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Diversity and Dynamics of Genomes (Seminar)


392217 Stoye, Wittler Summer 2014 Tuesday 14-16 in U10-155 or U10-146ekvv

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. Update on our research activities 69 - Better, Best, Worst
22.04. Paper 'Modeling 3D Facial Shape from DNA' 84 - Feel Versus Think
29.04. Paper 'Viral Quasispecies Assembly via Maximal Clique Enumeration' 99 - Neither Nor
06.05. Paper 'Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms' 113 - So Called
13.05. BREW
20.05. Paper 1: Phylogenetic Quantification of Intra-tumour Heterogeneity, Paper 2: Vascular and Neurogenic Rejuvenation of the Aging Mouse Brain by Young Systemic Factors 116 - Indices Versus Indexes
27.05. FRESCO: Referential Compression of Highly Similar Sequences 127 - Gender-Specific Words
02.06. "Models for DNA and RNA structure analysis" —
03.06. — (see instead: 02.06.)
10.06. Administratives 145 - Footnotes
17.06. Inferring human population size and separation history from multiple genome sequences, see also author post on Haldane's Sieve —
24.06. PBHoney: Identifying Genomic Variants via Long-Read Discordance and Interrupted Mapping PacBio Blog
01.07. — (Application workshop)
08.07. Whole-genome haplotyping using long reads and statistical methods and Supplement Corresponding Blog Entry
15.07. Update on our research activities

Papers we could/have read

Title Journal Read
The quest for a unified view of bacterial land colonization The ISME Journal
Modeling 3D Facial Shape from DNA Plos Genetics
Viral Quasispecies Assembly via Maximal Clique Enumeration Plos Comp Biol
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms Nature Biotechnology
FRESCO: Referential Compression of Highly Similar Sequences IEEE/ACM TCBB
Viruses in a 14th-Century Coprolite Applied and Environmental Microbiology
Phylogenetic Quantification of Intra-tumour Heterogeneity Plos Comp Biol
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

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