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List of works by Chi Zhang

A Comprehensive Image-based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa).

scientific article published in July 2017

A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize

scientific article published on 03 June 2016

A dataset for assessing temporal changes in gene expression during the aging process of adult Drosophila melanogaster

scientific article published on 06 May 2016

A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes

scientific article (publication date: 7 April 2005)

A novel function prediction approach using protein overlap networks ⬇️

scientific article published on July 17, 2013

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.

scientific article published in July 2004

Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.

scientific article

Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content.

scientific article

An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.

scientific article published on February 2004

Chemical and genetic variation in feral Cannabis sativa populations across the Nebraska climate gradient

scientific article published on 15 April 2022

Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods ⬇️

scientific article published on April 19, 2013

Deletion Mutagenesis and Identification of Causative Mutations in Maize.

scientific article

Deletion mutagenesis identifies a haploinsufficient role for γ-zein in opaque2 endosperm modification

scientific article published on 8 November 2013

Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization.

scientific article published on 3 August 2015

Distinct Pseudomonas type-III effectors use a cleavable transit peptide to target chloroplasts.

scientific article published on 28 December 2013

Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function

scientific article published in August 2005

Domain Graph ofArabidopsisProteome by Comparative Analysis

article

Editing of an Alpha-Kafirin Gene Family Increases, Digestibility and Protein Quality in Sorghum

scientific article published on 20 June 2018

Exomechip Analyses Identify Genes Affecting Mortality after HLA-Matched Unrelated Donor Blood and Marrow Transplantation.

scientific article published on 2 April 2018

Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast.

scientific article published on April 2006

Fast and accurate prediction of protein side-chain conformations ⬇️

scientific article published on August 27, 2011

Fold recognition by concurrent use of solvent accessibility and residue depth

scientific article published on 01 August 2007

Fuzzy clustering of CPP family in plants with evolution and interaction analyses

scientific article

Genetic and molecular characterization of submergence response identifies Subtol6 as a major submergence tolerance locus in maize

scientific article

Genome-Wide Gene Expression in relation to Age in Large Laboratory Cohorts of Drosophila melanogaster

scientific article published on 21 May 2015

Genome-wide Discovery of Circular RNAs in the Leaf and Seedling Tissues of Arabidopsis Thaliana.

scientific article published on August 2017

Heat stress yields a unique MADS box transcription factor in determining seed size and thermal sensitivity.

scientific article published on 2 March 2016

Identification of RNA silencing components in soybean and sorghum.

scientific article

Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling

scientific article

Insect and plant-derived miRNAs in greenbug (Schizaphis graminum) and yellow sugarcane aphid (Sipha flava) revealed by deep sequencing

scientific article published on 9 November 2016

L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier

scientific article

LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains

scientific article

MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities

scientific article published on 04 September 2020

MADS78 and MADS79 Are Essential Regulators of Early Seed Development in Rice

scientific article published on 09 December 2019

Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum.

scientific article published on 13 January 2016

Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of Arabidopsis thaliana

scientific article published on 22 June 2015

Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants

scientific article published on 10 February 2022

PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine.

scientific article published on 13 March 2014

Prediction of Protein Phosphorylation Sites by Integrating Secondary Structure Information and Other One-Dimensional Structural Properties.

scientific article

Prediction of antigenic epitopes on protein surfaces by consensus scoring

scientific article published on 22 September 2009

Prediction of immunogenicity for humanized and full human therapeutic antibodies

scientific article published on 31 August 2020

Protein Loop Modeling with Optimized Backbone Potential Functions

scientific article published on 18 April 2012

Protein binding site prediction using an empirical scoring function

scientific article

Protein flexibility prediction by an all-atom mean-field statistical theory.

scientific article

Protein loop selection using orientation-dependent force fields derived by parameter optimization

scientific article published on 13 May 2011

Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins.

scientific article published on 27 December 2015

Pyrophosphate-dependent fructose-6-phosphate 1-phosphotransferase induction and attenuation of Hsp gene expression during endosperm modification in quality protein maize

scientific article

Radiative Neutron β-Decay in Effective Field Theory.

scientific article published on August 2005

Scalable and physiologically relevant microenvironments for human pluripotent stem cell expansion and differentiation.

scientific article published on 10 January 2018

Sharpening low-energy, standard-model tests via correlation coefficients in neutron beta decay

scientific article published on 01 June 2001

Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3' tailing of small RNAs in Arabidopsis.

scientific article published on 30 April 2015

Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G.

scientific article published in May 2003

The DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation

scientific article published on 01 August 2012

The Pseudomonas syringae type III effector HopD1 suppresses effector-triggered immunity, localizes to the endoplasmic reticulum, and targets the Arabidopsis transcription factor NTL9.

scientific article

The dependence of all-atom statistical potentials on structural training database

scientific article

Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum.

scientific article

Virus-host mucosal interactions during early SIV rectal transmission.

scientific article published on 14 August 2014

What is a desirable statistical energy function for proteins and how can it be obtained?

scientific article published on January 2006

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