Special Topics on Bioinformatics: Intro to Biomolecular Structures and Genetics: Exercises and computational tools (2KV)

Course no.: 365.053
Lecturer: Noura Chelbat
Times/locations: room T212, 15:30-18:45 on
Wed March 3, 2010
Wed April 14, 2010
Wed April 28, 2010, room K009D
Wed May 5, 2010
Wed May 12, 2010
Wed May 26, 2010, room T212
Wed June 2, 2010
Tue June 15, 2010, room T 041 from 8:30-10:00
Mon June 21, 2010, room T 112 from 15:30-17:00
Start: Wed March 3, 2010
Mode: KV, 2h, blocked
Registration: KUSSS


PDF (Wed 03.03.2010)
PDF (Wed 28.04.2010)
PDF (Wed 03.05.2010)
PDF (Wed 12.05.2010)
PDF, PDF (Wed 26.05.2010)
EdgeFoundation.rar (330 MB): "Digitizing Biology" (Reading the genetic code by J.Craig Venter)

Students Reports:



Genomes, genetics, genomics, proteomics, microarrays, sequencing, protein structure, biological databases…why Bioinformatics? What is everything about? Where all these terms fit in? Under what fields can they be applied?
Scientific reports, magazines and journals, articles, abstracts, … would you like to be skilled enough to read, interpret and transfer the main information from a scientific paper within the field of Bioinformatics?

This and other related questions will be addressed in this special lecture.

To do so we will divide the lecture into two parts: The target audience for this lecture is, on the one hand those completely novel in the area of Bioinformatics but interested in getting to know about it for the first time, and on the other hand those who already know about Bioinformatics and would like to have a brainstorming and better understanding through the work on the scientific papers reading.
All of you are welcome.

Papers to be discussed:

  1. Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays
  2. Next-generation sequencing
  3. CNV-seq, a new method to detect copy number variation using high-throughput sequencing
  4. Salvaging Affymetrix probes after probe-level re-annotation
  5. FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
  6. Novel protein folds and their nonsequential structural analogs

Proposed Papers:

  1. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
  2. Probe signal correction for differential methylation hybridization experiments
  3. A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat
  4. Methods comparison for high- resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays
  5. A-MADMAN: Annotation-based microarray data meta-analysis tool
  6. ProbeMatchDB- a web database for finding equivalent probes across microarrays platforms and species
  7. Support vector machine classification and validation of cancer tissue samples using microarray expression data (Alois Regl)
  8. G-spots cause incorrect expression measurement in Affymetrix microarrays
  9. Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays
  10. Assessing Statistical Significance in Microarray Experiments Using the Distance Between Microarrays
  11. Cross-hybridization modeling on Affymetrix exon arrays
  12. Improved precision and accuracy for microarrays using updated probe set definitions
  13. Reliability and reproducibility issues in DNA microarray measurements (Johannes Palme)
  14. AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets
  15. Increased measurement accuracy for sequence-verified microarray probes
  16. Automated DNA Motif Disc (Thomas Unterthiner)
  17. MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads
  18. Fast and SNP-tolerant detection of complex variants and splicing in short reads
  19. Sequence dependence of cross-hybridization on short oligo microarrays
  20. Empirical Establishment of Oligonucleotide Probe Design Criteria
  21. SABERTOOTH: protein structural alignment based on a vectorial structure representation
  22. A new progressive-iterative algorithm for multiple structure alignment
  23. MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
  24. A structural alignment kernel for protein structures
  25. TM-align: a protein structure alignment algorithm based on the TM-score
  26. MULTICOM: A Multi-Level Combination Approach to Protein Structure Prediction and its Assessments in CASP8
  27. FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular Dynamics
  28. Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis (Johannes Palme)
  29. A Primer on Metagenomics (Alois Regl)
  30. An analysis of the feasibility of short read sequencing (Thomas Unterthiner)