Jianlin Cheng
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Computer Science Biology
Jianlin Cheng's Degrees
- PhD Bioinformatics University of California, San Francisco
- Masters Computer Science University of California, San Francisco
- Bachelors Computer Science Peking University
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(Suggest an Edit or Addition)Jianlin Cheng's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Genome sequence of the palaeopolyploid soybean (2010) (3615)
- SCRATCH: a protein structure and structural feature prediction server (2005) (902)
- A large-scale evaluation of computational protein function prediction (2013) (784)
- Prediction of protein stability changes for single‐site mutations using support vector machines (2005) (760)
- An expanded evaluation of protein function prediction methods shows an improvement in accuracy (2016) (316)
- 3Drefine: an interactive web server for efficient protein structure refinement (2016) (276)
- A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction (2015) (264)
- Improved residue contact prediction using support vector machines and a large feature set (2007) (241)
- A machine learning information retrieval approach to protein fold recognition (2006) (226)
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019) (219)
- Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data (2005) (208)
- NNcon: improved protein contact map prediction using 2D-recursive neural networks (2009) (161)
- A neural network approach to ordinal regression (2007) (157)
- 3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic‐level energy minimization (2013) (154)
- Predicting protein residue-residue contacts using deep networks and boosting (2012) (152)
- DeepSF: deep convolutional neural network for mapping protein sequences to folds (2017) (149)
- Large‐scale prediction of disulphide bridges using kernel methods, two‐dimensional recursive neural networks, and weighted graph matching (2005) (141)
- DeepQA: improving the estimation of single protein model quality with deep belief networks (2016) (141)
- CONFOLD: Residue‐residue contact‐guided ab initio protein folding (2015) (139)
- Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms (2005) (135)
- Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13 (2019) (133)
- Root hair systems biology. (2010) (132)
- DNCON2: improved protein contact prediction using two-level deep convolutional neural networks (2017) (129)
- Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment (2016) (126)
- SoyDB: a knowledge database of soybean transcription factors (2010) (119)
- DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks (2006) (111)
- Machine Learning Methods for Protein Structure Prediction (2008) (111)
- Improving Protein Fold Recognition by Deep Learning Networks (2015) (109)
- SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines (2014) (99)
- Evaluating the absolute quality of a single protein model using structural features and support vector machines (2009) (97)
- A comprehensive overview of computational protein disorder prediction methods. (2012) (95)
- Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics (2012) (94)
- Proteomic Quantification and Site-Mapping of S-Nitrosylated Proteins Using Isobaric iodoTMT Reagents (2014) (92)
- A multi-template combination algorithm for protein comparative modeling (2008) (92)
- PreDisorder: ab initio sequence-based prediction of protein disordered regions (2009) (91)
- MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8 (2010) (91)
- APOLLO: a quality assessment service for single and multiple protein models (2011) (88)
- DNdisorder: predicting protein disorder using boosting and deep networks (2013) (84)
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis (2020) (83)
- QAcon: single model quality assessment using protein structural and contact information with machine learning techniques (2016) (82)
- Protein single-model quality assessment by feature-based probability density functions (2016) (78)
- Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks. (2016) (76)
- A deep auto-encoder model for gene expression prediction (2017) (73)
- Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data (2014) (73)
- Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment (2019) (71)
- TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins (2008) (69)
- Prediction of global and local quality of CASP8 models by MULTICOM series (2009) (66)
- CONFOLD2: improved contact-driven ab initio protein structure modeling (2017) (66)
- Assessment of predictions submitted for the CASP7 domain prediction category (2007) (65)
- An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data (2019) (65)
- Bandgap prediction by deep learning in configurationally hybridized graphene and boron nitride (2019) (64)
- DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning (2011) (64)
- Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps (2019) (64)
- Large-scale model quality assessment for improving protein tertiary structure prediction (2015) (60)
- Protein disorder prediction at multiple levels of sensitivity and specificity (2008) (60)
- Estimation of model accuracy in CASP13 (2019) (58)
- Large-Scale Prediction of Disulphide Bond Connectivity (2004) (54)
- WeFold: A coopetition for protein structure prediction (2014) (53)
- Transcriptomic analysis identifies gene networks regulated by estrogen receptor α (ERα) and ERβ that control distinct effects of different botanical estrogens (2014) (49)
- Improving protein fold recognition by random forest (2014) (49)
- i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10 (2013) (48)
- Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants (2006) (46)
- MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data (2016) (45)
- DOMAC: an accurate, hybrid protein domain prediction server (2007) (45)
- The polycystic kidney disease-related proteins Bicc1 and SamCystin interact. (2009) (44)
- DeepDist: real-value inter-residue distance prediction with deep residual convolutional network (2020) (44)
- Deep learning methods for protein torsion angle prediction (2017) (44)
- UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling (2016) (43)
- Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing (2016) (43)
- Male-specific lethal complex in Drosophila counteracts histone acetylation and does not mediate dosage compensation (2013) (42)
- Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment (2014) (42)
- Dosage compensation and inverse effects in triple X metafemales of Drosophila (2013) (41)
- Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge (2021) (40)
- Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in Drosophila (2013) (39)
- Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa (2018) (39)
- A Protein Domain Co-Occurrence Network Approach for Predicting Protein Function and Inferring Species Phylogeny (2011) (38)
- The MULTICOM toolbox for protein structure prediction (2012) (37)
- A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data (2018) (36)
- Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment (2021) (36)
- Enzymatic Activity of the Soybean Ecto-Apyrase GS52 Is Essential for Stimulation of Nodulation1[W][OA] (2011) (36)
- The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types (2013) (36)
- ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data (2017) (34)
- 3D genome structure modeling by Lorentzian objective function (2016) (33)
- Evolutionary dynamics of protein domain architecture in plants (2012) (33)
- MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts (2011) (33)
- Erratum: Genome sequence of the palaeopolyploid soybean (Nature (2010) 463 (178-183)) (2010) (33)
- Ty3 Capsid Mutations Reveal Early and Late Functions of the Amino-Terminal Domain (2007) (32)
- A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks (2013) (31)
- Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks (2013) (30)
- Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11 (2016) (28)
- Inverse design of two-dimensional graphene/h-BN hybrids by a regressional and conditional GAN (2020) (27)
- Protein Residue Contacts and Prediction Methods. (2016) (27)
- Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data (2013) (27)
- TMBpro : Secondary Structure , β-contact , and Tertiary Structure Prediction of Transmembrane β-Barrel Proteins (2007) (26)
- NitroDIGE analysis reveals inhibition of protein S-nitrosylation by epigallocatechin gallates in lipopolysaccharide-stimulated microglial cells (2014) (26)
- Designing and benchmarking the MULTICOM protein structure prediction system (2013) (26)
- SeqRate: sequence-based protein folding type classification and rates prediction (2010) (24)
- Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction (2020) (23)
- ConEVA: a toolbox for comprehensive assessment of protein contacts (2016) (23)
- Genome sequence of the palaeopolyploid (2010) (23)
- HMMEditor: a visual editing tool for profile hidden Markov model (2008) (23)
- GMOL: An Interactive Tool for 3D Genome Structure Visualization (2015) (23)
- Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells (2012) (23)
- DNSS2: improved ab initio protein secondary structure prediction using advanced deep learning architectures (2019) (23)
- Proteomic Analysis of the Effects of Aged Garlic Extract and Its FruArg Component on Lipopolysaccharide-Induced Neuroinflammatory Response in Microglial Cells (2014) (23)
- DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks (2020) (22)
- De novo protein conformational sampling using a probabilistic graphical model (2015) (22)
- AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images (2019) (22)
- Genes targeted by the Hedgehog-signaling pathway can be regulated by Estrogen related receptor β (2015) (21)
- Effects of aged garlic extract and FruArg on gene expression and signaling pathways in lipopolysaccharide-activated microglial cells (2016) (21)
- Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution (2021) (20)
- DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM (2019) (20)
- 3D Genome Structure Modeling by Lorentzian Objective Function (2017) (20)
- From Analysis of Ischemic Mouse Brain Proteome to Identification of Human Serum Clusterin as a Potential Biomarker for Severity of Acute Ischemic Stroke (2018) (20)
- An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions (2015) (19)
- Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning (2018) (19)
- A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11 (2015) (19)
- An overview of bioinformatics methods for modeling biological pathways in yeast. (2016) (18)
- Deep convolutional neural networks for predicting the quality of single protein structural models (2019) (18)
- Analysis of several key factors influencing deep learning-based inter-residue contact prediction (2019) (17)
- An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 (2018) (17)
- Critical assessment of protein intrinsic disorder prediction (2021) (17)
- The MULTICOM Protein Structure Prediction Server Empowered by Deep Learning and Contact Distance Prediction. (2020) (16)
- A conformation ensemble approach to protein residue-residue contact (2011) (16)
- Proteomic Analysis and Biochemical Correlates of Mitochondrial Dysfunction after Low-Intensity Primary Blast Exposure. (2019) (16)
- GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure (2018) (16)
- Deciphering the association between gene function and spatial gene-gene interactions in 3D human genome conformation (2015) (15)
- Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data (2015) (15)
- Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize (2021) (15)
- Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions (2021) (15)
- Genomic imbalance determines positive and negative modulation of gene expression in diploid maize (2021) (15)
- An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11. (2015) (14)
- Structural and functional analysis of “non-smelly” proteins (2019) (14)
- Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14 (2021) (14)
- Genome sequence of the palaeopolyploid soybean (2010) (14)
- Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance. (2020) (14)
- Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9 (2011) (13)
- Geometric Transformers for Protein Interface Contact Prediction (2021) (13)
- Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes (2019) (13)
- A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers (2021) (13)
- Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins (2019) (13)
- Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells (2015) (12)
- Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts (2017) (12)
- DeepHCF: A Deep Learning Based Hybrid Collaborative Filtering Approach for Recommendation Systems (2018) (12)
- Sigmoid: a software infrastructure for pathway bioinformatics and systems biology (2005) (12)
- A predictive model of gene expression using a deep learning framework (2016) (12)
- Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods (2014) (11)
- Interpretable attention model in transcription factor binding site prediction with deep neural networks (2019) (11)
- From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data (2015) (10)
- FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling (2016) (10)
- GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data (2019) (10)
- Quantitative Proteomics Reveals Docosahexaenoic Acid-Mediated Neuroprotective Effects in Lipopolysaccharide-Stimulated Microglial Cells (2020) (9)
- Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14 (2021) (9)
- Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information (2014) (9)
- The MULTICOM protein tertiary structure prediction system. (2014) (9)
- The Gene Balance Hypothesis: Epigenetics and Dosage Effects in Plants. (2020) (9)
- DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning (2021) (9)
- High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function (2021) (8)
- DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling (2021) (8)
- Genetic dissection of Arabidopsis MAP kinase phosphatase 1-dependent PAMP-induced transcriptional responses (2017) (8)
- Predicting Protein Model Quality from Sequence Alignments by Support Vector Machines (2013) (8)
- DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction (2021) (7)
- Soft Labeling for Multi-Pass Document Review (2013) (7)
- VEHiCLE: a Variationally Encoded Hi-C Loss Enhancement algorithm for improving and generating Hi-C data (2020) (7)
- A Super-Clustering Approach for Fully Automated Single Particle Picking in Cryo-EM (2019) (7)
- Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution (2020) (7)
- Predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning (2020) (7)
- A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning (2016) (7)
- Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks (2022) (6)
- Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts (2021) (6)
- A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling (2016) (6)
- SAXSDom: Modeling multidomain protein structures using small‐angle X‐ray scattering data (2019) (6)
- Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph neural networks (2022) (6)
- Inhibition of Hedgehog-Signaling Driven Genes in Prostate Cancer Cells by Sutherlandia frutescens Extract (2015) (6)
- Effect of aneuploidy of a non‐essential chromosome on gene expression in maize (2022) (5)
- Collaborative Attentive Autoencoder for Scientific Article Recommendation (2019) (5)
- EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures (2022) (5)
- Heme oxygenase promotes B‐Raf‐dependent melanosphere formation (2020) (5)
- Deep Ranking in Template-free Protein Structure Prediction (2020) (5)
- Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction (2020) (5)
- DeepSF (2018) (5)
- Improving deep learning-based protein distance prediction in CASP14 (2021) (5)
- CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles (2020) (5)
- 3D-equivariant graph neural networks for protein model quality assessment (2022) (5)
- Evaluation of Protein Structural Models Using Random Forests (2016) (5)
- MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction (2021) (5)
- PairedFB: a full hierarchical Bayesian model for paired RNA‐seq data with heterogeneous treatment effects (2018) (5)
- DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network (2021) (4)
- Localized Deep-CNN Structure for Face Recognition (2018) (4)
- DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks (2021) (4)
- An iterative self‐refining and self‐evaluating approach for protein model quality estimation (2012) (4)
- DeepDist: real-value inter-residue distance prediction with deep residual convolutional network (2021) (4)
- CONFOLD: residue-residue contact-guided ab initio protein folding (2015) (4)
- A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data (2018) (3)
- Protein Structure Refinement by Iterative Fragment Exchange (2013) (3)
- Structural Bioinformatics MULTICOM : A Multi-Level Combination Approach to Protein Structure Prediction and its Assessments in CASP 8 (2010) (3)
- MSACompro: improving multiple protein sequence alignment by predicted structural features. (2014) (3)
- De novo centromere formation on chromosome fragments with an inactive centromere in maize (Zea mays) (2021) (3)
- Deep learning for reconstructing protein structures from cryo-EM density maps: recent advances and future directions (2022) (3)
- Localized Deep Norm-CNN Structure for Face Verification (2018) (3)
- Deep Learning For Denoising Hi-C Chromosomal Contact Data (2019) (3)
- Deep Learning-Based Recommender Systems (2020) (3)
- Does Concurrent Use of Some Botanicals Interfere with Treatment of Tuberculosis? (2016) (3)
- Title Improved residue contact prediction using support vector machines and a large feature set Permalink (2007) (3)
- A Contact-Assisted Approach to Protein Structure Structure Prediction and Its Assessment in CASP 10 (2013) (3)
- DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment (2022) (3)
- DNpro: A Deep Learning Network Approach to Predicting Protein Stability Changes Induced by Single-Site Mutations (2016) (2)
- Four-Dimensional Chromosome Structure Prediction (2021) (2)
- INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION, SIMULATION, AND BIOLOGY (2011) (2)
- Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks (2013) (2)
- Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome (2022) (2)
- Large-Scale Machine Learning and Optimization for Bioinformatics Data Analysis (2020) (2)
- Sigmoid : Towards an Intelligent , Scalable , Software Infrastructure for Pathway Bioinformatics and Systems Biology (2005) (2)
- Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods (2015) (2)
- Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge (2022) (2)
- AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images (2019) (2)
- Classifying protein structures into folds by convolutional neural networks, distance maps, and persistent homology (2020) (2)
- SMISS: a protein function prediction server by integrating multiple sources (2016) (2)
- Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network (2021) (2)
- A Gated Graph Transformer for Protein Complex Structure Quality Assessment and its Performance in CASP15 (2023) (1)
- Deep learning bandgaps of topologically doped graphene (2018) (1)
- A Deep Learning Bioinformatics Approach to Modeling Protein-Ligand Interaction with cryo-EM Data in 2021 Ligand Model Challenge (2022) (1)
- Hierarchical Reconstruction of High-Resolution 3D Models of Human Chromosomes (2018) (1)
- Drefine Software for Protein 3 D Structure Refinement and Its Assessment in CASP 10 (2013) (1)
- Geometry-Complete Diffusion for 3D Molecule Generation (2023) (1)
- Inverse Structural Design of Graphene/Boron Nitride Hybrids by Regressional GAN (2019) (1)
- DNdisorder: predicting protein disorder using boosting and deep networks (2013) (1)
- Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize (2022) (1)
- GNET2: an R package for constructing gene regulatory networks from transcriptomic data. (2020) (1)
- Geometry-Complete Perceptron Networks for 3D Molecular Graphs (2022) (1)
- High-throughput Identification of Novel Heat Tolerance Genes via Genome-wide Pooled Mutant Screens in the Model Green Alga Chlamydomonas reinhardtii (2022) (1)
- Isolation and functional diversification of dihydroflavonol 4-Reductase gene HvDFR from Hosta ventricosa indicate its role in driving anthocyanin accumulation (2021) (1)
- Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells (2012) (1)
- Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps (2022) (1)
- Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information (2014) (1)
- Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics (2012) (1)
- Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, et al. (2010 ) Genome sequence of the palaeopolyploid soybean (2010) (1)
- Genomic imbalance modulates transposable element expression in maize (2022) (1)
- Evolutionary dynamics of protein domain architecture in plants (2012) (1)
- Prediction of transcription factor binding site across cell-types using attention-based deep neural networks (2020) (1)
- The renoprotective effects of soy protein in the aging rat kidney. (2020) (1)
- The MULTICOM toolbox for protein structure prediction (2012) (1)
- Assessing Predicted Contacts for Building Protein Three-Dimensional Models. (2017) (1)
- A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks (2013) (1)
- Improving protein fold recognition by random forest (2014) (1)
- Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function (2023) (1)
- A Contact-assisted Approach to Protein Structure Prediction and Its Assessment in CASP 10 (2013) (1)
- Variability in Technology Assisted Review and Implications for Standards (2013) (1)
- Constructing proteome and metabolome maps for genetic improvement of energy-related traits in soybean [abstract] (2009) (0)
- A scalable and integrative system for pathway bioinformatics and systems biology. (2010) (0)
- Chapter 3 The MULTICOM Protein Tertiary Structure Prediction System (2014) (0)
- Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network (2021) (0)
- Experimentally motivated stepwise protein modeling via IOHMM sampling (2016) (0)
- Semi-Supervised Graph Learning Meets Dimensionality Reduction (2022) (0)
- HHMMVE: A Visual Editor for Profile Hidden Markov Model (2007) (0)
- Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer. (2023) (0)
- DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM (2020) (0)
- Integrative Protein Fold Recognition by Alignments and Machine Learning (2010) (0)
- A deep auto-encoder model for gene expression prediction (2017) (0)
- A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11 (2015) (0)
- Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15 (2023) (0)
- Faculty Opinions recommendation of De novo main-chain modeling for EM maps using MAINMAST. (2018) (0)
- Dissection of a down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome. (2023) (0)
- ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data (2017) (0)
- GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data (2020) (0)
- the official manuscript of predicting gene regulatory networks from RNASeq data (2013) (0)
- Machine Learning Algorithms for Protein Structure Prediction (2006) (0)
- Correction to: GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data (2020) (0)
- Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes (2019) (0)
- 4-28-2014 SMOQ : A Tool for Predicting the Absolute Residue-Specific Quality of a Single Protein Model with Support Vector Machine (2017) (0)
- Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines (2009) (0)
- SAXSDom: Modeling multi-domain protein structures using small-angle X-ray scattering data (2019) (0)
- Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing (2016) (0)
- Design and implementation of ICS Web Search Engine (0)
- Abstract 2366: Transcriptome analysis of human metastasis prostate cancer cells deciphers new function of Esrrb (2014) (0)
- SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines (2014) (0)
- Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction (2022) (0)
- MULTICOM: a large-scale conformation sampling and evaluation server for protein tertiary structure prediction (2015) (0)
- Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action (2023) (0)
- Deciphering the association between gene function and spatial gene-gene interactions in 3D human genome conformation (2015) (0)
- A deep reinforcement learning approach to reconstructing quaternary structures of protein dimers through self-learning (2022) (0)
- CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking (2023) (0)
- Automated protein structure refinement using i3Drefine software and its assessment in CASP10 (2013) (0)
- Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps (2022) (0)
- Author response for "DNSS2 : Improved ab initio protein secondary structure prediction using advanced deep learning architectures" (2020) (0)
- Integrated protein function prediction by mining protein sequences, function associations, protein interaction networks, and gene interaction networks (2015) (0)
- Statistical analysis using finite mixtures of normal linear models (1999) (0)
- Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps (2020) (0)
- An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data (2019) (0)
- Gene Expression Prediction based on Deep Learning (2016) (0)
- Deep learning methods for protein torsion angle prediction (2017) (0)
- Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction (2020) (0)
- TAPIOCA: Topological Attention and Predictive Inference of Chromatin Arrangement Using Epigenetic Features (2021) (0)
- Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15 (2023) (0)
- RNA Sequence Analysis Reveals Expected and Novel Immuno-Modulatory Activities by Sutherlandia frutescens (2018) (0)
- CONFOLD2: improved contact-driven ab initio protein structure modeling (2018) (0)
- REFINEpro: A novel conformation ensemble approach to protein structure refinement (2015) (0)
- Improving protein secondary structure prediction by deep language models and transformer networks (2022) (0)
- Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts (2017) (0)
- ConEVA: a toolbox for comprehensive assessment of protein contacts (2016) (0)
- Correction to: GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data (2020) (0)
- Introduction to 2019 ACM-BCB Highlights Session (2019) (0)
- Structural and functional analysis of “non-smelly” proteins (2019) (0)
- NitroDIGE analysis reveals inhibition of protein S-nitrosylation by epigallocatechin gallates in lipopolysaccharide-stimulated microglial cells (2014) (0)
- DeepQA: improving the estimation of single protein model quality with deep belief networks (2016) (0)
- Does Concurrent Use of Some Botanicals Interfere with Treatment of Tuberculosis? (2016) (0)
- Curation of the Deep Green list of unannotated green lineage proteins to enable structural and functional characterization (2022) (0)
- DRLComplex: Reconstruction of protein quaternary structures using deep reinforcement learning (2022) (0)
- Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data (2015) (0)
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019) (0)
- Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins (2019) (0)
- An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 (2018) (0)
- Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data (2013) (0)
- Prediction of the 4D Chromosome Structure From Time-Series Hi-C Data (2020) (0)
- Session introduction (2003) (0)
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What Schools Are Affiliated With Jianlin Cheng?
Jianlin Cheng is affiliated with the following schools:
