, 2009 (Thursday) ==
===Compute the Number of k-edge Subgraphs ===

The problem I'm working on is to calculate or estimate the number of n-edge subgraph in a larger graph, which can be used for Bonferroni correction for my multiple hypothesis testing problem. I've tried to google different keywords ("counting subgraph") in order to find previous methods, and most of the previous studies are kind of related with network motif finding. In brief, I could not find efficient algorithms or tools that can solve the problem I have. In graph motif finding, in order to find over- or under-represented motifs, generally two approaches are used: (1) Explicitly enumerate all n-edge subgraph, then count the frequencies, to see which motifs are abundant or depleted. This approaches is not applicable for large motif finding because of computation time. (2) Another approach I noticed is based on sampling (here is the paper [http://bioinformatics.oxfordjournals.org/cgi/reprint/bth163v1.pdf Kashtan N, Itzkovitz S, Milo R, Alon U: Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 2004, 20(11):1746-1758.]). Basically, they randomly sample some subgraphs and then estimate the subgraph concentrations. Hence, this method can only estimates the relative abundance of subgraphs, but not the frequencies. In addition, this method also only applies to motif detection of size less than 8 vertices.

My problem is a little bit simpler than the motif finding problem, because I'm not trying to find explicit motifs, but only the number of n-edge subgraphs. I tried two approaches (unfortunately, both failed): (1) Suppose the network has n edges, and we try to find the number of k-edge subgraphs. I randomly sample k edges (do not need to be connected), to see if they are connected with each other. If I sample 1000 times, and in 3 times the k edges are connected, then approximately 0.3% of all possible k edges are connected. Consequently, the total number of k-edge subgraph can be approximated by 0.3% X (n chooose k), where n choose k is the number of all possible combinations of k edges. However, the problem is n choose k is really huge, which means in order to get a good approximation, huge amount of samplings is needed. (2) Explicitly find all k-edge subgraph. Start from a node n1, expand to its neighbors n2, then expand to their (n1 and n2) neighbors until (k-1)th neighbor. This approach requires to keep track of all found subgraphs, because same k-edge subgraph could be found in different ways (multiple times). Again, this process is very expensive for large subgraphs (takes more than a hour for k=6).

=== Some Interesting Visualizations from Class===
1. [[Image:https://wiki.cs.umd.edu/cmsc734_09/images/9/9f/HispanicSurnames.jpg]] [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/want-to-be-rich-get-a-doctorate-de Want to be rich? Get a Doctorate Degree First!]

September 2009

2009-09-17T23:41:00Z

Boliu:

== September 17, 2009 (Thursday) ==
===Compute the Number of k-edge Subgraphs ===

The problem I'm working on is to calculate or estimate the number of n-edge subgraph in a larger graph, which can be used for Bonferroni correction for my multiple hypothesis testing problem. I've tried to google different keywords ("counting subgraph") in order to find previous methods, and most of the previous studies are kind of related with network motif finding. In brief, I could not find efficient algorithms or tools that can solve the problem I have. In graph motif finding, in order to find over- or under-represented motifs, generally two approaches are used: (1) Explicitly enumerate all n-edge subgraph, then count the frequencies, to see which motifs are abundant or depleted. This approaches is not applicable for large motif finding because of computation time. (2) Another approach I noticed is based on sampling (here is the paper [http://bioinformatics.oxfordjournals.org/cgi/reprint/bth163v1.pdf Kashtan N, Itzkovitz S, Milo R, Alon U: Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 2004, 20(11):1746-1758.]). Basically, they randomly sample some subgraphs and then estimate the subgraph concentrations. Hence, this method can only estimates the relative abundance of subgraphs, but not the frequencies. In addition, this method also only applies to motif detection of size less than 8 vertices.

My problem is a little bit simpler than the motif finding problem, because I'm not trying to find explicit motifs, but only the number of n-edge subgraphs. I tried two approaches (unfortunately, both failed): (1) Suppose the network has n edges, and we try to find the number of k-edge subgraphs. I randomly sample k edges (do not need to be connected), to see if they are connected with each other. If I sample 1000 times, and in 3 times the k edges are connected, then approximately 0.3% of all possible k edges are connected. Consequently, the total number of k-edge subgraph can be approximated by 0.3% X (n chooose k), where n choose k is the number of all possible combinations of k edges. However, the problem is n choose k is really huge, which means in order to get a good approximation, huge amount of samplings is needed. (2) Explicitly find all k-edge subgraph. Start from a node n1, expand to its neighbors n2, then expand to their (n1 and n2) neighbors until (k-1)th neighbor. This approach requires to keep track of all found subgraphs, because same k-edge subgraph could be found in different ways (multiple times). Again, this process is very expensive for large subgraphs (takes more than a hour for k=6).

=== Some Interesting Visualizations from Class===
1. [[Image:to_be_rich.jpg]] [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/want-to-be-rich-get-a-doctorate-de Want to be rich? Get a Doctorate Degree First!]

September 2009

2009-09-17T23:38:50Z

Boliu:

== September 17, 2009 (Thursday) ==
===Compute the Number of k-edge Subgraphs ===

The problem I'm working on is to calculate or estimate the number of n-edge subgraph in a larger graph, which can be used for Bonferroni correction for my multiple hypothesis testing problem. I've tried to google different keywords ("counting subgraph") in order to find previous methods, and most of the previous studies are kind of related with network motif finding. In brief, I could not find efficient algorithms or tools that can solve the problem I have. In graph motif finding, in order to find over- or under-represented motifs, generally two approaches are used: (1) Explicitly enumerate all n-edge subgraph, then count the frequencies, to see which motifs are abundant or depleted. This approaches is not applicable for large motif finding because of computation time. (2) Another approach I noticed is based on sampling (here is the paper [http://bioinformatics.oxfordjournals.org/cgi/reprint/bth163v1.pdf Kashtan N, Itzkovitz S, Milo R, Alon U: Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 2004, 20(11):1746-1758.]). Basically, they randomly sample some subgraphs and then estimate the subgraph concentrations. Hence, this method can only estimates the relative abundance of subgraphs, but not the frequencies. In addition, this method also only applies to motif detection of size less than 8 vertices.

My problem is a little bit simpler than the motif finding problem, because I'm not trying to find explicit motifs, but only the number of n-edge subgraphs. I tried two approaches (unfortunately, both failed): (1) Suppose the network has n edges, and we try to find the number of k-edge subgraphs. I randomly sample k edges (do not need to be connected), to see if they are connected with each other. If I sample 1000 times, and in 3 times the k edges are connected, then approximately 0.3% of all possible k edges are connected. Consequently, the total number of k-edge subgraph can be approximated by 0.3% X (n chooose k), where n choose k is the number of all possible combinations of k edges. However, the problem is n choose k is really huge, which means in order to get a good approximation, huge amount of samplings is needed. (2) Explicitly find all k-edge subgraph. Start from a node n1, expand to its neighbors n2, then expand to their (n1 and n2) neighbors until (k-1)th neighbor. This approach requires to keep track of all found subgraphs, because same k-edge subgraph could be found in different ways (multiple times). Again, this process is very expensive for large subgraphs (takes more than a hour for k=6).

=== Some Interesting Visualizations from Class===
1. [[Image:https://wiki.cs.umd.edu/cmsc734_09/index.php?title=Image:to_be_rich.jpg]] [http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/want-to-be-rich-get-a-doctorate-de Want to be rich? Get a Doctorate Degree First!]

September 2009

2009-09-17T23:33:14Z

Boliu: /* September 17, 2009 (Thursday) */

September 2009

2009-09-17T22:57:35Z

Boliu:

== September 17, 2009 (Thursday) ==
The problem I'm working on is to calculate or estimate the number of n-edge subgraph in a larger graph, which can be used for Bonferroni correction for my multiple hypothesis testing problem. I've tried to google different keywords ("counting subgraph") in order to find previous methods, and most of the previous studies are kind of related with network motif finding. In brief, I could not find efficient algorithms or tools that can solve the problem I have. In graph motif finding, in order to find over- or under-represented motifs, generally two approaches are used: (1) Explicitly enumerate all n-edge subgraph, then count the frequencies, to see which motifs are abundant or depleted. This approaches is not applicable for large motif finding because of computation time. (2) Another approach I noticed is based on sampling (here is the paper [http://bioinformatics.oxfordjournals.org/cgi/reprint/bth163v1.pdf Kashtan N, Itzkovitz S, Milo R, Alon U: Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 2004, 20(11):1746-1758.]). Basically, they randomly sample some subgraphs and then estimate the subgraph concentrations. Hence, this method can only estimates the relative abundance of subgraphs, but not the frequencies.

September 2009

2009-09-17T22:18:42Z

Boliu:

== September 17, 2009 (Thursday) ==

Cbcb:Pop-Lab:Bo-Report

2009-09-17T22:18:25Z

Boliu: /* Research Log */

== Research Log ==
* [[september 2009 | September 2009]]

== Metagenomic Date Sets ==
* [[Cbcb:Pop-Lab:Bo-Report:metagenomicsData| Metagenomic Datasets]]

September2009

2009-09-17T22:17:39Z

Boliu:

== September 17, 2009 (Thursday) ==

Cbcb:Pop-Lab:Bo-Report

2009-09-17T22:14:35Z

Boliu:

== Research Log ==
* [[september2009 | September 2009]]
== Metagenomic Date Sets ==
* [[Cbcb:Pop-Lab:Bo-Report:metagenomicsData| Metagenomic Datasets]]

Cbcb:Pop-Lab:Bo-Report:metagenomicsData

2009-08-31T16:20:02Z

Boliu:

== Metagenomic Date Sets ==
The following table shows some metagenomic datasets that are available locally. All the DNA sequences are downloaded directly from NCBI TraceArchive or Short Read Archive without any preprocessing.
 
{| class="wikitable" border="1" cellpadding="5"
|-
! Metagenomics Project
! Data Location
! More Information
|-
| UBA Acid Mine Drainage Biofilm Metagenome
| /fs/szdata/metagenomes/reads/acidMine/acidMineUba.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=18537 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=18537]
|-
| 5-Way (CG) Acid Mine Drainage Biofilm Metagenome
| /fs/szdata/metagenomes/reads/acidMine/acidMineCg.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13696 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13696]
|-
| Antarctica Aquatic Microbial Metagenome
| /fs/szdata/metagenomes/reads/antarctica/antarctica.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33179 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33179]
|-
| Metagenomic Water Samples from Rita Colwell
| /fs/szdata/metagenomes/reads/freshwaterUMIGS/freshwaterUMIGS1.fasta /fs/szdata/metagenomes/reads/freshwaterUMIGS/freshwaterUMIGS2.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33243 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33243]
|-
| Gut metagenomes collected from 13 healthy individuals (Japan)
| All 13 fasta files (with fasta suffix) in this directory: /fs/szdata/metagenomes/reads/gutJapan/F1S.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28117 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28117]
|-
| Human Gut Microbiome from Obese and Lean Twins
| All 18 fasta files (with fasta suffix) in this directory: /fs/szdata/metagenomes/reads/gutTwin
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32089 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32089]
|-
| Metagenome from Lake Washington
| All 5 fasta files in this directory: /fs/szdata/metagenomes/reads/lakeWash
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30541 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30541]
|-
| Sampling of Marine Metagenomes project at Broad Institute
| All 7 fasta files in this directory: /fs/szdata/metagenomes/reads/marineBroad
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30501 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30501]
|-
| Marine Metagenome from Coastal Waters project at Plymouth Marine Laboratory
| /fs/szdata/metagenomes/reads/marinePlymouth/plyM.fasta /fs/szdata/metagenomes/reads/marinePlymouth/plyT.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28969 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28969]
|-
| Metagenomics of the Human Intestinal Tract, MetaHit.
| All 5 fasta files in this directory: /fs/szdata/metagenomes/reads/metahit
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32811 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32811]
|-
| Metagenome isolated from Guerrero Negro hypersaline microbial mat in Mexico
| All 10 fasta files in this directory: /fs/szdata/metagenomes/reads/microbialMat
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29795 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29795]
|-
| Micro-Obes human intestinal tract metagenome project.
| All 5 fasta files in this dicrectory: /fs/szdata/metagenomes/reads/microobes
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33303 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33303]
|-
| Enhanced biological phosphorus removal (EBPR) sludge community.
| /fs/szdata/metagenomes/reads/sludge/sludgeOZ.fasta /fs/szdata/metagenomes/reads/sludge/sludgeUS.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=17663 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=17663]
|-
| Waseca County Farm Soil Metagenome
| /fs/szdata/metagenomes/reads/soilWaseca/soilWaseca.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13699 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13699]
|-
| Wastewater Metagenome MallardCreek032007AerobicBasin
| /fs/szdata/metagenomes/reads/wasteWater/wasteWater.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29421 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29421]
|-
| Whale Fall Metagenome
| /fs/szdata/metagenomes/reads/whale/bone.fasta /fs/szdata/metagenomes/reads/whale/microbialMat.fasta /fs/szdata/metagenomes/reads/whale/ribBone.fasta
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13700 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13700]
|-
| Yellowstone Bison Hot Spring Metagenome
| /fs/szdata/metagenomes/reads/ys/ysBisonP1.fasta /fs/szdata/metagenomes/reads/ys/ysBisonP3.fasta /fs/szdata/metagenomes/reads/ys/ysBisonP4.fasta /fs/szdata/metagenomes/reads/ys/ysBisonP5.fasta 
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=34795 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=34795]
|-
| Global Ocean Sampling Expedition Metagenome
| All 8 fasta files in this directory: /fs/szdata/metagenomes/reads/marineGlobe
| [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13694 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13694]
|}

Cbcb:Pop-Lab:Bo-Report

2009-08-31T16:16:17Z

Boliu: /* Feb 19, 2009 */

== Metagenomic Date Sets ==
* [[Cbcb:Pop-Lab:Bo-Report:metagenomicsData| Metagenomic Datasets]]

Cbcb:Pop-Lab:Bo-Report

2009-08-31T16:15:59Z

Boliu: /* Metagenomic Date Sets */

== Feb 19, 2009 ==
*'''Antibiotic Resistance Genes in MRSA.''' I am mainly working on the MRSA evolution paper. I have emailed the second version of this paper to Dr. Pop and I will get some comments from him early next week. Then I will probably spend another work improving it and submit it to [http://aac.asm.org/ Antimicrobial Agents and Chemotherapy]
*'''Antibiotic Resistance Genes in Metagenome.''' (more will come)
*'''Indexing and Query of Edge-Induced Subgraph of Metabolic Pathways''' (more will come)

== Metagenomic Date Sets ==
* [[Cbcb:Pop-Lab:Bo-Report:metagenomicsData| Metagenomic Datasets]]

Cbcb:Pop-Lab:Bo-Report:metagenomicsData

2009-08-31T16:12:30Z

Boliu: /* Metagenomic Date Sets */

Cbcb:Pop-Lab:Bo-Report:metagenomicsData

2009-08-31T15:10:33Z

Boliu: /* Metagenomic Date Sets */

Cbcb:Pop-Lab:Bo-Report:metagenomicsData

2009-08-31T15:05:53Z

Boliu: /* Metagenomic Date Sets */

Cbcb:Pop-Lab:Bo-Report:metagenomicsData

2009-08-31T14:48:50Z

Boliu:

== Metagenomic Date Sets ==

{| class="wikitable" border="1" cellpadding="5"
|-
! Metagenomics Project
! Data Location
! More Information
|-
| row 1, cell 1
| row 1, cell 2
| row 1, cell 3
|-
| row 2, cell 1
| row 2, cell 2
| row 2, cell 3
|}

Cbcb:Pop-Lab:Bo-Report

2009-08-31T14:39:55Z

Boliu: /* Feb 19, 2009 */

Cbcb:Pop-Lab:Bo-Report

2009-08-31T14:37:26Z

Boliu: /* Feb 19, 2009 */

Cbcb:Pop-Lab:Bo-Report

2009-02-20T19:40:03Z

Boliu: /* Feb 19, 2009 */

Cbcb:Pop-Lab:Bo-Report

2009-02-20T17:06:50Z

Boliu: /* Feb 19, 2009 */

== Feb 19, 2009 ==
*'''Antibiotic Resistance Genes in MRSA.''' I am mainly working on the MRSA evolution paper. I have emailed the second version of this paper to Dr. Pop and I will get some comments from him early next week. Then I will probably spend another work improving it and submit it to [http://aac.asm.org/ Antimicrobial Agents and Chemotherapy]
*'''Antibiotic Resistance Genes in Metagenome.'''
*'''Indexing and Query of Edge-Induced Subgraph of Metabolic Pathways'''

Cbcb:Pop-Lab:Bo-Report

2009-02-20T17:06:24Z

Boliu: /* Feb 19, 2009 */

== Feb 19, 2009 ==
*'''Antibiotic Resistance Genes in MRSA.''' I am mainly working on the MRSA evolution paper. I have emailed the second version of this paper to Dr. Pop and I will get some comments from him early next week. Then I will probably spend another work improving it and submit it to [http://aac.asm.org/ Antimicrobial Agents and Chemotherapy]
*"Antibiotic Resistance Genes in Metagenome."
*"Indexing and Query of Edge-Induced Subgraph of Metabolic Pathways"

Cbcb:Pop-Lab:Bo-Report

2009-02-20T17:04:59Z

Boliu: /* Feb 19, 2009 */

Cbcb:Pop-Lab:Bo-Report

2009-02-20T02:02:50Z

Boliu:

== Feb 19, 2009 ==
*I am mainly working on the MRSA evolution paper. I have emailed the second version of this paper to Dr. Pop and I will get some comments from him early next week. Then I will probably spend another work improving it and submit it to [http://aac.asm.org/ Antimicrobial Agents and Chemotherapy]

Cbcb:Pop-Lab:Bo-Report

2009-02-20T01:53:56Z

Boliu: /* Feb 19, 2009 */

== Feb 19, 2009 ==
== Mar 19, 2009 ==

Cbcb:Pop-Lab:Bo-Report

2009-02-20T01:53:06Z

Boliu:

== Feb 19, 2009 ==

Cbcb:Pop-Lab

2009-02-20T01:46:16Z

Boliu: /* Progress Reports */

= Important pages =
* Group members [[Cbcb:Pop-Lab:Members]]
* Blog: [http://genomes.blogspot.com Genomes.blogspot.com]
* How-tos: [[Cbcb:Pop-Lab:How-to]] - List of documentation on how to perform certain analyses, use different software, etc.
* Software developed by us: [[Cbcb:Pop-Lab:Software]]
* Metagenomics papers: [[Cbcb:Pop-Lab:Papers]]

= Meetings/seminars =
* [[Pop_group_meeting|Group meeting]]: every Monday from 2:30pm in corner conference room (3120 C)
* [[seminars|CBCB seminar]]: Thursdays 2-3pm during the semester in main conference room

= Progress Reports =
* [[Cbcb:Pop-Lab:Ben-Report|Ben]]
* [[Cbcb:Pop-Lab:Niranjan-Report|Niranjan]]
* [[Cbcb:Pop-Lab:Chris-Report|Chris]]
* [[Cbcb:Pop-Lab:James-Report|James]]
* [[Cbcb:Pop-Lab:Serge-Report|Serge]]
* [[Cbcb:Pop-Lab:Bo-Report|Bo]]

= Pop Lab Presentations =
* [[Media:Xoo_Cripsr.odg|Xanthomonas Crispr Slides (openoffice format)]]
* Listeria Monocytogenes Slides (powerpoint)
* Metagenome pipelines overview [[Media:Pipeline_outline.pdf|Presentation(pdf)]]

Cbcb:Pop-Lab

2009-02-20T01:46:02Z

Boliu: /* Progress Reports */

= Important pages =
* Group members [[Cbcb:Pop-Lab:Members]]
* Blog: [http://genomes.blogspot.com Genomes.blogspot.com]
* How-tos: [[Cbcb:Pop-Lab:How-to]] - List of documentation on how to perform certain analyses, use different software, etc.
* Software developed by us: [[Cbcb:Pop-Lab:Software]]
* Metagenomics papers: [[Cbcb:Pop-Lab:Papers]]

= Meetings/seminars =
* [[Pop_group_meeting|Group meeting]]: every Monday from 2:30pm in corner conference room (3120 C)
* [[seminars|CBCB seminar]]: Thursdays 2-3pm during the semester in main conference room

= Progress Reports =
* [[Cbcb:Pop-Lab:Ben-Report|Ben]]
* [[Cbcb:Pop-Lab:Niranjan-Report|Niranjan]]
* [[Cbcb:Pop-Lab:Chris-Report|Chris]]
* [[Cbcb:Pop-Lab:James-Report|James]]
* [[Cbcb:Pop-Lab:Serge-Report|Serge]]
* [[Cbcb:Pop-Lab:Serge-Report|Bo]]

= Pop Lab Presentations =
* [[Media:Xoo_Cripsr.odg|Xanthomonas Crispr Slides (openoffice format)]]
* Listeria Monocytogenes Slides (powerpoint)
* Metagenome pipelines overview [[Media:Pipeline_outline.pdf|Presentation(pdf)]]

Cbcb:Pop-Lab:Papers

2009-02-19T18:23:13Z

Boliu: /* DNA sequence binning */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

== DNA sequence binning ==
# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)
# [http://arxiv.org/abs/0708.3098 CompostBin] Principle Component Analysis (PCA)
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18218139 AMI] Mutual Information
# [http://www.ncbi.nlm.nih.gov/pubmed/18535082?dopt=Citation HSOM] Hierarchical Sef-Organizing Map
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18442374 GSOM] Growing SOM
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18285365 CARMA] Pfam and Phylogeny
# [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples] REVIEW

Cbcb:Pop-Lab:Papers

2009-02-19T18:22:37Z

Boliu: /* DNA sequence binning */

Cbcb:Pop-Lab:Papers

2009-02-19T18:22:12Z

Boliu: /* Metagenomics Reviews */

Cbcb:Pop-Lab:Papers

2009-02-19T18:20:01Z

Boliu: /* DNA sequence binning */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

== DNA sequence binning ==
# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)
# [http://arxiv.org/abs/0708.3098 CompostBin] Principle Component Analysis (PCA)
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18218139 AMI] Mutual Information
# [http://www.ncbi.nlm.nih.gov/pubmed/18535082?dopt=Citation HSOM] Hierarchical Sef-Organizing Map
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18442374 GSOM] Growing SOM
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18285365 CARMA] Pfam and Phylogeny

Cbcb:Pop-Lab:Papers

2009-02-19T18:18:42Z

Boliu: /* DNA sequence binning */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

== DNA sequence binning ==
# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)
# [http://arxiv.org/abs/0708.3098 CompostBin] Principle Component Analysis (PCA)
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18218139 AMI] Mutual Information
# [http://www.ncbi.nlm.nih.gov/pubmed/18535082?dopt=Citation HSOM] Hierarchical Sef-Organizing Map
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18442374 GSOM] Growing SOM

Cbcb:Pop-Lab:Papers

2009-02-19T18:13:15Z

Boliu: /* DNA sequence binning */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

== DNA sequence binning ==
# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)
# [http://arxiv.org/abs/0708.3098 CompostBin] Principle Component Analysis (PCA)
#

Cbcb:Pop-Lab:Papers

2009-02-19T18:11:55Z

Boliu: /* DNA sequence binning */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

== DNA sequence binning ==
# McHardy, A.C., et al., [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)
# []

Cbcb:Pop-Lab:Papers

2009-02-19T18:10:23Z

Boliu: /* DNA sequence binning */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

== DNA sequence binning ==
# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)

Cbcb:Pop-Lab:Papers

2009-02-19T18:09:53Z

Boliu: /* DNA sequence binning */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

== DNA sequence binning ==
# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia]

Cbcb:Pop-Lab:Papers

2009-02-19T17:55:13Z

Boliu:

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

== DNA sequence binning ==

Cbcb:Pop-Lab:Papers

2009-02-19T17:52:53Z

Boliu: /* Metagenomics Reviews */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

Cbcb:Pop-Lab:Papers

2009-02-19T17:51:53Z

Boliu: /* Metagenomics Reviews */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

Cbcb:Pop-Lab:Papers

2009-02-19T17:48:53Z

Boliu: /* Metagenomics Reviews */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

Cbcb:Pop-Lab:Papers

2009-02-19T17:47:05Z

Boliu: /* Metagenomics Reviews */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

Cbcb:Pop-Lab:Papers

2009-02-19T17:45:46Z

Boliu: /* Metagenomics Reviews */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]

== Pioneering papers ==

# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]

== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats

Cbcb:Pop-Lab:Papers

2009-02-19T17:41:33Z

Boliu: /* Metagenomics Reviews */

Cbcb:Pop-Lab:Papers

2009-02-19T17:38:33Z

Boliu: /* Metagenomics Reviews */

Cbcb:Pop-Lab:Papers

2009-02-19T17:37:37Z

Boliu: /* Metagenomics Reviews */