Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation

Development and evaluation of physiologically based pharmacokinetic drug-disease models for predicting captopril pharmacokinetics in chronic diseases

(2021) Muhammad F. Rasool et al.   Scientific Reports

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning

(2021) Derek M. Mason et al.   Nature Biomedical Engineering

The AIMe registry for artificial intelligence in biomedical research

(2021) Julian Matschinske et al.   NATURE METHODS

A guide to machine learning for biologists

(2021) Joe G. Greener et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The role of machine learning in clinical research: transforming the future of evidence generation

(2021) E. Hope Weissler et al.   Trials

Data‐driven personalization of a physiologically based pharmacokinetic model for caffeine: A systematic assessment

(2021) Rebekka Fendt et al.   CPT-Pharmacometrics & Systems Pharmacology

Scientific and regulatory evaluation of mechanistic in silico drug and disease models in drug development: Building model credibility

(2021) Flora T. Musuamba et al.   CPT-Pharmacometrics & Systems Pharmacology

Responsible use of polygenic risk scores in the clinic: potential benefits, risks and gaps

(2021) et al.   NATURE MEDICINE

SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks

(2021) Luca Csabai et al.   NUCLEIC ACIDS RESEARCH

Transparency of machine-learning in healthcare: The GDPR & European health law

(2021) Miranda Mourby et al.   Computer Law & Security Review

Clinically Applicable AI System for Accurate Diagnosis, Quantitative Measurements, and Prognosis of COVID-19 Pneumonia Using Computed Tomography

(2020) Kang Zhang et al.   CELL

Applications of personalised signalling network models in precision oncology

(2020) Jordan F. Hastings et al.   PHARMACOLOGY & THERAPEUTICS

Towards implementation of AI in New Zealand national diabetic screening program: Cloud-based, robust, and bespoke

(2020) Li Xie et al.   PLoS One

Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies

(2020) Federica Eduati et al.   Molecular Systems Biology

New machine learning method for image-based diagnosis of COVID-19

(2020) Mohamed Abd Elaziz et al.   PLoS One

The Atlas of Inflammation Resolution (AIR)

(2020) Charles N. Serhan et al.   MOLECULAR ASPECTS OF MEDICINE

Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI extension

(2020) Xiaoxuan Liu et al.   NATURE MEDICINE

Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI extension

(2020) Samantha Cruz Rivera et al.   NATURE MEDICINE

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

(2020) Samuel M D Seaver et al.   NUCLEIC ACIDS RESEARCH

Physiologically‐Based Pharmacokinetic Modeling in Renal and Hepatic Impairment Populations: A Pharmaceutical Industry Perspective

(2020) Tycho Heimbach et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Computer-assisted medical image classification for early diagnosis of oral cancer employing deep learning algorithm

(2019) Pandia Rajan Jeyaraj et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Correction: Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity

(2019) Akshata R. Udyavar et al.   CANCER RESEARCH

Intelligent Image De‐Blurring for Imaging Flow Cytometry

(2019) Fangzheng Zhang et al.   CYTOMETRY PART A

The role of polygenic risk score gene-set analysis in the context of the omnigenic model of schizophrenia

(2019) Alexandros Rammos et al.   NEUROPSYCHOPHARMACOLOGY

Analysis of polygenic risk score usage and performance in diverse human populations

(2019) L. Duncan et al.   Nature Communications

Patients with High Genome-Wide Polygenic Risk Scores for Coronary Artery Disease May Receive Greater Clinical Benefit from Alirocumab Treatment in the Odyssey Outcomes Trial

(2019) Amy Damask et al.   CIRCULATION

Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry

(2019) Tim B. Bigdeli et al.   MOLECULAR PSYCHIATRY

SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update

(2019) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

BioModels—15 years of sharing computational models in life science

(2019) Rahuman S Malik-Sheriff et al.   NUCLEIC ACIDS RESEARCH

The reactome pathway knowledgebase

(2019) Bijay Jassal et al.   NUCLEIC ACIDS RESEARCH

Explainable Artificial Intelligence (XAI): Concepts, taxonomies, opportunities and challenges toward responsible AI

(2019) Alejandro Barredo Arrieta et al.   Information Fusion

Prediction of olanzapine exposure in individual patients using physiologically based pharmacokinetic modelling and simulation

(2018) Thomas M. Polasek et al.   BRITISH JOURNAL OF CLINICAL PHARMACOLOGY

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

(2018) James J. Lee et al.   NATURE GENETICS

AsthmaMap: An expert-driven computational representation of disease mechanisms

(2018) Alexander Mazein et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Glaucoma diagnosis based on both hidden features and domain knowledge through deep learning models

(2018) Yidong Chai et al.   KNOWLEDGE-BASED SYSTEMS

Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations

(2018) Amit V. Khera et al.   NATURE GENETICS

New models of atherosclerosis and multi-drug therapeutic interventions

(2018) Andrew Parton et al.   BIOINFORMATICS

Generalizing polygenic risk scores from Europeans to Hispanics/Latinos

(2018) Kelsey E. Grinde et al.   GENETIC EPIDEMIOLOGY

Towards Further Verification of Physiologically-Based Kidney Models: Predictability of the Effects of Urine-Flow and Urine-pH on Renal Clearance

(2018) Takanobu Matsuzaki et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Multiethnic polygenic risk scores improve risk prediction in diverse populations

(2017) Carla Márquez-Luna et al.   GENETIC EPIDEMIOLOGY

An open-source solution for advanced imaging flow cytometry data analysis using machine learning

(2017) Holger Hennig et al.   METHODS

Fast learning method for convolutional neural networks using extreme learning machine and its application to lane detection

(2017) Jihun Kim et al.   NEURAL NETWORKS

BioModels: expanding horizons to include more modelling approaches and formats

(2017) Mihai Glont et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

(2017) Denise N Slenter et al.   NUCLEIC ACIDS RESEARCH

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures

(2017) Faiz M. Khan et al.   Nature Communications

A machine-learning heuristic to improve gene score prediction of polygenic traits

(2017) Guillaume Paré et al.   Scientific Reports

Development of a Whole-Body Physiologically Based Pharmacokinetic Approach to Assess the Pharmacokinetics of Drugs in Elderly Individuals

(2016) Jan-Frederik Schlender et al.   CLINICAL PHARMACOKINETICS

Towards patient stratification and treatment in the autoimmune disease lupus erythematosus using a systems pharmacology approach

(2016) M. Leire Ruiz-Cerdá et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Personalized risk prediction for type 2 diabetes: the potential of genetic risk scores

(2016) Kristi Läll et al.   GENETICS IN MEDICINE

Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation

(2016) Thomas J Hoffmann et al.   NATURE GENETICS

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

STARD 2015 guidelines for reporting diagnostic accuracy studies: explanation and elaboration

(2016) Jérémie F Cohen et al.   BMJ Open

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

(2015) Bjarni J. Vilhjálmsson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps

(2015) Cody R. Goodwin et al.   CHEMISTRY & BIOLOGY

Physiologically based pharmacokinetic modeling in drug discovery and development: A pharmaceutical industry perspective

(2015) HM Jones et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Deep learning

(2015) Yann LeCun et al.   NATURE

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Assessment of Age-Related Changes in Pediatric Gastrointestinal Solubility

(2015) Anil R. Maharaj et al.   PHARMACEUTICAL RESEARCH

Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients

(2015) D. Fey et al.   Science Signaling

Human metabolic atlas: an online resource for human metabolism

(2015) Natapol Pornputtapong et al.   Database-The Journal of Biological Databases and Curation

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes

(2015) Leif Väremo et al.   Cell Reports

Individual Participant Data (IPD) Meta-analyses of Diagnostic and Prognostic Modeling Studies: Guidance on Their Use

(2015) Thomas P. A. Debray et al.   PLOS MEDICINE

Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients

(2015) D. Fey et al.   Science Signaling

Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

(2015) I Kuperstein et al.   Oncogenesis

Clinical Decision Support Systems (CDSS) for preventive management of COPD patients

(2014) Filip Velickovski et al.   Journal of Translational Medicine

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

(2014) R. Agren et al.   Molecular Systems Biology

Correction: A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis

(2014) Gang Wu et al.   PLoS One

Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease

(2014) Shiri Stempler et al.   PLoS One

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

Enabling multiscale modeling in systems medicine

(2014) Olaf Wolkenhauer et al.   Genome Medicine

Regularized Machine Learning in the Genetic Prediction of Complex Traits

(2014) Sebastian Okser et al.   PLoS Genetics

Why model?

(2014) Olaf Wolkenhauer   Frontiers in Physiology

sybil – Efficient constraint-based modelling in R

(2013) Gabriel Gelius-Dietrich et al.   BMC Systems Biology

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

(2013) Claudine Chaouiya et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

The search for organizing principles as a cure against reductionism in systems medicine

(2013) Olaf Wolkenhauer et al.   FEBS Journal

Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map

(2013) Kazuhiro A. Fujita et al.   MOLECULAR NEUROBIOLOGY

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

The road from systems biology to systems medicine

(2013) Olaf Wolkenhauer et al.   PEDIATRIC RESEARCH

Correction: Power and Predictive Accuracy of Polygenic Risk Scores

(2013) Frank Dudbridge   PLoS Genetics

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

The Cell Collective: Toward an open and collaborative approach to systems biology

(2012) Tomáš Helikar et al.   BMC Systems Biology

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

The Physiome Model Repository 2

(2011) T. Yu et al.   BIOINFORMATICS

Clinical application of a systems model of apoptosis execution for the prediction of colorectal cancer therapy responses and personalisation of therapy

(2011) Suzanne Hector et al.   GUT

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

BoolNet—an R package for generation, reconstruction and analysis of Boolean networks

(2010) Christoph Müssel et al.   BIOINFORMATICS

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Logical modelling of regulatory networks with GINsim 2.3

(2009) A. Naldi et al.   BIOSYSTEMS

Common polygenic variation contributes to risk of schizophrenia and bipolar disorder

(2009) Shaun M. Purcell et al.   NATURE

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

Physiology-Based Simulations of a Pathological Condition

(2008) Andrea N Edginton et al.   CLINICAL PHARMACOKINETICS