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Improving protein fold recognition by random forest.CONFOLD: Residue-residue contact-guided ab initio protein folding.An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11Large-scale model quality assessment for improving protein tertiary structure prediction.Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11.Predicting Protein Model Quality from Sequence Alignments by Support Vector Machines.FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic samplingChromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealingQAcon: single model quality assessment using protein structural and contact information with machine learning techniques.Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data.From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data.What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment.Proteomic quantification and site-mapping of S-nitrosylated proteins using isobaric iodoTMT reagentsSMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machinesReconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methodsGenes targeted by the Hedgehog-signaling pathway can be regulated by Estrogen related receptor βMessenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells.Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks.Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in DrosophilaEffects of aged garlic extract and FruArg on gene expression and signaling pathways in lipopolysaccharide-activated microglial cells.NitroDIGE analysis reveals inhibition of protein S-nitrosylation by epigallocatechin gallates in lipopolysaccharide-stimulated microglial cells.GMOL: An Interactive Tool for 3D Genome Structure Visualization.Does Concurrent Use of Some Botanicals Interfere with Treatment of Tuberculosis?A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning.Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.DeepSF: deep convolutional neural network for mapping protein sequences to folds.CONFOLD2: improved contact-driven ab initio protein structure modeling.Genetic dissection of Arabidopsis MAP kinase phosphatase 1-dependent PAMP-induced transcriptional responses.An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C DataAnalysis of several key factors influencing deep learning-based inter-residue contact predictionEstimation of model accuracy in CASP13SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering dataAutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM imagesProtein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
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description
researcher
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name
Jianlin Cheng
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type
label
Jianlin Cheng
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prefLabel
Jianlin Cheng
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P108
P31
P496
0000-0003-0305-2853