Date |
Presenter |
Paper title |
Link to paper/powerpoint |
| 02/07 |
Nils Schimmelmann |
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions.
Chua HN. et al. Bioinformatics 2006 Jul 1;22(13):1623-30. Epub 2006 Apr 21 |
|
| 02/14 |
No lab meeting; |
| 02/21 |
Amrita Mohan |
Peer-review paper |
|
| 02/28 |
Arunima Ram |
Clustering Millions of Tandem Mass Spectra
Frank AM et al., J Proteome Res. 2008 Jan;7(1):113-22. Epub 2007 Dec 8 |
|
| 03/06 |
No lab meeting; Slobodan Vucetic's visit |
| 03/13 |
No lab meeting; Spring Recess |
| 03/20 |
Biao Li |
Predictive Pathway Models from Genotype to Phenotype
Li Biao et al. |
[In review] |
| 03/27 |
Yong Li |
A Bayesian approach to protein inference problem in shotgun proteomics
Li YF et al., RECOMB 08 |
|
| 04/03 |
Predrag Radivojac |
Linear-Time Computation of Similarity Measures for Sequential Data.
Konrad Rieck & Pavel Laskov. JMLR 9(Jan):23--48, 2008 |
|
| 04/10 |
Wyatt Clark |
Statistical Comparisons of Classifiers over Multiple Data Sets.
Janez Demšar; JMLR., 7(Jan):1--30, 2006 |
|
| 04/17 |
Dah Mee Ko |
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments
Lei Xie and Philip E. Bourne, PNAS 2008 105: 5441-5446 |
|
| 04/24 |
No lab meeting |
| 05/01 |
Amrita Mohan |
BLOSUM62 miscalculations improve search performance
Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G, Nat Biotechnol. 2008 Mar;26(3):274-5 |
|
| 05/08 |
Wyatt Clark |
Fourier Transforms |
|
| 05/15 |
Nils Schimmelmann |
Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes
English SB, Butte AJ. Bioinformatics. 2007 Nov 1;23(21):2910-7. Epub 2007 Oct 5 |
|
| 05/22 |
No lab meeting |
| 05/29 |
Biao Li |
Walking the interactome for prioritization of candidate disease genes
Am J Hum Genet 2008 Apr;82(4):949-58 |
|
| 06/05 |
No lab meeting |
| 06/12 |
Jim Costello |
Predicting Gene Function Through Integrating Genomics Data in Drosophila
(unpublished article) |
|
| 06/18 |
Predrag Radivojac |
Automated prediction of protein function and detection of functional sites from structure
Florencio Pazos, and Michael J. E. Sternberg PNAS | October 12, 2004 | vol. 101 | no. 41 | 14754-14759 |
|
| 06/26 |
Amrita Mohan |
Colander: A probability-based support vector machine learning algorithm for automatic screening of CID spectra of phospeptides prior to database search
Bingwen Lu, Cristian Ruse and John Yates; J.Prot.Res. |
|
| 07/03 |
Predrag Radivojac |
Review of protein function prediction methods using protein structure |
|
| 07/10 |
Fuxiao Xin |
The use of area under the ROC Curve in the evaluation of machine learning algorithms
Pattern Recognition, Vol. 30, No. 7, pp. 1145-1159, 1997 |
|
| 07/17 |
Predrag Radivojac |
Protein function prediction (presentation at ISMB 2008) |
|
| 07/24 |
Jun Ma |
Prediction of low-energy collision-induced dissociation spectra of peptides
Zhongqi Z, Anal Chem. 2004 Aug 1;76(15):291A. |
|
| 07/31 |
Vladimir Vacic |
Current research presentation |
|
| 08/07 |
Yong Li |
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Lukas Käll et.al. Nature. Methods - 4, 923 - 925 (2007)
|
|
| 08/14 |
No lab meeting |
| 08/21 |
Wyatt Clark |
Diffusion kernels on graphs and other discrete structures
Risi Imre Kondor, John Lafferty, In Proceedings of the ICML 2002 |
|
| 08/28 |
No lab meeting |
| 09/04 |
Biao Li |
Message-Passing Algorithms for the Prediction of Protein Domain Interactions from Protein-Protein Interaction Data
Bioinformatics. 2008 Jul 17. [Epub ahead of print] | |
| 09/17 |
Fuxiao Xin |
Global alignment of multiple protein interaction networks with application to functional orthology detection
Sing et al., Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12763-8. Epub 2008 Aug 25 |
|
| 09/24 |
Amrita Mohan |
Structural Insight into pH-Induced Conformational Changes within the Native Human
Transthyretin Tetramer (TTR)
Palaninathan SK et., JMB (2008) 382, 1157 - 1167 |
|
| 10/01 |
No lab meeting |
| 10/08 |
Nils Schimmelmann |
Capstone Project Presentation: Literature Mining for Gene/Disease Relationships |
|
| 10/15 |
Jun Ma |
On outliers and activity cliffs--why QSAR often disappoints.
Maggiora GM., J Chem Inf Model. 2006 Jul-Aug;46(4):1535 |
|
| 10/22 |
Yong Li |
A common sequence motif associated with recombination hot spots and genome instability in humans
Myers S. et al., Nature Genetics 40, 1124
- 1129 (2008) |
|
| 10/29 |
Wyatt Clark |
|
|
| 11/05 |
No lab meeting; MathWorks Workshop |
| 11/12 |
Discuss reviews for SIAM Data Mining |
| 11/19 |
Wyatt Clark |
Protein Function Prediction |
|
| 11/26 |
No lab meeting |
| 12/03 |
Biao Li |
Functional inference of mutation effects from protein sequences |
|
