Review
. 2018 Apr; 15(141):20170387.
doi: 10.1098/rsif.2017.0387.

Opportunities and obstacles for deep learning in biology and medicine

Travers Ching 1 Daniel S Himmelstein 2 Brett K Beaulieu-Jones 3 Alexandr A Kalinin 4 Brian T Do 5 Gregory P Way 2 Enrico Ferrero 6 Paul-Michael Agapow 7 Michael Zietz 2 Michael M Hoffman 8 Wei Xie 9 Gail L Rosen 10 Benjamin J Lengerich 11 Johnny Israeli 12 Jack Lanchantin 13 Stephen Woloszynek 10 Anne E Carpenter 14 Avanti Shrikumar 15 Jinbo Xu 16 Evan M Cofer 17 Christopher A Lavender 18 Srinivas C Turaga 19 Amr M Alexandari 15 Zhiyong Lu 20 David J Harris 21 Dave DeCaprio 22 Yanjun Qi 13 Anshul Kundaje 15 Yifan Peng 20 Laura K Wiley 23 Marwin H S Segler 24 Simina M Boca 25 S Joshua Swamidass 26 Austin Huang 27 Anthony Gitter 28 Casey S Greene 29 
Affiliations
  • PMID: 29618526
  •     274 References
  •     245 citations

Abstract

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

Keywords: deep learning; genomics; machine learning; precision medicine.

DNA binding sites: representation and discovery.
G D Stormo.
Bioinformatics, 2000 May 17; 16(1). PMID: 10812473
Highly Cited. Review.
Automated Melanoma Recognition in Dermoscopy Images via Very Deep Residual Networks.
Lequan Yu, Hao Chen, +2 authors, Pheng-Ann Heng.
IEEE Trans Med Imaging, 2016 Dec 28; 36(4). PMID: 28026754
Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network.
Tyler B Hughes, Na Le Dang, Grover P Miller, S Joshua Swamidass.
ACS Cent Sci, 2016 Sep 10; 2(8). PMID: 27610414    Free PMC article.
XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks.
Jed Zaretzki, Matthew Matlock, S Joshua Swamidass.
J Chem Inf Model, 2013 Nov 15; 53(12). PMID: 24224933
Big Data: Astronomical or Genomical?
Zachary D Stephens, Skylar Y Lee, +7 authors, Gene E Robinson.
PLoS Biol, 2015 Jul 08; 13(7). PMID: 26151137    Free PMC article.
Highly Cited.
Methods and dimensions of electronic health record data quality assessment: enabling reuse for clinical research.
Nicole Gray Weiskopf, Chunhua Weng.
J Am Med Inform Assoc, 2012 Jun 27; 20(1). PMID: 22733976    Free PMC article.
Highly Cited. Review.
Reproducibility of computational workflows is automated using continuous analysis.
Brett K Beaulieu-Jones, Casey S Greene.
Nat Biotechnol, 2017 Mar 14; 35(4). PMID: 28288103    Free PMC article.
Highly Cited.
Computer vision for high content screening.
Oren Z Kraus, Brendan J Frey.
Crit Rev Biochem Mol Biol, 2016 Jan 26; 51(2). PMID: 26806341
Review.
DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection.
Xiao Ding, Fudong Cheng, Changchang Cao, Xiao Sun.
BMC Bioinformatics, 2015 Oct 09; 16. PMID: 26446672    Free PMC article.
Metagenomic microbial community profiling using unique clade-specific marker genes.
Nicola Segata, Levi Waldron, +3 authors, Curtis Huttenhower.
Nat Methods, 2012 Jun 13; 9(8). PMID: 22688413    Free PMC article.
Highly Cited.
Generalization and dilution of association results from European GWAS in populations of non-European ancestry: the PAGE study.
Christopher S Carlson, Tara C Matise, +20 authors, PAGE Consortium.
PLoS Biol, 2013 Sep 27; 11(9). PMID: 24068893    Free PMC article.
Highly Cited.
Searching for exotic particles in high-energy physics with deep learning.
P Baldi, P Sadowski, D Whiteson.
Nat Commun, 2014 Jul 06; 5. PMID: 24986233
The Human Cell Atlas.
Aviv Regev, Sarah A Teichmann, +59 authors, Human Cell Atlas Meeting Participants.
Elife, 2017 Dec 06; 6. PMID: 29206104    Free PMC article.
Highly Cited.
NetMHCpan, a method for MHC class I binding prediction beyond humans.
Ilka Hoof, Bjoern Peters, +5 authors, Morten Nielsen.
Immunogenetics, 2008 Nov 13; 61(1). PMID: 19002680    Free PMC article.
Highly Cited.
CGBVS-DNN: Prediction of Compound-protein Interactions Based on Deep Learning.
Masatoshi Hamanaka, Kei Taneishi, +4 authors, Yasushi Okuno.
Mol Inform, 2016 Aug 16; 36(1-2). PMID: 27515489
Improved Automated Detection of Diabetic Retinopathy on a Publicly Available Dataset Through Integration of Deep Learning.
Michael David Abràmoff, Yiyue Lou, +4 authors, Meindert Niemeijer.
Invest Ophthalmol Vis Sci, 2016 Oct 05; 57(13). PMID: 27701631
Highly Cited.
Development and Validation of a Deep Learning Algorithm for Detection of Diabetic Retinopathy in Retinal Fundus Photographs.
Varun Gulshan, Lily Peng, +12 authors, Dale R Webster.
JAMA, 2016 Nov 30; 316(22). PMID: 27898976
Highly Cited.
Predicting drug-target interactions using restricted Boltzmann machines.
Yuhao Wang, Jianyang Zeng.
Bioinformatics, 2013 Jul 03; 29(13). PMID: 23812976    Free PMC article.
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.
Christopher Y Park, Aaron K Wong, +5 authors, Olga G Troyanskaya.
PLoS Comput Biol, 2013 Mar 22; 9(3). PMID: 23516347    Free PMC article.
Deep neural nets as a method for quantitative structure-activity relationships.
Junshui Ma, Robert P Sheridan, +2 authors, Vladimir Svetnik.
J Chem Inf Model, 2015 Jan 31; 55(2). PMID: 25635324
Highly Cited.
3D Deep Learning for Multi-modal Imaging-Guided Survival Time Prediction of Brain Tumor Patients.
Dong Nie, Han Zhang, +2 authors, Dinggang Shen.
Med Image Comput Comput Assist Interv, 2017 Feb 06; 9901. PMID: 28149967    Free PMC article.
Gene expression inference with deep learning.
Yifei Chen, Yi Li, +2 authors, Xiaohui Xie.
Bioinformatics, 2016 Feb 14; 32(12). PMID: 26873929    Free PMC article.
Highly Cited.
Deep Learning in Drug Discovery.
Erik Gawehn, Jan A Hiss, Gisbert Schneider.
Mol Inform, 2016 Aug 06; 35(1). PMID: 27491648
Highly Cited. Review.
Sequence-based prediction of protein protein interaction using a deep-learning algorithm.
Tanlin Sun, Bo Zhou, Luhua Lai, Jianfeng Pei.
BMC Bioinformatics, 2017 May 27; 18(1). PMID: 28545462    Free PMC article.
Deep architectures for protein contact map prediction.
Pietro Di Lena, Ken Nagata, Pierre Baldi.
Bioinformatics, 2012 Aug 01; 28(19). PMID: 22847931    Free PMC article.
Learning the Structural Vocabulary of a Network.
Saket Navlakha.
Neural Comput, 2016 Dec 29; 29(2). PMID: 28030777
Using goal-driven deep learning models to understand sensory cortex.
Daniel L K Yamins, James J DiCarlo.
Nat Neurosci, 2016 Feb 26; 19(3). PMID: 26906502
Highly Cited. Review.
Using neural networks for reducing the dimensions of single-cell RNA-Seq data.
Chieh Lin, Siddhartha Jain, Hannah Kim, Ziv Bar-Joseph.
Nucleic Acids Res, 2017 Oct 04; 45(17). PMID: 28973464    Free PMC article.
Highly Cited.
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.
Michael P Menden, Francesco Iorio, +4 authors, Julio Saez-Rodriguez.
PLoS One, 2013 May 07; 8(4). PMID: 23646105    Free PMC article.
Highly Cited.
Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes.
Matthew R Gazzara, Michael J Mallory, +4 authors, Yoseph Barash.
Genome Res, 2017 May 18; 27(8). PMID: 28512194    Free PMC article.
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.
David T Jones, Tanya Singh, Tomasz Kosciolek, Stuart Tetchner.
Bioinformatics, 2014 Nov 29; 31(7). PMID: 25431331    Free PMC article.
Highly Cited.
Imaging-based enrichment criteria using deep learning algorithms for efficient clinical trials in mild cognitive impairment.
Vamsi K Ithapu, Vikas Singh, +4 authors, Alzheimer's Disease Neuroimaging Initiative.
Alzheimers Dement, 2015 Jun 21; 11(12). PMID: 26093156    Free PMC article.
Evolution of microRNA diversity and regulation in animals.
Eugene Berezikov.
Nat Rev Genet, 2011 Nov 19; 12(12). PMID: 22094948
Highly Cited. Review.
A primer to single-particle cryo-electron microscopy.
Yifan Cheng, Nikolaus Grigorieff, Pawel A Penczek, Thomas Walz.
Cell, 2015 Apr 25; 161(3). PMID: 25910204    Free PMC article.
Highly Cited. Review.
Scalable metagenomic taxonomy classification using a reference genome database.
Sasha K Ames, David A Hysom, +3 authors, Jonathan E Allen.
Bioinformatics, 2013 Jul 06; 29(18). PMID: 23828782    Free PMC article.
Highly Cited.
Celebrating parasites.
Casey S Greene, Lana X Garmire, +2 authors, Lawrence E Hunter.
Nat Genet, 2017 Mar 31; 49(4). PMID: 28358134    Free PMC article.
Single-cell transcriptome sequencing: recent advances and remaining challenges.
Serena Liu, Cole Trapnell.
F1000Res, 2016 Mar 08; 5. PMID: 26949524    Free PMC article.
Highly Cited. Review.
A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.
Yanan Zhu, Qi Ouyang, Youdong Mao.
BMC Bioinformatics, 2017 Jul 25; 18(1). PMID: 28732461    Free PMC article.
What do we know and when do we know it?
Anthony Nicholls.
J Comput Aided Mol Des, 2008 Feb 07; 22(3-4). PMID: 18253702    Free PMC article.
Review.
RNA splicing is a primary link between genetic variation and disease.
Yang I Li, Bryce van de Geijn, +5 authors, Jonathan K Pritchard.
Science, 2016 Apr 30; 352(6285). PMID: 27126046    Free PMC article.
Highly Cited.
High-Throughput Classification of Radiographs Using Deep Convolutional Neural Networks.
Alvin Rajkomar, Sneha Lingam, +2 authors, John Mongan.
J Digit Imaging, 2016 Oct 13; 30(1). PMID: 27730417    Free PMC article.
Toward an Integration of Deep Learning and Neuroscience.
Adam H Marblestone, Greg Wayne, Konrad P Kording.
Front Comput Neurosci, 2016 Sep 30; 10. PMID: 27683554    Free PMC article.
Highly Cited.
The use of artificial neural networks in decision support in cancer: a systematic review.
Paulo J Lisboa, Azzam F G Taktak.
Neural Netw, 2006 Feb 18; 19(4). PMID: 16483741
Systematic Review.
Orphelia: predicting genes in metagenomic sequencing reads.
Katharina J Hoff, Thomas Lingner, Peter Meinicke, Maike Tech.
Nucleic Acids Res, 2009 May 12; 37(Web Server issue). PMID: 19429689    Free PMC article.
The path to personalized medicine.
Margaret A Hamburg, Francis S Collins.
N Engl J Med, 2010 Jun 17; 363(4). PMID: 20551152
Highly Cited.
Single-Cell and Single-Molecule Analysis of Gene Expression Regulation.
Maria Vera, Jeetayu Biswas, +2 authors, Hye Yoon Park.
Annu Rev Genet, 2016 Nov 29; 50. PMID: 27893965    Free PMC article.
Review.
Supervised classification of human microbiota.
Dan Knights, Elizabeth K Costello, Rob Knight.
FEMS Microbiol Rev, 2010 Nov 03; 35(2). PMID: 21039646
Highly Cited. Review.
Deep-Learning-Based Drug-Target Interaction Prediction.
Ming Wen, Zhimin Zhang, +4 authors, Hongmei Lu.
J Proteome Res, 2017 Mar 07; 16(4). PMID: 28264154
Highly Cited.
tmVar: a text mining approach for extracting sequence variants in biomedical literature.
Chih-Hsuan Wei, Bethany R Harris, Hung-Yu Kao, Zhiyong Lu.
Bioinformatics, 2013 Apr 09; 29(11). PMID: 23564842    Free PMC article.
Highly Cited.
Fast model-based protein homology detection without alignment.
Sepp Hochreiter, Martin Heusel, Klaus Obermayer.
Bioinformatics, 2007 May 10; 23(14). PMID: 17488755
Single-cell genome sequencing: current state of the science.
Charles Gawad, Winston Koh, Stephen R Quake.
Nat Rev Genet, 2016 Jan 26; 17(3). PMID: 26806412
Highly Cited. Review.
Semi-supervised learning of the electronic health record for phenotype stratification.
Brett K Beaulieu-Jones, Casey S Greene, Pooled Resource Open-Access ALS Clinical Trials Consortium.
J Biomed Inform, 2016 Oct 17; 64. PMID: 27744022
Deep learning as a tool for increased accuracy and efficiency of histopathological diagnosis.
Geert Litjens, Clara I Sánchez, +7 authors, Jeroen van der Laak.
Sci Rep, 2016 May 24; 6. PMID: 27212078    Free PMC article.
Highly Cited.
Deep Learning at Chest Radiography: Automated Classification of Pulmonary Tuberculosis by Using Convolutional Neural Networks.
Paras Lakhani, Baskaran Sundaram.
Radiology, 2017 Apr 25; 284(2). PMID: 28436741
Highly Cited.
High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.
Phaedra Agius, Aaron Arvey, +2 authors, Christina Leslie.
PLoS Comput Biol, 2010 Sep 15; 6(9). PMID: 20838582    Free PMC article.
Protein secondary structure prediction based on position-specific scoring matrices.
D T Jones.
J Mol Biol, 1999 Sep 24; 292(2). PMID: 10493868
Highly Cited.
Impact of electronic health record systems on information integrity: quality and safety implications.
Sue Bowman.
Perspect Health Inf Manag, 2013 Oct 26; 10. PMID: 24159271    Free PMC article.
Review.
Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction.
Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi.
IEEE/ACM Trans Comput Biol Bioinform, 2016 Sep 23; 16(5). PMID: 27654939
Large scale deep learning for computer aided detection of mammographic lesions.
Thijs Kooi, Geert Litjens, +5 authors, Nico Karssemeijer.
Med Image Anal, 2016 Aug 09; 35. PMID: 27497072
Highly Cited.
Multichannel Convolutional Neural Network for Biological Relation Extraction.
Chanqin Quan, Lei Hua, Xiao Sun, Wenjun Bai.
Biomed Res Int, 2017 Jan 06; 2016. PMID: 28053977    Free PMC article.
Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches.
Govindan Subramanian, Bharath Ramsundar, Vijay Pande, Rajiah Aldrin Denny.
J Chem Inf Model, 2016 Oct 01; 56(10). PMID: 27689393
A bootstrap based Neyman-Pearson test for identifying variable importance.
Gregory Ditzler, Robi Polikar, Gail Rosen.
IEEE Trans Neural Netw Learn Syst, 2015 Mar 21; 26(4). PMID: 25794384
Deep learning.
Yann LeCun, Yoshua Bengio, Geoffrey Hinton.
Nature, 2015 May 29; 521(7553). PMID: 26017442
Highly Cited. Review.
A review of approaches to identifying patient phenotype cohorts using electronic health records.
Chaitanya Shivade, Preethi Raghavan, +4 authors, Albert M Lai.
J Am Med Inform Assoc, 2013 Nov 10; 21(2). PMID: 24201027    Free PMC article.
Highly Cited. Review.
Absence of a simple code: how transcription factors read the genome.
Matthew Slattery, Tianyin Zhou, +3 authors, Remo Rohs.
Trends Biochem Sci, 2014 Aug 19; 39(9). PMID: 25129887    Free PMC article.
Highly Cited. Review.
Deep learning for computational chemistry.
Garrett B Goh, Nathan O Hodas, Abhinav Vishnu.
J Comput Chem, 2017 Mar 09; 38(16). PMID: 28272810
Highly Cited. Review.
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.
Morten Nielsen, Claus Lundegaard, +5 authors, Ole Lund.
Protein Sci, 2003 Apr 30; 12(5). PMID: 12717023    Free PMC article.
Highly Cited.
Large-Scale Discovery of Disease-Disease and Disease-Gene Associations.
Djordje Gligorijevic, Jelena Stojanovic, +4 authors, Zoran Obradovic.
Sci Rep, 2016 Sep 01; 6. PMID: 27578529    Free PMC article.
AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling.
Sheng Wang, Siqi Sun, Jinbo Xu.
Mach Learn Knowl Discov Databases, 2017 Sep 09; 9852. PMID: 28884168    Free PMC article.
DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Daniel Quang, Xiaohui Xie.
Nucleic Acids Res, 2016 Apr 17; 44(11). PMID: 27084946    Free PMC article.
Highly Cited.
ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.
Scott M Lundberg, William B Tu, +3 authors, Su-In Lee.
Genome Biol, 2016 May 04; 17. PMID: 27139377    Free PMC article.
DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.
Feng Wang, Huichao Gong, +5 authors, Jianyang Zeng.
J Struct Biol, 2016 Jul 18; 195(3). PMID: 27424268
Innovation in the pharmaceutical industry: New estimates of R&D costs.
Joseph A DiMasi, Henry G Grabowski, Ronald W Hansen.
J Health Econ, 2016 Mar 02; 47. PMID: 26928437
Highly Cited.
Class prediction and feature selection with linear optimization for metagenomic count data.
Zhenqiu Liu, Dechang Chen, Li Sheng, Amy Y Liu.
PLoS One, 2013 Apr 05; 8(3). PMID: 23555553    Free PMC article.
Caffe con Troll: Shallow Ideas to Speed Up Deep Learning.
Stefan Hadjis, Firas Abuzaid, Ce Zhang, Christopher Ré.
Proc Fourth Workshop Data Anal Scale Danac 2015 (2015), 2016 Jun 18; 2015. PMID: 27314106    Free PMC article.
Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.
Hui Yuan Xiong, Yoseph Barash, Brendan J Frey.
Bioinformatics, 2011 Aug 02; 27(18). PMID: 21803804
Dermatologist-level classification of skin cancer with deep neural networks.
Andre Esteva, Brett Kuprel, +4 authors, Sebastian Thrun.
Nature, 2017 Jan 25; 542(7639). PMID: 28117445
Highly Cited.
Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records.
Riccardo Miotto, Li Li, Brian A Kidd, Joel T Dudley.
Sci Rep, 2016 May 18; 6. PMID: 27185194    Free PMC article.
Highly Cited.
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.
Babak Alipanahi, Andrew Delong, Matthew T Weirauch, Brendan J Frey.
Nat Biotechnol, 2015 Jul 28; 33(8). PMID: 26213851
Highly Cited.
De Novo Design at the Edge of Chaos.
Petra Schneider, Gisbert Schneider.
J Med Chem, 2016 Feb 18; 59(9). PMID: 26881908
Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010.
Berry de Bruijn, Colin Cherry, +2 authors, Xiaodan Zhu.
J Am Med Inform Assoc, 2011 May 14; 18(5). PMID: 21565856    Free PMC article.
Learning a Local-Variable Model of Aromatic and Conjugated Systems.
Matthew K Matlock, Na Le Dang, S Joshua Swamidass.
ACS Cent Sci, 2018 Feb 03; 4(1). PMID: 29392176    Free PMC article.
Enhancers: five essential questions.
Len A Pennacchio, Wendy Bickmore, +2 authors, Gill Bejerano.
Nat Rev Genet, 2013 Mar 19; 14(4). PMID: 23503198    Free PMC article.
Highly Cited. Review.
Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks.
Ramzan Kh Umarov, Victor V Solovyev.
PLoS One, 2017 Feb 06; 12(2). PMID: 28158264    Free PMC article.
Advantages and disadvantages of using artificial neural networks versus logistic regression for predicting medical outcomes.
J V Tu.
J Clin Epidemiol, 1996 Nov 01; 49(11). PMID: 8892489
Highly Cited. Review.
Sequence and chromatin determinants of cell-type-specific transcription factor binding.
Aaron Arvey, Phaedra Agius, William Stafford Noble, Christina Leslie.
Genome Res, 2012 Sep 08; 22(9). PMID: 22955984    Free PMC article.
Highly Cited.
Removal of batch effects using distribution-matching residual networks.
Uri Shaham, Kelly P Stanton, +4 authors, Yuval Kluger.
Bioinformatics, 2017 Apr 19; 33(16). PMID: 28419223    Free PMC article.
Deep Learning in Medical Image Analysis.
Dinggang Shen, Guorong Wu, Heung-Il Suk.
Annu Rev Biomed Eng, 2017 Mar 17; 19. PMID: 28301734    Free PMC article.
Highly Cited. Review.
A survey of current trends in computational drug repositioning.
Jiao Li, Si Zheng, +3 authors, Zhiyong Lu.
Brief Bioinform, 2015 Apr 03; 17(1). PMID: 25832646    Free PMC article.
Highly Cited. Review.
Identification of direct residue contacts in protein-protein interaction by message passing.
Martin Weigt, Robert A White, +2 authors, Terence Hwa.
Proc Natl Acad Sci U S A, 2009 Jan 01; 106(1). PMID: 19116270    Free PMC article.
Highly Cited.
Predicting protein residue-residue contacts using deep networks and boosting.
Jesse Eickholt, Jianlin Cheng.
Bioinformatics, 2012 Oct 11; 28(23). PMID: 23047561    Free PMC article.
Use of an artificial neural network for the diagnosis of myocardial infarction.
W G Baxt.
Ann Intern Med, 1991 Dec 01; 115(11). PMID: 1952470
Mitosis detection in breast cancer histology images with deep neural networks.
Dan C Cireşan, Alessandro Giusti, Luca M Gambardella, Jürgen Schmidhuber.
Med Image Comput Comput Assist Interv, 2014 Mar 01; 16(Pt 2). PMID: 24579167
Highly Cited.
Why Patient Matching Is a Challenge: Research on Master Patient Index (MPI) Data Discrepancies in Key Identifying Fields.
Beth Haenke Just, David Marc, Megan Munns, Ryan Sandefer.
Perspect Health Inf Manag, 2016 May 03; 13. PMID: 27134610    Free PMC article.
Influence relevance voting: an accurate and interpretable virtual high throughput screening method.
S Joshua Swamidass, Chloé-Agathe Azencott, +3 authors, Pierre Baldi.
J Chem Inf Model, 2009 Apr 28; 49(4). PMID: 19391629    Free PMC article.
$\mathtt {Deepr}$: A Convolutional Net for Medical Records.
Phuoc Nguyen, Truyen Tran, Nilmini Wickramasinghe, Svetha Venkatesh.
IEEE J Biomed Health Inform, 2016 Dec 04; 21(1). PMID: 27913366
Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach.
Muxuan Liang, Zhizhong Li, Ting Chen, Jianyang Zeng.
IEEE/ACM Trans Comput Biol Bioinform, 2015 Sep 12; 12(4). PMID: 26357333
Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning.
Tanel Pärnamaa, Leopold Parts.
G3 (Bethesda), 2017 Apr 10; 7(5). PMID: 28391243    Free PMC article.
Highly Cited.
Evaluating word representation features in biomedical named entity recognition tasks.
Buzhou Tang, Hongxin Cao, +2 authors, Hua Xu.
Biomed Res Int, 2014 Apr 15; 2014. PMID: 24729964    Free PMC article.
Hit discovery and hit-to-lead approaches.
György M Keseru, Gergely M Makara.
Drug Discov Today, 2006 Jul 19; 11(15-16). PMID: 16846802
Review.
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing.
Hansaim Lim, Aleksandar Poleksic, +5 authors, Lei Xie.
PLoS Comput Biol, 2016 Oct 08; 12(10). PMID: 27716836    Free PMC article.
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.
Edoardo Pasolli, Duy Tin Truong, +2 authors, Nicola Segata.
PLoS Comput Biol, 2016 Jul 12; 12(7). PMID: 27400279    Free PMC article.
Highly Cited.
Enabling Privacy-Preserving GWASs in Heterogeneous Human Populations.
Sean Simmons, Cenk Sahinalp, Bonnie Berger.
Cell Syst, 2016 Jul 28; 3(1). PMID: 27453444    Free PMC article.
New approaches to population stratification in genome-wide association studies.
Alkes L Price, Noah A Zaitlen, David Reich, Nick Patterson.
Nat Rev Genet, 2010 Jun 16; 11(7). PMID: 20548291    Free PMC article.
Highly Cited. Review.
Influence of microbiome species in hard-to-heal wounds on disease severity and treatment duration.
Dagmar Chudobova, Kristyna Cihalova, +8 authors, Rene Kizek.
Braz J Infect Dis, 2015 Nov 01; 19(6). PMID: 26518264
Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action.
Dušica Vidović, Amar Koleti, Stephan C Schürer.
Front Genet, 2014 Oct 18; 5. PMID: 25324859    Free PMC article.
Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.
David A Van Valen, Takamasa Kudo, +7 authors, Markus W Covert.
PLoS Comput Biol, 2016 Nov 05; 12(11). PMID: 27814364    Free PMC article.
Highly Cited.
Retraction.
Paola Sebastiani, Nadia Solovieff, +10 authors, Thomas T Perls.
Science, 2011 Jul 23; 333(6041). PMID: 21778381
Have DRG-based prospective payment systems influenced the number of secondary diagnoses in health care administrative data?
Lisbeth Serdén, Rikard Lindqvist, Måns Rosén.
Health Policy, 2003 Jul 10; 65(2). PMID: 12849909
Identifying and mitigating biases in EHR laboratory tests.
Rimma Pivovarov, David J Albers, Jorge L Sepulveda, Noémie Elhadad.
J Biomed Inform, 2014 Apr 15; 51. PMID: 24727481    Free PMC article.
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks.
Javier De Las Rivas, Celia Fontanillo.
PLoS Comput Biol, 2010 Jul 01; 6(6). PMID: 20589078    Free PMC article.
Highly Cited.
A unified architecture of transcriptional regulatory elements.
Robin Andersson, Albin Sandelin, Charles G Danko.
Trends Genet, 2015 Jun 16; 31(8). PMID: 26073855
Highly Cited. Review.
Deep convolutional neural networks for annotating gene expression patterns in the mouse brain.
Tao Zeng, Rongjian Li, +2 authors, Shuiwang Ji.
BMC Bioinformatics, 2015 May 08; 16. PMID: 25948335    Free PMC article.
STRATEGIES FOR EQUITABLE PHARMACOGENOMIC-GUIDED WARFARIN DOSING AMONG EUROPEAN AND AFRICAN AMERICAN INDIVIDUALS IN A CLINICAL POPULATION.
Laura K Wiley, Jacob P Vanhouten, +4 authors, Joshua C Denny.
Pac Symp Biocomput, 2016 Nov 30; 22. PMID: 27897005    Free PMC article.
The PDBbind database: methodologies and updates.
Renxiao Wang, Xueliang Fang, +2 authors, Shaomeng Wang.
J Med Chem, 2005 Jun 10; 48(12). PMID: 15943484
Highly Cited.
Improving Computer-Aided Detection Using Convolutional Neural Networks and Random View Aggregation.
Holger R Roth, Le Lu, +5 authors, Ronald M Summers.
IEEE Trans Med Imaging, 2015 Oct 07; 35(5). PMID: 26441412    Free PMC article.
Highly Cited.
From vital signs to clinical outcomes for patients with sepsis: a machine learning basis for a clinical decision support system.
Eren Gultepe, Jeffrey P Green, +3 authors, Ilias Tagkopoulos.
J Am Med Inform Assoc, 2013 Aug 21; 21(2). PMID: 23959843    Free PMC article.
NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads.
Gail L Rosen, Erin R Reichenberger, Aaron M Rosenfeld.
Bioinformatics, 2010 Nov 11; 27(1). PMID: 21062764    Free PMC article.
MECHANISMS IN ENDOCRINOLOGY: Alternative splicing: the new frontier in diabetes research.
Jonàs Juan-Mateu, Olatz Villate, Décio L Eizirik.
Eur J Endocrinol, 2015 Dec 03; 174(5). PMID: 26628584    Free PMC article.
Review.
Drug repositioning: a machine-learning approach through data integration.
Francesco Napolitano, Yan Zhao, +4 authors, Dario Greco.
J Cheminform, 2013 Jun 27; 5(1). PMID: 23800010    Free PMC article.
A logical calculus of the ideas immanent in nervous activity. 1943.
W S McCulloch, W Pitts.
Bull Math Biol, 1990 Jan 01; 52(1-2). PMID: 2185863
Highly Cited.
Mastering the game of Go with deep neural networks and tree search.
David Silver, Aja Huang, +17 authors, Demis Hassabis.
Nature, 2016 Jan 29; 529(7587). PMID: 26819042
Highly Cited.
TaggerOne: joint named entity recognition and normalization with semi-Markov Models.
Robert Leaman, Zhiyong Lu.
Bioinformatics, 2016 Jun 11; 32(18). PMID: 27283952    Free PMC article.
Trans-species learning of cellular signaling systems with bimodal deep belief networks.
Lujia Chen, Chunhui Cai, Vicky Chen, Xinghua Lu.
Bioinformatics, 2015 May 23; 31(18). PMID: 25995230    Free PMC article.
Imputation for transcription factor binding predictions based on deep learning.
Qian Qin, Jianxing Feng.
PLoS Comput Biol, 2017 Feb 25; 13(2). PMID: 28234893    Free PMC article.
Analysis of computational footprinting methods for DNase sequencing experiments.
Eduardo G Gusmao, Manuel Allhoff, Martin Zenke, Ivan G Costa.
Nat Methods, 2016 Feb 24; 13(4). PMID: 26901649
Highly Cited.
Network-based prediction of protein function.
Roded Sharan, Igor Ulitsky, Ron Shamir.
Mol Syst Biol, 2007 Mar 14; 3. PMID: 17353930    Free PMC article.
Highly Cited. Review.
DNorm: disease name normalization with pairwise learning to rank.
Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu.
Bioinformatics, 2013 Aug 24; 29(22). PMID: 23969135    Free PMC article.
Highly Cited.
Drug-disease association and drug-repositioning predictions in complex diseases using causal inference-probabilistic matrix factorization.
Jihong Yang, Zheng Li, Xiaohui Fan, Yiyu Cheng.
J Chem Inf Model, 2014 Aug 15; 54(9). PMID: 25116798
MoleculeNet: a benchmark for molecular machine learning.
Zhenqin Wu, Bharath Ramsundar, +5 authors, Vijay Pande.
Chem Sci, 2018 Apr 10; 9(2). PMID: 29629118    Free PMC article.
Highly Cited.
Gapped sequence alignment using artificial neural networks: application to the MHC class I system.
Massimo Andreatta, Morten Nielsen.
Bioinformatics, 2015 Oct 31; 32(4). PMID: 26515819    Free PMC article.
Highly Cited.
Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics.
Ehsaneddin Asgari, Mohammad R K Mofrad.
PLoS One, 2015 Nov 12; 10(11). PMID: 26555596    Free PMC article.
Highly Cited.
Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction.
Edgar D Coelho, Joel P Arrais, José Luís Oliveira.
PLoS Comput Biol, 2016 Nov 29; 12(11). PMID: 27893735    Free PMC article.
ViPAR: a software platform for the Virtual Pooling and Analysis of Research Data.
Kim W Carter, Richard W Francis, +28 authors, International Collaboration for Autism Registry Epidemiology.
Int J Epidemiol, 2015 Oct 11; 45(2). PMID: 26452388    Free PMC article.
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.
Jellert T Gaublomme, Nir Yosef, +10 authors, Aviv Regev.
Cell, 2015 Nov 27; 163(6). PMID: 26607794    Free PMC article.
Highly Cited.
Neuroscience-Inspired Artificial Intelligence.
Demis Hassabis, Dharshan Kumaran, Christopher Summerfield, Matthew Botvinick.
Neuron, 2017 Jul 21; 95(2). PMID: 28728020
Highly Cited. Review.
Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.
Rhys Heffernan, Kuldip Paliwal, +6 authors, Yaoqi Zhou.
Sci Rep, 2015 Jun 23; 5. PMID: 26098304    Free PMC article.
Highly Cited.
Confidence interval prediction for neural network models.
G Chryssolouris, M Lee, A Ramsey.
IEEE Trans Neural Netw, 1996 Jan 01; 7(1). PMID: 18255575
A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.
Domonkos Tikk, Philippe Thomas, +2 authors, Ulf Leser.
PLoS Comput Biol, 2010 Jul 10; 6. PMID: 20617200    Free PMC article.
The case for cloud computing in genome informatics.
Lincoln D Stein.
Genome Biol, 2010 May 06; 11(5). PMID: 20441614    Free PMC article.
Highly Cited.
How sample size influences research outcomes.
Jorge Faber, Lilian Martins Fonseca.
Dental Press J Orthod, 2014 Oct 04; 19(4). PMID: 25279518    Free PMC article.
A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, +15 authors, Mark J Daly.
Nat Genet, 2011 Apr 12; 43(5). PMID: 21478889    Free PMC article.
Highly Cited.
Computational phenotype discovery using unsupervised feature learning over noisy, sparse, and irregular clinical data.
Thomas A Lasko, Joshua C Denny, Mia A Levy.
PLoS One, 2013 Jul 05; 8(6). PMID: 23826094    Free PMC article.
Highly Cited.
Single-Particle Cryo-EM at Crystallographic Resolution.
Yifan Cheng.
Cell, 2015 Apr 25; 161(3). PMID: 25910205    Free PMC article.
Highly Cited. Review.
Supervised risk predictor of breast cancer based on intrinsic subtypes.
Joel S Parker, Michael Mullins, +17 authors, Philip S Bernard.
J Clin Oncol, 2009 Feb 11; 27(8). PMID: 19204204    Free PMC article.
Highly Cited.
Deep learning for regulatory genomics.
Yongjin Park, Manolis Kellis.
Nat Biotechnol, 2015 Aug 08; 33(8). PMID: 26252139
Chemical-induced disease relation extraction via convolutional neural network.
Jinghang Gu, Fuqing Sun, Longhua Qian, Guodong Zhou.
Database (Oxford), 2017 Apr 18; 2017(1). PMID: 28415073    Free PMC article.
Embedding assisted prediction architecture for event trigger identification.
Yifan Nie, Wenge Rong, +2 authors, Zhang Xiong.
J Bioinform Comput Biol, 2015 Feb 12; 13(3). PMID: 25669328
Epidemiological research labelled as a violation of privacy: the case of Estonia.
Mati Rahu, Martin McKee.
Int J Epidemiol, 2008 Feb 29; 37(3). PMID: 18304955
WGSQuikr: fast whole-genome shotgun metagenomic classification.
David Koslicki, Simon Foucart, Gail Rosen.
PLoS One, 2014 Mar 15; 9(3). PMID: 24626336    Free PMC article.
A renaissance of neural networks in drug discovery.
Igor I Baskin, David Winkler, Igor V Tetko.
Expert Opin Drug Discov, 2016 Jun 14; 11(8). PMID: 27295548
Review.
An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium.
Nature, 2012 Sep 08; 489(7414). PMID: 22955616    Free PMC article.
Highly Cited.
Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction.
Connor W Coley, Regina Barzilay, +2 authors, Klavs F Jensen.
J Chem Inf Model, 2017 Jul 12; 57(8). PMID: 28696688
Secondary Use of EHR: Data Quality Issues and Informatics Opportunities.
Taxiarchis Botsis, Gunnar Hartvigsen, Fei Chen, Chunhua Weng.
Summit Transl Bioinform, 2011 Feb 25; 2010. PMID: 21347133    Free PMC article.
Improved contact predictions using the recognition of protein like contact patterns.
Marcin J Skwark, Daniele Raimondi, Mirco Michel, Arne Elofsson.
PLoS Comput Biol, 2014 Nov 07; 10(11). PMID: 25375897    Free PMC article.
Highly Cited.
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.
Sheng Wang, Siqi Sun, +2 authors, Jinbo Xu.
PLoS Comput Biol, 2017 Jan 06; 13(1). PMID: 28056090    Free PMC article.
Highly Cited.
DeepPPI: Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks.
Xiuquan Du, Shiwei Sun, +3 authors, Yanping Zhang.
J Chem Inf Model, 2017 May 18; 57(6). PMID: 28514151
Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition.
Sabrina Jaeger, Simone Fulle, Samo Turk.
J Chem Inf Model, 2017 Dec 23; 58(1). PMID: 29268609
Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D.
Yun Niu, David Otasek, Igor Jurisica.
Bioinformatics, 2009 Oct 24; 26(1). PMID: 19850753    Free PMC article.
Applications in image-based profiling of perturbations.
Juan C Caicedo, Shantanu Singh, Anne E Carpenter.
Curr Opin Biotechnol, 2016 Apr 19; 39. PMID: 27089218
Review.
DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Christof Angermueller, Heather J Lee, Wolf Reik, Oliver Stegle.
Genome Biol, 2017 Apr 12; 18(1). PMID: 28395661    Free PMC article.
Highly Cited.
Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.
Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu.
Sci Rep, 2016 Jan 12; 6. PMID: 26752681    Free PMC article.
Highly Cited.
Cloud computing and the DNA data race.
Michael C Schatz, Ben Langmead, Steven L Salzberg.
Nat Biotechnol, 2010 Jul 14; 28(7). PMID: 20622843    Free PMC article.
Extraction of skin lesions from non-dermoscopic images for surgical excision of melanoma.
M Hossein Jafari, Ebrahim Nasr-Esfahani, +3 authors, Kayvan Najarian.
Int J Comput Assist Radiol Surg, 2017 Mar 28; 12(6). PMID: 28342106
Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory.
Chien-Hung Huang, Peter Mu-Hsin Chang, +2 authors, Ka-Lok Ng.
BMC Bioinformatics, 2016 Jan 29; 17 Suppl 1. PMID: 26817825    Free PMC article.
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.
Hui Y Xiong, Babak Alipanahi, +14 authors, Brendan J Frey.
Science, 2014 Dec 20; 347(6218). PMID: 25525159    Free PMC article.
Highly Cited.
High-order neural networks and kernel methods for peptide-MHC binding prediction.
Pavel P Kuksa, Martin Renqiang Min, Rishabh Dugar, Mark Gerstein.
Bioinformatics, 2015 Jul 25; 31(22). PMID: 26206306
Large-scale machine learning for metagenomics sequence classification.
Kévin Vervier, Pierre Mahé, +2 authors, Jean-Philippe Vert.
Bioinformatics, 2015 Nov 22; 32(7). PMID: 26589281    Free PMC article.
The Framingham Heart Study and the epidemiology of cardiovascular disease: a historical perspective.
Syed S Mahmood, Daniel Levy, Ramachandran S Vasan, Thomas J Wang.
Lancet, 2013 Oct 03; 383(9921). PMID: 24084292    Free PMC article.
Highly Cited. Review.
Structure-based virtual screening for drug discovery: a problem-centric review.
Tiejun Cheng, Qingliang Li, +2 authors, Stephen H Bryant.
AAPS J, 2012 Jan 28; 14(1). PMID: 22281989    Free PMC article.
Highly Cited. Review.
Is Multitask Deep Learning Practical for Pharma?
Bharath Ramsundar, Bowen Liu, +4 authors, Vijay Pande.
J Chem Inf Model, 2017 Jul 12; 57(8). PMID: 28692267
Highly Cited.
Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting.
Laura K Wiley, Peter Tarczy-Hornoch, +5 authors, Indra Neil Sarkar.
J Am Med Inform Assoc, 2016 Feb 26; 23(2). PMID: 26911808    Free PMC article.
ChEMBL: a large-scale bioactivity database for drug discovery.
Anna Gaulton, Louisa J Bellis, +8 authors, John P Overington.
Nucleic Acids Res, 2011 Sep 29; 40(Database issue). PMID: 21948594    Free PMC article.
Highly Cited.
A deep learning approach for the analysis of masses in mammograms with minimal user intervention.
Neeraj Dhungel, Gustavo Carneiro, Andrew P Bradley.
Med Image Anal, 2017 Feb 09; 37. PMID: 28171807
Biomedical informatics for computer-aided decision support systems: a survey.
Ashwin Belle, Mark A Kon, Kayvan Najarian.
ScientificWorldJournal, 2013 Feb 23; 2013. PMID: 23431259    Free PMC article.
Review.
Predicting protein-protein interactions from protein sequences by a stacked sparse autoencoder deep neural network.
Yan-Bin Wang, Zhu-Hong You, +4 authors, Lei Wang.
Mol Biosyst, 2017 Jun 13; 13(7). PMID: 28604872
Deep learning for healthcare: review, opportunities and challenges.
Riccardo Miotto, Fei Wang, +2 authors, Joel T Dudley.
Brief Bioinform, 2017 May 10; 19(6). PMID: 28481991    Free PMC article.
Highly Cited. Review.
Enhancing reproducibility for computational methods.
Victoria Stodden, Marcia McNutt, +6 authors, Michela Taufer.
Science, 2016 Dec 13; 354(6317). PMID: 27940837
Highly Cited.
Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.
Tianchuan Du, Li Liao, Cathy H Wu, Bilin Sun.
Methods, 2016 Jun 11; 110. PMID: 27282356
Data Sharing.
Dan L Longo, Jeffrey M Drazen.
N Engl J Med, 2016 Jan 21; 374(3). PMID: 26789876
Highly Cited.
Mining electronic health records: towards better research applications and clinical care.
Peter B Jensen, Lars J Jensen, Søren Brunak.
Nat Rev Genet, 2012 May 03; 13(6). PMID: 22549152
Highly Cited. Review.
Evaluation of methods for modeling transcription factor sequence specificity.
Matthew T Weirauch, Atina Cote, +13 authors, Timothy R Hughes.
Nat Biotechnol, 2013 Jan 29; 31(2). PMID: 23354101    Free PMC article.
Highly Cited.
Deep learning for computational biology.
Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle.
Mol Syst Biol, 2016 Jul 31; 12(7). PMID: 27474269    Free PMC article.
Highly Cited. Review.
DANN: a deep learning approach for annotating the pathogenicity of genetic variants.
Daniel Quang, Yifei Chen, Xiaohui Xie.
Bioinformatics, 2014 Oct 24; 31(5). PMID: 25338716    Free PMC article.
Highly Cited.
Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients.
Anders Boeck Jensen, Pope L Moseley, +6 authors, Søren Brunak.
Nat Commun, 2014 Jun 25; 5. PMID: 24959948    Free PMC article.
Highly Cited.
Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters.
Yifeng Li, Chih-Yu Chen, Wyeth W Wasserman.
J Comput Biol, 2016 Jan 23; 23(5). PMID: 26799292
Applications of Deep Learning in Biomedicine.
Polina Mamoshina, Armando Vieira, Evgeny Putin, Alex Zhavoronkov.
Mol Pharm, 2016 Mar 24; 13(5). PMID: 27007977
Highly Cited. Review.
Predicting effects of noncoding variants with deep learning-based sequence model.
Jian Zhou, Olga G Troyanskaya.
Nat Methods, 2015 Aug 25; 12(10). PMID: 26301843    Free PMC article.
Highly Cited.
A general framework for estimating the relative pathogenicity of human genetic variants.
Martin Kircher, Daniela M Witten, +3 authors, Jay Shendure.
Nat Genet, 2014 Feb 04; 46(3). PMID: 24487276    Free PMC article.
Highly Cited.
FragGeneScan: predicting genes in short and error-prone reads.
Mina Rho, Haixu Tang, Yuzhen Ye.
Nucleic Acids Res, 2010 Sep 02; 38(20). PMID: 20805240    Free PMC article.
Highly Cited.
Metagenomic taxonomic classification using extreme learning machines.
Zeehasham Rasheed, Huzefa Rangwala.
J Bioinform Comput Biol, 2012 Aug 02; 10(5). PMID: 22849369
Exploring the application of deep learning techniques on medical text corpora.
José Antonio Minarro-Giménez, Oscar Marín-Alonso, Matthias Samwald.
Stud Health Technol Inform, 2014 Aug 28; 205. PMID: 25160253
A unified multitask architecture for predicting local protein properties.
Yanjun Qi, Merja Oja, Jason Weston, William Stafford Noble.
PLoS One, 2012 Mar 31; 7(3). PMID: 22461885    Free PMC article.
A comprehensive evaluation of multicategory classification methods for microbiomic data.
Alexander Statnikov, Mikael Henaff, +7 authors, Alexander V Alekseyenko.
Microbiome, 2014 Jan 25; 1(1). PMID: 24456583    Free PMC article.
SwarmPS: rapid, semi-automated single particle selection software.
David Woolford, Geoffery Ericksson, +8 authors, Jasmine Banks.
J Struct Biol, 2006 Jun 16; 157(1). PMID: 16774837
Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data.
Alexander Aliper, Sergey Plis, +3 authors, Alex Zhavoronkov.
Mol Pharm, 2016 May 21; 13(7). PMID: 27200455    Free PMC article.
Highly Cited.
DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads.
Vladimír Boža, Broňa Brejová, Tomáš Vinař.
PLoS One, 2017 Jun 06; 12(6). PMID: 28582401    Free PMC article.
Highly Cited.
DEEP: a general computational framework for predicting enhancers.
Dimitrios Kleftogiannis, Panos Kalnis, Vladimir B Bajic.
Nucleic Acids Res, 2014 Nov 08; 43(1). PMID: 25378307    Free PMC article.
A survey on deep learning in medical image analysis.
Geert Litjens, Thijs Kooi, +6 authors, Clara I Sánchez.
Med Image Anal, 2017 Aug 05; 42. PMID: 28778026
Highly Cited. Review.
Compositional biases of bacterial genomes and evolutionary implications.
S Karlin, J Mrázek, A M Campbell.
J Bacteriol, 1997 Jun 01; 179(12). PMID: 9190805    Free PMC article.
Highly Cited.
Electronic medical record phenotyping using the anchor and learn framework.
Yoni Halpern, Steven Horng, Youngduck Choi, David Sontag.
J Am Med Inform Assoc, 2016 Apr 24; 23(4). PMID: 27107443    Free PMC article.
Highly Cited.
Using electronic health records for clinical research: the case of the EHR4CR project.
Georges De Moor, Mats Sundgren, +13 authors, Pascal Coorevits.
J Biomed Inform, 2014 Dec 03; 53. PMID: 25463966
Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules.
Alessandro Lusci, Gianluca Pollastri, Pierre Baldi.
J Chem Inf Model, 2013 Jun 26; 53(7). PMID: 23795551    Free PMC article.
Highly Cited.
DataSHIELD: taking the analysis to the data, not the data to the analysis.
Amadou Gaye, Yannick Marcon, +46 authors, Paul R Burton.
Int J Epidemiol, 2014 Sep 30; 43(6). PMID: 25261970    Free PMC article.
On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation.
Sebastian Bach, Alexander Binder, +3 authors, Wojciech Samek.
PLoS One, 2015 Jul 15; 10(7). PMID: 26161953    Free PMC article.
Highly Cited.
Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.
Lujia Chen, Chunhui Cai, Vicky Chen, Xinghua Lu.
BMC Bioinformatics, 2016 Jan 29; 17 Suppl 1. PMID: 26818848    Free PMC article.
Automated analysis of high-content microscopy data with deep learning.
Oren Z Kraus, Ben T Grys, +4 authors, Brenda J Andrews.
Mol Syst Biol, 2017 Apr 20; 13(4). PMID: 28420678    Free PMC article.
Highly Cited.
The Cancer Genome Atlas Pan-Cancer analysis project.
Cancer Genome Atlas Research Network, John N Weinstein, +7 authors, Joshua M Stuart.
Nat Genet, 2013 Sep 28; 45(10). PMID: 24071849    Free PMC article.
Highly Cited.
An analysis of the attrition of drug candidates from four major pharmaceutical companies.
Michael J Waring, John Arrowsmith, +9 authors, Alex Weir.
Nat Rev Drug Discov, 2015 Jun 20; 14(7). PMID: 26091267
Highly Cited. Review.
A review of connectivity map and computational approaches in pharmacogenomics.
Aliyu Musa, Laleh Soltan Ghoraie, +5 authors, Frank Emmert-Streib.
Brief Bioinform, 2017 Jan 11; 19(3). PMID: 28069634    Free PMC article.
Review.
Causal Phenotype Discovery via Deep Networks.
David C Kale, Zhengping Che, +3 authors, Randall Wetzel.
AMIA Annu Symp Proc, 2015 Jan 01; 2015. PMID: 26958203    Free PMC article.
L1000CDS2: LINCS L1000 characteristic direction signatures search engine.
Qiaonan Duan, St Patrick Reid, +13 authors, Avi Ma'ayan.
NPJ Syst Biol Appl, 2016 Jan 01; 2. PMID: 28413689    Free PMC article.
Highly Cited.
Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.
Jiayi Wu, Yong-Bei Ma, +5 authors, Youdong Mao.
PLoS One, 2017 Aug 09; 12(8). PMID: 28786986    Free PMC article.
Prospective identification of hematopoietic lineage choice by deep learning.
Felix Buggenthin, Florian Buettner, +10 authors, Carsten Marr.
Nat Methods, 2017 Feb 22; 14(4). PMID: 28218899    Free PMC article.
Extracting interactions between proteins from the literature.
Deyu Zhou, Yulan He.
J Biomed Inform, 2008 Jan 22; 41(2). PMID: 18207462
Review.
Protein 3D structure computed from evolutionary sequence variation.
Debora S Marks, Lucy J Colwell, +4 authors, Chris Sander.
PLoS One, 2011 Dec 14; 6(12). PMID: 22163331    Free PMC article.
Highly Cited.
A network-biology perspective of microRNA function and dysfunction in cancer.
Cameron P Bracken, Hamish S Scott, Gregory J Goodall.
Nat Rev Genet, 2016 Nov 01; 17(12). PMID: 27795564
Highly Cited. Review.
Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders.
Jie Tan, Matthew Ung, Chao Cheng, Casey S Greene.
Pac Symp Biocomput, 2015 Jan 17;. PMID: 25592575    Free PMC article.
Combining gene prediction methods to improve metagenomic gene annotation.
Non G Yok, Gail L Rosen.
BMC Bioinformatics, 2011 Jan 15; 12. PMID: 21232129    Free PMC article.
The real cost of sequencing: scaling computation to keep pace with data generation.
Paul Muir, Shantao Li, +8 authors, Mark Gerstein.
Genome Biol, 2016 Mar 25; 17. PMID: 27009100    Free PMC article.
Highly Cited.
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu.
Bioinformatics, 2015 Aug 16; 31(21). PMID: 26275894    Free PMC article.
Extended-connectivity fingerprints.
David Rogers, Mathew Hahn.
J Chem Inf Model, 2010 Apr 30; 50(5). PMID: 20426451
Highly Cited.
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli.
Minseung Kim, Navneet Rai, Violeta Zorraquino, Ilias Tagkopoulos.
Nat Commun, 2016 Oct 08; 7. PMID: 27713404    Free PMC article.
Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning.
Hoo-Chang Shin, Holger R Roth, +6 authors, Ronald M Summers.
IEEE Trans Med Imaging, 2016 Feb 18; 35(5). PMID: 26886976    Free PMC article.
Highly Cited.
New strategies for triple-negative breast cancer--deciphering the heterogeneity.
Ingrid A Mayer, Vandana G Abramson, Brian D Lehmann, Jennifer A Pietenpol.
Clin Cancer Res, 2014 Feb 19; 20(4). PMID: 24536073    Free PMC article.
Highly Cited. Review.
Semi-automated selection of cryo-EM particles in RELION-1.3.
Sjors H W Scheres.
J Struct Biol, 2014 Dec 09; 189(2). PMID: 25486611    Free PMC article.
Highly Cited.
ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions.
Jie Tan, John H Hammond, Deborah A Hogan, Casey S Greene.
mSystems, 2016 Nov 09; 1(1). PMID: 27822512    Free PMC article.
Low Data Drug Discovery with One-Shot Learning.
Han Altae-Tran, Bharath Ramsundar, Aneesh S Pappu, Vijay Pande.
ACS Cent Sci, 2017 May 05; 3(4). PMID: 28470045    Free PMC article.
Highly Cited.
Overcoming the winner's curse: estimating penetrance parameters from case-control data.
Sebastian Zollner, Jonathan K Pritchard.
Am J Hum Genet, 2007 Mar 16; 80(4). PMID: 17357068    Free PMC article.
Highly Cited.
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
Toshiyuki Shiraki, Shinji Kondo, +14 authors, Yoshihide Hayashizaki.
Proc Natl Acad Sci U S A, 2003 Dec 10; 100(26). PMID: 14663149    Free PMC article.
Highly Cited.
Informatics for unveiling hidden genome signatures.
Takashi Abe, Shigehiko Kanaya, +3 authors, Toshimichi Ikemura.
Genome Res, 2003 Apr 03; 13(4). PMID: 12671005    Free PMC article.
An open investigation of the reproducibility of cancer biology research.
Timothy M Errington, Elizabeth Iorns, +3 authors, Brian A Nosek.
Elife, 2014 Dec 11; 3. PMID: 25490932    Free PMC article.
Highly Cited.
A machine learning-based framework to identify type 2 diabetes through electronic health records.
Tao Zheng, Wei Xie, +5 authors, You Chen.
Int J Med Inform, 2016 Dec 07; 97. PMID: 27919371    Free PMC article.
Detection of RNA polymerase II promoters and polyadenylation sites in human DNA sequence.
S Matis, Y Xu, +4 authors, E Uberbacher.
Comput Chem, 1996 Mar 01; 20(1). PMID: 8867844
Clustering metagenomic sequences with interpolated Markov models.
David R Kelley, Steven L Salzberg.
BMC Bioinformatics, 2010 Nov 04; 11. PMID: 21044341    Free PMC article.
Leveraging uncertainty information from deep neural networks for disease detection.
Christian Leibig, Vaneeda Allken, +2 authors, Siegfried Wahl.
Sci Rep, 2017 Dec 21; 7(1). PMID: 29259224    Free PMC article.
A review of validation strategies for computational drug repositioning.
Adam S Brown, Chirag J Patel.
Brief Bioinform, 2016 Nov 25; 19(1). PMID: 27881429    Free PMC article.
Systematic Review.
Bidirectional RNN for Medical Event Detection in Electronic Health Records.
Abhyuday N Jagannatha, Hong Yu.
Proc Conf, 2016 Nov 26; 2016. PMID: 27885364    Free PMC article.
Highly Cited.
Realizing the full potential of electronic health records: the role of natural language processing.
Lucila Ohno-Machado.
J Am Med Inform Assoc, 2011 Aug 19; 18(5). PMID: 21846784    Free PMC article.
TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions.
Zixuan Cang, Guo-Wei Wei.
PLoS Comput Biol, 2017 Jul 28; 13(7). PMID: 28749969    Free PMC article.
Multi-Layer and Recursive Neural Networks for Metagenomic Classification.
Gregory Ditzler, Robi Polikar, Gail Rosen.
IEEE Trans Nanobioscience, 2015 Sep 01; 14(6). PMID: 26316190
Enhanced regulatory sequence prediction using gapped k-mer features.
Mahmoud Ghandi, Dongwon Lee, Morteza Mohammad-Noori, Michael A Beer.
PLoS Comput Biol, 2014 Jul 18; 10(7). PMID: 25033408    Free PMC article.
Highly Cited.
Sex bias in neuroscience and biomedical research.
Annaliese K Beery, Irving Zucker.
Neurosci Biobehav Rev, 2010 Jul 14; 35(3). PMID: 20620164    Free PMC article.
Highly Cited. Review.
Convolutional neural network architectures for predicting DNA-protein binding.
Haoyang Zeng, Matthew D Edwards, Ge Liu, David K Gifford.
Bioinformatics, 2016 Jun 17; 32(12). PMID: 27307608    Free PMC article.
Highly Cited.
Clinical prediction rules. Applications and methodological standards.
J H Wasson, H C Sox, R K Neff, L Goldman.
N Engl J Med, 1985 Sep 26; 313(13). PMID: 3897864
Highly Cited. Review.
Large-scale image-based screening and profiling of cellular phenotypes.
Nicola Bougen-Zhukov, Sheng Yang Loh, Hwee Kuan Lee, Lit-Hsin Loo.
Cytometry A, 2016 Jul 20; 91(2). PMID: 27434125
Review.
HLA class I binding prediction via convolutional neural networks.
Yeeleng S Vang, Xiaohui Xie.
Bioinformatics, 2017 Apr 27; 33(17). PMID: 28444127
NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets.
Morten Nielsen, Massimo Andreatta.
Genome Med, 2016 Apr 01; 8(1). PMID: 27029192    Free PMC article.
Highly Cited.
Boosting Docking-Based Virtual Screening with Deep Learning.
Janaina Cruz Pereira, Ernesto Raúl Caffarena, Cicero Nogueira Dos Santos.
J Chem Inf Model, 2016 Dec 28; 56(12). PMID: 28024405
Molecular graph convolutions: moving beyond fingerprints.
Steven Kearnes, Kevin McCloskey, +2 authors, Patrick Riley.
J Comput Aided Mol Des, 2016 Aug 26; 30(8). PMID: 27558503    Free PMC article.
Highly Cited.
Improving chemical disease relation extraction with rich features and weakly labeled data.
Yifan Peng, Chih-Hsuan Wei, Zhiyong Lu.
J Cheminform, 2017 Mar 21; 8. PMID: 28316651    Free PMC article.
Deciphering the splicing code.
Yoseph Barash, John A Calarco, +5 authors, Brendan J Frey.
Nature, 2010 May 07; 465(7294). PMID: 20445623
Highly Cited.
Machines that learn to segment images: a crucial technology for connectomics.
Viren Jain, H Sebastian Seung, Srinivas C Turaga.
Curr Opin Neurobiol, 2010 Aug 31; 20(5). PMID: 20801638    Free PMC article.
Review.
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks.
David R Kelley, Jasper Snoek, John L Rinn.
Genome Res, 2016 May 20; 26(7). PMID: 27197224    Free PMC article.
Highly Cited.
The state of the art of mammalian promoter recognition.
Thomas Werner.
Brief Bioinform, 2003 Apr 29; 4(1). PMID: 12715831
Review.
Accurate phylogenetic classification of variable-length DNA fragments.
Alice Carolyn McHardy, Héctor García Martín, +2 authors, Isidore Rigoutsos.
Nat Methods, 2006 Dec 21; 4(1). PMID: 17179938
Highly Cited.
Learning the sequence determinants of alternative splicing from millions of random sequences.
Alexander B Rosenberg, Rupali P Patwardhan, Jay Shendure, Georg Seelig.
Cell, 2015 Oct 27; 163(3). PMID: 26496609
Highly Cited.
RNA mis-splicing in disease.
Marina M Scotti, Maurice S Swanson.
Nat Rev Genet, 2015 Nov 26; 17(1). PMID: 26593421    Free PMC article.
Highly Cited. Review.
Accurate and efficient target prediction using a potency-sensitive influence-relevance voter.
Alessandro Lusci, Michael Browning, +2 authors, Pierre Baldi.
J Cheminform, 2016 Jan 01; 7. PMID: 26719774    Free PMC article.
Drug drug interaction extraction from biomedical literature using syntax convolutional neural network.
Zhehuan Zhao, Zhihao Yang, +2 authors, Jian Wang.
Bioinformatics, 2016 Jul 29; 32(22). PMID: 27466626    Free PMC article.
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.
Riu Yamashita, Nuankanya P Sathira, +7 authors, Yutaka Suzuki.
Genome Res, 2011 Mar 05; 21(5). PMID: 21372179    Free PMC article.
A neural joint model for entity and relation extraction from biomedical text.
Fei Li, Meishan Zhang, Guohong Fu, Donghong Ji.
BMC Bioinformatics, 2017 Apr 01; 18(1). PMID: 28359255    Free PMC article.
MEME SUITE: tools for motif discovery and searching.
Timothy L Bailey, Mikael Boden, +6 authors, William S Noble.
Nucleic Acids Res, 2009 May 22; 37(Web Server issue). PMID: 19458158    Free PMC article.
Highly Cited.
A Shortest Dependency Path Based Convolutional Neural Network for Protein-Protein Relation Extraction.
Lei Hua, Chanqin Quan.
Biomed Res Int, 2016 Aug 06; 2016. PMID: 27493967    Free PMC article.
Somatic mutation in single human neurons tracks developmental and transcriptional history.
Michael A Lodato, Mollie B Woodworth, +11 authors, Christopher A Walsh.
Science, 2015 Oct 03; 350(6256). PMID: 26430121    Free PMC article.
Highly Cited.
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
Justin Lamb, Emily D Crawford, +17 authors, Todd R Golub.
Science, 2006 Sep 30; 313(5795). PMID: 17008526
Highly Cited.
Deep learning in neural networks: an overview.
Jürgen Schmidhuber.
Neural Netw, 2014 Dec 03; 61. PMID: 25462637
Highly Cited. Review.
Fizzy: feature subset selection for metagenomics.
Gregory Ditzler, J Calvin Morrison, Yemin Lan, Gail L Rosen.
BMC Bioinformatics, 2015 Nov 06; 16. PMID: 26538306    Free PMC article.
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.
Xiaoyong Pan, Hong-Bin Shen.
BMC Bioinformatics, 2017 Mar 02; 18(1). PMID: 28245811    Free PMC article.
Highly Cited.
Children of the 90s: Coming of age.
Helen Pearson.
Nature, 2012 Apr 14; 484(7393). PMID: 22498607
Hit and lead generation: beyond high-throughput screening.
Konrad H Bleicher, Hans-Joachim Böhm, Klaus Müller, Alexander I Alanine.
Nat Rev Drug Discov, 2003 May 17; 2(5). PMID: 12750740
Highly Cited. Review.
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.
Matt Spencer, Jesse Eickholt, Jianlin Cheng.
IEEE/ACM Trans Comput Biol Bioinform, 2015 Mar 10; 12(1). PMID: 25750595    Free PMC article.
Predicting effective microRNA target sites in mammalian mRNAs.
Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel.
Elife, 2015 Aug 13; 4. PMID: 26267216    Free PMC article.
Highly Cited.
Machine learning and computer vision approaches for phenotypic profiling.
Ben T Grys, Dara S Lo, +4 authors, Brenda J Andrews.
J Cell Biol, 2016 Dec 13; 216(1). PMID: 27940887    Free PMC article.
Review.
The Novel Roles of Connexin Channels and Tunneling Nanotubes in Cancer Pathogenesis.
Silvana Valdebenito, Emil Lou, +2 authors, Eliseo Eugenin.
Int J Mol Sci, 2018 Apr 27; 19(5). PMID: 29695070    Free PMC article.
Review.
Deep learning in pharmacogenomics: from gene regulation to patient stratification.
Alexandr A Kalinin, Gerald A Higgins, +5 authors, Brian D Athey.
Pharmacogenomics, 2018 Apr 27; 19(7). PMID: 29697304    Free PMC article.
Review.
Patient-Centered Mobile Health Data Management Solution for the German Health Care System (The DataBox Project).
Titus Josef Brinker, Stefanie Rudolph, Daniela Richter, Christof von Kalle.
JMIR Cancer, 2018 May 13; 4(1). PMID: 29752255    Free PMC article.
Opportunities and challenges in developing deep learning models using electronic health records data: a systematic review.
Cao Xiao, Edward Choi, Jimeng Sun.
J Am Med Inform Assoc, 2018 Jun 13; 25(10). PMID: 29893864    Free PMC article.
Highly Cited. Systematic Review.
Extracting chemical-protein relations with ensembles of SVM and deep learning models.
Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu.
Database (Oxford), 2018 Jul 19; 2018. PMID: 30020437    Free PMC article.
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integration in Precision Medicine.
Dmitry Grapov, Johannes Fahrmann, Kwanjeera Wanichthanarak, Sakda Khoomrung.
OMICS, 2018 Aug 21; 22(10). PMID: 30124358    Free PMC article.
Review.
Systems Medicine Disease: Disease Classification and Scalability Beyond Networks and Boundary Conditions.
Richard Berlin, Russell Gruen, James Best.
Front Bioeng Biotechnol, 2018 Aug 23; 6. PMID: 30131956    Free PMC article.
Deep learning in biomedicine.
Michael Wainberg, Daniele Merico, Andrew Delong, Brendan J Frey.
Nat Biotechnol, 2018 Sep 07; 36(9). PMID: 30188539
Highly Cited.
3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification.
Alexandr A Kalinin, Ari Allyn-Feuer, +15 authors, Ivo D Dinov.
Sci Rep, 2018 Sep 14; 8(1). PMID: 30209281    Free PMC article.
The Human Interface of Biomedical Informatics.
Edward C Klatt.
J Pathol Inform, 2018 Sep 22; 9. PMID: 30237909    Free PMC article.
Review.
Multi-omic and multi-view clustering algorithms: review and cancer benchmark.
Nimrod Rappoport, Ron Shamir.
Nucleic Acids Res, 2018 Oct 09; 46(20). PMID: 30295871    Free PMC article.
Highly Cited. Review.
Universal cancer screening: revolutionary, rational, and realizable.
David A Ahlquist.
NPJ Precis Oncol, 2018 Nov 06; 2. PMID: 30393772    Free PMC article.
Review.
A reference set of curated biomedical data and metadata from clinical case reports.
J Harry Caufield, Yijiang Zhou, +13 authors, Peipei Ping.
Sci Data, 2018 Nov 21; 5. PMID: 30457569    Free PMC article.
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.
Žiga Avsec, Roman Kreuzhuber, +10 authors, Julien Gagneur.
Nat Biotechnol, 2019 May 30; 37(6). PMID: 31138913    Free PMC article.
Highly Cited.
Computational pathology definitions, best practices, and recommendations for regulatory guidance: a white paper from the Digital Pathology Association.
Esther Abels, Liron Pantanowitz, +9 authors, Cleopatra Kozlowski.
J Pathol, 2019 Jul 30; 249(3). PMID: 31355445    Free PMC article.
Review.
Artificial intelligence in digital pathology - new tools for diagnosis and precision oncology.
Kaustav Bera, Kurt A Schalper, +2 authors, Anant Madabhushi.
Nat Rev Clin Oncol, 2019 Aug 11; 16(11). PMID: 31399699    Free PMC article.
Highly Cited. Review.
Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests.
Jesse G Meyer, Shengchao Liu, +2 authors, Anthony Gitter.
J Chem Inf Model, 2019 Sep 14; 59(10). PMID: 31518132    Free PMC article.
Inferring Disease-Associated MicroRNAs Using Semi-supervised Multi-Label Graph Convolutional Networks.
Xiaoyong Pan, Hong-Bin Shen.
iScience, 2019 Oct 13; 20. PMID: 31605942    Free PMC article.
DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data.
Cédric Arisdakessian, Olivier Poirion, +2 authors, Lana X Garmire.
Genome Biol, 2019 Oct 20; 20(1). PMID: 31627739    Free PMC article.
Highly Cited.
Trends and Focus of Machine Learning Applications for Health Research.
Brett Beaulieu-Jones, Samuel G Finlayson, +7 authors, Tristan Naumann.
JAMA Netw Open, 2019 Oct 28; 2(10). PMID: 31651969    Free PMC article.
The second information revolution: digitalization brings opportunities and concerns for public health.
Martin McKee, May C I van Schalkwyk, David Stuckler.
Eur J Public Health, 2019 Nov 19; 29(Supplement_3). PMID: 31738440    Free PMC article.
Deep spectral learning for label-free optical imaging oximetry with uncertainty quantification.
Rongrong Liu, Shiyi Cheng, Lei Tian, Ji Yi.
Light Sci Appl, 2019 Nov 23; 8. PMID: 31754429    Free PMC article.
Extracting a biologically latent space of lung cancer epigenetics with variational autoencoders.
Zhenxing Wang, Yadong Wang.
BMC Bioinformatics, 2019 Nov 26; 20(Suppl 18). PMID: 31760935    Free PMC article.
From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology.
Vahid H Gazestani, Nathan E Lewis.
Curr Opin Syst Biol, 2019 Nov 30; 15. PMID: 31777764    Free PMC article.
tRNA functional signatures classify plastids as late-branching cyanobacteria.
Travis J Lawrence, Katherine Ch Amrine, Wesley D Swingley, David H Ardell.
BMC Evol Biol, 2019 Dec 11; 19(1). PMID: 31818253    Free PMC article.
Graph Embedding Deep Learning Guides Microbial Biomarkers' Identification.
Qiang Zhu, Xingpeng Jiang, +2 authors, Tingting He.
Front Genet, 2019 Dec 12; 10. PMID: 31824573    Free PMC article.
A Deep Learning Approach for Meibomian Gland Atrophy Evaluation in Meibography Images.
Jiayun Wang, Thao N Yeh, +2 authors, Meng C Lin.
Transl Vis Sci Technol, 2019 Dec 24; 8(6). PMID: 31867138    Free PMC article.
Digital Health and the State of Interoperable Electronic Health Records.
Jessica Germaine Shull.
JMIR Med Inform, 2019 Nov 05; 7(4). PMID: 31682583    Free PMC article.
Evolving the pulmonary nodules diagnosis from classical approaches to deep learning-aided decision support: three decades' development course and future prospect.
Bo Liu, Wenhao Chi, +5 authors, Jianxing He.
J Cancer Res Clin Oncol, 2019 Dec 02; 146(1). PMID: 31786740
Review.
Brain Imaging Genomics: Integrated Analysis and Machine Learning.
Li Shen, Paul M Thompson.
Proc IEEE Inst Electr Electron Eng, 2020 Jan 07; 108(1). PMID: 31902950    Free PMC article.
Co-expression Networks Identify DHX15 RNA Helicase as a B Cell Regulatory Factor.
Thiago Detanico, Richard Virgen-Slane, +8 authors, Carl F Ware.
Front Immunol, 2020 Jan 11; 10. PMID: 31921164    Free PMC article.
Applications of Machine Learning Using Electronic Medical Records in Spine Surgery.
John T Schwartz, Michael Gao, +3 authors, Samuel K Cho.
Neurospine, 2020 Jan 07; 16(4). PMID: 31905452    Free PMC article.
Multiset sparse partial least squares path modeling for high dimensional omics data analysis.
Attila Csala, Aeilko H Zwinderman, Michel H Hof.
BMC Bioinformatics, 2020 Jan 11; 21(1). PMID: 31918677    Free PMC article.
deepDR: a network-based deep learning approach to in silico drug repositioning.
Xiangxiang Zeng, Siyi Zhu, +3 authors, Feixiong Cheng.
Bioinformatics, 2019 May 23; 35(24). PMID: 31116390    Free PMC article.
Highly Cited.
Cloud bursting galaxy: federated identity and access management.
Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks.
Bioinformatics, 2019 Jun 15; 36(1). PMID: 31197310    Free PMC article.
Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming.
Jake P Taylor-King, Asbjørn N Riseth, Will Macnair, Manfred Claassen.
PLoS Comput Biol, 2020 Jan 11; 16(1). PMID: 31923173    Free PMC article.
Knowledge Generation with Rule Induction in Cancer Omics.
Giovanni Scala, Antonio Federico, +2 authors, Barbara Majello.
Int J Mol Sci, 2019 Dec 22; 21(1). PMID: 31861438    Free PMC article.
Review.
Molecular Insights from Conformational Ensembles via Machine Learning.
Oliver Fleetwood, Marina A Kasimova, Annie M Westerlund, Lucie Delemotte.
Biophys J, 2020 Jan 19; 118(3). PMID: 31952811    Free PMC article.
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.
Christopher A Lavender, Andrew J Shapiro, Frank S Day, David C Fargo.
PLoS Comput Biol, 2020 Jan 25; 16(1). PMID: 31978042    Free PMC article.
Deep learning in clinical natural language processing: a methodical review.
Stephen Wu, Kirk Roberts, +9 authors, Hua Xu.
J Am Med Inform Assoc, 2019 Dec 04; 27(3). PMID: 31794016    Free PMC article.
Review.
Deep learning cardiac motion analysis for human survival prediction.
Ghalib A Bello, Timothy J W Dawes, +8 authors, Declan P O'Regan.
Nat Mach Intell, 2019 Feb 26; 1. PMID: 30801055    Free PMC article.
Highly Cited.
Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing.
Brett K Beaulieu-Jones, Zhiwei Steven Wu, +4 authors, Casey S Greene.
Circ Cardiovasc Qual Outcomes, 2019 Jul 10; 12(7). PMID: 31284738    Free PMC article.
Neural computational model GrowthEstimate: A model for studying living resources through digestive efficiency.
Krisna Rungruangsak-Torrissen, Poramate Manoonpong.
PLoS One, 2019 Aug 29; 14(8). PMID: 31461459    Free PMC article.
The discovery BPD (D-BPD) program: study protocol of a prospective translational multicenter collaborative study to investigate determinants of chronic lung disease in very low birth weight infants.
Gaston Ofman, Mauricio T Caballero, +22 authors, Fernando P Polack.
BMC Pediatr, 2019 Jul 08; 19(1). PMID: 31279333    Free PMC article.
Characterization of a novel cotton MYB gene, GhMYB108-like responsive to abiotic stresses.
Abid Ullah, Muhammad Tahir Ul Qamar, +8 authors, Xiyan Yang.
Mol Biol Rep, 2020 Jan 15; 47(3). PMID: 31933260
Learning to predict the cosmological structure formation.
Siyu He, Yin Li, +4 authors, Barnabás Póczos.
Proc Natl Acad Sci U S A, 2019 Jun 27; 116(28). PMID: 31235606    Free PMC article.
Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.
Alberto Romagnoni, Simon Jégou, +3 authors, International Inflammatory Bowel Disease Genetics Consortium (IIBDGC).
Sci Rep, 2019 Jul 19; 9(1). PMID: 31316157    Free PMC article.
Technical considerations of multi-parametric tissue outcome prediction methods in acute ischemic stroke patients.
Anthony J Winder, Susanne Siemonsen, +3 authors, Nils D Forkert.
Sci Rep, 2019 Sep 15; 9(1). PMID: 31519923    Free PMC article.
Latent Risk Intrahepatic Cholangiocarcinoma Susceptible to Adjuvant Treatment After Resection: A Clinical Deep Learning Approach.
Seogsong Jeong, Yang Ge, +11 authors, Lei Chen.
Front Oncol, 2020 Mar 07; 10. PMID: 32140448    Free PMC article.
Evolving systems biology approaches to understanding non-coding RNAs in pulmonary hypertension.
Lloyd D Harvey, Stephen Y Chan.
J Physiol, 2018 Aug 17; 597(4). PMID: 30113078    Free PMC article.
Review.
How to rekindle drug discovery process through integrative therapeutic targeting?
Ashok Vaidya, Anuradha Roy, Rathnam Chaguturu.
Expert Opin Drug Discov, 2018 Aug 28; 13(10). PMID: 30146919    Free PMC article.
DeepSeeNet: A Deep Learning Model for Automated Classification of Patient-based Age-related Macular Degeneration Severity from Color Fundus Photographs.
Yifan Peng, Shazia Dharssi, +5 authors, Zhiyong Lu.
Ophthalmology, 2018 Nov 25; 126(4). PMID: 30471319    Free PMC article.
Practical Model Selection for Prospective Virtual Screening.
Shengchao Liu, Moayad Alnammi, +6 authors, Anthony Gitter.
J Chem Inf Model, 2018 Dec 01; 59(1). PMID: 30500183    Free PMC article.
Deep Learning in Image Cytometry: A Review.
Anindya Gupta, Philip J Harrison, +9 authors, Carolina Wählby.
Cytometry A, 2018 Dec 20; 95(4). PMID: 30565841    Free PMC article.
Review.
Single cell RNA-sequencing: replicability of cell types.
Megan Crow, Jesse Gillis.
Curr Opin Neurobiol, 2019 Jan 18; 56. PMID: 30654233    Free PMC article.
Review.
Unsupervised classification of multi-omics data during cardiac remodeling using deep learning.
Neo Christopher Chung, Bilal Mirza, +4 authors, Wei Wang.
Methods, 2019 Mar 12; 166. PMID: 30853547    Free PMC article.
Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis.
Beau Norgeot, Benjamin S Glicksberg, +6 authors, Atul J Butte.
JAMA Netw Open, 2019 Mar 16; 2(3). PMID: 30874779    Free PMC article.
MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction.
Nathan LaPierre, Chelsea J-T Ju, Guangyu Zhou, Wei Wang.
Methods, 2019 Mar 20; 166. PMID: 30885720    Free PMC article.
Artificial intelligence in reproductive medicine.
Renjie Wang, Wei Pan, +7 authors, Shujie Liao.
Reproduction, 2019 Apr 11; 158(4). PMID: 30970326    Free PMC article.
Review.
A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.
Jason H Yang, Sarah N Wright, +9 authors, James J Collins.
Cell, 2019 May 14; 177(6). PMID: 31080069    Free PMC article.
Highly Cited.
A Brief History of Protein Sorting Prediction.
Henrik Nielsen, Konstantinos D Tsirigos, Søren Brunak, Gunnar von Heijne.
Protein J, 2019 May 24; 38(3). PMID: 31119599    Free PMC article.
Review.
Reproduction study using public data of: Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs.
Mike Voets, Kajsa Møllersen, Lars Ailo Bongo.
PLoS One, 2019 Jun 07; 14(6). PMID: 31170223    Free PMC article.
Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays.
Rajiv Movva, Peyton Greenside, +3 authors, Anshul Kundaje.
PLoS One, 2019 Jun 18; 14(6). PMID: 31206543    Free PMC article.
Open collaborative writing with Manubot.
Daniel S Himmelstein, Vincent Rubinetti, +4 authors, Anthony Gitter.
PLoS Comput Biol, 2019 Jun 25; 15(6). PMID: 31233491    Free PMC article.
Machine and deep learning meet genome-scale metabolic modeling.
Guido Zampieri, Supreeta Vijayakumar, Elisabeth Yaneske, Claudio Angione.
PLoS Comput Biol, 2019 Jul 12; 15(7). PMID: 31295267    Free PMC article.
Review.
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework.
Jinyu Yang, Anjun Ma, +6 authors, Qin Ma.
Nucleic Acids Res, 2019 Aug 03; 47(15). PMID: 31372637    Free PMC article.
Designing combination therapies with modeling chaperoned machine learning.
Yin Zhang, Julie M Huynh, +4 authors, Tongli Zhang.
PLoS Comput Biol, 2019 Sep 10; 15(9). PMID: 31498788    Free PMC article.
DeepSynth: Three-dimensional nuclear segmentation of biological images using neural networks trained with synthetic data.
Kenneth W Dunn, Chichen Fu, +4 authors, Edward J Delp.
Sci Rep, 2019 Dec 05; 9(1). PMID: 31797882    Free PMC article.
Precision Psychiatry Applications with Pharmacogenomics: Artificial Intelligence and Machine Learning Approaches.
Eugene Lin, Chieh-Hsin Lin, Hsien-Yuan Lane.
Int J Mol Sci, 2020 Feb 07; 21(3). PMID: 32024055    Free PMC article.
Review.
Predicting or Pretending: Artificial Intelligence for Protein-Ligand Interactions Lack of Sufficiently Large and Unbiased Datasets.
Jincai Yang, Cheng Shen, Niu Huang.
Front Pharmacol, 2020 Mar 13; 11. PMID: 32161539    Free PMC article.
Classifying T cell activity in autofluorescence intensity images with convolutional neural networks.
Zijie J Wang, Alex J Walsh, Melissa C Skala, Anthony Gitter.
J Biophotonics, 2019 Oct 30; 13(3). PMID: 31661592    Free PMC article.
MethylNet: an automated and modular deep learning approach for DNA methylation analysis.
Joshua J Levy, Alexander J Titus, +3 authors, Brock C Christensen.
BMC Bioinformatics, 2020 Mar 19; 21(1). PMID: 32183722    Free PMC article.
The Roles of the NLRP3 Inflammasome in Neurodegenerative and Metabolic Diseases and in Relevant Advanced Therapeutic Interventions.
Rameez Hassan Pirzada, Nasir Javaid, Sangdun Choi.
Genes (Basel), 2020 Feb 06; 11(2). PMID: 32012695    Free PMC article.
Review.
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data.
Aaron M Smith, Jonathan R Walsh, +9 authors, Charles K Fisher.
BMC Bioinformatics, 2020 Mar 22; 21(1). PMID: 32197580    Free PMC article.
Prediction of the miRNA interactome - Established methods and upcoming perspectives.
Moritz Schäfer, Constance Ciaudo.
Comput Struct Biotechnol J, 2020 Mar 27; 18. PMID: 32211130    Free PMC article.
Review.
Technical and imaging factors influencing performance of deep learning systems for diabetic retinopathy.
Michelle Y T Yip, Gilbert Lim, +16 authors, Daniel S W Ting.
NPJ Digit Med, 2020 Mar 29; 3. PMID: 32219181    Free PMC article.
How Machine Learning Will Transform Biomedicine.
Jeremy Goecks, Vahid Jalili, Laura M Heiser, Joe W Gray.
Cell, 2020 Apr 04; 181(1). PMID: 32243801    Free PMC article.
Review.
Selene: a PyTorch-based deep learning library for sequence data.
Kathleen M Chen, Evan M Cofer, Jian Zhou, Olga G Troyanskaya.
Nat Methods, 2019 Mar 30; 16(4). PMID: 30923381    Free PMC article.
Tyrosine Kinase Inhibitors in Cancer: Breakthrough and Challenges of Targeted Therapy.
Charles Pottier, Margaux Fresnais, +3 authors, Nor Eddine Sounni.
Cancers (Basel), 2020 Apr 05; 12(3). PMID: 32244867    Free PMC article.
Review.
Emerging role of deep learning-based artificial intelligence in tumor pathology.
Yahui Jiang, Meng Yang, +2 authors, Yan Sun.
Cancer Commun (Lond), 2020 Apr 12; 40(4). PMID: 32277744    Free PMC article.
Review.
Brain Morphometry Estimation: From Hours to Seconds Using Deep Learning.
Michael Rebsamen, Yannick Suter, +2 authors, Christian Rummel.
Front Neurol, 2020 Apr 24; 11. PMID: 32322235    Free PMC article.
Molecular Generation for Desired Transcriptome Changes With Adversarial Autoencoders.
Rim Shayakhmetov, Maksim Kuznetsov, +4 authors, Daniil Polykovskiy.
Front Pharmacol, 2020 May 05; 11. PMID: 32362822    Free PMC article.
Discovering the hidden messages within cell trajectories using a deep learning approach for in vitro evaluation of cancer drug treatments.
A Mencattini, D Di Giuseppe, +8 authors, E Martinelli.
Sci Rep, 2020 May 08; 10(1). PMID: 32376840    Free PMC article.
Predicting cancer origins with a DNA methylation-based deep neural network model.
Chunlei Zheng, Rong Xu.
PLoS One, 2020 May 10; 15(5). PMID: 32384093    Free PMC article.
MOLI: multi-omics late integration with deep neural networks for drug response prediction.
Hossein Sharifi-Noghabi, Olga Zolotareva, Colin C Collins, Martin Ester.
Bioinformatics, 2019 Sep 13; 35(14). PMID: 31510700    Free PMC article.
Artificial intelligence in oncology.
Hideyuki Shimizu, Keiichi I Nakayama.
Cancer Sci, 2020 Mar 07; 111(5). PMID: 32133724    Free PMC article.
Review.
Specific histone modifications associate with alternative exon selection during mammalian development.
Qiwen Hu, Casey S Greene, Elizabeth A Heller.
Nucleic Acids Res, 2020 Apr 23; 48(9). PMID: 32319526    Free PMC article.
Automated abnormality classification of chest radiographs using deep convolutional neural networks.
Yu-Xing Tang, You-Bao Tang, +8 authors, Ronald M Summers.
NPJ Digit Med, 2020 May 22; 3. PMID: 32435698    Free PMC article.
Developing Real-world Evidence-Ready Datasets: Time for Clinician Engagement.
James M Snyder, Jacob A Pawloski, Laila M Poisson.
Curr Oncol Rep, 2020 Apr 17; 22(5). PMID: 32297007
Review.
Automated quantitative analysis of Ki-67 staining and HE images recognition and registration based on whole tissue sections in breast carcinoma.
Min Feng, Yang Deng, +10 authors, Hong Bu.
Diagn Pathol, 2020 May 31; 15(1). PMID: 32471471    Free PMC article.
Assistant diagnosis with Chinese electronic medical records based on CNN and BiLSTM with phrase-level and word-level attentions.
Tong Wang, Ping Xuan, Zonglin Liu, Tiangang Zhang.
BMC Bioinformatics, 2020 Jun 07; 21(1). PMID: 32503424    Free PMC article.
An image-based data-driven analysis of cellular architecture in a developing tissue.
Jonas Hartmann, Mie Wong, Elisa Gallo, Darren Gilmour.
Elife, 2020 Jun 06; 9. PMID: 32501214    Free PMC article.
HISTOBREAST, a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue.
Roxana M Buga, Tiberiu Totu, +4 authors, Stefan G Stanciu.
Sci Data, 2020 Jun 07; 7(1). PMID: 32503988    Free PMC article.
Drug Resistance Prediction Using Deep Learning Techniques on HIV-1 Sequence Data.
Margaret C Steiner, Keylie M Gibson, Keith A Crandall.
Viruses, 2020 May 23; 12(5). PMID: 32438586    Free PMC article.
Integrative computational epigenomics to build data-driven gene regulation hypotheses.
Tyrone Chen, Sonika Tyagi.
Gigascience, 2020 Jun 17; 9(6). PMID: 32543653    Free PMC article.
Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study.
Anupama Jha, Joseph K Aicher, +2 authors, Yoseph Barash.
Genome Biol, 2020 Jun 21; 21(1). PMID: 32560708    Free PMC article.
Putting deep learning in perspective for pest management scientists.
Robert D Clark.
Pest Manag Sci, 2020 Mar 17; 76(7). PMID: 32173969    Free PMC article.
Don't dismiss logistic regression: the case for sensible extraction of interactions in the era of machine learning.
Joshua J Levy, A James O'Malley.
BMC Med Res Methodol, 2020 Jul 01; 20(1). PMID: 32600277    Free PMC article.
An artificial neural network approach for predicting hypertension using NHANES data.
Fernando López-Martínez, Edward Rolando Núñez-Valdez, Rubén González Crespo, Vicente García-Díaz.
Sci Rep, 2020 Jul 02; 10(1). PMID: 32606434    Free PMC article.
Links between Nutrition, Infectious Diseases, and Microbiota: Emerging Technologies and Opportunities for Human-Focused Research.
Manuela Cassotta, Tamara Yuliett Forbes-Hernández, +4 authors, Maurizio Battino.
Nutrients, 2020 Jun 25; 12(6). PMID: 32575399    Free PMC article.
Review.
Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome.
Vuong Le, Thomas P Quinn, Truyen Tran, Svetha Venkatesh.
BMC Genomics, 2020 Jul 22; 21(Suppl 4). PMID: 32689932    Free PMC article.
Methodological Challenges of Deep Learning in Optical Coherence Tomography for Retinal Diseases: A Review.
Ryan T Yanagihara, Cecilia S Lee, Daniel Shu Wei Ting, Aaron Y Lee.
Transl Vis Sci Technol, 2020 Jul 25; 9(2). PMID: 32704417    Free PMC article.
Review.
Convolutional Neural Networks Can Predict Retinal Differentiation in Retinal Organoids.
Evgenii Kegeles, Anton Naumov, +2 authors, Petr Baranov.
Front Cell Neurosci, 2020 Jul 29; 14. PMID: 32719585    Free PMC article.
Artificial intelligence in digital breast pathology: Techniques and applications.
Asmaa Ibrahim, Paul Gamble, +4 authors, Emad A Rakha.
Breast, 2020 Jan 15; 49. PMID: 31935669    Free PMC article.
Review.
A refined cell-of-origin classifier with targeted NGS and artificial intelligence shows robust predictive value in DLBCL.
Zijun Y Xu-Monette, Hongwei Zhang, +25 authors, Ken H Young.
Blood Adv, 2020 Jul 30; 4(14). PMID: 32722783    Free PMC article.
Relevant Applications of Generative Adversarial Networks in Drug Design and Discovery: Molecular De Novo Design, Dimensionality Reduction, and De Novo Peptide and Protein Design.
Eugene Lin, Chieh-Hsin Lin, Hsien-Yuan Lane.
Molecules, 2020 Jul 28; 25(14). PMID: 32708785    Free PMC article.
Review.
Artificial Intelligence and Health Technology Assessment: Anticipating a New Level of Complexity.
Hassane Alami, Pascale Lehoux, +7 authors, Jean-Paul Fortin.
J Med Internet Res, 2020 May 15; 22(7). PMID: 32406850    Free PMC article.
Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data.
Nikolaus Fortelny, Christoph Bock.
Genome Biol, 2020 Aug 05; 21(1). PMID: 32746932    Free PMC article.
A hybrid unsupervised-Deep learning tandem for electrooculography time series analysis.
Ruxandra Stoean, Catalin Stoean, +5 authors, Gonzalo Joya.
PLoS One, 2020 Jul 22; 15(7). PMID: 32692779    Free PMC article.
A Review on the Challenges in Indian Genomics Research for Variant Identification and Interpretation.
Sandhya Kiran Pemmasani, Rasika Raman, +2 authors, Anuradha Acharya.
Front Genet, 2020 Aug 15; 11. PMID: 32793285    Free PMC article.
Review.
An annotated fluorescence image dataset for training nuclear segmentation methods.
Florian Kromp, Eva Bozsaky, +11 authors, Sabine Taschner-Mandl.
Sci Data, 2020 Aug 13; 7(1). PMID: 32782410    Free PMC article.
Investigation on the impacts of COVID-19 quarantine on society and environment: Preventive measures and supportive technologies.
Santhosh Kumar Kumaravel, Ranjith Kumar Subramani, +4 authors, Umashankar Subramaniam.
3 Biotech, 2020 Aug 22; 10(9). PMID: 32821645    Free PMC article.
Review.
Integrative Methods and Practical Challenges for Single-Cell Multi-omics.
Anjun Ma, Adam McDermaid, +2 authors, Qin Ma.
Trends Biotechnol, 2020 Aug 21; 38(9). PMID: 32818441    Free PMC article.
Review.
Futuristic CRISPR-based biosensing in the cloud and internet of things era: an overview.
Abdullahi Umar Ibrahim, Fadi Al-Turjman, Zubaida Sa'id, Mehmet Ozsoz.
Multimed Tools Appl, 2020 Aug 25;. PMID: 32837247    Free PMC article.
Towards Building a Plant Cell Atlas.
Seung Y Rhee, Kenneth D Birnbaum, David W Ehrhardt.
Trends Plant Sci, 2019 Feb 20; 24(4). PMID: 30777643    Free PMC article.
Review.
Deep learning and feature based medication classifications from EEG in a large clinical data set.
David O Nahmias, Eugene F Civillico, Kimberly L Kontson.
Sci Rep, 2020 Aug 28; 10(1). PMID: 32848165    Free PMC article.
Using Deep Learning with Convolutional Neural Network Approach to Identify the Invasion Depth of Endometrial Cancer in Myometrium Using MR Images: A Pilot Study.
Hsiang-Chun Dong, Hsiang-Kai Dong, +2 authors, Cheng-Chang Chang.
Int J Environ Res Public Health, 2020 Aug 23; 17(16). PMID: 32824765    Free PMC article.
Histopathological Classification of Breast Cancer Images Using a Multi-Scale Input and Multi-Feature Network.
Taimoor Shakeel Sheikh, Yonghee Lee, Migyung Cho.
Cancers (Basel), 2020 Jul 30; 12(8). PMID: 32722111    Free PMC article.
Predicting risk of late age-related macular degeneration using deep learning.
Yifan Peng, Tiarnan D Keenan, +5 authors, Zhiyong Lu.
NPJ Digit Med, 2020 Sep 10; 3. PMID: 32904246    Free PMC article.
Deep learning with noisy labels: Exploring techniques and remedies in medical image analysis.
Davood Karimi, Haoran Dou, Simon K Warfield, Ali Gholipour.
Med Image Anal, 2020 Jul 06; 65. PMID: 32623277    Free PMC article.
Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics.
Georgia Doing, Katja Koeppen, +2 authors, Deborah A Hogan.
PLoS Genet, 2020 Aug 20; 16(8). PMID: 32813693    Free PMC article.
Objective assessment of stored blood quality by deep learning.
Minh Doan, Joseph A Sebastian, +16 authors, Anne E Carpenter.
Proc Natl Acad Sci U S A, 2020 Aug 26; 117(35). PMID: 32839303    Free PMC article.
Breast cancer detection using deep convolutional neural networks and support vector machines.
Dina A Ragab, Maha Sharkas, Stephen Marshall, Jinchang Ren.
PeerJ, 2019 Feb 05; 7. PMID: 30713814    Free PMC article.
Artificial intelligence systems for complex decision-making in acute care medicine: a review.
Lawrence A Lynn.
Patient Saf Surg, 2019 Feb 09; 13. PMID: 30733829    Free PMC article.
Review.
Artificial intelligence for precision oncology: beyond patient stratification.
Francisco Azuaje.
NPJ Precis Oncol, 2019 Mar 02; 3. PMID: 30820462    Free PMC article.
Review.
Embedded deep learning in ophthalmology: making ophthalmic imaging smarter.
Petteri Teikari, Raymond P Najjar, Leopold Schmetterer, Dan Milea.
Ther Adv Ophthalmol, 2019 Mar 27; 11. PMID: 30911733    Free PMC article.
Review.
Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging.
Sigita Cinciute.
PeerJ, 2019 Apr 04; 7. PMID: 30941269    Free PMC article.
Recent Advances of Deep Learning in Bioinformatics and Computational Biology.
Binhua Tang, Zixiang Pan, Kang Yin, Asif Khateeb.
Front Genet, 2019 Apr 12; 10. PMID: 30972100    Free PMC article.
Review.
Introduction to Digital Image Analysis in Whole-slide Imaging: A White Paper from the Digital Pathology Association.
Famke Aeffner, Mark D Zarella, +11 authors, Douglas Bowman.
J Pathol Inform, 2019 Apr 16; 10. PMID: 30984469    Free PMC article.
Highly Cited. Review.
A roadmap for semi-automatically extracting predictive and clinically meaningful temporal features from medical data for predictive modeling.
Gang Luo.
Glob Transit, 2019 Apr 30; 1. PMID: 31032483    Free PMC article.
Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review.
Seyedmostafa Sheikhalishahi, Riccardo Miotto, +3 authors, Venet Osmani.
JMIR Med Inform, 2019 May 09; 7(2). PMID: 31066697    Free PMC article.
Review.
Deep Learning Methods for Predicting Disease Status Using Genomic Data.
Qianfan Wu, Adel Boueiz, +5 authors, Weiliang Qiu.
J Biom Biostat, 2018 Jan 01; 9(5). PMID: 31131151    Free PMC article.
With an eye to AI and autonomous diagnosis.
Pearse A Keane, Eric J Topol.
NPJ Digit Med, 2019 Jul 16; 1. PMID: 31304321    Free PMC article.
Physician perspectives on integration of artificial intelligence into diagnostic pathology.
Shihab Sarwar, Anglin Dent, +4 authors, Phedias Diamandis.
NPJ Digit Med, 2019 Jul 16; 2. PMID: 31304375    Free PMC article.
Machine Learning Approaches for the Estimation of Biological Aging: The Road Ahead for Population Studies.
Alessandro Gialluisi, Augusto Di Castelnuovo, +3 authors, Moli-sani Study Investigators.
Front Med (Lausanne), 2019 Jul 25; 6. PMID: 31338367    Free PMC article.
Convolutional Neural Networks for the Automatic Identification of Plant Diseases.
Justine Boulent, Samuel Foucher, Jérôme Théau, Pierre-Luc St-Charles.
Front Plant Sci, 2019 Aug 10; 10. PMID: 31396250    Free PMC article.
Review.
Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks.
Baiba Vilne, Irēna Meistere, Lelde Grantiņa-Ieviņa, Juris Ķibilds.
Front Microbiol, 2019 Aug 27; 10. PMID: 31447800    Free PMC article.
Review.
A machine-learning algorithm for neonatal seizure recognition: a multicentre, randomised, controlled trial.
Andreea M Pavel, Janet M Rennie, +17 authors, Geraldine B Boylan.
Lancet Child Adolesc Health, 2020 Aug 31; 4(10). PMID: 32861271    Free PMC article.
Clinical features of COVID-19 mortality: development and validation of a clinical prediction model.
Arjun S Yadaw, Yan-Chak Li, +3 authors, Gaurav Pandey.
Lancet Digit Health, 2020 Sep 29; 2(10). PMID: 32984797    Free PMC article.
Enhancing scientific discoveries in molecular biology with deep generative models.
Romain Lopez, Adam Gayoso, Nir Yosef.
Mol Syst Biol, 2020 Sep 26; 16(9). PMID: 32975352    Free PMC article.
Review.
A bird's-eye view of deep learning in bioimage analysis.
Erik Meijering.
Comput Struct Biotechnol J, 2020 Oct 01; 18. PMID: 32994890    Free PMC article.
Review.
Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist.
Beau Norgeot, Giorgio Quer, +10 authors, Atul J Butte.
Nat Med, 2020 Sep 11; 26(9). PMID: 32908275    Free PMC article.
Preparing next-generation scientists for biomedical big data: artificial intelligence approaches.
Jason H Moore, Mary Regina Boland, +9 authors, John H Holmes.
Per Med, 2019 Feb 15; 16(3). PMID: 30760118    Free PMC article.
Review.
Accelerated knowledge discovery from omics data by optimal experimental design.
Xiaokang Wang, Navneet Rai, +2 authors, Ilias Tagkopoulos.
Nat Commun, 2020 Oct 08; 11(1). PMID: 33024104    Free PMC article.
Sequence-to-function deep learning frameworks for engineered riboregulators.
Jacqueline A Valeri, Katherine M Collins, +4 authors, Diogo M Camacho.
Nat Commun, 2020 Oct 09; 11(1). PMID: 33028819    Free PMC article.
Codon optimization with deep learning to enhance protein expression.
Hongguang Fu, Yanbing Liang, +6 authors, Zhong Liu.
Sci Rep, 2020 Oct 21; 10(1). PMID: 33077783    Free PMC article.
Pattern recognition based on machine learning identifies oil adulteration and edible oil mixtures.
Kevin Lim, Kun Pan, Zhe Yu, Rong Hui Xiao.
Nat Commun, 2020 Oct 25; 11(1). PMID: 33097723    Free PMC article.
Analyzing Malaria Disease Using Effective Deep Learning Approach.
Krit Sriporn, Cheng-Fa Tsai, Chia-En Tsai, Paohsi Wang.
Diagnostics (Basel), 2020 Sep 30; 10(10). PMID: 32987888    Free PMC article.
Deep metabolome: Applications of deep learning in metabolomics.
Yotsawat Pomyen, Kwanjeera Wanichthanarak, +3 authors, Sakda Khoomrung.
Comput Struct Biotechnol J, 2020 Nov 03; 18. PMID: 33133423    Free PMC article.
Review.
Adversarial attacks on medical machine learning.
Samuel G Finlayson, John D Bowers, +3 authors, Isaac S Kohane.
Science, 2019 Mar 23; 363(6433). PMID: 30898923    Free PMC article.
Highly Cited.
Designing accurate emulators for scientific processes using calibration-driven deep models.
Jayaraman J Thiagarajan, Bindya Venkatesh, +4 authors, Brian Spears.
Nat Commun, 2020 Nov 08; 11(1). PMID: 33159053    Free PMC article.
Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation.
Michael Rebsamen, Christian Rummel, +2 authors, Richard McKinley.
Hum Brain Mapp, 2020 Aug 14; 41(17). PMID: 32786059    Free PMC article.
A Review of Integrative Imputation for Multi-Omics Datasets.
Meng Song, Jonathan Greenbaum, +6 authors, Hong-Wen Deng.
Front Genet, 2020 Nov 17; 11. PMID: 33193667    Free PMC article.
Review.
Neuromorphic on-chip recognition of saliva samples of COPD and healthy controls using memristive devices.
Pouya Soltani Zarrin, Finn Zahari, +3 authors, Christian Wenger.
Sci Rep, 2020 Nov 14; 10(1). PMID: 33184439    Free PMC article.
Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids.
Tobias Goris, Álvaro Pérez-Valero, +7 authors, Juan Nogales.
Microb Biotechnol, 2020 Oct 14; 14(1). PMID: 33047877    Free PMC article.
Review.
Automatic Grading of Individual Knee Osteoarthritis Features in Plain Radiographs Using Deep Convolutional Neural Networks.
Aleksei Tiulpin, Simo Saarakkala.
Diagnostics (Basel), 2020 Nov 14; 10(11). PMID: 33182830    Free PMC article.
Machine Learning Methods in Drug Discovery.
Lauv Patel, Tripti Shukla, +2 authors, Shanzhi Wang.
Molecules, 2020 Nov 18; 25(22). PMID: 33198233    Free PMC article.
Review.
Rethinking glottal midline detection.
Andreas M Kist, Julian Zilker, +2 authors, Michael Döllinger.
Sci Rep, 2020 Nov 28; 10(1). PMID: 33244031    Free PMC article.
Multi-omics integration in biomedical research - A metabolomics-centric review.
Maria A Wörheide, Jan Krumsiek, Gabi Kastenmüller, Matthias Arnold.
Anal Chim Acta, 2020 Nov 30; 1141. PMID: 33248648    Free PMC article.
Review.
PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data.
Jie Hao, Youngsoon Kim, Tae-Kyung Kim, Mingon Kang.
BMC Bioinformatics, 2018 Dec 19; 19(1). PMID: 30558539    Free PMC article.
An integrative approach for building personalized gene regulatory networks for precision medicine.
Monique G P van der Wijst, Dylan H de Vries, +2 authors, Lude Franke.
Genome Med, 2018 Dec 21; 10(1). PMID: 30567569    Free PMC article.
Review.
Application of machine learning in rheumatic disease research.
Ki-Jo Kim, Ilias Tagkopoulos.
Korean J Intern Med, 2019 Jan 09; 34(4). PMID: 30616329    Free PMC article.
Review.
Detecting Adverse Drug Events with Rapidly Trained Classification Models.
Alec B Chapman, Kelly S Peterson, +2 authors, Olga V Patterson.
Drug Saf, 2019 Jan 17; 42(1). PMID: 30649737    Free PMC article.
A deep learning method to more accurately recall known lysine acetylation sites.
Meiqi Wu, Yingxi Yang, Hui Wang, Yan Xu.
BMC Bioinformatics, 2019 Jan 25; 20(1). PMID: 30674277    Free PMC article.
16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses.
Stephen Woloszynek, Zhengqiao Zhao, Jian Chen, Gail L Rosen.
PLoS Comput Biol, 2019 Feb 27; 15(2). PMID: 30807567    Free PMC article.
Learning Contextual Hierarchical Structure of Medical Concepts with Poincairé Embeddings to Clarify Phenotypes.
Brett K Beaulieu-Jones, Isaac S Kohane, Andrew L Beam.
Pac Symp Biocomput, 2019 Mar 14; 24. PMID: 30864306    Free PMC article.
Systems biology intertwines with single cell and AI.
Yong Wang, Xiang-Sun Zhang, Luonan Chen.
BMC Bioinformatics, 2019 May 11; 20(Suppl 7). PMID: 31074375    Free PMC article.
Genomic data mining for functional annotation of human long noncoding RNAs.
Brian L Gudenas, Jun Wang, +3 authors, Liang-Jiang Wang.
J Zhejiang Univ Sci B, 2019 May 16; 20(6). PMID: 31090273    Free PMC article.
Review.
ProteinNet: a standardized data set for machine learning of protein structure.
Mohammed AlQuraishi.
BMC Bioinformatics, 2019 Jun 13; 20(1). PMID: 31185886    Free PMC article.
Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction.
Chinmay Belthangady, Loic A Royer.
Nat Methods, 2019 Jul 10; 16(12). PMID: 31285623
Review.
Region Extraction and Classification of Skin Cancer: A Heterogeneous framework of Deep CNN Features Fusion and Reduction.
Tanzila Saba, Muhammad Attique Khan, Amjad Rehman, Souad Larabi Marie-Sainte.
J Med Syst, 2019 Jul 22; 43(9). PMID: 31327058
HetEnc: a deep learning predictive model for multi-type biological dataset.
Leihong Wu, Xiangwen Liu, Joshua Xu.
BMC Genomics, 2019 Aug 10; 20(1). PMID: 31395005    Free PMC article.
Joint Banknote Recognition and Counterfeit Detection Using Explainable Artificial Intelligence.
Miseon Han, Jeongtae Kim.
Sensors (Basel), 2019 Aug 23; 19(16). PMID: 31430971    Free PMC article.
Identifying Methylation Pattern and Genes Associated with Breast Cancer Subtypes.
Lei Chen, Tao Zeng, +3 authors, Yu-Dong Cai.
Int J Mol Sci, 2019 Sep 05; 20(17). PMID: 31480430    Free PMC article.
Deep learning predicts short non-coding RNA functions from only raw sequence data.
Teresa Maria Rosaria Noviello, Francesco Ceccarelli, Michele Ceccarelli, Luigi Cerulo.
PLoS Comput Biol, 2020 Nov 12; 16(11). PMID: 33175836    Free PMC article.
The impact of different negative training data on regulatory sequence predictions.
Louisa-Marie Krützfeldt, Max Schubach, Martin Kircher.
PLoS One, 2020 Dec 02; 15(12). PMID: 33259518    Free PMC article.
Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives.
Tanvir Alam, Hamada R H Al-Absi, Sebastian Schmeier.
Noncoding RNA, 2020 Dec 04; 6(4). PMID: 33266128    Free PMC article.
Review.
Identifying Mouse Autoimmune Uveitis from Fundus Photographs Using Deep Learning.
Jian Sun, Xiaoqin Huang, +4 authors, Siamak Yousefi.
Transl Vis Sci Technol, 2020 Dec 10; 9(2). PMID: 33294300    Free PMC article.
Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells.
Brent M Kuenzi, Jisoo Park, +5 authors, Trey Ideker.
Cancer Cell, 2020 Oct 24; 38(5). PMID: 33096023    Free PMC article.
Identifying Ethical Considerations for Machine Learning Healthcare Applications.
Danton S Char, Michael D Abràmoff, Chris Feudtner.
Am J Bioeth, 2020 Oct 27; 20(11). PMID: 33103967    Free PMC article.
Methods for correcting inference based on outcomes predicted by machine learning.
Siruo Wang, Tyler H McCormick, Jeffrey T Leek.
Proc Natl Acad Sci U S A, 2020 Nov 20; 117(48). PMID: 33208538    Free PMC article.
Axes of a revolution: challenges and promises of big data in healthcare.
Smadar Shilo, Hagai Rossman, Eran Segal.
Nat Med, 2020 Jan 15; 26(1). PMID: 31932803
Review.
Machine learning-enabled multiplexed microfluidic sensors.
Sajjad Rahmani Dabbagh, Fazle Rabbi, +2 authors, Savas Tasoglu.
Biomicrofluidics, 2020 Dec 22; 14(6). PMID: 33343782    Free PMC article.
Review.
Augmented Realities, Artificial Intelligence, and Machine Learning: Clinical Implications and How Technology Is Shaping the Future of Medicine.
Gaby N Moawad, Jad Elkhalil, +3 authors, Ibrahim Alkatout.
J Clin Med, 2020 Dec 02; 9(12). PMID: 33255705    Free PMC article.
Review.
Learning to detect the onset of slow activity after a generalized tonic-clonic seizure.
Carroll Vance, Yejin Kim, +5 authors, Xiaoqian Jiang.
BMC Med Inform Decis Mak, 2020 Dec 29; 20(Suppl 12). PMID: 33357225    Free PMC article.
Deep Learning in Proteomics.
Bo Wen, Wen-Feng Zeng, +4 authors, Bing Zhang.
Proteomics, 2020 Sep 18; 20(21-22). PMID: 32939979    Free PMC article.
Review.
State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing.
Michal Krassowski, Vivek Das, Sangram K Sahu, Biswapriya B Misra.
Front Genet, 2020 Dec 29; 11. PMID: 33362867    Free PMC article.
Review.
Applications of machine learning methods in kidney disease: hope or hype?
Lili Chan, Akhil Vaid, Girish N Nadkarni.
Curr Opin Nephrol Hypertens, 2020 Apr 03; 29(3). PMID: 32235273    Free PMC article.
Review.
Application of deep learning in genomics.
Jianxiao Liu, Jiying Li, Hai Wang, Jianbing Yan.
Sci China Life Sci, 2020 Oct 15; 63(12). PMID: 33051704
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models.
Daniil Polykovskiy, Alexander Zhebrak, +13 authors, Alex Zhavoronkov.
Front Pharmacol, 2021 Jan 05; 11. PMID: 33390943    Free PMC article.
Teasing out Artificial Intelligence in Medicine: An Ethical Critique of Artificial Intelligence and Machine Learning in Medicine.
Mark Henderson Arnold.
J Bioeth Inq, 2021 Jan 09; 18(1). PMID: 33415596    Free PMC article.
Pneumonia Classification Using Deep Learning from Chest X-ray Images During COVID-19.
Abdullahi Umar Ibrahim, Mehmet Ozsoz, +2 authors, Polycarp Shizawaliyi Yakoi.
Cognit Comput, 2021 Jan 12;. PMID: 33425044    Free PMC article.
DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach.
Yash Khemchandani, Stephen O'Hagan, +4 authors, Douglas B Kell.
J Cheminform, 2021 Jan 13; 12(1). PMID: 33431037    Free PMC article.
Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach.
João Figueira Silva, João Rafael Almeida, Sérgio Matos.
JMIR Med Inform, 2020 Dec 30; 8(12). PMID: 33372893    Free PMC article.
Artificial intelligence and computational pathology.
Miao Cui, David Y Zhang.
Lab Invest, 2021 Jan 18; 101(4). PMID: 33454724    Free PMC article.
Review.
Multi-classifier-based identification of COVID-19 from chest computed tomography using generalizable and interpretable radiomics features.
Lu Wang, Brendan Kelly, +11 authors, Jiangdian Song.
Eur J Radiol, 2021 Jan 27; 136. PMID: 33497881    Free PMC article.
Single-cell cytometry via multiplexed fluorescence prediction by label-free reflectance microscopy.
Shiyi Cheng, Sipei Fu, +5 authors, Lei Tian.
Sci Adv, 2021 Feb 02; 7(3). PMID: 33523908    Free PMC article.
Translating research findings into clinical practice: a systematic and critical review of neuroimaging-based clinical tools for brain disorders.
C Scarpazza, M Ha, +4 authors, A Mechelli.
Transl Psychiatry, 2020 Apr 22; 10(1). PMID: 32313006    Free PMC article.
Review.
The physician-scientist, 75 years after Vannevar Bush-rethinking the 'bench' and 'bedside' dichotomy.
Gopal P Sarma, Allan Levey, Victor Faundez.
Nat Med, 2020 Apr 11; 26(4). PMID: 32273602
Unraveling the deep learning gearbox in optical coherence tomography image segmentation towards explainable artificial intelligence.
Peter M Maloca, Philipp L Müller, +12 authors, Nora Denk.
Commun Biol, 2021 Feb 07; 4(1). PMID: 33547415    Free PMC article.

;. PMID: 33597680
Artificial intelligence for good health: a scoping review of the ethics literature.
Kathleen Murphy, Erica Di Ruggiero, +6 authors, Jennifer Gibson.
BMC Med Ethics, 2021 Feb 17; 22(1). PMID: 33588803    Free PMC article.
Prevalence of low high-density lipoprotein among young adults receiving antiretroviral therapy in Zambia: An opportunity to consider non-communicable diseases in resource-limited settings.
Benson M Hamooya, Patrick Musonda, +8 authors, Douglas C Heimburger.
PLoS One, 2021 Feb 17; 16(2). PMID: 33592027    Free PMC article.
Rethinking drug design in the artificial intelligence era.
Petra Schneider, W Patrick Walters, +15 authors, Gisbert Schneider.
Nat Rev Drug Discov, 2019 Dec 06; 19(5). PMID: 31801986
Review.
Machine Learning to Predict Delayed Cerebral Ischemia and Outcomes in Subarachnoid Hemorrhage.
Jude P J Savarraj, Georgene W Hergenroeder, +7 authors, H Alex Choi.
Neurology, 2020 Nov 14; 96(4). PMID: 33184232    Free PMC article.
A deep learning algorithm using CT images to screen for Corona virus disease (COVID-19).
Shuai Wang, Bo Kang, +8 authors, Bo Xu.
Eur Radiol, 2021 Feb 26;. PMID: 33629156    Free PMC article.
TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations.
Qiao Liu, Lei Xie.
PLoS Comput Biol, 2021 Feb 13; 17(2). PMID: 33577560    Free PMC article.
SynTEG: a framework for temporal structured electronic health data simulation.
Ziqi Zhang, Chao Yan, +2 authors, Bradley A Malin.
J Am Med Inform Assoc, 2020 Dec 06; 28(3). PMID: 33277896    Free PMC article.
Deep learning-based high-throughput phenotyping can drive future discoveries in plant reproductive biology.
Cedar Warman, John E Fowler.
Plant Reprod, 2021 Mar 17; 34(2). PMID: 33725183    Free PMC article.
Artificial Intelligence Based Approaches to Identify Molecular Determinants of Exceptional Health and Life Span-An Interdisciplinary Workshop at the National Institute on Aging.
Jason H Moore, Nalini Raghavachari, Workshop Speakers.
Front Artif Intell, 2019 Aug 06; 2. PMID: 33733101    Free PMC article.
Review.
Biological network analysis with deep learning.
Giulia Muzio, Leslie O'Bray, Karsten Borgwardt.
Brief Bioinform, 2020 Nov 11; 22(2). PMID: 33169146    Free PMC article.
Human-interpretable image features derived from densely mapped cancer pathology slides predict diverse molecular phenotypes.
James A Diao, Jason K Wang, +19 authors, Amaro Taylor-Weiner.
Nat Commun, 2021 Mar 14; 12(1). PMID: 33712588    Free PMC article.
Complementary performances of convolutional and capsule neural networks on classifying microfluidic images of dividing yeast cells.
Mehran Ghafari, Justin Clark, +4 authors, Hong Qin.
PLoS One, 2021 Mar 18; 16(3). PMID: 33730031    Free PMC article.
Executable cancer models: successes and challenges.
Matthew A Clarke, Jasmin Fisher.
Nat Rev Cancer, 2020 Apr 29; 20(6). PMID: 32341552
Review.
Review of deep learning: concepts, CNN architectures, challenges, applications, future directions.
Laith Alzubaidi, Jinglan Zhang, +7 authors, Laith Farhan.
J Big Data, 2021 Apr 06; 8(1). PMID: 33816053    Free PMC article.
Genome annotation across species using deep convolutional neural networks.
Ghazaleh Khodabandelou, Etienne Routhier, Julien Mozziconacci.
PeerJ Comput Sci, 2021 Apr 06; 6. PMID: 33816929    Free PMC article.
Helixer: Cross-species gene annotation of large eukaryotic genomes using deep learning.
Felix Stiehler, Marvin Steinborn, +3 authors, Alisandra K Denton.
Bioinformatics, 2020 Dec 17;. PMID: 33325516    Free PMC article.
Artificial intelligence and leukocyte epigenomics: Evaluation and prediction of late-onset Alzheimer's disease.
Ray O Bahado-Singh, Sangeetha Vishweswaraiah, +11 authors, Uppala Radhakrishna.
PLoS One, 2021 Apr 01; 16(3). PMID: 33788842    Free PMC article.
Typing methods based on whole genome sequencing data.
Laura Uelze, Josephine Grützke, +5 authors, Burkhard Malorny.
One Health Outlook, 2020 Feb 18; 2. PMID: 33829127    Free PMC article.
Review.
A large-scale internal validation study of unsupervised virtual trichrome staining technologies on nonalcoholic steatohepatitis liver biopsies.
Joshua J Levy, Nasim Azizgolshani, +7 authors, Louis J Vaickus.
Mod Pathol, 2020 Dec 11; 34(4). PMID: 33299110    Free PMC article.
Artificial intelligence in cancer research: learning at different levels of data granularity.
Davide Cirillo, Iker Núñez-Carpintero, Alfonso Valencia.
Mol Oncol, 2021 Feb 04; 15(4). PMID: 33533192    Free PMC article.
Review.
Machine learning, the kidney, and genotype-phenotype analysis.
Rachel S G Sealfon, Laura H Mariani, Matthias Kretzler, Olga G Troyanskaya.
Kidney Int, 2020 May 04; 97(6). PMID: 32359808    Free PMC article.
Review.
Machine learning for patient risk stratification: standing on, or looking over, the shoulders of clinicians?
Brett K Beaulieu-Jones, William Yuan, +4 authors, Isaac S Kohane.
NPJ Digit Med, 2021 Apr 01; 4(1). PMID: 33785839    Free PMC article.
Automated detection and segmentation of thoracic lymph nodes from CT using 3D foveal fully convolutional neural networks.
Andra-Iza Iuga, Heike Carolus, +6 authors, Michael Püsken.
BMC Med Imaging, 2021 Apr 15; 21(1). PMID: 33849483    Free PMC article.
Action detection using a neural network elucidates the genetics of mouse grooming behavior.
Brian Q Geuther, Asaf Peer, +3 authors, Vivek Kumar.
Elife, 2021 Mar 18; 10. PMID: 33729153    Free PMC article.
Machine learning analysis to predict the need for ankle foot orthosis in patients with stroke.
Yoo Jin Choo, Jeoung Kun Kim, +2 authors, Donghwi Park.
Sci Rep, 2021 Apr 21; 11(1). PMID: 33875716    Free PMC article.
Opportunities and challenges for the computational interpretation of rare variation in clinically important genes.
Gregory McInnes, Andrew G Sharo, +11 authors, Russ B Altman.
Am J Hum Genet, 2021 Apr 03; 108(4). PMID: 33798442    Free PMC article.
Review.
Pretreatment MRI Radiomics Based Response Prediction Model in Locally Advanced Cervical Cancer.
Benedetta Gui, Rosa Autorino, +15 authors, Giovanni Scambia.
Diagnostics (Basel), 2021 Apr 04; 11(4). PMID: 33807494    Free PMC article.
G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data.
Simone Rampelli, Marco Fabbrini, +3 authors, Silvia Turroni.
Front Genet, 2021 Apr 27; 12. PMID: 33897763    Free PMC article.
Machine learning-based investigation of the cancer protein secretory pathway.
Rasool Saghaleyni, Azam Sheikh Muhammad, +2 authors, Jonathan L Robinson.
PLoS Comput Biol, 2021 Apr 06; 17(4). PMID: 33819271    Free PMC article.
Single-cell transcriptomics in cancer: computational challenges and opportunities.
Jean Fan, Kamil Slowikowski, Fan Zhang.
Exp Mol Med, 2020 Sep 16; 52(9). PMID: 32929226    Free PMC article.
Review.
Multi-Layer Picture of Neurodegenerative Diseases: Lessons from the Use of Big Data through Artificial Intelligence.
Andrea Termine, Carlo Fabrizio, +5 authors, Raffaella Cascella.
J Pers Med, 2021 May 01; 11(4). PMID: 33917161    Free PMC article.
Review.
The pursuit of mechanism of action: uncovering drug complexity in TB drug discovery.
Tianao Yuan, Joshua M Werman, Nicole S Sampson.
RSC Chem Biol, 2021 May 01; 2(2). PMID: 33928253    Free PMC article.
Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces.
Jiarui Ding, Aviv Regev.
Nat Commun, 2021 May 07; 12(1). PMID: 33953202    Free PMC article.
Text mining for modeling of protein complexes enhanced by machine learning.
Varsha D Badal, Petras J Kundrotas, Ilya A Vakser.
Bioinformatics, 2020 Sep 23; 37(4). PMID: 32960948    Free PMC article.
The Importance of Image Resolution in Building Deep Learning Models for Medical Imaging.
Paras Lakhani.
Radiol Artif Intell, 2020 Jan 22; 2(1). PMID: 33939779    Free PMC article.
Deep learning methods allow fully automated segmentation of metacarpal bones to quantify volumetric bone mineral density.
Lukas Folle, Timo Meinderink, +5 authors, Andreas Maier.
Sci Rep, 2021 May 08; 11(1). PMID: 33958664    Free PMC article.
CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies.
Matthew Waas, Jack Littrell, Rebekah L Gundry.
J Am Soc Mass Spectrom, 2020 Mar 28; 31(7). PMID: 32212654    Free PMC article.
Smart Video Surveillance System Based on Edge Computing.
Antonio Carlos Cob-Parro, Cristina Losada-Gutiérrez, +2 authors, Ignacio Bravo-Muñoz.
Sensors (Basel), 2021 May 01; 21(9). PMID: 33922548    Free PMC article.
Machine learning for sperm selection.
Jae Bem You, Christopher McCallum, +3 authors, David Sinton.
Nat Rev Urol, 2021 May 19;. PMID: 34002070
Review.
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator.
Adrian L Sanborn, Benjamin T Yeh, +5 authors, Roger D Kornberg.
Elife, 2021 Apr 28; 10. PMID: 33904398    Free PMC article.
Hybrid modelling for stroke care: Review and suggestions of new approaches for risk assessment and simulation of scenarios.
Tilda Herrgårdh, Vince I Madai, +5 authors, Gunnar Cedersund.
Neuroimage Clin, 2021 May 18; 31. PMID: 34000646    Free PMC article.
Review.
Dual-scale categorization based deep learning to evaluate programmed cell death ligand 1 expression in non-small cell lung cancer.
Xiangyun Wang, Peilin Chen, +5 authors, Qiang Fu.
Medicine (Baltimore), 2021 May 21; 100(20). PMID: 34011092    Free PMC article.
Predicting youth diabetes risk using NHANES data and machine learning.
Nita Vangeepuram, Bian Liu, +2 authors, Gaurav Pandey.
Sci Rep, 2021 May 29; 11(1). PMID: 34045491    Free PMC article.
Translational precision medicine: an industry perspective.
Dominik Hartl, Valeria de Luca, +11 authors, Adrian Roth.
J Transl Med, 2021 Jun 07; 19(1). PMID: 34090480    Free PMC article.
Review.