Code

Open research data and software

Research software impact. Mature open source projects are listed below.

Statistical ecology and machine learning

Microbiome bioinformatics software and tutorials

earlywarnings Methods for identification of critical transitions between ecosystem states from time series data (CRAN). Co-developer. CRAN/Github. WICI Data Challenge 2013 runner-up / Waterloo Institute for Complex Systems and Innovation.

DMT Dependency Modeling Toolkit. Probabilistic tools for dependency analysis between multiple data sources (R/CRAN). Probabilistic PCA, factor analysis, CCA, regularized variants, dependency-based dimensionality reduction etc. ICML/MLOSS workshop, Israel 2010.

Bioinformatics

netresponse Modeling context-specific activation patterns in genome-wide interaction networks (R/Matlab). Originally applied to study transcriptional responses in genome-scale interaction networks across organism-wide collections of gene expression data. doi:10.18129/B9.BIOC.NETRESPONSE

RPA (R/Bioconductor). Scalable probabilistic method for preprocessing short oligo microarray data. NAR 2013. doi:10.18129/B9.BIOC.RPA

intcomp Benchmarking for integrative cancer gene discovery algorithms. Briefings in Bioinformatics 2012

pint Probabilistic data integration for DNA/RNA data in functional genomics (R/Bioc). MLSP 2009.

Digital Humanities and Computational Social Science

rOpenGov R package ecosystem for open government data analytics (R/GitHub). introduced in NIPS Machine Learning Open Source Software workshop 2013.

COMHIS Helsinki Computational History Group data analytics infrastructure.

Data

Full agreement texts for academic publisher agreements. The agreements were released by the FinELib consortium of research libraries following our FOI request in April 2018.

Scientific journal subscription costs in Finland 2010-2017; MoE/ATT. The data set was released by Finnish Ministry of Education (Open Science and Research Initiative) following my Freedom of Information Request (summary). Finland became the first country to systematically collect and release this information.

Human Gut Microbiota Atlas (Data Dryad); Genus level profiling of the human gut microbiota for 1006 western adults; Lahti et al. Nature Communications 5:4344, 2014

Gut microbiota profiling in African-American diet swap experiment; Data Dryad; O’Keefe et al. Nature Communications 6:6342, 2015

Probiotics intervention data with high-throughput profiling of the gut microbiome and serum lipidome (RData format); from Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data. Lahti et al. PeerJ 1:e32, 2013