Call for Papers & Highlight track abstracts: 10th International Workshop Machine Learning in Systems Biology (MLSB-2016) Organized as a ECCB pre-conference workshop, September 3-4, 2016, World Forum, The Hague, Netherlands SUMMARY Biology is rapidly turning into an information science, thanks to enormous advances in the ability to observe the molecular properties of cells, organs and individuals. This wealth of data allows us to model molecular systems at an unprecedented level of detail and to start to understand the underlying biological mechanisms. This field of systems biology creates a huge need for methods from machine learning, which find statistical dependencies and patterns in these large-scale datasets and that use them to establish models of complex molecular systems. MLSB is a scientific forum for the exchange between researchers from Systems Biology and Machine Learning, to promote the exchange of ideas, interactions and collaborations between these communities. TARGET AUDIENCE The aim of this workshop is to contribute to the cross­-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. WORKSHOP TOPICS (NON EXHAUSTIVE) Methods: Active learning/Experimental design, Bayesian Methods, Clustering/Biclustering, Data integration/fusion/multi­-view learning, Feature/subspace selection, Graph inference/completion, Kernel Methods, Machine Learning Algorithms, Multi­task/Structured output prediction, Probabilistic inference, Semi­-supervised learning, Systems identification, Time­-series analysis Applications: Biomarker identification, Epigenetics, Genome­-wide association studies, Metabolic modeling and reconstruction, Metabolomics, Protein function and structure prediction, Protein­-protein interaction networks, Rational drug design methods, Regulatory genomics, Sequence Annotation, Signaling networks, Synthetic biology IMPORTANT DATES May 30, 2016: Full length manuscript submission May 30, 2016: Highlight track abstract submission June 30, 2016: Decision notifications for manuscripts and abstracts July 20, 2016: Final camera-ready manuscript submission August 19, 2016: Registration deadline September 3-4, 2016: Workshop INVITED SPEAKERS Prof. Ziv Bar­-Joseph, School of Computer Science Carnegie­-Mellon University, USA Prof. Jukka Corander, Department of Mathematics and Statistics, University of Helsinki, Finland Prof. Lodewyk Wessels, The Delft Bioinformatics Lab, Delft University of Technology, The Netherlands Prof. Yvan Saeys, VIB Inflammation Research Center, Ghent University, Belgium SUBMISSIONS We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures), statistical machine learning methods for analysis of various high-throughput ­omics data, and methods supporting systems­-level data analysis. The submissions are organized into the following two tracks: 1. Manuscripts (preferentially up to 5000 words) describing original work on machine learning in systems biology. These should describe method development and applications broadly in the topics listed above (see Workshop topics). Accepted proceedings track papers will be published in BMC Bioinformatics. The publications need to match the standards of the journal; please prepare your submissions using the BMC instructions (http://www.bioinformatics.nl/MLSB2016/BMC_guidelines.pdf). The publication is subject to open access fee (special reduced price negotiated by MLSB). 2. Highlights Track abstracts (1­-2 pages) describing computational aspects of work that has been recently published in a journal (or are “in press”) as well as unpublished/on-going work. Submissions will be evaluated by at least three reviewers from an international programme committee of experts in the field. The most relevant and most original submissions will be accepted as full oral presentations and/or as poster presentations at the workshop. Submission is through the Easychair system: https://easychair.org/conferences/?conf=mlsb2016 REGISTRATION Registration via the general ECCB2016 registration system http://www.eccb2016.org/registration/ PROGRAMME COMMITTEE Antti Airola Chloé-Agathe Azencott Alexis Battle Michael A. Beer Andreas Beyer Karsten Borgwardt Céline Brouard Gal Chechik Chao Cheng Manfred Claassen Florence D’Alché-buc Dick de Ridder Saso Dzeroski Pierre Geurts Markus Heinonen James Hensman Lars Kaderali David Knowles Stefan Kramer Anshul Kundaje Harri Lähdesmäki François Laviolette Christina Leslie Hiroshi Mamitsuka Martin Renqiang Min Yves Moreau Alan Moses Sara Mostafavi Bernard Ng Mahesan Niranjan William Noble Uwe Ohler Tapio Pahikkala Nico Pfeifer Gerald Quon Magnus Rattray Juho Rousu Yvan Saeys Guido Sanguinetti Li Shen Motoki Shiga Oliver Stegle Koji Tsuda Giorgio Valentini Aalt-Jan van Dijk Jinbo Xu