Seminar Algorithms in Bioinformatics
- Mehmet Tekman
- Milad Miladi
- Van Dinh Tran
- Initial compulsory meeting 17. October 2018, 14:00, room 02 006, building 106
- Block seminar: TBA January 2018, 10am - 6pm, room 02 006, building 106
The MEME Suite
Assigned to: Angeloose, Diana Das
INFO-RNA-a fast approach to inverse RNA folding
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
antaRNA: ant colony-based RNA sequence design
Comparative genomics boosts target prediction for bacterial small RNAs
Assigned to: Prasad, Janani Rajendra
GraphClust: alignment-free structural clustering of local RNA secondary structures
Assigned to: Bindemann, Daniel
GraphProt: modeling binding preferences of RNA-binding proteins
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.
Assigned to: Todorov, Haralambi
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
Convolutional neural networks for classification of alignments of non-coding RNA sequences
Assigned to: Tsapenko, Olesya
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach
Assigned to: Sudharsan, Subhadhra
Sequence, Structure, and Context Preferences of Human RNA Binding Proteins
cDeepbind: A context sensitive deep learning model of RNA-protein binding
Assigned to: Bešić, Borna
LEARNA: Learning to Design RNA
Assigned to: Runge, Tim Frederic
- The seminar will be held in English.
- Hand in presentation a week before seminar begins.
- Active participation for all talks.
- Give 25 min presentation. (+ ~5-10 min discussion after)
- One page summary (no copy paste).
- Order of talks is based on order of submission.
- Previous participation in at least one bioinformatics lecture
- Basic knowledge of algorithms, molecular biology and interest in biologically relevant problems