Methods included: standardizing computational reuse and portability with the common workflow language

…, A Iosup, P Amstutz, J Chilton, N Tijanić… - Communications of the …, 2022 - dl.acm.org
… CRUSOE, SANNE ABELN, ALEXANDRU IOSUP, PETER AMSTUTZ, JOHN CHILTON,
NEBOJŠA TIJANIC, HERVÉ MÉNAGER, STIAN SOILAND-REYES, BOGDAN GAVRILOVIC …

Common workflow language, v1. 0

P Amstutz, MR Crusoe, N Tijanić, B Chapman… - 2016 - research.manchester.ac.uk
The Common Workflow Language (CWL) is an informal, multi-vendor working group
consisting of various organizations and individuals that have an interest in portability of data …

Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness

…, V Blay, C Kohnert, JT Stanton, A Brown, N Tijanic… - BioRxiv, 2022 - biorxiv.org
Traditional antibody optimization approaches involve screening a small subset of the
available sequence space, often resulting in drug candidates with suboptimal binding affinity, …

Rabix: an open-source workflow executor supporting recomputability and interoperability of workflow descriptions

G Kaushik, S Ivkovic, J Simonovic, N Tijanic… - PACIFIC …, 2017 - World Scientific
As biomedical data has become increasingly easy to generate in large quantities, the
methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are …

Improved scaffold hopping in ligand-based virtual screening using neural representation learning

L Stojanovic, M Popovic, N Tijanic… - Journal of Chemical …, 2020 - ACS Publications
Deep learning has demonstrated significant potential in advancing state of the art in many
problem domains, especially those benefiting from automated feature extraction. Yet, the …

[HTML][HTML] A community-powered search of machine learning strategy space to find NMR property prediction models

…, W Reade, W Song, L Stojanovic, EH Thiede, N Tijanic… - Plos one, 2021 - journals.plos.org
The rise of machine learning (ML) has created an explosion in the potential strategies for
using data to make scientific predictions. For physical scientists wishing to apply ML strategies …

Large-scale uniform analysis of cancer whole genomes in multiple computing environments

…, HJ Sofia, J Spring, AJ Struck, G Tiao, N Tijanic… - BioRxiv, 2017 - biorxiv.org
The International Cancer Genome Consortium (ICGC)’s Pan-Cancer Analysis of Whole
Genomes (PCAWG) project aimed to categorize somatic and germline variations in both coding …

Common workflow language, draft 3

…, J Randall, S Soiland-Reyes, L Stojanovic, N Tijanić - 2016 - escholarship.org
The Common Workflow Language (CWL) is an informal, multi-vendor working group
consisting of various organizations and individuals that have an interest in portability of data …

Portable workflow and tool descriptions with the CWL

P Amstutz, N Tijanić… - Bioinformatics …, 2015 - research.manchester.ac.uk
Bioinformatics workflow platforms provide provenance tracking, execution and data management,
repeatability, and an environment for data exploration and visualization. Example F/…

Graph Theory Approaches For Optimizing Biomedical Data Analysis Using Reproducible Workflows

G Kaushik, S Ivkovic, J Simonovic, N Tijanic… - bioRxiv, 2016 - biorxiv.org
As biomedical data becomes increasingly easy to generate in large quantities, the methods
used to analyze it have proliferated rapidly. However, for the insights gained from these …