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List of works by Juho Rousu

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

scientific article

Analysis of Fluxomic Experiments with Principal Metabolic Flux Mode Analysis

scientific article published on 01 January 2018

Bayesian metabolic flux analysis reveals intracellular flux couplings

scientific article published on 01 July 2019

Biomarker discovery by sparse canonical correlation analysis of complex clinical phenotypes of tuberculosis and malaria

scientific article

CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology.

scientific article

Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species

scientific article (publication date: February 2014)

Computational methods for metabolic reconstruction

scientific article published on 18 February 2010

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors.

scientific article published on 07 August 2017

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism ⬇️

scientific article published on January 1, 2011

Computing positional isotopomer distributions from tandem mass spectrometric data

scientific article

Critical Assessment of Small Molecule Identification 2016: automated methods

scientific article

Erratum: CamOptimus: a tool for exploiting complex adaptive evolution to optimise experiments and processes in biotechnology.

scientific article

Fast metabolite identification with Input Output Kernel Regression

scientific article published on June 2016

FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data

scientific article

Identification of drug candidates and repurposing opportunities through compound-target interaction networks

scientific article published on October 2015

Improved Small Molecule Identification through Learning Combinations of Kernel Regression Models

scientific article published on 01 August 2019

Inferring branching pathways in genome-scale metabolic networks

scientific article

Information theoretic methods for bioinformatics

scientific article published on January 2007

Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra

scientific article published in 2005

Learning with multiple pairwise kernels for drug bioactivity prediction.

scientific article published in July 2018

Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects

scientific article published on 01 December 2020

Liquid-chromatography retention order prediction for metabolite identification

scientific article published on 01 September 2018

Machine Learning of Protein Interactions in Fungal Secretory Pathways.

scientific article published on 21 July 2016

Metabolite Identification through Machine Learning- Tackling CASMI Challenge Using FingerID

scientific article published on 6 June 2013

Metabolite identification and molecular fingerprint prediction through machine learning.

scientific article

Metabolite identification through multiple kernel learning on fragmentation trees

scientific article published on June 2014

Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks ⬇️

scientific article published in January 2014

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes

scientific article published on 27 February 2006

Principal Metabolic Flux Mode Analysis

scientific article published on 6 February 2018

Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification

scientific article published on 27 November 2020

Probabilistic modeling and machine learning in structural and systems biology

scientific article published on 3 May 2007

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy

scientific article

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions

scientific article published in 2021

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

scientific article published on 18 March 2019

Searching molecular structure databases with tandem mass spectra using CSI:FingerID.

scientific article published on 21 September 2015

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016.

scientific article

Strain design optimization using reinforcement learning

scientific article published on 03 June 2022

Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods

scientific article published on 04 November 2020

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae

scientific article

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

scientific article published on 23 November 2020

Towards structured output prediction of enzyme function

scientific article

metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis

scientific article published on 19 February 2016

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