Papers to go through

A curated list of awesome deep learning applications in the field of computational biology

2012-07 | Deep architectures for protein contact map prediction | Pietro Di Lena, Ken Nagata and Pierre Baldi Bioinformatics

2012-10 | Predicting protein residue–residue contacts using deep networks and boosting | Jesse Eickholt and Jianlin Cheng | Bioinformatics

2013-03 | DNdisorder: predicting protein disorder using boosting and deep networks | Jesse Eickholt and Jianlin Cheng | BMC Bioinformatics

2014-06 | Deep learning of the tissue-regulated splicing code | Michael K. K. Leung, Hui Yuan Xiong, Leo J. Lee and Brendan J. Frey | Bioinformatics

2014-10 | DANN: a deep learning approach for annotating the pathogenicity of genetic variants | Daniel Quang, Yifei Chen and Xiaohui Xie | Bioinformatics

2014-11 | Pairwise input neural network for target-ligand interaction prediction | Caihua Wang, Juan Liu, Fei Luo, Yafang Tan, Zixin Deng, Qian-Nan Hu | 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2015-01 | Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. | Jie Tan, Matt Ung, Chao Cheng, Casey Greene | Pacific Symposium on Biocomputing (PSB) | Models & Data

2015-01 | The human splicing code reveals new insights into the genetic determinants of disease | Hui Y. Xiong, Babak Alipanahi, Leo J. Lee, Hannes Bretschneider, Daniele Merico, Ryan K. C. Yuen, Yimin Hua, Serge Gueroussov, Hamed S. Najafabadi, Timothy R. Hughes, Quaid Morris, Yoseph Barash, Adrian R. Krainer, Nebojsa Jojic, Stephen W. Scherer, Benjamin J. Blencowe, Brendan J. Frey | Science

2015-03 | Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters | Yifeng Li, Chih-Yu Chen, and Wyeth W. Wasserman | 19th Annual International Conference, RECOMB 2015, Warsaw, Proceedings

2015-05 | Trans-species learning of cellular signaling systems with bimodal deep belief networks | Lujia Chen, Chunhui Cai, Vicky Chen and Xinghua Lu | Bioinformatics

2015-05 | Deep convolutional neural networks for annotating gene expression patterns in the mouse brain | Tao Zeng, Rongjian Li, Ravi Mukkamala, Jieping Ye and Shuiwang Ji | BMC Bioinformatics

2015-07 | DeepBind: Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning | Babak Alipanahi,	Andrew Delong,	Matthew T. Weirauch & Brendan J. Frey | Nature Biotechnology

2015-08 | Deep learning for regulatory genomics | Yongjin Park & Manolis Kellis | Nature Biotechnology

2015-08 | DeepSEA: Predicting effects of noncoding variants with deep learning–based sequence model | Jian Zhou & Olga G. Troyanskaya | Nature Methods: Short intro & Nature Methods

2015-08 | Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach | Muxuan Liang, Zhizhong Li, Ting Chen, Jianyang Zeng | IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

2015-10 | A deep learning framework for modeling structural features of RNA-binding protein targets | Sai Zhang, Jingtian Zhou, Hailin Hu, Haipeng Gong, Ligong Chen, Chao Cheng, and Jianyang Zeng | NAR

2015-10 | Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks | David R. Kelley, Jasper Snoek, John Rinn | Biorxiv | code

2015-10 | Deep Learning for Drug-Induced Liver Injury | Youjun Xu, Ziwei Dai, Fangjin Chen, Shuaishi Gao, Jianfeng Pei, and Luhua Lai | ASC Journal of Chemical Information and Modeling

2016-01 | Convolutional neural network architectures for predicting DNA–protein binding | * Haoyang Zeng, Matthew D. Edwards, Ge Liu, David K. Gifford* | Bioinformatics | code

2016-01 | ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions | mSystems | code

2015-11 | De novo identification of replication-timing domains in the human genome by deep learning | Feng Liu, Chao Ren, Hao Li, Pingkun Zhou, Xiaochen Bo and Wenjie Shu | Bioinformatics

2015-11 | Recurrent Neural Network Based Hybrid Model of Gene Regulatory Network | Khalid Raza, Mansaf Alam | Arxiv

2015-11 | Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics | Ehsaneddin Asgari, Mohammad R. K. Mofrad | PloS one

2016-01 | Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model | Lujia Chen, Chunhui Cai, Vicky Chen and Xinghua Lu | BMC Bioinformatics

2016-01 | PEDLA: predicting enhancers with a deep learning-based algorithmic framework | Feng Liu, Hao Li, Chao Ren, Xiaochen Bo, Wenjie Shu | Biorxiv

2016-01 | TensorFlow: Biology’s Gateway to Deep Learning? | Ladislav Rampasek, Anna Goldenberg | Cell Systems

2016-01 | ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions | mSystems | code

2016-01 | Deep Learning in Drug Discovery | Erik Gawehn, Jan A. Hiss and Gisbert Schneider | Molecular Informatics

2016-02 | Gene expression inference with deep learning | Yifei Chen, Yi Li, Rajiv Narayan, Aravind Subramanian, Xiaohui Xie | Bioinformatics

2016-02 | Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification | Brett Beaulieu-Jones, Casey Greene | bioRxiv

2016-03 | Genome-Wide Prediction of cis-Regulatory Regions Using Supervised Deep Learning Methods | Yifeng Li, Wenqiang Shi, Wyeth W Wasserman | Biorxiv

2016-03 | Applications of deep learning in biomedicine | Polina Mamoshina, Armando Vieira, Evgeny Putin, and Alex Zhavoronkov | ACS Molecular Pharmaceutics

2016-03 | Deep Learning in Bioinformatics | Seonwoo Min, Byunghan Lee, Sungroh Yoon | Arxiv

2016-03 | DeepNano: Deep Recurrent Neural Networks for Base Calling in MinION Nanopore Reads | Vladimír Boža, Broňa Brejová, Tomáš Vinař | Arxiv | code

2016-03 | deepTarget: End-to-end Learning Framework for microRNA Target Prediction using Deep Recurrent Neural Networks | Byunghan Lee, Junghwan Baek, Seunghyun Park, Sungroh Yoon | Arxiv

2016-03 | Deep Learning in Label-free Cell Classification | Claire Lifan Chen, Ata Mahjoubfar, Li-Chia Tai, Ian K. Blaby, Allen Huang, Kayvan Reza Niazi & Bahram Jalali | Nature Scientific Reports

2016-04 | Accurate classification of protein subcellular localization from high throughput microscopy images using deep learning | Tanel Pärnamaa, Leopold Parts | bioRxiv

2016-04 | DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences | Daniel Quang & Xiaohui Xie | Nucleic Acids Research | code

2016-04 | deepMiRGene: Deep Neural Network based Precursor microRNA Prediction | Seunghyun Park, Seonwoo Min, Hyun-soo Choi, and Sungroh Yoon | Arxiv

2016-04 | Microscopy cell counting and detection with fully convolutional regression networks | Weidi Xie, J. Alison Noble and Andrew Zisserman | Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization

2016-04 | Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks | Zhen Li and Yizhou Yu | Arxiv

2016-05 | Denoising genome-wide histone ChIP-seq with convolutional neural networks | Pang Wei Koh, Emma Pierson, Anshul Kundaje | Biorxiv

2016-05 | Deep Motif: Visualizing Genomic Sequence Classifications | Jack Lanchantin, Ritambhara Singh, Zeming Lin, Yanjun Qi | Arxiv

2016-05 | Not Just a Black Box: Learning Important Features Through Propagating Activation Differences | Avanti Shrikumar, Peyton Greenside, Anna Shcherbina, Anshul Kundaje | Arxiv

2016-05 | Deep biomarkers of human aging: Application of deep neural networks to biomarker development | Evgeny Putin, Polina Mamoshina, Alexander Aliper, Mikhail Korzinkin, Alexey Moskalev, Alexey Kolosov, Alexander Ostrovskiy, Charles Cantor, Jan Vijg, and Alex Zhavoronkov | Aging

2016-05 | Deep learning applications for predicting pharmacological properties of drugs and drug repurposing using transcriptomic data | Alexander Aliper, Sergey Plis, Artem Artemov, Alvaro Ulloa, Polina Mamoshina, and Alex Zhavoronkov | ACS Molecular Pharmaceutics

2016-05 | Accurate prediction of single-cell DNA methylation states using deep learning | Christof Angermueller, Heather Lee, Wolf Reik, Oliver Stegle | Biorxiv

2016-05 | Deep Machine Learning provides state-of-the-art performance in image-based plant phenotyping | Michael P. Pound, Alexandra J. Burgess, Michael H. Wilson, Jonathan A. Atkinson, Marcus Griffiths, Aaron S. Jackson, Adrian Bulat, Yorgos Tzimiropoulos, Darren M. Wells, Erik H. Murchie, Tony P. Pridmore, Andrew P. French | Biorxiv

2016-05 | Genetic Architect: Discovering Genomic Structure with Learned Neural Architectures | Laura Deming, Sasha Targ, Nate Sauder, Diogo Almeida, Chun Jimmie Ye | Arxiv

2016-05 | DeepCyTOF: Automated Cell Classification of Mass Cytometry Data by Deep Learning and Domain Adaptation | Huamin Li, Uri Shaham, Yi Yao, Ruth Montgomery, Yuval Kluger | Biorxiv

2016-06 | Classifying and segmenting microscopy images with deep multiple instance learning | Oren Z. Kraus, Jimmy Lei Ba and Brendan J. Frey | Bioinformatics

2016-06 | Convolutional neural network architectures for predicting DNA–protein binding | Haoyang Zeng, Matthew D. Edwards, Ge Liu and David K. Gifford | Bioinformatics

2016-06 | DeepLNC, a long non-coding RNA prediction tool using deep neural network | Rashmi Tripathi, Sunil Patel, Vandana Kumari, Pavan Chakraborty, Pritish Kumar Varadwaj | Network Modeling Analysis in Health Informatics and Bioinformatics

2016-06 | Virtual Screening: A Challenge for Deep Learning | Javier Pérez-Sianes, Horacio Pérez-Sánchez, Fernando Díaz | 10th International Conference on Practical Applications of Computational Biology & Bioinformatics

2016-07 | DeepChrome: Deep-learning for predicting gene expression from histone modifications | Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi | Arxiv

2016-07 | Deep learning for computational biology | Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle | Molecular Systems Biology

2016-08 | Deep Artificial Neural Networks and Neuromorphic Chips for Big Data Analysis: Pharmaceutical and Bioinformatics Applications | Lucas Antón Pastur-Romay, Francisco Cedrón, Alejandro Pazos and Ana Belén Porto-Pazos | International Journal of Molecular Sciences

2016-08 | Deep GDashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks | Jack Lanchantin, Ritambhara Singh, Beilun Wang, Yanjun Qi | Arxiv

2016-08 | Modeling translation elongation dynamics by deep learning reveals new insights into the landscape of ribosome stalling | Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He and Jianyang Zeng | bioRxiv

2016-08 | DeepWAS: Directly integrating regulatory information into GWAS using deep learning supports master regulator MEF2C as risk factor for major depressive disorder | Gökcen Eraslan, Janine Arloth, Jade Martins, Stella Iurato, Darina Czamara, Elisabeth B. Binder, Fabian J. Theis, Nikola S. Mueller | bioRxiv

2016-09 | The Next Era: Deep Learning in Pharmaceutical Research | Sean Ekins | Pharmaceutical Research

2016-09 | Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model | Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu | Arxiv

2016-10 | Automatic chemical design using a data-driven continuous representation of molecules | Rafael Gómez-Bombarelli, David Duvenaud, José Miguel Hernández-Lobato, Jorge Aguilera-Iparraguirre, Timothy D. Hirzel, Ryan P. Adams, Alán Aspuru-Guzik | Arxiv

2016-10 | FIDDLE: An integrative deep learning framework for functional genomic data inference | Umut Eser, L. Stirling Churchman | bioRxiv

2016-10 | Deep Learning for Imaging Flow Cytometry: Cell Cycle Analysis of Jurkat Cells | Philipp Eulenberg, Niklas Koehler, Thomas Blasi, Andrew Filby, Anne E. Carpenter, Paul Rees, Fabian J. Theis, F. Alexander Wolf | bioRxiv

2016-10 | Leveraging uncertainty information from deep neural networks for disease detection | Christian Leibig, Vaneeda Allken, Philipp Berens, Siegfried Wahl | bioRxiv

2016-11 | Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks | Shashank Singh, Yang Yang, Barnabas Poczos, Jian Ma | bioRxiv

2016-11 | RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach | Xiaoyong Pan, Hong-Bin Shen | bioRxiv

2016-11 | Low Data Drug Discovery with One-shot Learning | Han Altae-Tran, Bharath Ramsundar, Aneesh S. Pappu, Vijay Pande | Arxiv

2016-11 | Diet Networks: Thin Parameters for Fat Genomic | Adriana Romero, Pierre Luc Carrier, Akram Erraqabi, Tristan Sylvain, Alex Auvolat, Etienne Dejoie, Marc-André Legault, Marie-Pierre Dubé, Julie G. Hussin, Yoshua Bengio | Arxiv

2016-11 | DeeperBind: Enhancing Prediction of Sequence Specificities of DNA Binding Proteins | Hamid Reza Hassanzadeh, May D. Wang | Arxiv

2016-11 | Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model | Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu | bioRxiv

2016-11 | Deep learning with feature embedding for compound-protein interaction prediction | Fangping Wan, Jianyang Zeng | bioRxiv

2016-12 | Creating a universal SNP and small indel variant caller with deep neural networks | Ryan Poplin, Dan Newburger, Jojo Dijamco, Nam Nguyen, Dion Loy, Sam S. Gross, Cory Y. McLean, Mark A. DePristo | bioRxiv

2016-12 | DeepCancer: Detecting Cancer through Gene Expressions via Deep Generative Learning | Rajendra Rana Bhat, Vivek Viswanath, Xiaolin Li | Arxiv

2016-12 | Cox-nnet: an artificial neural network Cox regression for prognosis prediction | Travers Ching, Xun Zhu, Lana Garmire | bioRxiv

2016-12 | Deep learning is effective for the classification of OCT images of normal versus Age-related Macular Degeneration | Cecilia S Lee, Doug M Baughman, Aaron Y Lee | bioRxiv

2016-12 | Partitioned learning of deep Boltzmann machines for SNP data | Moritz Hess, Stefan Lenz, Tamara Blaette, Lars Bullinger, Harald Binder | bioRxiv

2016-12 | DeepAD: Alzheimer′s Disease Classification via Deep Convolutional Neural Networks using MRI and fMRI | Saman Sarraf, John Anderson, Ghassem Tofighi, for the Alzheimer's Disease Neuroimaging Initiativ | bioRxiv

2016-12 | Training Genotype Callers with Neural Networks | Rémi Torracinta, Fabien Campagne | bioRxiv

2016-12 | EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm | Seong Gon Kim, Mrudul Harwani, Ananth Grama, Somali Chaterji | Nature Scientific Reports

2016-12 | EnhancerPred: a predictor for discovering enhancers based on the combination and selection of multiple features | Cangzhi Jia, Wenying He | Nature Scientific Reports

2016-12 | DeepEnhancer: Predicting enhancers by convolutional neural networks | Min, Xu, Ning Chen, Ting Chen, and Rui Jiang | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | DeepSplice: Deep classification of novel splice junctions revealed by RNA-seq | Zhang, Yi, Xinan Liu, James N. MacLeod, and Jinze Liu | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy | Li, Rongjian, Dong Si, Tao Zeng, Shuiwang Ji, and Jing He | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Towards recognition of protein function based on its structure using deep convolutional networks | Tavanaei, Amirhossein, Anthony S. Maida, Arun Kaniymattam, and Rasiah Loganantharaj | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Emotion recognition from multi-channel EEG data through Convolutional Recurrent Neural Network | Li, Xiang, Dawei Song, Peng Zhang, Guangliang Yu, Yuexian Hou, and Bin Hu | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Coarse-to-Fine Stacked Fully Convolutional Nets for lymph node segmentation in ultrasound images | Zhang, Yizhe, Michael TC Ying, Lin Yang, Anil T. Ahuja, and Danny Z. Chen | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | CNNsite: Prediction of DNA-binding residues in proteins using Convolutional Neural Network with sequence features | Zhou, Jiyun, Qin Lu, Ruifeng Xu, Lin Gui, and Hongpeng Wang | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | A predictive model of gene expression using a deep learning framework | Xie, Rui, Andrew Quitadamo, Jianlin Cheng, and Xinghua Shi | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Deep convolutional neural network for survival analysis with pathological images | Zhu, Xinliang, Jiawen Yao, and Junzhou Huang | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Dependency-based convolutional neural network for drug-drug interaction extraction | Liu, Shengyu, Kai Chen, Qingcai Chen, and Buzhou Tang | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Pervasive EEG diagnosis of depression using Deep Belief Network with three-electrodes EEG collector | Cai, Hanshu, Xiaocong Sha, Xue Han, Shixin Wei, and Bin Hu | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Cardiac left ventricular volumes prediction method based on atlas location and deep learning | Luo, Gongning, Suyu Dong, Kuanquan Wang, and Henggui Zhang | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | A high-precision shallow Convolutional Neural Network based strategy for the detection of Genomic Deletions | Wang, Jing, Cheng Ling, and Jingyang Gao | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2016-12 | Predicting the impact of non-coding variants on DNA methylation | Zeng, Haoyang, and David K. Gifford | bioRxiv

2016-12 | The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology | Kadurin, Artur, Alexander Aliper, Andrey Kazennov, Polina Mamoshina, Quentin Vanhaelen, Kuzma Khrabrov, and Alex Zhavoronkov | Oncotarget

2016-12 | Medical Image Synthesis with Context-Aware Generative Adversarial Networks | Dong Nie, Roger Trullo, Caroline Petitjean, Su Ruan, Dinggang Shen | Arxiv

2017-01 | A Deep Learning Approach for Cancer Detection and Relevant Gene Identification | Wang, Jing, Cheng Ling, and Jingyang Gao | Pacific Symposium on Biocomputing 2017

2017-01 | Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks | Lanchantin, Jack, Ritambhara Singh, Beilun Wang, and Yanjun Qi | Pacific Symposium on Biocomputing 2017

2017-01 | HLA class I binding prediction via convolutional neural networks | Yeeleng Scott Vang, Xiaohui Xie | bioRxiv

2017-01 | DeadNet: Identifying Phototoxicity from Label-free Microscopy Images of Cells using Deep ConvNets | David Richmond, Anna Payne-Tobin Jost, Talley Lambert, Jennifer Waters, Hunter Elliott | arXiv

2017-01 | Dermatologist-level classification of skin cancer with deep neural networks | Andre Esteva, Brett Kuprel, Roberto A. Novoa, Justin Ko, Susan M. Swetter, Helen M. Blau & Sebastian Thrun | Nature

2016-07 | Deep Learning in Bioinformatics | Seonwoo Min, Byunghan Lee, Sungroh Yoon | Briefings in Bioinformatics

2016-07 | Deep learning for computational biology | Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle | Molecular systems biology

2016-08 | DeepChrome: deep-learning for predicting gene expression from histone modifications | Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi | Bioinformatics

2017-01 | Understanding sequence conservation with deep learning | Yi Li, Daniel Quang, Xiaohui Xie | Biorxiv

2017-01 | Learning the Structural Vocabulary of a Network | Saket Navlakha | Neural Computation

2017-01 | Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms | Sierra S. Nishizaki, Alan P. Boyle | Trends in Genetics