Research about Deep Learning Application in Biology Published in bioRxiv

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Deep learning is a set of machine learning algorithms that attempt to model high-level abstractions in input data using multiple non-linear transformations. Some of the major advances in deep learning have been made in speech recognition , computer vision, and natural language processing. Considering that data volume is growing exponentially, deep learning is becoming increasingly important in the predictive analysis of big data (Li et. al, 2016). I have tried to collect and curate some publications form bioRxiv that related to the deep learning application in biology, and the results were listed here. Please enjoy it!

Last updated: May 17, 2020
Source : bioRxiv

No. Year Title URL
1 2020 Polishing Copy Number Variant Calls on Exome Sequencing Data via Deep Learning View
2 2020 JavaDL: a Java-based Deep Learning Tool to Predict Drug Responses View
3 2020 Leverging Deep Learning to Simulate Coronavirus Spike proteins has the potential to predict future Zoonotic sequences View
4 2020 Deep Learning Improves Macromolecules Localization and Identification in 3D Cellular Cryo-Electron Tomograms View
5 2020 Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model View
6 2020 Interpretable Deep Learning for De Novo Design of Cell-Penetrating Abiotic Polymers View
7 2020 On the Relation of Gene Essentiality to Intron Structure: A Computational and Deep Learning Approach View
8 2020 DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning View
9 2020 Deep Learning Enable Untargeted Metabolite Extraction from High Throughput Coverage Data-Independent Acquisition View
10 2020 Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning View
11 2020 Phenotype Prediction using a Tensor Representation and Deep Learning from Data Independent Acquisition Mass Spectrometry View
12 2020 Predicting Endometrial Cancer Subtypes and Molecular Features from Histopathology Images Using Multi-resolution Deep Learning Models View
13 2020 Predicting and Visualizing STK11 Mutation in Lung Adenocarcinoma Histopathology Slides Using Deep Learning View
14 2019 Deep Docking - a Deep Learning Approach for Virtual Screening of Big Chemical Datasets View
15 2019 A Deep Learning approach predicts the impact of point mutations in intronic flanking regions on micro-exon splicing definition View
16 2019 DeepSleep: Fast and Accurate Delineation of Sleep Arousals at Millisecond Resolution by Deep Learning View
17 2019 DeepSide: A Deep Learning Framework for Drug Side Effect Prediction View
18 2019 UPCLASS: a Deep Learning-based Classifier for UniProtKB Entry Publications View
19 2019 Modeling Abiotic Niches of Crops and Wild Ancestors Using Deep Learning: A Generalized Approach View
20 2019 Linnaeus: Interpretable Deep Learning Classification of Single Cell Transcript Data View
21 2019 Image-based Cell Phenotyping Using Deep Learning View
22 2019 DAVI:Deep Learning Based Tool for Alignment and Single Nucleotide Variant identification View
23 2019 Detection and Classification of Cardiac Arrhythmias by a Challenge-Best Deep Learning Neural Network Model View
24 2019 DeepCLIP: Predicting the effect of mutations on protein-RNA binding with Deep Learning View
25 2019 NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded Cells View
26 2019 DeepMF: Deciphering the Latent Patterns in Omics Profiles with a Deep Learning Method View
27 2019 Deep Learning-Based Point-Scanning Super-Resolution Imaging View
28 2019 Intercostal Space Prediction Using Deep Learning In Fully Endoscopic Mitral Valve Surgery View
29 2019 RootNav 2 View
30 2019 DeepPrime2Sec: Deep Learning for Protein Secondary Structure Prediction from the Primary Sequences View
31 2019 Janggu: Deep Learning for Genomics View
32 2019 MethylNet: A Modular Deep Learning Approach to Methylation Prediction View
33 2019 A Simple Deep Learning Approach for Detecting Duplications and Deletions in Next-Generation Sequencing Data View
34 2019 CRISPRpred(SEQ): a sequence based tool for sgRNA on target activity prediction [(almost) beating Deep Learning pipelines by View
35 2019 An Accurate Bioinformatics Tool For Anti-Cancer Peptide Generation Through Deep Learning Omics View
36 2019 Feasibility of Automated Deep Learning Design for Medical Image Classification by Healthcare Professionals with Limited Coding Experience View
37 2019 Detecting Novel Sequence Signals in Targeting Peptides Using Deep Learning View
38 2019 Deep Learning Approach to Identifying Breast Cancer Subtypes Using High-Dimensional Genomic Data View
39 2019 Using Deep Learning to Annotate the Protein Universe View
40 2019 Modeling the Language of Life - Deep Learning Protein Sequences View
41 2019 Deep Learning with Multimodal Representation for Pancancer Prognosis Prediction View
42 2019 Deep Learning on Chaos Game Representation for Proteins View
43 2019 Viral host prediction with Deep Learning View
44 2019 Deep Learning of Representations for Transcriptomics-based Phenotype Prediction View
45 2019 Recognition Genes Which Are Relative With Cancer By Deep Learning Algorithm View
46 2019 MuStARD: Deep Learning for intra- and inter-species scanning of functional genomic patterns View
47 2019 E2M: A Deep Learning Framework for Associating Combinatorial Methylation Patterns with Gene Expression View
48 2018 A Deep Learning Genome-Mining Strategy Improves Biosynthetic Gene Cluster Prediction View
49 2018 Predicting Methylation from Sequence and Gene Expression Using Deep Learning with Attention View
50 2018 DeepCapTail: A Deep Learning Framework to Predict Capsid and Tail Proteins of Phage Genomes View
51 2018 Distance-based Protein Folding Powered by Deep Learning View
52 2018 Root Anatomy based on Root Cross-Section Image Analysis with Deep Learning View
53 2018 Systematic Prediction of Regulatory Motifs from Human ChIP-Sequencing Data Based on a Deep Learning Framework View
54 2018 Tensorflow Based Deep Learning Model and Snakemake Workflow for Peptide-Protein Binding Predictions View
55 2018 Taxonomic Classification of Ants (Formicidae) from Images using Deep Learning View
56 2018 Robust Automated Assessment of Human Blastocyst Quality using Deep Learning View
57 2018 rawMSA: Proper Deep Learning makes protein sequence profiles and feature extraction obsolete View
58 2018 Skin Lesion Classification Via Combining Deep Learning Features and Clinical Criteria Representations View
59 2018 Lesion Attributes Segmentation for Melanoma Detection with Deep Learning View
60 2018 On the Depth of Deep Learning Models for Splice Site Identification View
61 2018 Deep Learning Based Tumor Type Classification Using GeneExpression Data View
62 2018 Taking a Dive: Experiments in Deep Learning for Automatic Ontology-based Annotation of Scientific Literature View
63 2018 DeepAffinity: Interpretable Deep Learning of Compound Protein Affinity through Unified Recurrent and Convolutional Neural Networks View
64 2018 Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images View
65 2018 A Deep Learning Approach for Learning Intrinsic Protein-RNA Binding Preferences View
66 2018 Deep Learning meets Topology-preserving Active Contours: towards scalable quantitative histology of cortical cytoarchitecture View
67 2018 Forecasting Future Humphrey Visual Fields Using Deep Learning View
68 2018 Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections View
69 2018 Deep Learning Predicts Tuberculosis Drug Resistance Status from Whole-Genome Sequencing Data View
70 2018 Enhancer Identification using Transfer and Adversarial Deep Learning of DNA Sequences View
71 2018 COSSMO: Predicting Competitive Alternative Splice Site Selection using Deep Learning View
72 2018 DeepNeuron: An Open Deep Learning Toolbox for Neuron Tracing View
73 2018 Link Prediction through Deep Learning View
74 2018 Deep Learning Based Proarrhythmia Analysis Using Field Potentials Recorded from Human Pluripotent Stem Cells Derived Cardiomyocytes View
75 2018 Breast Cancer Histopathological Image Classification: A Deep Learning Approach View
76 2017 DeepGS: Predicting phenotypes from genotypes using Deep Learning View
77 2017 Edge Detection of Cryptic Lamellipodia Assisted by Deep Learning View
78 2017 Mapping Patient Trajectories using Longitudinal Extraction and Deep Learning in the View
79 2017 A Deep Learning Model for Predicting Tumor Suppressor Genes and Oncogenes from PDB Structure View
80 2017 Beyond Homology Transfer: Deep Learning for Automated Annotation of Proteins View
81 2017 Separable Fully Connected Layers Improve Deep Learning Models For Genomics View
82 2017 Opportunities And Obstacles For Deep Learning In Biology And Medicine View
83 2017 Generalising Better: Applying Deep Learning To Integrate Deleteriousness Prediction Scores View
84 2017 Deep Learning based multi-omics integration robustly predicts survival in liver cancer View
85 2016 Adaptive Somatic Mutations Calls with Deep Learning and Semi-Simulated Data View
86 2016 Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model View
87 2016 Deep Learning and Association Rule Mining for Predicting Drug Response in Cancer View
88 2016 Deep Learning-based Pipeline to Recognize Alzheimer’s Disease using fMRI Data View