====== Diversity and Dynamics of Genomes (Seminar) ======
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|392217 |Stoye, Wittler | Summer 2014 |Tuesday 14-16 in U10-155 or U10-146|[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=44147758|ekvv]] |

===== Course Description =====
In this seminar, research of the DiDy Group is presented, and other research related topics are discussed. This semester, we focus on literature research. Each participant is responsible for scanning a few journals and extracting DiDy-relevant articles. Some selected articles will be discussed. 



===== Schedule =====

|  **Date** | **Topic**  | **Bugs Chapter/Blog Entry** |
| 08.04. | Distribution of journals |  |
| 15.04. | [[:Teaching:2014summer:DiDySeminar:topicsbuzzwords|Update on our research activities]] | 69 - //Better, Best, Worst// |
| 22.04. |  Paper [[http://dx.doi.org/10.1371/journal.pgen.1004224|'Modeling 3D Facial Shape from DNA']] |  84 - //Feel Versus Think// |
| 29.04. | Paper [[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003515|'Viral Quasispecies Assembly via Maximal Clique Enumeration']] |  99 - // Neither Nor// |
| 06.05. | Paper [[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2862.html|'Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms']]  | 113 - //So Called// |
| 13.05. | [[http://wiki.techfak.uni-bielefeld.de/didy/brew|BREW]] |  |
| 20.05. | Paper 1: [[http://dx.doi.org/10.1371/journal.pcbi.1003535|Phylogenetic Quantification of Intra-tumour Heterogeneity]], Paper 2: [[http://www.sciencemag.org/content/early/2014/05/02/science.1251141|Vascular and Neurogenic Rejuvenation of the Aging Mouse Brain by Young Systemic Factors]] |  116 - //Indices Versus Indexes// |
| 27.05. | [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6616534|FRESCO: Referential Compression of Highly Similar Sequences]] |  127 - //Gender-Specific Words// |
| 02.06. | [[workshopdnarna|"Models for DNA and RNA structure analysis"]] |  --- |
| 03.06. | --- (see instead: 02.06.) | |
| 10.06. | Administratives |  145 - //Footnotes// |
| 17.06. | [[http://dx.doi.org/10.1101/005348|Inferring human population size and separation history from multiple genome sequences]], see also [[http://haldanessieve.org/2014/06/04/uthor-post-inferring-human-population-size-and-separation-history-from-multiple-genome-sequences/|author post on Haldane's Sieve]] |  --- |
| 24.06. | [[http://www.biomedcentral.com/1471-2105/15/180/abstract|PBHoney: Identifying Genomic Variants via Long-Read Discordance and Interrupted Mapping]] | [[http://blog.pacificbiosciences.com/2014/03/agbt-2014-presentation-videos-smrt.html|PacBio Blog]] |
| 01.07. | --- (Application workshop) |  |
| 08.07. | [[http://www.nature.com/nbt/journal/v32/n3/full/nbt.2833.html|Whole-genome haplotyping using long reads and statistical methods]] and Supplement |  [[http://nextgenseek.com/2014/02/moleculo-long-reads-in-action-for-haplotyping-whole-human-genome/|Corresponding Blog Entry]] |
| 15.07. | Update on our research activities |  |

===== Papers we could/have read =====

| **Title** | **Journal** | **Read** |
| [[http://www.nature.com/ismej/journal/v8/n7/full/ismej2013247a.html?WT.ec_id=ISMEJ-201407|The quest for a unified view of bacterial land colonization]] | The ISME Journal | |
| [[http://dx.doi.org/10.1371/journal.pgen.1004224|Modeling 3D Facial Shape from DNA]] | Plos Genetics |  |
| [[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003515|Viral Quasispecies Assembly via Maximal Clique Enumeration]] | Plos Comp Biol |  |
| [[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2862.html|Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms]] | Nature Biotechnology |  |
| [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6616534|FRESCO: Referential Compression of Highly Similar Sequences]] | IEEE/ACM TCBB |  |
| [[http://aem.asm.org/content/80/9/2648.abstract.html|Viruses in a 14th-Century Coprolite]] | Applied and Environmental Microbiology | |
| [[http://dx.doi.org/10.1371/journal.pcbi.1003535|Phylogenetic Quantification of Intra-tumour Heterogeneity]] | Plos Comp Biol |  |
| [[http://www.sciencemag.org/content/early/2014/05/02/science.1251141|Vascular and Neurogenic Rejuvenation of the Aging Mouse Brain by Young Systemic Factors]] | Science |  |

===== Journal Scanning =====

| **Participant** | **Journals** |
| Benedikt B. | Nature Biotechnology, IEEE TVCG |
| Andreas     | arXiv, bioRxiv, PeerJ, ISME Journal, Applied and Environmental Microbiology |
| Guillaume   | Journal of Computational Biology, PLoS Computational Biology |
| Jan         | Oxford Bioinformatics, Nature Methods  |
| Benedikt L. | PLoS Biology, RNA |
| Nina        | Genome Research, IEEE TCBB |
| Madis       | BMC Systems Biology, Data Mining and Knowledge Discovery |
| Linda  | Nucleic Acids Research, Briefings in Bioinformatics |
| Roland      | PLoS One |
| Tina        | BMC Bioinformatics, Genome Biology |

===== Topics to come (or not) =====

  * Update on our research activities (beginning and end of each semester) 
  * Faculty members introduce themselves 
  * Work/life balance 
  * Mission statement 
  * Scientific superhero 
  * Conference smalltalk 
  * Slam session 
  * Author order and other publishing related questions 
Back to [[:Teaching|Teaching]]