Computational Mathematics, Science & Engineering · Michigan State University
Hou Lab
AI and machine learning for biomolecular structure, omics, and health
Publications
57Publications
24h-index
22h-index since 2019
The complete and continuously updated list of published work is available in NCBI My Bibliography and on Google Scholar. Selected publications are grouped by topic below (most recent first); Dr. Hou's name is highlighted.
Protein/RNA Structure, Contact & Function Prediction
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2024Exploring the efficiency of deep graph neural networks for RNA secondary structure predictionInternational Conference on Intelligent Biology and Medicine (ICIBM 2024), oral presentation; recommended for journal submission
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2023Protein Structure Refinement via DeepTracer and AlphaFold2Briefings in Bioinformatics (bioRxiv 2023.08.16.553616)
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2023Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM mapsBriefings in Bioinformatics 24(2):bbac632
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2023AnglesRefine: refinement of 3D protein structures using Transformer based on torsion anglesbioRxiv 2023-07; presented at ACM SIGKDD BioKDD 2023
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2022Artificial intelligence advances for de novo molecular structure modeling in cryo-electron microscopyWIREs Computational Molecular Science 12(2):e1542
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2022Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14Proteins 90(1):58–72
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2021Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14Scientific Reports 11:1–12
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2021Improving deep learning-based protein distance prediction in CASP14Bioinformatics 37(19):3190–3196
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2021Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challengeNature Methods 18(2):156–164
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2021DeepDist: real-value inter-residue distance prediction with deep residual convolutional networkBMC Bioinformatics 22:1–17
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2021DISTEVAL: A web server for evaluating predicted protein distancesBMC Bioinformatics 22:1–9
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2021DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networksBMC Bioinformatics 22:1–18
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2021DNSS2: improved ab initio protein secondary structure prediction using advanced deep learning architecturesProteins 89(2):207–217
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2020SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering dataProteins 88(6):775–787. PMID 31860156
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2020Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density MapsScientific Reports 10:4282. PMID 32152330
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2020Analysis of several key factors influencing deep learning-based inter-residue contact predictionBioinformatics 36(4):1091–1098. PMID 31504181
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2019The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screensGenome Biology 20:244. PMID 31744546
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2019Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experimentProteins 87(12):1200–1221. PMID 31612567
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2019Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13Proteins 87(12):1165–1178. PMID 30985027
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2018An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12Scientific Reports 8:9939. PMID 29967418
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2018DNCON2: improved protein contact prediction using two-level deep convolutional neural networksBioinformatics 34(9):1466–1472. PMID 29228185
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2018DeepSF: deep convolutional neural network for mapping protein sequences to foldsBioinformatics 34(8):1295–1303. PMID 29228193
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2018Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learningProteins 86(S1):84–96. PMID 29047157
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2017Deep learning methods for protein torsion angle predictionBMC Bioinformatics 18:417. PMID 28923002
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2016ConEVA: a toolbox for comprehensive assessment of protein contactsBMC Bioinformatics 17:517. PMID 27923350
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2015Improving Protein Fold Recognition by Deep Learning NetworksScientific Reports 5:17573. PMID 26634993
Protein Structure Quality Assessment
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2023ComplexQA: A deep graph learning approach for protein complex structure assessmentBriefings in Bioinformatics 24(6):bbad287
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2022Deep graph learning to estimate protein model quality using structural constraints from multiple sequence alignmentsProceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), 1–10
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2022ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural featuresBriefings in Bioinformatics 23(1):bbab384
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2019
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2017QAcon: single model quality assessment using protein structural and contact information with machine learning techniquesBioinformatics 33(4):586–588. PMID 28035027
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2016DeepQA: improving the estimation of single protein model quality with deep belief networksBMC Bioinformatics 17:495. PMID 27919220
Omics Data Analysis
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2023A novel f-divergence based generative adversarial imputation method for scRNA-seq data analysisPLOS ONE 18(11):e0292792
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2023Genomic imbalance modulates transposable element expression in maizePlant Communications 4(2)
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2022Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maizeNature Communications 13:3014
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2022Effect of aneuploidy of a non-essential chromosome on gene expression in maizeThe Plant Journal 110(1):193–211
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2021Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolutionProceedings of the National Academy of Sciences 118(23):e2104254118
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2021Genomic imbalance determines positive and negative modulation of gene expression in diploid maizeThe Plant Cell 33(4):917–939
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2021Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maizeThe Plant Cell 33(4):901–916
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2020Bioinformatics methods for mass spectrometry-based proteomics data analysisInternational Journal of Molecular Sciences 21(8):2873
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2020GNET2: An R package for constructing gene regulatory networks from transcriptomic dataBioinformatics
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2020The renoprotective effects of soy protein in the aging kidneyMedical Research Archives 8(3)
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2020Heme oxygenase promotes B-Raf-dependent melanosphere formationPigment Cell & Melanoma Research. PMID 32558263
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2020Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalanceJournal of Genetics and Genomics 47(2):93–103. PMID 32178980
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2020The Gene Balance Hypothesis: Epigenetics and Dosage Effects in PlantsMethods in Molecular Biology 2093:161–171. PMID 32088896
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2019PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effectsBioinformatics 35(5):787–797. PMID 30753300
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2019From Analysis of Ischemic Mouse Brain Proteome to Identification of Human Serum Clusterin as a Potential Biomarker for Severity of Acute Ischemic StrokeTranslational Stroke Research 10(5):546–556. PMID 30465328
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2018Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxaProceedings of the National Academy of Sciences 115(48):E11321–E11330. PMID 30429332
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2017Genetic dissection of Arabidopsis MAP kinase phosphatase 1-dependent PAMP-induced transcriptional responsesJournal of Experimental Botany 68(18):5207–5220. PMID 29045691
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2016Effects of aged garlic extract and FruArg on gene expression and signaling pathways in lipopolysaccharide-activated microglial cellsScientific Reports 6:35323. PMID 27734935
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2016An overview of bioinformatics methods for modeling biological pathways in yeastBriefings in Functional Genomics 15(2):95–108. PMID 26476430
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2015Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methodsEURASIP Journal on Bioinformatics and Systems Biology 2015:5. PMID 28194174
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2015From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics DataPLOS ONE 10(4):e0125000. PMID 25902288
Education, Health Analytics, Privacy-preserving ML & Community
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2025Teaching Coding in the Age of AI: A Hands-on Tutorial on Process FeedbackProceedings of the 56th ACM Technical Symposium on Computer Science Education (SIGCSE TS), V.2
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2025Improving Warfarin Therapy Safety with Accurate International Normalized Ratio (INR) Prediction Algorithms33rd Congress of the International Society on Thrombosis and Haemostasis (ISTH 2025), poster presentation
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2023A Stealthy Inference Attack on Split Learning with a Split-Fuse Defensive Measure2023 IEEE Conference on Communications and Network Security (CNS), 1–9
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202322nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023)Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 5897–5898