Published in J Chem Theory Comput on March 26, 2012
To milliseconds and beyond: challenges in the simulation of protein folding. Curr Opin Struct Biol (2012) 1.77
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput (2012) 1.65
Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. J Exp Med (2014) 1.56
Lipid14: The Amber Lipid Force Field. J Chem Theory Comput (2014) 1.50
New insights on the mechanism of the K(+-) independent activity of crenarchaeota pyruvate kinases. PLoS One (2015) 1.39
Markov state models of biomolecular conformational dynamics. Curr Opin Struct Biol (2014) 1.28
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide. J Chem Theory Comput (2013) 1.25
Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding. Proc Natl Acad Sci U S A (2012) 1.12
Mechanism for priming DNA synthesis by yeast DNA polymerase α. Elife (2013) 1.10
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J Chem Theory Comput (2013) 1.09
The FHA and BRCT domains recognize ADP-ribosylation during DNA damage response. Genes Dev (2013) 1.09
Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations. J Phys Chem B (2013) 1.08
Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent. J Am Chem Soc (2014) 1.07
Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly. J Cell Biol (2014) 1.03
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Res (2013) 1.02
LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B (2012) 1.02
Native states of fast-folding proteins are kinetic traps. J Am Chem Soc (2013) 1.01
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput (2014) 1.01
Enzymatic basis for N-glycan sialylation: structure of rat α2,6-sialyltransferase (ST6GAL1) reveals conserved and unique features for glycan sialylation. J Biol Chem (2013) 1.01
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochim Biophys Acta (2014) 0.98
The local dinucleotide preference of APOBEC3G can be altered from 5'-CC to 5'-TC by a single amino acid substitution. J Mol Biol (2013) 0.97
Synchronous opening and closing motions are essential for cAMP-dependent protein kinase A signaling. Structure (2014) 0.96
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. J Chem Theory Comput (2014) 0.96
Dynamic architecture of a protein kinase. Proc Natl Acad Sci U S A (2014) 0.94
Predicting drug metabolism: experiment and/or computation? Nat Rev Drug Discov (2015) 0.93
Molecular Dynamics Study of Helicobacter pylori Urease. J Chem Theory Comput (2014) 0.93
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. J Comput Chem (2015) 0.92
Extein residues play an intimate role in the rate-limiting step of protein trans-splicing. J Am Chem Soc (2013) 0.92
Presentation, presentation, presentation! Molecular-level insight into linker effects on glycan array screening data. Glycobiology (2013) 0.91
Fucosylated chondroitin sulfates from the body wall of the sea cucumber Holothuria forskali: conformation, selectin binding, and biological activity. J Biol Chem (2014) 0.90
Accelerated molecular dynamics simulations of protein folding. J Comput Chem (2015) 0.89
Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package. J Chem Theory Comput (2013) 0.88
Novel COL9A3 mutation in a family diagnosed with multiple epiphyseal dysplasia: a case report. BMC Musculoskelet Disord (2014) 0.88
Identification of two poorly prognosed ovarian carcinoma subtypes associated with CHEK2 germ-line mutation and non-CHEK2 somatic mutation gene signatures. Cell Cycle (2014) 0.88
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields. RNA (2015) 0.88
Probing the paramyxovirus fusion (F) protein-refolding event from pre- to postfusion by oxidative footprinting. Proc Natl Acad Sci U S A (2014) 0.87
On the absence of intrahelical DNA dynamics on the μs to ms timescale. Nat Commun (2014) 0.87
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J Chem Theory Comput (2015) 0.86
On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. J Chem Theory Comput (2014) 0.86
Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA. Nucleic Acids Res (2014) 0.86
Computational assay of H7N9 influenza neuraminidase reveals R292K mutation reduces drug binding affinity. Sci Rep (2013) 0.86
Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nat Commun (2015) 0.85
Perspective: Markov models for long-timescale biomolecular dynamics. J Chem Phys (2014) 0.85
Loop-loop interactions regulate KaiA-stimulated KaiC phosphorylation in the cyanobacterial KaiABC circadian clock. Biochemistry (2013) 0.84
Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate. Nat Commun (2014) 0.84
Distal loop flexibility of a regulatory domain modulates dynamics and activity of C-terminal SRC kinase (csk). PLoS Comput Biol (2013) 0.84
Bridging scales through multiscale modeling: a case study on protein kinase A. Front Physiol (2015) 0.84
MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery. Int J Mol Sci (2015) 0.83
Multipolar Ewald methods, 2: applications using a quantum mechanical force field. J Chem Theory Comput (2015) 0.83
Unraveling cellulose microfibrils: a twisted tale. Biopolymers (2013) 0.83
Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J (2015) 0.83
Predicting the Origins of Anti-Blood Group Antibody Specificity: A Case Study of the ABO A- and B-Antigens. Front Immunol (2014) 0.83
All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields. Chem Commun (Camb) (2015) 0.82
Influence of N-myristylation and ligand binding on the flexibility of the catalytic subunit of protein kinase A. Biochemistry (2013) 0.81
Molecular dynamics study of the opening mechanism for DNA polymerase I. PLoS Comput Biol (2014) 0.81
Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. J Chem Theory Comput (2014) 0.81
The Interaction of Heparin Tetrasaccharides with Chemokine CCL5 Is Modulated by Sulfation Pattern and pH. J Biol Chem (2015) 0.80
Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions. Mol Cell Proteomics (2016) 0.80
Effects of hypoxanthine substitution in peptide nucleic acids targeting KRAS2 oncogenic mRNA molecules: theory and experiment. J Phys Chem B (2013) 0.80
The PAKs come of age: Celebrating 18 years of discovery. Cell Logist (2012) 0.80
Assessing the Current State of Amber Force Field Modifications for DNA. J Chem Theory Comput (2016) 0.80
A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field. J Phys Chem B (2015) 0.80
An additional substrate binding site in a bacterial phenylalanine hydroxylase. Eur Biophys J (2013) 0.80
Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly. Proc Natl Acad Sci U S A (2015) 0.80
Antiviral mechanism of polyanionic carbosilane dendrimers against HIV-1. Int J Nanomedicine (2016) 0.79
Recognition of the disordered p53 transactivation domain by the transcriptional adapter zinc finger domains of CREB-binding protein. Proc Natl Acad Sci U S A (2016) 0.79
Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case. Biopolymers (2016) 0.79
Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations. Biochim Biophys Acta (2016) 0.79
Long-ranged contributions to solvation free energies from theory and short-ranged models. Proc Natl Acad Sci U S A (2016) 0.79
Proteomic-coupled-network analysis of T877A-androgen receptor interactomes can predict clinical prostate cancer outcomes between White (non-Hispanic) and African-American groups. PLoS One (2014) 0.79
Modeling the assembly of the multiple domains of α-actinin-4 and its role in actin cross-linking. Biophys J (2013) 0.79
A theoretical investigation of DNA dynamics and desolvation kinetics for zinc finger proteinZif268. BMC Genomics (2015) 0.79
Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering. J Chem Theory Comput (2014) 0.79
Analysis of site-specific N-glycan remodeling in the endoplasmic reticulum and the Golgi. Glycobiology (2015) 0.79
Investigating changes in the gas-phase conformation of Antithrombin III upon binding of Arixtra using traveling wave ion mobility spectrometry (TWIMS). Analyst (2015) 0.79
Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics. J Chem Theory Comput (2016) 0.78
Structural model of weak binding actomyosin in the prepowerstroke state. J Biol Chem (2014) 0.78
Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations. J Chem Theory Comput (2015) 0.78
Structure and Function of the Su(H)-Hairless Repressor Complex, the Major Antagonist of Notch Signaling in Drosophila melanogaster. PLoS Biol (2016) 0.78
Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins. J Chem Theory Comput (2015) 0.78
A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Eng Des Sel (2016) 0.78
Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules. Biophys J (2014) 0.78
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories. BMC Bioinformatics (2014) 0.78
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol (2016) 0.78
Computing the relative stabilities and the per-residue components in protein conformational changes. Structure (2013) 0.78
Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach. Biopolymers (2014) 0.78
Peroxidase activation of cytoglobin by anionic phospholipids: Mechanisms and consequences. Biochim Biophys Acta (2016) 0.78
Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity. Sci Rep (2016) 0.78
O-Acetyl Side-Chains in Monosaccharides: Redundant NMR Spin-Couplings and Statistical Models for Acetate Ester Conformational Analysis. J Phys Chem B (2016) 0.78
Impact of sulfation pattern on the conformation and dynamics of sulfated fucan oligosaccharides as revealed by NMR and MD. Glycobiology (2014) 0.78
Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation. Sci Rep (2016) 0.77
A composite approach towards a complete model of the myosin rod. Proteins (2015) 0.77
Understanding the cross-resistance of oseltamivir to H1N1 and H5N1 influenza A neuraminidase mutations using multidimensional computational analyses. Drug Des Devel Ther (2015) 0.77
An aromatic residue switch in enhancer-dependent bacterial RNA polymerase controls transcription intermediate complex activity. Nucleic Acids Res (2013) 0.77
Protein dynamics of the HIF-2α PAS-B domain upon heterodimerization and ligand binding. PLoS One (2014) 0.77
Recent advances in QM/MM free energy calculations using reference potentials. Biochim Biophys Acta (2014) 0.77
Enrichment of druggable conformations from apo protein structures using cosolvent-accelerated molecular dynamics. Biology (Basel) (2015) 0.77
Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. Biochim Biophys Acta (2016) 0.77
Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly. PLoS Comput Biol (2015) 0.77
Protonation states and catalysis: Molecular dynamics studies of intermediates in tryptophan synthase. Protein Sci (2015) 0.77
All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B (1998) 54.00
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem (2004) 17.97
Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol (1987) 9.19
Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins (2004) 9.15
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (1998) 8.46
Dynamics of folded proteins. Nature (1977) 7.82
All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc (2002) 4.99
Accelerating molecular modeling applications with graphics processors. J Comput Chem (2007) 4.83
Molecular dynamics and protein function. Proc Natl Acad Sci U S A (2005) 4.70
Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers (2001) 4.68
Accelerating molecular dynamic simulation on graphics processing units. J Comput Chem (2009) 4.58
Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol (2009) 3.81
Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A (2005) 2.91
Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. Biopolymers (1992) 2.86
Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure (2006) 2.71
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. J Chem Theory Comput (2009) 2.70
Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput (2007) 2.10
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. J Phys Chem B (2008) 1.90
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J (2010) 1.75
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. J Am Chem Soc (2002) 1.69
Quantitative molecular ensemble interpretation of NMR dipolar couplings without restraints. J Am Chem Soc (2007) 1.62
Three-dimensional structure of ubiquitin at 2.8 A resolution. Proc Natl Acad Sci U S A (1985) 1.60
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J Comput Chem (2010) 1.55
Analytical electrostatics for biomolecules: beyond the generalized Born approximation. J Chem Phys (2006) 1.26
Molecular dynamics simulations of hydrophobic collapse of ubiquitin. Protein Sci (1998) 1.25
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. J Chem Theory Comput (2009) 1.17
Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality. Biophys J (2008) 1.01
FASTRUN: a special purpose, hardwired computer for molecular simulation. Proteins (1991) 0.97
Determining the Numerical Stability of Quantum Chemistry Algorithms. J Chem Theory Comput (2011) 0.85
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Long-term monitoring shows hepatitis B virus resistance to entecavir in nucleoside-naïve patients is rare through 5 years of therapy. Hepatology (2009) 4.00
Enhanced computer vision with Microsoft Kinect sensor: a review. IEEE Trans Cybern (2013) 3.75
Slug antagonizes p53-mediated apoptosis of hematopoietic progenitors by repressing puma. Cell (2005) 3.73
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res (2007) 3.40
Graph embedding and extensions: a general framework for dimensionality reduction. IEEE Trans Pattern Anal Mach Intell (2007) 3.06
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49
B lymphocyte stimulator overexpression in patients with systemic lupus erythematosus: longitudinal observations. Arthritis Rheum (2003) 2.47
An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J (2010) 2.41
Visualization of nitric oxide in living cells by a copper-based fluorescent probe. Nat Chem Biol (2006) 2.33
Local production of B lymphocyte stimulator protein and APRIL in arthritic joints of patients with inflammatory arthritis. Arthritis Rheum (2003) 2.21
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Understanding the unique characteristics of suicide in China: national psychological autopsy study. Biomed Environ Sci (2005) 1.90
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics (2002) 1.81
Microarray analysis of chitin elicitation in Arabidopsis thaliana. Mol Plant Pathol (2002) 1.80
Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics (2012) 1.80
Epidermal growth factor-like domain 7 protects endothelial cells from hyperoxia-induced cell death. Am J Physiol Lung Cell Mol Physiol (2007) 1.75
Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques (2004) 1.74
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res (2013) 1.72
Photoaffinity isolation and identification of proteins in cancer cell extracts that bind to platinum-modified DNA. Chembiochem (2009) 1.71
Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res (2004) 1.71
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput (2012) 1.65
Efficacy of entecavir in chronic hepatitis B patients with mildly elevated alanine aminotransferase and biopsy-proven histological damage. Hepatology (2010) 1.61
Long-term treatment with entecavir induces reversal of advanced fibrosis or cirrhosis in patients with chronic hepatitis B. Clin Gastroenterol Hepatol (2010) 1.60
Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics (2010) 1.55
Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics (2007) 1.53
CUBIC: identification of regulatory binding sites through data clustering. J Bioinform Comput Biol (2003) 1.47
No supernovae associated with two long-duration gamma-ray bursts. Nature (2006) 1.47
catena-Poly[[bis(thiocyanato-kappa N)cadmium(II)]-di-mu-thiourea-kappa(4)S:S]. Acta Crystallogr C (2002) 1.45
SNP discovery by high-throughput sequencing in soybean. BMC Genomics (2010) 1.45
Preoperative rosuvastatin protects patients with coronary artery disease undergoing noncardiac surgery. Cardiology (2015) 1.43
Single feature polymorphism discovery in rice. PLoS One (2007) 1.42
MUFOLD: A new solution for protein 3D structure prediction. Proteins (2010) 1.42
SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol (2010) 1.40
Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc (2009) 1.40
Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics (2010) 1.39
Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun (2011) 1.39
Chemical markup, XML, and the World Wide Web. 5. Applications of chemical metadata in RSS aggregators. J Chem Inf Comput Sci (2004) 1.37
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics (2008) 1.35
Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PLoS One (2009) 1.34
BAFF overexpression and accelerated glomerular disease in mice with an incomplete genetic predisposition to systemic lupus erythematosus. Arthritis Rheum (2005) 1.33
P3DB: a plant protein phosphorylation database. Nucleic Acids Res (2008) 1.31
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol (2004) 1.30
Legume transcription factor genes: what makes legumes so special? Plant Physiol (2009) 1.30
Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model (2012) 1.29
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics (2012) 1.29
Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. J Bacteriol (2007) 1.29
Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Mol Plant Microbe Interact (2005) 1.27
Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A (2007) 1.27
Genomic and genetic evidence for the loss of umami taste in bats. Genome Biol Evol (2011) 1.27
Using Internet search engines to obtain medical information: a comparative study. J Med Internet Res (2012) 1.25
Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. OMICS (2004) 1.25
Understanding protein dispensability through machine-learning analysis of high-throughput data. Bioinformatics (2004) 1.24
A protocol for computer-based protein structure and function prediction. J Vis Exp (2011) 1.23
Root hair systems biology. Trends Plant Sci (2010) 1.21
Genome-scale probe and primer design with PRIMEGENS. Methods Mol Biol (2007) 1.20
Mosaic: making biological sense of complex networks. Bioinformatics (2012) 1.19
A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23. Nat Genet (2013) 1.19
Homolog-specific PCR primer design for profiling splice variants. Nucleic Acids Res (2011) 1.19
PROSPECT II: protein structure prediction program for genome-scale applications. Protein Eng (2003) 1.19
Visual event recognition in videos by learning from Web data. IEEE Trans Pattern Anal Mach Intell (2012) 1.18
Regulation of cellular oncosis by uncoupling protein 2. J Biol Chem (2002) 1.17
Contrast-enhanced whole-heart coronary MRA at 3.0T for the evaluation of cardiac venous anatomy. Int J Cardiovasc Imaging (2010) 1.17
An oligonucleotide microarray resource for transcriptional profiling of Bradyrhizobium japonicum. Mol Plant Microbe Interact (2007) 1.17
ProteinDBS: a real-time retrieval system for protein structure comparison. Nucleic Acids Res (2004) 1.17
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res (2011) 1.15
Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis. PLoS One (2010) 1.15
Establishment of a protein reference map for soybean root hair cells. Plant Physiol (2008) 1.14
Automated Tongue Feature Extraction for ZHENG Classification in Traditional Chinese Medicine. Evid Based Complement Alternat Med (2012) 1.12
Improving the performance of DomainParser for structural domain partition using neural network. Nucleic Acids Res (2003) 1.12
Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics (2007) 1.12
Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Mol Plant Microbe Interact (2008) 1.11
Multilinear discriminant analysis for face recognition. IEEE Trans Image Process (2007) 1.11
Targeting oncogenic miR-335 inhibits growth and invasion of malignant astrocytoma cells. Mol Cancer (2011) 1.11
Clinical features and prognosis in adult-onset Still's disease: a study of 104 cases. Clin Rheumatol (2010) 1.08
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Res (2013) 1.08
A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST. Proteomics (2004) 1.08
Systems analysis of seed filling in Arabidopsis: using general linear modeling to assess concordance of transcript and protein expression. Plant Physiol (2010) 1.07
Computational analyses of high-throughput protein-protein interaction data. Curr Protein Pept Sci (2003) 1.07
Inhibition of MDR1 expression with altritol-modified siRNAs. Nucleic Acids Res (2007) 1.06
Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS One (2010) 1.06
PDCD5 interacts with Tip60 and functions as a cooperator in acetyltransferase activity and DNA damage-induced apoptosis. Neoplasia (2009) 1.06
ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics (2013) 1.05
Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method. Int J Bioinform Res Appl (2006) 1.05
Identification of genes and pathways involved in kidney renal clear cell carcinoma. BMC Bioinformatics (2014) 1.05
A link between SIN1 (MAPKAP1) and poly(rC) binding protein 2 (PCBP2) in counteracting environmental stress. Proc Natl Acad Sci U S A (2008) 1.04
Phosphoproteomic analysis of seed maturation in Arabidopsis, rapeseed, and soybean. Plant Physiol (2012) 1.04
Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. BMC Plant Biol (2010) 1.04
PyADF--a scripting framework for multiscale quantum chemistry. J Comput Chem (2011) 1.03
Quantitative phosphoproteomic analysis of soybean root hairs inoculated with Bradyrhizobium japonicum. Mol Cell Proteomics (2012) 1.03
Domain adaptation from multiple sources: a domain-dependent regularization approach. IEEE Trans Neural Netw Learn Syst (2012) 1.03
Image clustering using local discriminant models and global integration. IEEE Trans Image Process (2010) 1.03
A typical N-terminal extensions confer novel regulatory properties on GTP cyclohydrolase isoforms in Drosophila melanogaster. J Biol Chem (2006) 1.02
Bioinformatics and its applications in plant biology. Annu Rev Plant Biol (2006) 1.02
Correlation between posttranslational modification and intrinsic disorder in protein. Pac Symp Biocomput (2012) 1.02
LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B (2012) 1.02
MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction. Proteins (2011) 1.01
Domain transfer multiple kernel learning. IEEE Trans Pattern Anal Mach Intell (2012) 0.99