On the public citation graph

A deep learning approach to pattern recognition for short DNA sequences

https://doi.org/10.1101/353474
0 signed · 112 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/prot.10508openalex-snapshot
Gaps in structurally similar proteins: Towards improvement of multiple sequence alignment
inferredcites →https://doi.org/10.1016/j.mimet.2007.02.005openalex-snapshot
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1017/cbo9780511790492openalex-snapshot
Biological Sequence Analysis
inferredcites →https://doi.org/10.1038/nature11209openalex-snapshot
A framework for human microbiome research
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nbt.3300openalex-snapshot
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
inferredcites →https://doi.org/10.1038/nbt1004-1315openalex-snapshot
What is a hidden Markov model?
inferredcites →https://doi.org/10.1038/nmeth.1358openalex-snapshot
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
inferredcites →https://doi.org/10.1038/nmeth.2066openalex-snapshot
Metagenomic microbial community profiling using unique clade-specific marker genes
inferredcites →https://doi.org/10.1038/nmeth.3547openalex-snapshot
Predicting effects of noncoding variants with deep learning–based sequence model
inferredcites →https://doi.org/10.1038/nmeth.4458openalex-snapshot
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/s41591-018-0316-zopenalex-snapshot
A guide to deep learning in healthcare
inferredcites →https://doi.org/10.1038/s41598-018-29334-5openalex-snapshot
Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
inferredcites →https://doi.org/10.1073/pnas.74.11.5088openalex-snapshot
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
inferredcites →https://doi.org/10.1073/pnas.75.10.4801openalex-snapshot
Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli.
inferredcites →https://doi.org/10.1080/10635150802032982openalex-snapshot
Inferring Species Membership Using DNA Sequences with Back-Propagation Neural Networks
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btu745openalex-snapshot
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods
inferredcites →https://doi.org/10.1093/nar/27.23.4636openalex-snapshot
Improved microbial gene identification with GLIMMER
inferredcites →https://doi.org/10.1093/nar/gki038openalex-snapshot
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
inferredcites →https://doi.org/10.1093/nar/gkq967openalex-snapshot
The European Nucleotide Archive
inferredcites →https://doi.org/10.1093/nar/gkr1178openalex-snapshot
The NCBI Taxonomy database
inferredcites →https://doi.org/10.1093/nar/gku1341openalex-snapshot
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
inferredcites →https://doi.org/10.1098/rsif.2017.0387openalex-snapshot
Opportunities and obstacles for deep learning in biology and medicine
inferredcites →https://doi.org/10.1109/cvpr.2013.163openalex-snapshot
Rotation, Scaling and Deformation Invariant Scattering for Texture Discrimination
inferredcites →https://doi.org/10.1126/science.1171700openalex-snapshot
Topographical and Temporal Diversity of the Human Skin Microbiome
inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/aem.49.6.1379-1384.1985openalex-snapshot
Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences
inferredcites →https://doi.org/10.1145/3097983.3098043openalex-snapshot
Google Vizier
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-16-s11-s2openalex-snapshot
VisRseq: R-based visual framework for analysis of sequencing data
inferredcites →https://doi.org/10.1186/1471-2105-16-s6-s2openalex-snapshot
Probabilistic topic modeling for the analysis and classification of genomic sequences
inferredcites →https://doi.org/10.1186/1471-2164-12-s2-s4openalex-snapshot
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
inferredcites →https://doi.org/10.1186/gb-2011-12-s1-p11openalex-snapshot
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12859-016-0976-yopenalex-snapshot
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
inferredcites →https://doi.org/10.1186/s12864-015-2194-9openalex-snapshot
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
inferredcites →https://doi.org/10.1371/journal.pcbi.1004957openalex-snapshot
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pone.0094249openalex-snapshot
Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys
inferredcites →https://doi.org/10.2174/138920209789177575openalex-snapshot
Hidden Markov Models and their Applications in Biological Sequence Analysis
inferredcites →https://doi.org/10.3390/genes8110326openalex-snapshot
Taxonomic Classification for Living Organisms Using Convolutional Neural Networks
inferredcites →https://doi.org/10.48550/arxiv.1505.00853openalex-snapshot
Empirical Evaluation of Rectified Activations in Convolutional Network
inferredcites →https://doi.org/10.48550/arxiv.1603.04467openalex-snapshot
TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems
inferredcites →https://doi.org/10.48550/arxiv.1704.04861openalex-snapshot
MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications
inferredcites →https://doi.org/10.48550/arxiv.1706.03059openalex-snapshot
Depthwise Separable Convolutions for Neural Machine Translation
inferredcites →https://doi.org/10.7717/peerj.1603openalex-snapshot
PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/edn3.232openalex-snapshot
Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
inferred← citeshttps://doi.org/10.1007/978-1-0716-1103-6_9openalex-snapshot
Deep Learning Applied on Next Generation Sequencing Data Analysis
inferred← citeshttps://doi.org/10.1007/978-3-030-34139-8_33openalex-snapshot
Applications of Machine Learning Tools in Genomics: A Review
inferred← citeshttps://doi.org/10.1007/978-3-030-57821-3_25openalex-snapshot
Deep Ensemble Models for 16S Ribosomal Gene Classification
inferred← citeshttps://doi.org/10.1007/978-3-030-82469-3_11openalex-snapshot
Searching Pattern in DNA Sequence Using ECC-Diffie-Hellman Exchange Based Hash Function: An Efficient Approach
inferred← citeshttps://doi.org/10.1007/978-3-030-87240-3_57openalex-snapshot
MG-NET: Leveraging Pseudo-imaging for Multi-modal Metagenome Analysis
inferred← citeshttps://doi.org/10.1007/978-3-031-96852-5_6openalex-snapshot
Making It Work
inferred← citeshttps://doi.org/10.1007/978-981-15-2449-3_17openalex-snapshot
Deep Recurrent Neural Network (Deep-RNN) for Classification of Nonlinear Data
inferred← citeshttps://doi.org/10.1007/s12275-021-0632-8openalex-snapshot
Application of computational approaches to analyze metagenomic data
inferred← citeshttps://doi.org/10.1007/s12275-021-0698-3openalex-snapshot
Omics-based microbiome analysis in microbial ecology: from sequences to information
inferred← citeshttps://doi.org/10.1016/b978-0-443-26765-9.00010-xopenalex-snapshot
Case studies and use cases of deep learning for biomedical applications
inferred← citeshttps://doi.org/10.1016/b978-0-443-33633-1.00016-2openalex-snapshot
AI models and metagenomics in crop breeding: Advancing soil and plant microbiome analysis through machine learning and deep learning approaches
inferred← citeshttps://doi.org/10.1016/j.bspc.2021.102539openalex-snapshot
Taxonomic classification of metagenomic sequences from Relative Abundance Index profiles using deep learning
inferred← citeshttps://doi.org/10.1016/j.drudis.2020.10.002openalex-snapshot
Deep learning in next-generation sequencing
inferred← citeshttps://doi.org/10.1016/j.eswa.2022.117972openalex-snapshot
BERT contextual embeddings for taxonomic classification of bacterial DNA sequences
inferred← citeshttps://doi.org/10.1016/j.imu.2020.100318openalex-snapshot
DeepDBP: Deep neural networks for identification of DNA-binding proteins
inferred← citeshttps://doi.org/10.1016/j.istruc.2022.09.107openalex-snapshot
A computationally efficient crack detection approach based on deep learning assisted by stockwell transform and linear discriminant analysis
inferred← citeshttps://doi.org/10.1016/j.procs.2025.04.187openalex-snapshot
Enhancing Nucleotide Pattern Recognition: A Hybrid Encoding Approach with Bi-LSTM and GRU
inferred← citeshttps://doi.org/10.1016/j.ymeth.2020.05.018openalex-snapshot
CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning
inferred← citeshttps://doi.org/10.1038/s41467-021-22206-zopenalex-snapshot
Variable number tandem repeats mediate the expression of proximal genes
inferred← citeshttps://doi.org/10.1038/s41598-021-02703-3openalex-snapshot
ACP-MHCNN: an accurate multi-headed deep-convolutional neural network to predict anticancer peptides
inferred← citeshttps://doi.org/10.1038/s41598-022-13412-wopenalex-snapshot
Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem
inferred← citeshttps://doi.org/10.1038/s41598-025-09846-7openalex-snapshot
Creating interpretable deep learning models to identify species using environmental DNA sequences
inferred← citeshttps://doi.org/10.1073/pnas.2122636119openalex-snapshot
Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks
inferred← citeshttps://doi.org/10.1093/bioadv/vbag166openalex-snapshot
DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification
inferred← citeshttps://doi.org/10.1093/nargab/lqaa009openalex-snapshot
DeepMicrobes: taxonomic classification for metagenomics with deep learning
inferred← citeshttps://doi.org/10.1099/mgen.0.001231openalex-snapshot
Deep learning methods in metagenomics: a review
inferred← citeshttps://doi.org/10.1101/2025.01.27.634943openalex-snapshot
Phylo-HS: A phylogenetic hierarchical softmax for taxonomic classification
inferred← citeshttps://doi.org/10.1101/537795openalex-snapshot
GeNet: Deep Representations for Metagenomics
inferred← citeshttps://doi.org/10.1109/i-smac52330.2021.9640852openalex-snapshot
A Novel Detection Approach of Ground Level Ozone using Machine Learning Classifiers
inferred← citeshttps://doi.org/10.1109/icdmw53433.2021.00067openalex-snapshot
Metagenome2Vec: Building Contextualized Representations for Scalable Metagenome Analysis
inferred← citeshttps://doi.org/10.1109/iceeict62016.2024.10534520openalex-snapshot
A Study to Classify Virus Genome Through Analyzing DNA Sequences Using Transformer Model
inferred← citeshttps://doi.org/10.1109/icicat62666.2024.10922903openalex-snapshot
Prediction of Transposon Insertion Sites in the Human Genome Using Deep Learning Techniques
inferred← citeshttps://doi.org/10.1109/jbhi.2024.3358842openalex-snapshot
TEPI: Taxonomy-Aware Embedding and Pseudo-Imaging for Scarcely-Labeled Zero-Shot Genome Classification
inferred← citeshttps://doi.org/10.1109/synasc51798.2020.00036openalex-snapshot
Machine Learning based models for examining differences between modern and ancient DNA in dental calculus
inferred← citeshttps://doi.org/10.1111/1755-0998.14006openalex-snapshot
MycoAI : Fast and accurate taxonomic classification for fungal ITS sequences
inferred← citeshttps://doi.org/10.1155/2021/1835056openalex-snapshot
Analysis of DNA Sequence Classification Using CNN and Hybrid Models
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009345openalex-snapshot
Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network
inferred← citeshttps://doi.org/10.14569/ijacsa.2020.0111065openalex-snapshot
Very Deep Neural Networks for Extracting MITE Families Features and Classifying them based on DNA Scalograms
inferred← citeshttps://doi.org/10.1515/jisys-2023-0041openalex-snapshot
A deep neural network model for paternity testing based on 15-loci STR for Iraqi families
inferred← citeshttps://doi.org/10.21608/ajbas.2020.34160.1023openalex-snapshot
Machine and Deep Learning Approaches in Genome: Review Article
inferred← citeshttps://doi.org/10.2174/9789815079005123050011openalex-snapshot
Deep Learning Techniques for Biomedical Research and Significant Gene Identification using Next Generation Sequencing (NGS) Data: - A Review
inferred← citeshttps://doi.org/10.2174/9789815313321125010007openalex-snapshot
Data-Driven Approach of Species DNA Sequencing Based on Similar Patterns Using Machine Learning
inferred← citeshttps://doi.org/10.23860/thesis-cres-cecile-2020openalex-snapshot
TAXONOMIC PROFILING OF METAGENOMIC READS USING DEEP LEARNING
inferred← citeshttps://doi.org/10.3389/fimmu.2021.661437openalex-snapshot
Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression
inferred← citeshttps://doi.org/10.3389/fmicb.2021.644487openalex-snapshot
Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences
inferred← citeshttps://doi.org/10.3389/fmicb.2024.1516667openalex-snapshot
Deep learning in microbiome analysis: a comprehensive review of neural network models
inferred← citeshttps://doi.org/10.3390/biom13040585openalex-snapshot
DL-TODA: A Deep Learning Tool for Omics Data Analysis
inferred← citeshttps://doi.org/10.3390/biomedicines11051323openalex-snapshot
Classification of Highly Divergent Viruses from DNA/RNA Sequence Using Transformer-Based Models
inferred← citeshttps://doi.org/10.3390/geomatics5010004openalex-snapshot
Examining Deep Learning Pixel-Based Classification Algorithms for Mapping Weed Canopy Cover in Wheat Production Using Drone Data
inferred← citeshttps://doi.org/10.48550/arxiv.1909.13146openalex-snapshot
META$^\mathbf{2}$: Memory-efficient taxonomic classification and abundance estimation for metagenomics with deep learning
inferred← citeshttps://doi.org/10.48550/arxiv.2007.14062openalex-snapshot
Big Bird: Transformers for Longer Sequences
inferred← citeshttps://doi.org/10.48550/arxiv.2011.00485openalex-snapshot
Comparing Machine Learning Algorithms with or without Feature Extraction for DNA Classification
inferred← citeshttps://doi.org/10.53555/kuey.v30i4.1551openalex-snapshot
Pattern Matching Of DNA Sequence Using FRCT Algorithm
inferred← citeshttps://doi.org/10.54097/yay6zs23openalex-snapshot
A Novel Feature Fusion Method Based on RSCU and K-mer to Classify the SARS-Cov-2
inferred← citeshttps://doi.org/10.57709/18808634openalex-snapshot
Biomedical Data Classification with Improvised Deep Learning Architectures
inferred← citeshttps://doi.org/10.5772/intechopen.114972openalex-snapshot
Integrating MLSecOps in the Biotechnology Industry 5.0
inferred← citeshttps://doi.org/10.70675/9b8f6b3czd015z48afzb458z22d7510f2953openalex-snapshot
Conception de séquences génomiques artificielles chez la levure par apprentissage profond
inferred← citeshttps://doi.org/10.70675/bc11fdd1z0c3az45c3z9f9ez65301994b39dopenalex-snapshot
Continuous embeddings for large-scale machine learning with DNA sequences
inferred← citeshttps://doi.org/10.7287/peerj.13613v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Genomics enters the deep learning era (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.13613v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Genomics enters the deep learning era (v0.1)"
inferred← citeshttps://doi.org/10.7717/peerj.13613openalex-snapshot
Genomics enters the deep learning era
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.