Protein function in precision medicine: deep understanding with machine learning

Improving condition severity classification with an efficient active learning based framework

(2016) Nir Nissim et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Google AI algorithm masters ancient game of Go

(2016) Elizabeth Gibney   NATURE

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

Predicted Molecular Effects of Sequence Variants Link to System Level of Disease

(2016) Jonas Reeb et al.   PLoS Computational Biology

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

(2016) David Lamparter et al.   PLoS Computational Biology

Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants

(2016) David L. Masica et al.   PLoS Computational Biology

Evolutionary profiles improve protein–protein interaction prediction from sequence

(2015) Tobias Hamp et al.   BIOINFORMATICS

More challenges for machine-learning protein interactions

(2015) Tobias Hamp et al.   BIOINFORMATICS

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

The DNA of a nation

(2015) Vivien Marx   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Human-level control through deep reinforcement learning

(2015) Volodymyr Mnih et al.   NATURE

Predicting drug metabolism: experiment and/or computation?

(2015) Johannes Kirchmair et al.   NATURE REVIEWS DRUG DISCOVERY

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

The neXtProt knowledgebase on human proteins: current status

(2015) Pascale Gaudet et al.   NUCLEIC ACIDS RESEARCH

Unexpected features of the dark proteome

(2015) Nelson Perdigão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat: Figure 1.

(2015) Patricia C. Babbitt et al.   Database-The Journal of Biological Databases and Curation

Deep Question Answering for protein annotation

(2015) Julien Gobeill et al.   Database-The Journal of Biological Databases and Curation

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

A Method for Gene-Based Pathway Analysis Using Genomewide Association Study Summary Statistics Reveals Nine New Type 1 Diabetes Associations

(2014) Marina Evangelou et al.   GENETIC EPIDEMIOLOGY

Class Prior Estimation from Positive and Unlabeled Data

(2014) Marthinus Christoffel DU PLESSIS et al.   IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Large Scale Analysis of Phenotype-Pathway Relationships Based on GWAS Results

(2014) Aharon Brodie et al.   PLoS One

Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

(2014) Anders Boeck Jensen et al.   Nature Communications

I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study

(2014) Kunlin Zhang et al.   Protein & Cell

Pathway-based Analysis Tools for Complex Diseases: A Review

(2014) Lv Jin et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Information-theoretic evaluation of predicted ontological annotations

(2013) Wyatt T. Clark et al.   BIOINFORMATICS

Predicting the functional consequences of non-synonymous DNA sequence variants — evaluation of bioinformatics tools and development of a consensus strategy

(2013) Kimon Frousios et al.   GENOMICS

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Building a Genome Analysis Pipeline to Predict Disease Risk and Prevent Disease

(2013) Y. Bromberg   JOURNAL OF MOLECULAR BIOLOGY

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants

(2013) Thomas A. Peterson et al.   JOURNAL OF MOLECULAR BIOLOGY

The Effects of Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) on Protein–Protein Interactions

(2013) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

Momentum grows to make 'personalized' medicine more 'precise'

(2013) Alla Katsnelson   NATURE MEDICINE

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Neutral and weakly nonneutral sequence variants may define individuality

(2013) Y. Bromberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

(2013) Alexandra M. Schnoes et al.   PLoS Computational Biology

Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset

(2013) Tjaart A. P. de Beer et al.   PLoS Computational Biology

Chapter 15: Disease Gene Prioritization

(2013) Yana Bromberg   PLoS Computational Biology

Disease-related mutations predicted to impact protein function

(2012) Christian Schaefer et al.   BMC GENOMICS

Bioinformatics for personal genome interpretation

(2012) E. Capriotti et al.   BRIEFINGS IN BIOINFORMATICS

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Computational tools for prioritizing candidate genes: boosting disease gene discovery

(2012) Yves Moreau et al.   NATURE REVIEWS GENETICS

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Pathway analysis of genomic data: concepts, methods, and prospects for future development

(2012) Vijay K. Ramanan et al.   TRENDS IN GENETICS

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

(2012) Vladimir Vacic et al.   PLoS Computational Biology

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Bioinformatics challenges for personalized medicine

(2011) Guy Haskin Fernald et al.   BIOINFORMATICS

Protein disorder—a breakthrough invention of evolution?

(2011) Avner Schlessinger et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Computational Methods for Identification of Functional Residues in Protein Structures

(2011) Fuxiao Xin et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

Disease mutations in disordered regions—exception to the rule?

(2011) Vladimir Vacic et al.   Molecular BioSystems

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

(2011) G. De Baets et al.   NUCLEIC ACIDS RESEARCH

Type 1 Diabetes: Etiology, Immunology, and Therapeutic Strategies

(2011) Tom L. Van Belle et al.   PHYSIOLOGICAL REVIEWS

Development and validation of a nomogram for prediction of survival and local control in laryngeal carcinoma patients treated with radiotherapy alone: A cohort study based on 994 patients

(2011) Ada G.T.M. Egelmeer et al.   RADIOTHERAPY AND ONCOLOGY

Using bioinformatics to predict the functional impact of SNVs

(2010) M. S. Cline et al.   BIOINFORMATICS

A comparative study of cancer proteins in the human protein-protein interaction network

(2010) Jingchun Sun et al.   BMC GENOMICS

The Human Phenotype Ontology

(2010) PN Robinson et al.   CLINICAL GENETICS

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions

(2010) Matthew Mort et al.   HUMAN MUTATION

Rapid-Learning System for Cancer Care

(2010) Amy P. Abernethy et al.   JOURNAL OF CLINICAL ONCOLOGY

Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits

(2010) Ayellet V. Segrè et al.   PLoS Genetics

Gene Ontology Analysis of GWA Study Data Sets Provides Insights into the Biology of Bipolar Disorder

(2009) Peter Holmans et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Epistasis and Its Implications for Personal Genetics

(2009) Jason H. Moore et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Detecting gene–gene interactions that underlie human diseases

(2009) Heather J Cordell   NATURE REVIEWS GENETICS

Protein function prediction – the power of multiplicity

(2009) Robert Rentzsch et al.   TRENDS IN BIOTECHNOLOGY

Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins

(2009) Amrita Mohan et al.   PLoS Computational Biology

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Intrinsically Disordered Proteins in Human Diseases: Introducing the D2 Concept

(2008) Vladimir N. Uversky et al.   Annual Review of Biophysics

Gain and loss of phosphorylation sites in human cancer

(2008) P. Radivojac et al.   BIOINFORMATICS

Presence-Only Data and the EM Algorithm

(2008) Gill Ward et al.   BIOMETRICS

From protein-disease associations to disease informatics

(2008) Mehmet et al.   Frontiers in Bioscience-Landmark

The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program

(2008) Michel Schneider et al.   Journal of Proteomics