Opportunities and obstacles for deep learning in biology and medicine

Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition

(2018) Sabrina Jaeger et al.   Journal of Chemical Information and Modeling

MoleculeNet: a benchmark for molecular machine learning

(2018) Zhenqin Wu et al.   Chemical Science

Learning a Local-Variable Model of Aromatic and Conjugated Systems

(2018) Matthew K. Matlock et al.   ACS Central Science

Automated Melanoma Recognition in Dermoscopy Images via Very Deep Residual Networks

(2017) Lequan Yu et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

A machine learning-based framework to identify type 2 diabetes through electronic health records

(2017) Tao Zheng et al.   INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS

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

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

Is Multitask Deep Learning Practical for Pharma?

(2017) Bharath Ramsundar et al.   Journal of Chemical Information and Modeling

Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction

(2017) Connor W. Coley et al.   Journal of Chemical Information and Modeling

Deep learning for computational chemistry

(2017) Garrett B. Goh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Deep-Learning-Based Drug–Target Interaction Prediction

(2017) Ming Wen et al.   JOURNAL OF PROTEOME RESEARCH

A deep learning approach for the analysis of masses in mammograms with minimal user intervention

(2017) Neeraj Dhungel et al.   MEDICAL IMAGE ANALYSIS

Large scale deep learning for computer aided detection of mammographic lesions

(2017) Thijs Kooi et al.   MEDICAL IMAGE ANALYSIS

A survey on deep learning in medical image analysis

(2017) Geert Litjens et al.   MEDICAL IMAGE ANALYSIS

Predicting protein–protein interactions from protein sequences by a stacked sparse autoencoder deep neural network

(2017) Yan-Bin Wang et al.   Molecular BioSystems

Automated analysis of high‐content microscopy data with deep learning

(2017) Oren Z Kraus et al.   Molecular Systems Biology

Dermatologist-level classification of skin cancer with deep neural networks

(2017) Andre Esteva et al.   NATURE

Reproducibility of computational workflows is automated using continuous analysis

(2017) Brett K Beaulieu-Jones et al.   NATURE BIOTECHNOLOGY

Celebrating parasites

(2017) Casey S Greene et al.   NATURE GENETICS

Prospective identification of hematopoietic lineage choice by deep learning

(2017) Felix Buggenthin et al.   NATURE METHODS

Learning the Structural Vocabulary of a Network

(2017) Saket Navlakha   NEURAL COMPUTATION

Neuroscience-Inspired Artificial Intelligence

(2017) Demis Hassabis et al.   NEURON

Using neural networks for reducing the dimensions of single-cell RNA-Seq data

(2017) Chieh Lin et al.   NUCLEIC ACIDS RESEARCH

Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning

(2017) Jiayi Wu et al.   PLoS One

Deep Learning at Chest Radiography: Automated Classification of Pulmonary Tuberculosis by Using Convolutional Neural Networks

(2017) Paras Lakhani et al.   RADIOLOGY

Chemical-induced disease relation extraction via convolutional neural network

(2017) Jinghang Gu et al.   Database-The Journal of Biological Databases and Curation

Extraction of skin lesions from non-dermoscopic images for surgical excision of melanoma

(2017) M. Hossein Jafari et al.   International Journal of Computer Assisted Radiology and Surgery

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

(2017) Zixuan Cang et al.   PLoS Computational Biology

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

Imputation for transcription factor binding predictions based on deep learning

(2017) Qian Qin et al.   PLoS Computational Biology

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

$\mathtt {Deepr}$: A Convolutional Net for Medical Records

(2017) Phuoc Nguyen et al.   IEEE Journal of Biomedical and Health Informatics

Low Data Drug Discovery with One-Shot Learning

(2017) Han Altae-Tran et al.   ACS Central Science

Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks

(2017) Ramzan Kh. Umarov et al.   PLoS One

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

(2017) Vladimír Boža et al.   PLoS One

Leveraging uncertainty information from deep neural networks for disease detection

(2017) Christian Leibig et al.   Scientific Reports

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation

(2016) Maria Vera et al.   Annual Review of Genetics

Drug drug interaction extraction from biomedical literature using syntax convolutional neural network

(2016) Zhehuan Zhao et al.   BIOINFORMATICS

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

(2016) Robert Leaman et al.   BIOINFORMATICS

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model

(2016) Lujia Chen et al.   BMC BIOINFORMATICS

Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory

(2016) Chien-Hung Huang et al.   BMC BIOINFORMATICS

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

A review of validation strategies for computational drug repositioning

(2016) Adam S Brown et al.   BRIEFINGS IN BIOINFORMATICS

Computer vision for high content screening

(2016) Oren Z. Kraus et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Applications in image-based profiling of perturbations

(2016) Juan C Caicedo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Large-scale image-based screening and profiling of cellular phenotypes

(2016) Nicola Bougen-Zhukov et al.   CYTOMETRY PART A

A renaissance of neural networks in drug discovery

(2016) Igor I. Baskin et al.   Expert Opinion on Drug Discovery

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Improving Computer-Aided Detection Using_newlineConvolutional Neural Networks and Random View Aggregation

(2016) Holger R. Roth et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning

(2016) Hoo-Chang Shin et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Visualizing Deep Convolutional Neural Networks Using Natural Pre-images

(2016) Aravindh Mahendran et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

A general protein-protein interaction extraction architecture based on word representation and feature selection

(2016) Zhenchao Jiang et al.   International Journal of Data Mining and Bioinformatics

Development and Validation of a Deep Learning Algorithm for Detection of Diabetic Retinopathy in Retinal Fundus Photographs

(2016) Varun Gulshan et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Semi-supervised learning of the electronic health record for phenotype stratification

(2016) Brett K. Beaulieu-Jones et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Machine learning and computer vision approaches for phenotypic profiling

(2016) Ben T. Grys et al.   JOURNAL OF CELL BIOLOGY

Boosting Docking-Based Virtual Screening with Deep Learning

(2016) Janaina Cruz Pereira et al.   Journal of Chemical Information and Modeling

Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches

(2016) Govindan Subramanian et al.   Journal of Chemical Information and Modeling

Molecular graph convolutions: moving beyond fingerprints

(2016) Steven Kearnes et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

High-Throughput Classification of Radiographs Using Deep Convolutional Neural Networks

(2016) Alvin Rajkomar et al.   JOURNAL OF DIGITAL IMAGING

Innovation in the pharmaceutical industry: New estimates of R&D costs

(2016) Joseph A. DiMasi et al.   JOURNAL OF HEALTH ECONOMICS

De Novo Design at the Edge of Chaos

(2016) Petra Schneider et al.   JOURNAL OF MEDICINAL CHEMISTRY

DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM

(2016) Feng Wang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Harnessing next-generation informatics for personalizing medicine: a report from AMIA’s 2014 Health Policy Invitational Meeting

(2016) Laura K Wiley et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Electronic medical record phenotyping using the anchor and learn framework

(2016) Yoni Halpern et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning

(2016) Tianchuan Du et al.   METHODS

CGBVS-DNN: Prediction of Compound-protein Interactions Based on Deep Learning

(2016) Masatoshi Hamanaka et al.   Molecular Informatics

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

Classification evaluation

(2016) Jake Lever et al.   NATURE METHODS

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

Using goal-driven deep learning models to understand sensory cortex

(2016) Daniel L K Yamins et al.   NATURE NEUROSCIENCE

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

A network-biology perspective of microRNA function and dysfunction in cancer

(2016) Cameron P. Bracken et al.   NATURE REVIEWS GENETICS

Data Sharing

(2016) Dan L. Longo et al.   NEW ENGLAND JOURNAL OF MEDICINE

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Enhancing reproducibility for computational methods

(2016) V. Stodden et al.   SCIENCE

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Toward an Integration of Deep Learning and Neuroscience

(2016) Adam H. Marblestone et al.   Frontiers in Computational Neuroscience

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

(2016) Minseung Kim et al.   Nature Communications

Improving chemical disease relation extraction with rich features and weakly labeled data

(2016) Yifan Peng et al.   Journal of Cheminformatics

Large-Scale Discovery of Disease-Disease and Disease-Gene Associations

(2016) Djordje Gligorijevic et al.   Scientific Reports

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing

(2016) Hansaim Lim et al.   PLoS Computational Biology

Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction

(2016) Edgar D. Coelho et al.   PLoS Computational Biology

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

(2016) David A. Van Valen et al.   PLoS Computational Biology

Predicting Complications in Critical Care Using Heterogeneous Clinical Data

(2016) Vijay Huddar et al.   IEEE Access

Enabling Privacy-Preserving GWASs in Heterogeneous Human Populations

(2016) Sean Simmons et al.   Cell Systems

Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network

(2016) Tyler B. Hughes et al.   ACS Central Science

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

(2016) Jie Tan et al.   mSystems

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

(2016) Sheng Wang et al.   Scientific Reports

Deep learning as a tool for increased accuracy and efficiency of histopathological diagnosis

(2016) Geert Litjens et al.   Scientific Reports

Imaging-based enrichment criteria using deep learning algorithms for efficient clinical trials in mild cognitive impairment

(2015) Vamsi K. Ithapu et al.   Alzheimers & Dementia

Trans-species learning of cellular signaling systems with bimodal deep belief networks

(2015) Lujia Chen et al.   BIOINFORMATICS

Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning

(2015) Jianzhu Ma et al.   BIOINFORMATICS

High-order neural networks and kernel methods for peptide-MHC binding prediction

(2015) Pavel P. Kuksa et al.   BIOINFORMATICS

Large-scale machine learning for metagenomics sequence classification

(2015) Kévin Vervier et al.   BIOINFORMATICS

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

(2015) Bie Verbist et al.   BMC BIOINFORMATICS

Deep convolutional neural networks for annotating gene expression patterns in the mouse brain

(2015) Tao Zeng et al.   BMC BIOINFORMATICS

DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection

(2015) Xiao Ding et al.   BMC BIOINFORMATICS

Influence of microbiome species in hard-to-heal wounds on disease severity and treatment duration

(2015) Dagmar Chudobova et al.   Brazilian Journal of Infectious Diseases

A survey of current trends in computational drug repositioning

(2015) Jiao Li et al.   BRIEFINGS IN BIOINFORMATICS

A Primer to Single-Particle Cryo-Electron Microscopy

(2015) Yifan Cheng et al.   CELL

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

Single-Particle Cryo-EM at Crystallographic Resolution

(2015) Yifan Cheng   CELL

Growing pains for deep learning

(2015) Chris Edwards   COMMUNICATIONS OF THE ACM

MECHANISMS IN ENDOCRINOLOGY: Alternative splicing: the new frontier in diabetes research

(2015) Jonàs Juan-Mateu et al.   EUROPEAN JOURNAL OF ENDOCRINOLOGY

Multi-Layer and Recursive Neural Networks for Metagenomic Classification

(2015) Gregory Ditzler et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach

(2015) Muxuan Liang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

(2015) Matt Spencer et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

ImageNet Large Scale Visual Recognition Challenge

(2015) Olga Russakovsky et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

ViPAR: a software platform for the Virtual Pooling and Analysis of Research Data

(2015) Kim W Carter et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Using electronic health records for clinical research: The case of the EHR4CR project

(2015) Georges De Moor et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Deep Neural Nets as a Method for Quantitative Structure–Activity Relationships

(2015) Junshui Ma et al.   Journal of Chemical Information and Modeling

Semi-automated selection of cryo-EM particles in RELION-1.3

(2015) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Deep Learning in Drug Discovery

(2015) Erik Gawehn et al.   Molecular Informatics

Deep learning

(2015) Yann LeCun et al.   NATURE

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Deep learning for regulatory genomics

(2015) Yongjin Park et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

An analysis of the attrition of drug candidates from four major pharmaceutical companies

(2015) Michael J. Waring et al.   NATURE REVIEWS DRUG DISCOVERY

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Accurate and efficient target prediction using a potency-sensitive influence-relevance voter

(2015) Alessandro Lusci et al.   Journal of Cheminformatics

Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning

(2015) Rhys Heffernan et al.   Scientific Reports

A Bootstrap Based Neyman-Pearson Test for Identifying Variable Importance

(2015) Gregory Ditzler et al.   IEEE Transactions on Neural Networks and Learning Systems

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Embedding assisted prediction architecture for event trigger identification

(2015) Yifan Nie et al.   Journal of Bioinformatics and Computational Biology

On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation

(2015) Sebastian Bach et al.   PLoS One

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

New Strategies for Triple-Negative Breast Cancer--Deciphering the Heterogeneity

(2014) I. A. Mayer et al.   CLINICAL CANCER RESEARCH

DataSHIELD: taking the analysis to the data, not the data to the analysis

(2014) Amadou Gaye et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Identifying and mitigating biases in EHR laboratory tests

(2014) Rimma Pivovarov et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Drug–Disease Association and Drug-Repositioning Predictions in Complex Diseases Using Causal Inference–Probabilistic Matrix Factorization

(2014) Jihong Yang et al.   Journal of Chemical Information and Modeling

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification

(2014) David Koslicki et al.   PLoS One

Correction: Class Prediction and Feature Selection with Linear Optimization for Metagenomic Count Data

(2014) Zhenqiu Liu et al.   PLoS One

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2014) Anders Boeck Jensen et al.   Nature Communications

Searching for exotic particles in high-energy physics with deep learning

(2014) P. Baldi et al.   Nature Communications

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

(2014) Marcin J. Skwark et al.   PLoS Computational Biology

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Mucosal Immunity in the Female Genital Tract, HIV/AIDS

(2014) Juliana Reis Machado et al.   Biomed Research International

An open investigation of the reproducibility of cancer biology research

(2014) Timothy M Errington et al.   eLife

DNorm: disease name normalization with pairwise learning to rank

(2013) R. Leaman et al.   BIOINFORMATICS

tmVar: a text mining approach for extracting sequence variants in biomedical literature

(2013) C.-H. Wei et al.   BIOINFORMATICS

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules

(2013) Alessandro Lusci et al.   Journal of Chemical Information and Modeling

XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks

(2013) Jed Zaretzki et al.   Journal of Chemical Information and Modeling

From vital signs to clinical outcomes for patients with sepsis: a machine learning basis for a clinical decision support system

(2013) Eren Gultepe et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A review of approaches to identifying patient phenotype cohorts using electronic health records

(2013) Chaitanya Shivade et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

The Framingham Heart Study and the epidemiology of cardiovascular disease: a historical perspective

(2013) Syed S Mahmood et al.   LANCET

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties

(2013) Michael P. Menden et al.   PLoS One

Computational Phenotype Discovery Using Unsupervised Feature Learning over Noisy, Sparse, and Irregular Clinical Data

(2013) Thomas A. Lasko et al.   PLoS One

Biomedical Informatics for Computer-Aided Decision Support Systems: A Survey

(2013) Ashwin Belle et al.   TheScientificWorldJOURNAL

Leakage in data mining

(2013) Shachar Kaufman et al.   ACM Transactions on Knowledge Discovery from Data

Drug Repositioning: A Machine-Learning Approach through Data Integration

(2013) Francesco Napolitano et al.   Journal of Cheminformatics

Generalization and Dilution of Association Results from European GWAS in Populations of Non-European Ancestry: The PAGE Study

(2013) Christopher S. Carlson et al.   PLOS BIOLOGY

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

(2013) Christopher Y. Park et al.   PLoS Computational Biology

A comprehensive evaluation of multicategory classification methods for microbiomic data

(2013) Alexander Statnikov et al.   Microbiome

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

(2012) Tiejun Cheng et al.   AAPS Journal

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Predicting protein residue–residue contacts using deep networks and boosting

(2012) Jesse Eickholt et al.   BIOINFORMATICS

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Methods and dimensions of electronic health record data quality assessment: enabling reuse for clinical research

(2012) N. G. Weiskopf et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Children of the 90s: Coming of age

(2012) Helen Pearson   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Mining electronic health records: towards better research applications and clinical care

(2012) Peter B. Jensen et al.   NATURE REVIEWS GENETICS

A Unified Multitask Architecture for Predicting Local Protein Properties

(2012) Yanjun Qi et al.   PLoS One

The enumeration of chemical space

(2012) Jean-Louis Reymond et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

METAGENOMIC TAXONOMIC CLASSIFICATION USING EXTREME LEARNING MACHINES

(2012) ZEEHASHAM RASHEED et al.   Journal of Bioinformatics and Computational Biology

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context

(2011) Hui Yuan Xiong et al.   BIOINFORMATICS

Combining gene prediction methods to improve metagenomic gene annotation

(2011) Non G Yok et al.   BMC BIOINFORMATICS

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

(2011) R. Yamashita et al.   GENOME RESEARCH

Realizing the full potential of electronic health records: the role of natural language processing

(2011) Lucila Ohno-Machado   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010

(2011) Berry de Bruijn et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Evolution of microRNA diversity and regulation in animals

(2011) Eugene Berezikov   NATURE REVIEWS GENETICS

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Retraction

(2011) P. Sebastiani et al.   SCIENCE

Enabling future drug discovery by de novo design

(2011) Markus Hartenfeller et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

Clustering metagenomic sequences with interpolated Markov models

(2010) David R Kelley et al.   BMC BIOINFORMATICS

A view of cloud computing

(2010) Michael Armbrust et al.   COMMUNICATIONS OF THE ACM

Machines that learn to segment images: a crucial technology for connectomics

(2010) Viren Jain et al.   CURRENT OPINION IN NEUROBIOLOGY

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Cloud computing and the DNA data race

(2010) Michael C Schatz et al.   NATURE BIOTECHNOLOGY

New approaches to population stratification in genome-wide association studies

(2010) Alkes L. Price et al.   NATURE REVIEWS GENETICS

Sex bias in neuroscience and biomedical research

(2010) Annaliese K. Beery et al.   NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS

The Path to Personalized Medicine

(2010) Margaret A. Hamburg et al.   NEW ENGLAND JOURNAL OF MEDICINE

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature

(2010) Domonkos Tikk et al.   PLoS Computational Biology

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions

(2010) Phaedra Agius et al.   PLoS Computational Biology

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational Biology

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D

(2009) Yun Niu et al.   BIOINFORMATICS

Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method

(2009) S. Joshua Swamidass et al.   Journal of Chemical Information and Modeling

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Orphelia: predicting genes in metagenomic sequencing reads

(2009) Katharina J. Hoff et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Epidemiological research labelled as a violation of privacy: the case of Estonia

(2008) M. Rahu et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Extracting interactions between proteins from the literature

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