Currents in Bioinformatics

  • Seminarleiter: Purva Kulkarni
  • Termin: Di 16-18h, SR 3423 EAP

Im Journal Club wird wöchentlich ein aktueller Artikel aus der bioinformatischen Forschung vorgestellt und diskutiert.
Details werden in der ersten Veranstaltung besprochen.

Vorläufiger Ablaufplan

Date Paper Presenter
20.10 Organisatorisches, Besprechen der Themen
27.10 Lukas Käll, Jesse D Canterbury, Jason Weston, William Stafford Noble & Michael J MacCoss
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Nature Methods – 4, 923 – 925 (2007), doi:10.1038/nmeth1113Viktor Granholm, Sangtae Kim, José C. F. Navarro, Erik Sjölund, Richard D. Smith, and Lukas Käll
Fast and Accurate Database Searches with MS-GF+Percolator
J. Proteome Res., 2014, 13 (2), pp 890–897, doi: 10.1021/pr400937n
Marcus
3.11 Sara Forcisi, Franco Moritz, Marianna Lucio, Rainer Lehmann, Norbert Stefan, and Philippe Schmitt-Kopplin
Solutions for Low and High Accuracy Mass Spectrometric Data Matching: A Data-Driven Annotation Strategy in Nontargeted Metabolomics
Anal. Chem., 2015, 87 (17), pp 8917–8924, doi:10.1021/acs.analchem.5b02049
Kai
10.11 Richard S. Barr, Bruce L. Golden, James P. Kelly, Mauricio G. C. Resende, William R. StewartJr.
Designing and reporting on computational experiments with heuristic methods
Journal of Heuristics, September 1995, Volume 1, Issue 1, pp 9-32, doi:10.1007/BF02430363
Tim
17.11 Presenting computational methods
Discussion on FT and CSI:FingerID resultsKarin Kleigrewe, Jehad Almaliti, Isaac Yuheng Tian, Robin B. Kinnel, Anton Korobeynikov, Emily A. Monroe, Brendan M. Duggan, Vincenzo Di Marzo, David H. Sherman, Pieter C. Dorrestein, Lena Gerwick, and William H. Gerwick
Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria
J. Nat. Prod., 2015, 78 (7), pp 1671–1682, doi: 10.1021/acs.jnatprod.5b00301
Sebastian

Bertram

24.11 Scientific Tuesday
10-min presentation by group members
 –
01.12 Theodore Alexandrov and Andreas Bartels
Testing for presence of known and unknown molecules in imaging mass spectrometry
Bioinformatics (2013) 29 (18):2335-2342. doi: 10.1093/bioinformatics/btt388
Purva
08.12  No journal club
15.12 JCB Seminar
Over the hedge: proteomics algorithms that could serve metabolomics
  Prof. Dr. Lennart Martens
22.12  No journal club (Weihnachts-/Silvesterpause)
29.12  No journal club (Weihnachts-/Silvesterpause)
05.01 No journal club
12.01 Anastasia V. Rudik, Alexander V. Dmitriev, Alexey A. Lagunin, Dmitry A. Filimonov, and Vladimir V. Poroikov
Metabolism Site Prediction Based on Xenobiotic Structural Formulas and PASS Prediction Algorithm
J. Chem. Inf. Model., 2014, 54 (2), pp 498–507, doi:10.1021/ci400472j
Marvin
19.01 Md Shamsuzzoha Bayzid, Tyler Hunt, Tandy Warnow
Disk covering methods improve phylogenomic analyses
BMC Genomics 2014, 15(Suppl 6):S7 doi:10.1186/1471-2164-15-S6-S7
Markus
26.01 Tobias Petri, Stefan Altmann, Ludwig Geistlinger, Ralf Zimmer and Robert Küffner
Addressing false discoveries in network inference
Bioinformatics(2015) 31 (17): 2836-2843, doi: 10.1093/bioinformatics/btv215
Franzi
02.02  No journal club
09.02 Eudes Barbosa, Richard Ro«ttger, Anne-Christin Hauschild, Vasco Azevedo and Jan Baumbach
On the limits of computational functional genomics for bacterial lifestyle prediction
Briefings in Functional Genomics(2014) 13 (5): 398-408 doi: 10.1093/bfgp/elu014
 Eudes