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 and Backup
04.04  Organisatorisches, Besprechen der Themen Purva
12.04  How to read a scientific paper? Sebastian
19.04 Nicholas W. Kwiecien†‡, Derek J. Bailey†‡, Matthew J. P. Rush†‡, Jason S. Cole§, Arne Ulbrich†‡, Alexander S. Hebert†, Michael S. Westphall†, and Joshua J. Coon
High-Resolution Filtering for Improved Small Molecule Identification via GC/MS
Anal. Chem., 2015, 87 (16), pp 8328–8335
Franzi
26.04 André C. A. NascimentoEmail author, Ricardo B. C. Prudêncio and Ivan G. Costa
A multiple kernel learning algorithm for drug-target interaction prediction
BMC Bioinformatics, 2016, 17:46 DOI: 10.1186/s12859-016-0890-3
Marcus
03.05 Michael Hanselmann, Ullrich Köthe, Marc Kirchner, Bernhard Y. Renard, Erika R. Amstalden, Kristine Glunde§, Ron M. A. Heeren and Fred A. Hamprecht
Toward Digital Staining using Imaging Mass Spectrometry and Random Forests
J. Proteome Res., 2009, 8 (7), pp 3558–3567 DOI: 10.1021/pr900253y
Daniel and Purva
10.05 Simona Constantinescu1,2, Ewa Szczurek1,2, Pejman Mohammadi1,2, Jörg Rahnenführer3 and Niko Beerenwinkel1,2
TiMEx: a waiting time model for mutually exclusive cancer alterations
Bioinformatics (2016) 32 (7): 968-975.
Florian and Tim
17.05 Grzegorz Mrukwa, Grzegorz Drazek, Monika Pietrowska, Piotr Widlak, Joanna Polanska
A Novel Divisive iK-Means Algorithm with Region-Driven Feature Selection as a Tool for Automated Detection of Tumour Heterogeneity in MALDI IMS Experiments
Bioinformatics and Biomedical Engineering
Volume 9656 of the series Lecture Notes in Computer Science pp 113-124
Bastian and Purva
 24.05 Robin Genuer, Jean-Michel Poggi and Christine Tuleau-Malot
VSURF: An R Package for Variable Selection Using Random Forests
CONTRIBUTED RESEARCH ARTICLES, R Project
Anna and Eudes
31.05 Dries Verdegem, Diether Lambrechts, Peter Carmeliet, Bart Ghesquiere
Improved metabolite identification with MIDAS and MAGMa through MS/MS spectral dataset-driven parameter optimization
Metabolomics (2016) 12:98, DOI 10.1007/s11306-016-1036-3
Kai
 07.06 Nam-phuong D. Nguyen, Siavash Mirarab, Keerthana Kumar and Tandy Warnow
Ultra-large alignments using phylogeny-aware profiles
Genome Biology2015, 16:124
Ruman and Markus
14.06 Cancelled
21.06  Julian R Marchesi1,2, David H Adams3, Francesca Fava4, Gerben D A Hermes, Gideon M Hirschfield3, Georgina Hold7, Mohammed
Nabil Quraishi3, James Kinross8, Hauke Smidt5, Kieran M Tuohy4, Linda V Thomas9, Erwin G Zoetendal5,6, Ailsa Hart10
The gut microbiota and host health: a new clinical frontier
Gut 2016;65:330-339
 Marvin
28.06  Cancelled
05.07 Michael E. Kurczy1, Julijana Ivanisevic1, Caroline H. Johnson1, Winnie Uritboonthai1, Linh Hoang1, Mingliang Fang1, Matthew Hicks1, Anthony Aldebot1, Duane Rinehart1, Lisa J. Mellander2, Ralf Tautenhahn1, Gary J. Patti3,4, Mary E. Spilker5, H. Paul Benton1 and Gary Siuzdak
Determining conserved metabolic biomarkers from a million database queries
Bioinformatics (2015) 31 (23): 3721-3724. doi: 10.1093/bioinformatics/btv475
 Moritz and Purva

Additional papers:

  1. Aleksandra Skirycz, Sylwia Kierszniowska, Michaël Méret, Lothar Willmitzer, George Tzotzos
    Medicinal Bioprospecting of the Amazon Rainforest: A Modern Eldorado?
    Trends in Biotechnology, Cell Press, Available online 21 April 2016
  2. Isidro Cortes‑Ciriano
    Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets
    Cortes‑Ciriano J Cheminform (2016) 8:13
  3. Andrés M. Castillo, Andrés Bernal, Reiner Dieden, Luc Patiny and Julien Wist
    “Ask Ernö”: a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra
    Journal of Cheminformatics 2016 8:26 DOI: 10.1186/s13321-016-0134-6