Artificial Intelligence in Molecular Medicine

Global detection of human variants and isoforms by deep proteome sequencing

(2023) Pavel Sinitcyn et al.   NATURE BIOTECHNOLOGY

Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland

(2023) Caroline F. Wright et al.   NEW ENGLAND JOURNAL OF MEDICINE

Using deep learning to annotate the protein universe

(2022) Maxwell L. Bileschi et al.   NATURE BIOTECHNOLOGY

Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting

(2022) John E. Gorzynski et al.   NEW ENGLAND JOURNAL OF MEDICINE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly

(2022) Denis Beslic et al.   BRIEFINGS IN BIOINFORMATICS

Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk

(2021) Christopher Y. Park et al.   NATURE GENETICS

Genome-wide detection of cytosine methylation by single molecule real-time sequencing

(2021) O. Y. Olivia Tse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of aberrant splicing events in RNA-seq data using FRASER

(2021) Christian Mertes et al.   Nature Communications

Using machine learning approaches for multi-omics data analysis: A review

(2021) Parminder S. Reel et al.   BIOTECHNOLOGY ADVANCES

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Artificial intelligence for proteomics and biomarker discovery

(2021) Matthias Mann et al.   Cell Systems

Comparison of Untargeted Metabolomic Profiling vs Traditional Metabolic Screening to Identify Inborn Errors of Metabolism

(2021) Ning Liu et al.   JAMA Network Open

The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy

(2021) Siyuan Chen et al.   BMC CANCER

Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus

(2021) Damien J. Downes et al.   NATURE GENETICS

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

(2021) Kishwar Shafin et al.   NATURE METHODS

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

(2021) Robbin Bouwmeester et al.   NATURE METHODS

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

(2021) Francisco M. De La Vega et al.   Genome Medicine

Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network

(2020) Kaiyuan Liu et al.   ANALYTICAL CHEMISTRY

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Integrated analysis of metabolomic profiling and exome data supplements sequence variant interpretation, classification, and diagnosis

(2020) Joseph T. Alaimo et al.   GENETICS IN MEDICINE

Video-based AI for beat-to-beat assessment of cardiac function

(2020) David Ouyang et al.   NATURE

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature

(2020) Johannes Birgmeier et al.   Science Translational Medicine

Reaching the End-Game for GWAS: Machine Learning Approaches for the Prioritization of Complex Disease Loci

(2020) Hannah L. Nicholls et al.   Frontiers in Genetics

Untargeted metabolomics as an unbiased approach to the diagnosis of inborn errors of metabolism of the non-oxidative branch of the pentose phosphate pathway

(2020) Brian J. Shayota et al.   MOLECULAR GENETICS AND METABOLISM

Untargeted metabolic profiling in dried blood spots identifies disease fingerprint for pyruvate kinase deficiency

(2020) Birgit Van Dooijeweert et al.   HAEMATOLOGICA

Deep learning in proteomics

(2020) Bo Wen et al.   PROTEOMICS

Transcriptomic signatures across human tissues identify functional rare genetic variation

(2020) Nicole M. Ferraro et al.   SCIENCE

Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing

(2020) Suhua Feng et al.   Epigenetics & Chromatin

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins

(2019) Hongli Fu et al.   BMC BIOINFORMATICS

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

(2019) Peng Ni et al.   BIOINFORMATICS

Sequencing of human genomes with nanopore technology

(2019) Rory Bowden et al.   Nature Communications

MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning

(2019) Wen-Feng Zeng et al.   ANALYTICAL CHEMISTRY

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts

(2019) Laure Frésard et al.   NATURE MEDICINE

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

(2019) Qian Liu et al.   Nature Communications

Plasma protein patterns as comprehensive indicators of health

(2019) Stephen A. Williams et al.   NATURE MEDICINE

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease

(2018) Kimberly Splinter et al.   NEW ENGLAND JOURNAL OF MEDICINE

The impact of rare variation on gene expression across tissues

(2017) Xin Li et al.   NATURE

A wellness study of 108 individuals using personal, dense, dynamic data clouds

(2017) Nathan D Price et al.   NATURE BIOTECHNOLOGY

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome Sequencing of a Large Human Family Identifies the Impact of Rare Noncoding Variants

(2014) Xin Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders

(2014) Hane Lee et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Protein post-translational modifications and regulation of pluripotency in human stem cells

(2013) Yu-Chieh Wang et al.   CELL RESEARCH

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

(2010) Sujun Li et al.   ANALYTICAL CHEMISTRY

Clinical assessment incorporating a personal genome

(2010) Euan A Ashley et al.   LANCET