List of works - Jianlin Cheng

A Protein Domain Co-Occurrence Network Approach for Predicting Protein Function and Inferring Species Phylogeny ⬇️

scientific article published on March 24, 2011

A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning

scientific article published on 12 December 2016

An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11

scientific article

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data

scientific article published on 24 April 2019

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

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An iterative self‐refining and self‐evaluating approach for protein model quality estimation ⬇️

scientific article published on November 23, 2011

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

scientific article published on 01 February 2020

AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images

scientific article published on 13 June 2019

CONFOLD2: improved contact-driven ab initio protein structure modeling

scientific article published on 25 January 2018

CONFOLD: Residue-residue contact-guided ab initio protein folding.

scientific article

Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing

scientific article

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

scientific article published on 04 February 2021

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction

scientific article published in 2023

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

scientific article published on 06 September 2020

DNdisorder: predicting protein disorder using boosting and deep networks ⬇️

scientific article published on March 6, 2013

DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM

scientific article published on 09 November 2020

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

scientific article published on 8 December 2017

Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in Drosophila

scientific article published on 23 September 2013

DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning ⬇️

scientific article published on February 1, 2011

Does Concurrent Use of Some Botanicals Interfere with Treatment of Tuberculosis?

scientific article published on 7 May 2016

Dosage compensation and inverse effects in triple X metafemales of Drosophila ⬇️

scientific article published on April 15, 2013

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

scientific article published on 13 October 2016

Estimation of model accuracy in CASP13

scientific article published on 16 July 2019

Evolutionary dynamics of protein domain architecture in plants ⬇️

scientific article (publication date: 17 January 2012)

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling

scientific article

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

scientific article

GMOL: An Interactive Tool for 3D Genome Structure Visualization

scientific article published on 12 February 2016

GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data

scientific article published on 05 August 2020

Genes targeted by the Hedgehog-signaling pathway can be regulated by Estrogen related receptor β

scientific article published on 23 November 2015

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

scientific article

Improving protein fold recognition by random forest.

scientific article

Improving protein function prediction by learning and integrating representations of protein sequences and function labels

scientific article published in 2024

Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks

scientific article published on 11 September 2015

Large-scale model quality assessment for improving protein tertiary structure prediction.

scientific article

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

scientific article

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts ⬇️

scientific article published on December 14, 2011

Male-specific lethal complex in Drosophila counteracts histone acetylation and does not mediate dosage compensation ⬇️

scientific article published on February 4, 2013

Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11.

scientific article

Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells

scientific article published in December 2015

NitroDIGE analysis reveals inhibition of protein S-nitrosylation by epigallocatechin gallates in lipopolysaccharide-stimulated microglial cells

scientific article published on 28 January 2014

Predicted structural proteome of <i>Sphagnum divinum</i> and proteome-scale annotation

scientific article published in 2023

Predicting Protein Model Quality from Sequence Alignments by Support Vector Machines.

scientific article

Predicting protein residue–residue contacts using deep networks and boosting ⬇️

scientific article published on October 9, 2012

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

scientific article published on 19 October 2017

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13

scientific article published on 25 April 2019

Proteomic quantification and site-mapping of S-nitrosylated proteins using isobaric iodoTMT reagents

scientific article

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

scientific article

Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods

scientific article

Recursive protein modeling: a divide and conquer strategy for Protein Structure Prediction and its case study in CASP9 ⬇️

scientific article published on June 1, 2012

Root hair systems biology ⬇️

scientific article published on September 17, 2010

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

scientific article published on 20 December 2019

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

scientific article

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

scientific article published on 19 November 2019

The MULTICOM toolbox for protein structure prediction ⬇️

scientific article published on April 30, 2012

Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks ⬇️

scientific article published on February 28, 2013

UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling

scientific article

What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment

scientific article

List of works by Jianlin Cheng

A Protein Domain Co-Occurrence Network Approach for Predicting Protein Function and Inferring Species Phylogeny ⬇️

A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning

An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data

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

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

An iterative self‐refining and self‐evaluating approach for protein model quality estimation ⬇️

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

AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images

CONFOLD2: improved contact-driven ab initio protein structure modeling

CONFOLD: Residue-residue contact-guided ab initio protein folding.

Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing

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

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction

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

DNdisorder: predicting protein disorder using boosting and deep networks ⬇️

DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM

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

Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in Drosophila

DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning ⬇️

Does Concurrent Use of Some Botanicals Interfere with Treatment of Tuberculosis?

Dosage compensation and inverse effects in triple X metafemales of Drosophila ⬇️

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

Estimation of model accuracy in CASP13

Evolutionary dynamics of protein domain architecture in plants ⬇️

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling

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

GMOL: An Interactive Tool for 3D Genome Structure Visualization

GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data

Genes targeted by the Hedgehog-signaling pathway can be regulated by Estrogen related receptor β

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

Improving protein fold recognition by random forest.

Improving protein function prediction by learning and integrating representations of protein sequences and function labels

Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks

Large-scale model quality assessment for improving protein tertiary structure prediction.

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts ⬇️

Male-specific lethal complex in Drosophila counteracts histone acetylation and does not mediate dosage compensation ⬇️

Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11.

Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells

NitroDIGE analysis reveals inhibition of protein S-nitrosylation by epigallocatechin gallates in lipopolysaccharide-stimulated microglial cells

Predicted structural proteome of <i>Sphagnum divinum</i> and proteome-scale annotation

Predicting Protein Model Quality from Sequence Alignments by Support Vector Machines.

Predicting protein residue–residue contacts using deep networks and boosting ⬇️

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13

Proteomic quantification and site-mapping of S-nitrosylated proteins using isobaric iodoTMT reagents

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

Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods

Recursive protein modeling: a divide and conquer strategy for Protein Structure Prediction and its case study in CASP9 ⬇️

Root hair systems biology ⬇️

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

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

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

The MULTICOM toolbox for protein structure prediction ⬇️

Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks ⬇️

UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling

What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment