Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks

(2019) Ljubisa Miskovic et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Supervised Machine Learning for Population Genetics: A New Paradigm

(2018) Daniel R. Schrider et al.   TRENDS IN GENETICS

Machine Learning in Medical Imaging

(2018) Maryellen L. Giger   Journal of the American College of Radiology

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

(2018) Tuure Hameri et al.   METABOLIC ENGINEERING

DeepPPI: Boosting Prediction of Protein–Protein Interactions with Deep Neural Networks

(2017) Xiuquan Du et al.   Journal of Chemical Information and Modeling

Machine Learning: Discovering the Future of Medical Imaging

(2017) Bradley J. Erickson   JOURNAL OF DIGITAL IMAGING

Machine Learning for Medical Imaging

(2017) Bradley J. Erickson et al.   RADIOGRAPHICS

Editorial (Thematic Issue: Machine Learning Techniques for Protein Structure, Genomics Function Analysis and Disease Prediction)

(2016) Quan Zou   Current Proteomics

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

(2016) Stefano Andreozzi et al.   METABOLIC ENGINEERING

iSCHRUNK – I n S ilico Approach to Ch aracterization and R eduction of Un certainty in the K inetic Models of Genome-scale Metabolic Networks

(2016) Stefano Andreozzi et al.   METABOLIC ENGINEERING

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

(2016) Ali Khodayari et al.   Nature Communications

Deep Learning for Population Genetic Inference

(2016) Sara Sheehan et al.   PLoS Computational Biology

Thermodynamic and Probabilistic Metabolic Control Analysis of Riboflavin (Vitamin B2) Biosynthesis in Bacteria

(2015) Markus Birkenmeier et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

(2015) Ljubisa Miskovic et al.   CURRENT OPINION IN BIOTECHNOLOGY

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

(2015) Meric Ataman et al.   CURRENT OPINION IN BIOTECHNOLOGY

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Machine learning for biomarker identification in cancer research – developments toward its clinical application

(2015) Zeenia Jagga et al.   Personalized Medicine

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

(2015) N. Hadadi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Machine learning: Trends, perspectives, and prospects

(2015) M. I. Jordan et al.   SCIENCE

Erratum to: A coupled thermodynamic and metabolic control analysis methodology and its evaluation on glycerol biosynthesis in Saccharomyces cerevisiae

(2014) Markus Birkenmeier et al.   BIOTECHNOLOGY LETTERS

A computational method of predicting regulatory interactions in Arabidopsis based on gene expression data and sequence information

(2014) Xiaoqing Yu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways

(2014) Yun Lee et al.   METABOLIC ENGINEERING

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

(2014) Ali Khodayari et al.   METABOLIC ENGINEERING

Kinetic models in industrial biotechnology – Improving cell factory performance

(2014) Joachim Almquist et al.   METABOLIC ENGINEERING

Monte-Carlo Modeling of the Central Carbon Metabolism of Lactococcus lactis: Insights into Metabolic Regulation

(2014) Ettore Murabito et al.   PLoS One

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM

(2013) Andrew J. Sedgewick et al.   BIOINFORMATICS

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

(2013) Anirikh Chakrabarti et al.   Biotechnology Journal

Machine learning in cell biology – teaching computers to recognize phenotypes

(2013) Christoph Sommer et al.   JOURNAL OF CELL SCIENCE

Application of Machine Learning to Proteomics Data: Classification and Biomarker Identification in Postgenomics Biology

(2013) Anna Louise Swan et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

(2013) Natalie J. Stanford et al.   PLoS One

A global machine learning based scoring function for protein structure prediction

(2013) Eshel Faraggi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Approximate Bayesian Computation

(2013) Mikael Sunnåker et al.   PLoS Computational Biology

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

(2012) Ida Schomburg et al.   NUCLEIC ACIDS RESEARCH

From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

(2011) Keng Cher Soh et al.   FEMS YEAST RESEARCH

SABIO-RK--database for biochemical reaction kinetics

(2011) U. Wittig et al.   NUCLEIC ACIDS RESEARCH

Modeling of uncertainties in biochemical reactions

(2010) Ljubiša Mišković et al.   BIOTECHNOLOGY AND BIOENGINEERING

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC Systems Biology

Network thermodynamics in the post-genomic era

(2010) Keng Cher Soh et al.   CURRENT OPINION IN MICROBIOLOGY

A probabilistic approach to identify putative drug targets in biochemical networks

(2010) E. Murabito et al.   Journal of the Royal Society Interface

Production of biofuels and biochemicals: in need of an ORACLE

(2010) Ljubisa Miskovic et al.   TRENDS IN BIOTECHNOLOGY

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

(2008) Matthew D. Jankowski et al.   BIOPHYSICAL JOURNAL