Published in J Am Chem Soc on December 29, 2007
Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys (2012) 1.39
Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. J Chem Theory Comput (2012) 1.01
Simulations of allosteric motions in the zinc sensor CzrA. J Am Chem Soc (2011) 0.93
Characterization of the cofactor-induced folding mechanism of a zinc-binding peptide using computationally designed mutants. J Mol Biol (2009) 0.85
Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin. Biophys J (2010) 0.83
Engineering a zinc binding site into the de novo designed protein DS119 with a βαβ structure. Protein Cell (2012) 0.83
Using simulations to provide the framework for experimental protein folding studies. Arch Biochem Biophys (2012) 0.81
Sequence-specific binding of recombinant Zbed4 to DNA: insights into Zbed4 participation in gene transcription and its association with other proteins. PLoS One (2012) 0.80
Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. J Biomol NMR (2013) 0.79
Substrate binding activates the designed triple mutant of the colicin E7 metallonuclease. J Biol Inorg Chem (2014) 0.77
Stability and folding behavior analysis of zinc-finger using simple models. Int J Mol Sci (2010) 0.76
Effect of His-Tag on Expression, Purification, and Structure of Zinc Finger Protein, ZNF191(243-368). Bioinorg Chem Appl (2016) 0.75
Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly. Sci Rep (2016) 0.75
Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine. J Biol Phys (2016) 0.75
The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase-like HHCC zinc finger. Nat Commun (2017) 0.75
Sodium binding to hH3R and hH 4R--a molecular modeling study. J Mol Model (2014) 0.75
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Enterotypes of the human gut microbiome. Nature (2011) 24.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res (2004) 19.62
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet (2008) 12.51
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res (2002) 12.20
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature (2009) 11.27
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
The Protein Information Resource. Nucleic Acids Res (2003) 11.17
PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res (2009) 11.05
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell (2004) 8.06
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model (2006) 7.93
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol (2009) 7.59
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res (2008) 7.45
Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell (2012) 7.36
Acute renal failure and sepsis. N Engl J Med (2004) 7.18
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
High-performance neuroprosthetic control by an individual with tetraplegia. Lancet (2012) 6.66
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Aberrant excitatory neuronal activity and compensatory remodeling of inhibitory hippocampal circuits in mouse models of Alzheimer's disease. Neuron (2007) 6.60
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One (2011) 5.64
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
New loci associated with kidney function and chronic kidney disease. Nat Genet (2010) 5.58
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med (2008) 5.54
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Building the sequence map of the human pan-genome. Nat Biotechnol (2009) 5.53
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
Predictive value for the Chinese population of the Framingham CHD risk assessment tool compared with the Chinese Multi-Provincial Cohort Study. JAMA (2004) 5.34
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
The pediatric preclinical testing program: description of models and early testing results. Pediatr Blood Cancer (2007) 5.28
Adeno-associated virus serotype 8 efficiently delivers genes to muscle and heart. Nat Biotechnol (2005) 5.27
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
De novo mutations in histone-modifying genes in congenital heart disease. Nature (2013) 5.15
Evidence for HIV-associated B cell exhaustion in a dysfunctional memory B cell compartment in HIV-infected viremic individuals. J Exp Med (2008) 5.14
MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. Cancer Res (2007) 4.95
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Hippo pathway inhibits Wnt signaling to restrain cardiomyocyte proliferation and heart size. Science (2011) 4.76
An overview of the PubChem BioAssay resource. Nucleic Acids Res (2009) 4.75
Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ (2011) 4.50
Hepatocyte growth factor induces gefitinib resistance of lung adenocarcinoma with epidermal growth factor receptor-activating mutations. Cancer Res (2008) 4.30
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol (2010) 4.25
Probable limited person-to-person transmission of highly pathogenic avian influenza A (H5N1) virus in China. Lancet (2008) 4.17
EpCAM and alpha-fetoprotein expression defines novel prognostic subtypes of hepatocellular carcinoma. Cancer Res (2008) 4.17
Regression of castrate-recurrent prostate cancer by a small-molecule inhibitor of the amino-terminus domain of the androgen receptor. Cancer Cell (2010) 4.16
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics (2006) 4.15
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Dynamic T cell migration program provides resident memory within intestinal epithelium. J Exp Med (2010) 4.09
Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proc Natl Acad Sci U S A (2008) 4.07
Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet (2012) 4.07
Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet (2010) 4.06
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell (2012) 4.03
Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. Cell (2004) 3.98
Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature (2010) 3.95
Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat Genet (2013) 3.87
Pelvic Organ Support Study (POSST): the distribution, clinical definition, and epidemiologic condition of pelvic organ support defects. Am J Obstet Gynecol (2005) 3.85
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol (2012) 3.83
Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance. Lancet (2013) 3.83
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81
Epidemiological transition of stroke in China: twenty-one-year observational study from the Sino-MONICA-Beijing Project. Stroke (2008) 3.81
Natural selection on EPAS1 (HIF2alpha) associated with low hemoglobin concentration in Tibetan highlanders. Proc Natl Acad Sci U S A (2010) 3.78
Comparative population genomics of maize domestication and improvement. Nat Genet (2012) 3.78