Jie Hou

发表

Improving Protein Fold Recognition by Deep Learning Networks

Taeho Jo, Jianlin Cheng, Jesse Eickholt, 2015, Scientific Reports.

An overview of bioinformatics methods for modeling biological pathways in yeast.

Jianlin Cheng, Lipi Acharya, Lipi R. Acharya, 2016, Briefings in functional genomics.

DeepDist: real-value inter-residue distance prediction with deep residual convolutional network

Jianlin Cheng, Jie Hou, Tianqi Wu, 2020, bioRxiv.

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

Jianlin Cheng, J. Tanner, Jie Hou, 2020, International journal of molecular sciences.

Interpretable attention model in transcription factor binding site prediction with deep neural networks

Chen Chen, Jianlin Cheng, Hua Yang, 2019, bioRxiv.

Synthqa - Hierarchical Machine Learning-Based Protein Quality Assessment

Renzhi Cao, Jie Hou, Dong Si, 2021, bioRxiv.

Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network

Jianlin Cheng, Jie Hou, Tianqi Wu, 2021, BMC Bioinform..

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

RNA Sequence Analysis Reveals Expected and Novel Immuno-Modulatory Activities by Sutherlandia frutescens

Jianlin Cheng, D. Lubahn, W. Folk, 2018 .

Estimation of model accuracy in CASP13

Arne Elofsson, Karolis Uziela, Björn Wallner, 2019, Proteins.

Heme oxygenase promotes B‐Raf‐dependent melanosphere formation

Jianlin Cheng, Jie Hou, M. Hannink, 2020, Pigment cell & melanoma research.

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data

Chad E. Niederhuth, Jianlin Cheng, D. Lubahn, 2015, PloS one.

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Jianlin Cheng, Jie Hou, Tianqi Wu, 2021, bioRxiv.

Effect of aneuploidy of a non‐essential chromosome on gene expression in maize

J. Birchler, Jianlin Cheng, Jie Hou, 2022, The Plant journal : for cell and molecular biology.

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

Jianlin Cheng, J. Birchler, Jie Hou, 2020, BMC Bioinform..

Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance.

Jianlin Cheng, J. Birchler, Jie Hou, 2020, Journal of genetics and genomics = Yi chuan xue bao.

Deep graph learning to estimate protein model quality using structural constraints from multiple sequence alignments

Renzhi Cao, Jie Hou, Mahdi Rahbar, 2022, BCB.

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

Jianlin Cheng, J. Birchler, Jie Hou, 2020, BMC Bioinformatics.

The MULTICOM Protein Structure Prediction Server Empowered by Deep Learning and Contact Distance Prediction.

Jianlin Cheng, Jie Hou, Tianqi Wu, 2020, Methods in molecular biology.

SAXSDom: Modeling multi-domain protein structures using small-angle X-ray scattering data

Badri Adhikari, Jie Hou, Jianlin Cheng, 2019, bioRxiv.

From Analysis of Ischemic Mouse Brain Proteome to Identification of Human Serum Clusterin as a Potential Biomarker for Severity of Acute Ischemic Stroke

Jiankun Cui, Jianlin Cheng, Jilong Li, 2018, Translational Stroke Research.

Genomic imbalance determines positive and negative modulation of gene expression in diploid maize

Jianlin Cheng, J. Birchler, Jie Hou, 2021, The Plant cell.

Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize

Jianlin Cheng, J. Birchler, Jie Hou, 2021, The Plant cell.

Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa

Jianlin Cheng, J. Birchler, M. Matzke, 2018, Proceedings of the National Academy of Sciences.

Improving deep learning-based protein distance prediction in CASP14

Jianlin Cheng, Tianqi Wu, Zhiye Guo, 2021, bioRxiv.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

DeepDist: real-value inter-residue distance prediction with deep residual convolutional network

Jianlin Cheng, Jie Hou, Tianqi Wu, 2021, BMC Bioinformatics.

DNCON2: improved protein contact prediction using two-level deep convolutional neural networks

Jie Hou, Badri Adhikari, Jianlin Cheng, 2017, bioRxiv.

DeepSF: deep convolutional neural network for mapping protein sequences to folds

Jie Hou, Badri Adhikari, Jianlin Cheng, 2017, Bioinform..

Analysis of several key factors influencing deep learning-based inter-residue contact prediction

Jie Hou, Badri Adhikari, Jianlin Cheng, 2019, Bioinform..

DNSS2: improved ab initio protein secondary structure prediction using advanced deep learning architectures

Jianlin Cheng, Jie Hou, Zhiye Guo, 2019, bioRxiv.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Christopher J. Williams, Soon Wen Hoh, Colin M. Palmer, 2021, Nature Methods.

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

Genki Terashi, Daisuke Kihara, Grigore D. Pintilie, 2020, bioRxiv.

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Elodie Laine, Alessandra Carbone, Adam Liwo, 2019, Proteins.

Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution

Jing Zhang, Jianlin Cheng, F. Han, 2021, Proceedings of the National Academy of Sciences.

The Gene Balance Hypothesis: Epigenetics and Dosage Effects in Plants.

Jianlin Cheng, R. Veitia, J. Birchler, 2020, Methods in molecular biology.

Effects of aged garlic extract and FruArg on gene expression and signaling pathways in lipopolysaccharide-activated microglial cells

Jiankun Cui, Jianlin Cheng, D. Lubahn, 2016, Scientific Reports.

Genetic dissection of Arabidopsis MAP kinase phosphatase 1-dependent PAMP-induced transcriptional responses

Jianlin Cheng, Jie Hou, S. Peck, 2017, Journal of experimental botany.

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data

Lin Sun, Yuan Lu, Jie Hou, 2015, BCB.

DeepQA: improving the estimation of single protein model quality with deep belief networks

Jie Hou, Renzhi Cao, Debswapna Bhattacharya, 2016, BMC Bioinformatics.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features

H. Ding, Renzhi Cao, Jie Hou, 2021, Briefings Bioinform..

Recent Progress of Machine Learning in Gene Therapy.

H. Ding, Renzhi Cao, Jie Hou, 2021, Current gene therapy.

QAcon: single model quality assessment using protein structural and contact information with machine learning techniques

Miao Sun, Jie Hou, Renzhi Cao, 2016, Bioinform..

Performance Evaluation of Viral Infection Diagnosis using T-Cell Receptor Sequence and Artificial Intelligence

Jie Hou, Tim Kosfeld, Jonathan McMillan, 2020, BCB.

Artificial intelligence advances for de novo molecular structure modeling in cryo‐electron microscopy pdf

Dong Si, Renzhi Cao, Kyle Hippe, 2021, WIREs Computational Molecular Science.

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps

Dong Si, Renzhi Cao, Jianlin Cheng, 2019, bioRxiv.

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

Jianlin Cheng, J. Birchler, Jie Hou, 2022, Nature Communications.

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

Jianlin Cheng, Jie Hou, Tianqi Wu, 2021, Scientific Reports.

Deep Ranking in Template-free Protein Structure Prediction

Nasrin Akhter, Amarda Shehu, Jianlin Cheng, 2020, BCB.

Deep learning methods for protein torsion angle prediction

Jie Hou, Badri Adhikari, Jianlin Cheng, 2017, BMC Bioinformatics.

Deep convolutional neural networks for predicting the quality of single protein structural models

Renzhi Cao, Jianlin Cheng, Jie Hou, 2019, bioRxiv.

Protein Structure Refinement via DeepTracer and AlphaFold2

Fengbin Wang, Renzhi Cao, Jie Hou, 2023, bioRxiv.

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

Jianlin Cheng, J. Birchler, Jie Hou, 2021, BMC Bioinformatics.

The renoprotective effects of soy protein in the aging rat kidney.

Jianlin Cheng, B. Valliyodan, Jilong Li, 2020, Medical research archives.

Fast and Automated Protein-DNA/RNA Macromolecular Complex Modeling from Cryo-EM Maps

Andrew Nakamura, Fengbin Wang, Renzhi Cao, 2022, bioRxiv.

PairedFB: a full hierarchical Bayesian model for paired RNA‐seq data with heterogeneous treatment effects

Chong He, Jie Hou, Jianlin Cheng, 2018, Bioinform..

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps

Dong Si, Renzhi Cao, Jianlin Cheng, 2020, Scientific Reports.

SAXSDom: Modeling multidomain protein structures using small‐angle X‐ray scattering data

Badri Adhikari, Jianlin Cheng, Jie Hou, 2019, Proteins.

Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods

Gary Stacey, Jie Hou, Jianlin Cheng, 2015, EURASIP J. Bioinform. Syst. Biol..

AnglesRefine: refinement of 3D protein structures using Transformer based on torsion angles

Renzhi Cao, Jie Hou, Lei Zhang, 2023, bioRxiv.

A novel f-divergence based generative adversarial imputation method for scRNA-seq data analysis

Jie Hou, Tong Si, Zackary Hopkins, 2023, bioRxiv.

From Analysis of Ischemic Mouse Brain Proteome to Identification of Human Serum Clusterin as a Potential Biomarker for Severity of Acute Ischemic Stroke

Jiankun Cui, Jianlin Cheng, Jilong Li, 2018, Translational Stroke Research.

DISTEVAL: a web server for evaluating predicted protein distances

Badri Adhikari, Bikash Shrestha, Matthew Bernardini, 2021, BMC Bioinformatics.

ComplexQA: a deep graph learning approach for protein complex structure assessment.

Jie Hou, Dong Si, Junyong Zhu, 2023, Briefings in bioinformatics.

Artificial Intelligence Advances for De Novo Molecular Structure Modeling in Cryo-EM

Andrew Nakamura, Renzhi Cao, Jie Hou, 2021, ArXiv.

ConEVA: a toolbox for comprehensive assessment of protein contacts

Jie Hou, Debswapna Bhattacharya, Badri Adhikari, 2016, BMC Bioinformatics.

Genomic imbalance modulates transposable element expression in maize

J. Birchler, Jianlin Cheng, Jie Hou, 2022, Plant communications.