Currents on Bioinformatics

  • Seminarleiter: Purva Kulkarni
  • Termin: Di 16-18h, SR 3423 EAP
  • Beginn: 25.10.2016

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 and Backup
18.10. verschoben
25.10. Organisatorisches, Besprechen der Themen  Purva
01.11. Huibin Shen , Sandor Szedmak, Céline Brouard, Juho Rousu
Soft Kernel Target Alignment for Two-Stage Multiple Kernel Learning
Volume 9956 of the series Lecture Notes in Computer Science pp 427-441
08.11. Battista Biggio, Blaine Nelson, Pavel Laskov
Support Vector Machines Under Adversarial Label Noise
JMLR: Workshop and Conference Proceedings 20 (2011) 97–112, Asian Conference on Machine Learning
15.11. Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner and David S. Wishart
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy
Journal of Cheminformatics 2016 8:61 DOI: 10.1186/s13321-016-0174-y
22.11. Andrew Palmer, Prasad Phapale, Ilya Chernyavsky, Regis Lavigne, Dominik Fay, Artem Tarasov, Vitaly Kovalev, Jens Fuchser, Sergey Nikolenko, Charles Pineau, Michael Becker & Theodore Alexandrov
FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry
Nature Methods (2016) doi:10.1038/nmeth.4072
29.11. Andreas Mayr, Günter Klambauer, Thomas Unterthiner and Sepp Hochreiter
DeepTox: Toxicity Prediction using Deep Learning
Front. Environ. Sci., 02 February 2016
Priyanka Banerjee, Vishal B. Siramshetty, Malgorzata N. Drwal and Robert Preissner
Computational methods for prediction of in vitro effects of new chemical structures
Journal of Cheminformatics20168:51 DOI: 10.1186/s13321-016-0162-2
Daniel and Marcus
06.12. Visit to weihnachtsmarkt
13.12. Visit to weihnachtsmarkt
20.12. Pranjal Vachaspati and Tandy Warnow
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization
Bioinformatics (2016) doi: 10.1093/bioinformatics/btw600 First published online: September 23, 2016
Claudia and Markus
03.01. Mikko I. MalinenPasi Fränti
Balanced K-Means for Clustering
Joint IAPR International Workshops on Statistical Techniques in Pattern
S+SSPR 2014: Structural, Syntactic, and Statistical Pattern Recognition pp 32-41  DOI: 10.1007/978-3-662-44415-3_4
Frederik and Tim
17.01.  Justin Johan Jozias van der Hooft, Joe Wandya, Michael P. Barretta, Karl E. V. Burgessa, and Simon Rogers
Topic modeling for untargeted substructure exploration in metabolomics
doi: 10.1073/pnas.1608041113
24.01.  Shahaf et al
The WEIZMASS spectral library for high-confidence metabolite identification
Nature Communications 7, Article number: 12423 (2016), doi:10.1038/ncomms12423
 Beatrice and Kai

List of papers:

  1. Abate-Pellaa et al
    Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods
    Journal of Chromatography A, Volume 1412, 18 September 2015, Pages 43–51, DOI: 10.1016/j.chroma.2015.07.108
  2. Aicheler et al
    Retention Time Prediction Improves Identification in Nontargeted Lipidomics Approaches
    Anal. Chem., 2015, 87 (15), pp 7698–7704, DOI: 10.1021/acs.analchem.5b01139
  3. Shunichi Takeda, Hiromasa Kaneko, and Kimito Funatsu
    Chemical-Space-Based de Novo Design Method To Generate Drug-Like Molecules
    J. Chem. Inf. Model., 2016, 56 (10), pp 1885–1893 DOI: 10.1021/acs.jcim.6b00038
  4. Corey D. Broeckling, Andrea Ganna, Mark Layer, Kevin Brown, Ben Sutton, Erik Ingelsson, Graham Peers, and Jessica E. Prenni
    Enabling Efficient and Confident Annotation of LC−MS Metabolomics Data through MS1 Spectrum and Time Prediction
    Anal. Chem., 2016, 88 (18), pp 9226–9234 DOI: 10.1021/acs.analchem.6b02479
  5. Mariana González-Medina, Fernando D. Prieto-Martínez, John R. Owen and José L. Medina-Franco
    Consensus Diversity Plots: a global diversity analysis of chemical libraries
    Journal of Cheminformatics 20168:63 DOI: 10.1186/s13321-016-0176-9