Bioinformatics

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  Subject Areas on Research

  • - : Exploring the outer limits of bacterial pseudogenes 
  • 3D maps of RNA interhelical junctions. 
  • A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data. 
  • A Bayesian network approach to operon prediction. 
  • A Bayesian non-parametric mixed-effects model of microbial growth curves. 
  • A Cayley tree immune network model with antibody dynamics. 
  • A Model for Migratory B Cell Oscillations from Receptor Down-Regulation Induced by External Chemokine Fields 
  • A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal. 
  • A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks. 
  • A bayesian analysis strategy for cross-study translation of gene expression biomarkers. 
  • A behavioral summary for completely random nets 
  • A biometrical genome search in rats reveals the multigenic basis of blood pressure variation. 
  • A brave new synthetic world. A report of the first meeting on 'Frontiers in Synthetic Biology', Boston, USA, 1-2 December 2008. 
  • A carrageenan hydrogel stabilized colloidal gold multi-enzyme biosensor electrode utilizing immobilized horseradish peroxidase and cholesterol oxidase/cholesterol esterase to detect cholesterol in serum and whole blood. 
  • A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila. 
  • A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. 
  • A collection of bioconductor methods to visualize gene-list annotations. 
  • A compact CMOS biochip immunosensor towards the detection of a single bacteria. 
  • A comparative analysis of the information content in long and short SAGE libraries. 
  • A comparison of different bivariate correlated frailty models and estimation strategies. 
  • A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits. 
  • A comparison of methods for RNA extraction from lymphocytes for RT-PCR. 
  • A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes. 
  • A computational model of epithelial solute and water transport along a human nephron. 
  • A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. 
  • A dynamic numerical method for models of renal tubules. 
  • A facile approach to immobilize protein for biosensor: self-assembled supported bilayer lipid membranes on glassy carbon electrode. 
  • A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information. 
  • A forecasting model of disease prevalence based on the McKendrick-von Foerster equation. 
  • A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. 
  • A generalized workflow for conducting electric field-optimized, fMRI-guided, transcranial magnetic stimulation. 
  • A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs. 
  • A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation. 
  • A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat. 
  • A hybrid bayesian approach for genome-wide association studies on related individuals. 
  • A kinetic model for the intramolecular distribution of ¹⁵ N in uric acid in patients with primary gout fed ¹⁵ N-glycine 
  • A machine learning approach for the prediction of protein surface loop flexibility. 
  • A map of 75 human ribosomal protein genes. 
  • A map of human cancer signaling. 
  • A mathematical model for LH release in response to continuous and pulsatile exposure of gonadotrophs to GnRH. 
  • A mathematical model for histamine synthesis, release, and control in varicosities. 
  • A mathematical model for persistent post-CSD vasoconstriction. 
  • A mathematical model of glutathione metabolism. 
  • A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions. 
  • A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity. 
  • A model for migratory B cell oscillations from receptor down-regulation induced by external chemokine fields. 
  • A new analysis tool for individual-level allele frequency for genomic studies. 
  • A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS. 
  • A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. 
  • A novel cross-disciplinary multi-institute approach to translational cancer research: Lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC) 
  • A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status. 
  • A nucleosome-guided map of transcription factor binding sites in yeast. 
  • A numerical method for renal models that represent tubules with abrupt changes in membrane properties. 
  • A permutation-based multiple testing method for time-course microarray experiments. 
  • A phased strategy to differentiate human CD14+monocytes into classically and alternatively activated macrophages and dendritic cells 
  • A power-law dependence of bacterial invasion on mammalian host receptors. 
  • A preliminary gene map for the Van der Woude syndrome critical region derived from 900 kb of genomic sequence at 1q32-q41. 
  • A protocol for imaging alternative splicing regulation in vivo using fluorescence reporters in transgenic mice. 
  • A region-based model framework for the rat urine concentrating mechanism. 
  • A resistor interpretation of general anisotropic cardiac tissue. 
  • A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data. 
  • A second locus for hereditary hemorrhagic telangiectasia maps to chromosome 12. 
  • A semiclassical theory for nerve excitation by a low intensity electromagnetic field. 
  • A simple BASIC program allows the rapid entry of DNA nucleotide sequences into personal computers. 
  • A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. 
  • A statistical and biological response to an informatics appraisal of healthy aging gene signatures. 
  • A stele-enriched gene regulatory network in the Arabidopsis root. 
  • A study of the repetitive structure and distribution of short motifs in human genomic sequences. 
  • A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. 
  • A synthetic Escherichia coli predator-prey ecosystem. 
  • A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease. 
  • A transcription factor affinity-based code for mammalian transcription initiation. 
  • A two-current model for the dynamics of cardiac membrane. 
  • A xanthine oxidase/colloidal gold enzyme electrode for amperometric biosensor applications 
  • Abrupt population changes along smooth environmental gradients 
  • Advances to Bayesian network inference for generating causal networks from observational biological data. 
  • Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. 
  • Advantages of mRNA amplification for microarray analysis. 
  • Age trends in the prevalence of cervical squamous intraepithelial lesions among HIV-positive women in Cameroon: a cross-sectional study. 
  • Alginate encapsulation is a highly reproducible method for tumor cell implantation in dorsal skinfold chambers. 
  • Algorithm for backrub motions in protein design. 
  • All-Atom Contacts: A New Approach to Structure Validation 
  • All-atom contacts: a new approach to structure validation. 
  • Alternative ion channel splicing in mesial temporal lobe epilepsy and Alzheimer's disease. 
  • Amperometric glucose biosensor based on lipid film. 
  • Amplification of antigen-antibody interactions based on biotin labeled protein-streptavidin network complex using impedance spectroscopy. 
  • An RNA tertiary switch by modifying how helices are tethered. 
  • An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes. 
  • An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. 
  • An approach to modelling in immunology. 
  • An asymptotic solution for traveling waves of a nonlinear-diffusion Fisher's equation 
  • An automated decision-tree approach to predicting protein interaction hot spots. 
  • An efficient numerical method for distributed-loop models of the urine concentrating mechanism. 
  • An empirical analysis of training protocols for probabilistic gene finders 
  • An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. 
  • An encyclopedia of mouse DNA elements (Mouse ENCODE) 
  • An encyclopedia of mouse DNA elements (Mouse ENCODE). 
  • An ensemble model of competitive multi-factor binding of the genome. 
  • An image processing approach to computing distances between RNA secondary structures dot plots. 
  • An individualized predictor of health and disease using paired reference and target samples. 
  • An integrated YAC map of the human X chromosome. 
  • An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer. 
  • An inverse algorithm for a mathematical model of an avian urine concentrating mechanism. 
  • An ionically based mapping model with memory for cardiac restitution. 
  • An optimization algorithm for a distributed-loop model of an avian urine concentrating mechanism. 
  • Analysis of Homeostatic Mechanisms in Biochemical Networks. 
  • Analysis of the mouse transcriptome for genes involved in the function of the nervous system. 
  • Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. 
  • Angiogenesis: an adaptive dynamic biological patterning problem. 
  • Annotating the human genome with Disease Ontology. 
  • Antibody Fab-Fc properties outperform titer in predictive models of SIV vaccine-induced protection. 
  • Application of Bayesian evidence synthesis to modelling the effect of ketogenic therapy on survival of high grade glioma patients. 
  • Application of a miniature biochip using the molecular beacon probe in breast cancer gene BRCA1 detection. 
  • Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma. 
  • Applications of a rat multiple tissue gene expression data set. 
  • Applying family analyses to electronic health records to facilitate genetic research. 
  • Artifactual frame-shift p53 mutation at codon 249 detected with the Cyclist DNA sequencing method. 
  • Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists. 
  • Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster 
  • Assessment of LD matrix measures for the analysis of biological pathway association. 
  • Assessment of protein dynamics and DNA repair following generation of DNA double-strand breaks at defined genomic sites. 
  • Association of calmodulin and smooth muscle myosin light chain kinase: application of a label selection technique with trace acetylated calmodulin. 
  • Attachment of gold nanoparticles to glassy carbon electrode and its application for the direct electrochemistry and electrocatalytic behavior of hemoglobin. 
  • AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes. 
  • Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields. 
  • Automated constraint-based nucleotide sequence selection for DNA computation. 
  • Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study. 
  • Automatic annotation of spatial expression patterns via sparse Bayesian factor models. 
  • Avianbase: a community resource for bird genomics. 
  • BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. 
  • Bacterial artificial chromosome cloning and mapping of a 630-kb human extrachromosomal structure. 
  • Bacterial infection remodels the DNA methylation landscape of human dendritic cells. 
  • Bacterial temporal dynamics enable optimal design of antibiotic treatment. 
  • Balancing selection and trans-specific polymorphisms. 
  • Bang-bang control of feeding: Role of hypothalamic and satiety signals 
  • Barriers to adopting a healthy lifestyle: insight from postpartum women. 
  • Basophile: accurate fragment charge state prediction improves peptide identification rates. 
  • BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. 
  • Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. 
  • Bayesian consensus clustering. 
  • Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. 
  • Bayesian estimation of the number of inversions in the history of two chromosomes. 
  • Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions. 
  • Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies. 
  • Bayesian joint analysis of heterogeneous genomics data. 
  • Bayesian learning from marginal data in bionetwork models. 
  • Bayesian network-response regression. 
  • Bayesian segmentation of protein secondary structure. 
  • Beyond a 'skeleton': Understanding cellular functions of the cytoskeleton 
  • Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. 
  • Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. 
  • BioWarehouse: a bioinformatics database warehouse toolkit. 
  • Biological control with nonlocal interactions. 
  • Biological pathway selection through Bayesian integrative modeling (Statistical Applications in Genetics and Molecular Biology) 
  • Biological pathway selection through Bayesian integrative modeling. 
  • Bioplasmonic calligraphy for multiplexed label-free biodetection. 
  • Biosensor system for continuous monitoring of organophosphate aerosols. 
  • Biotinylated tags for recovery and characterization of ribonucleoprotein complexes. 
  • Block-diagonal discriminant analysis and its bias-corrected rules. 
  • Bone-associated gene evolution and the origin of flight in birds. 
  • Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer. 
  • Building pathway clusters from Random Forests classification using class votes. 
  • COVID19 antibody detection using lateral flow assay tests in a cohort of convalescent plasma donors. 
  • CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. 
  • Callipyge mutation affects gene expression in cis: a potential role for chromatin structure. 
  • Cancer characterization and feature set extraction by discriminative margin clustering. 
  • Capacitive detection of glucose using molecularly imprinted polymers. 
  • Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling. 
  • Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. 
  • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. 
  • Characterising phase variations in MALDI-TOF data and correcting them by peak alignment. 
  • Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. 
  • Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types. 
  • Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. 
  • Characterizing disease-specific pathways and their coordination by integrative microarray analysis with application to cancer 
  • Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. 
  • Checkpoints couple transcription network oscillator dynamics to cell-cycle progression 
  • Checkpoints couple transcription network oscillator dynamics to cell-cycle progression. 
  • Chemical carcinogenesis and toxicity models: matching complexity to objectives. 
  • Chemical carcinogenesis and toxity models: Matching complexity to objectives 
  • Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes 
  • Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. 
  • Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila. 
  • Chromatin signatures of the Drosophila replication program. 
  • Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions. 
  • Clustering gene expression time series data using an infinite Gaussian process mixture model. 
  • Clusters of adjacent and similarly expressed genes across normal human tissues complicate comparative transcriptomic discovery. 
  • Colonoscopy-based colorectal cancer modeling in mice with CRISPR-Cas9 genome editing and organoid transplantation. 
  • Combined genotype and haplotype tests for region-based association studies. 
  • Combining gene expression, demographic and clinical data in modeling disease: a case study of bipolar disorder and schizophrenia. 
  • Community assembly and food web stability 
  • Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen 
  • Comparative RNA sequencing reveals substantial genetic variation in endangered primates. 
  • Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. 
  • Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. 
  • Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. 
  • Comparative genomics reveals molecular features unique to the songbird lineage. 
  • Comparative genomics search for losses of long-established genes on the human lineage. 
  • Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. 
  • Comparing reference-based RNA-Seq mapping methods for non-human primate data. 
  • Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. 
  • Comparison of colloidal gold electrode fabrication methods: the preparation of a horseradish peroxidase enzyme electrode. 
  • Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling. 
  • Complex-trait analysis in plants. 
  • Complexity reduction in context-dependent DNA substitution models. 
  • Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates. 
  • Computation of mutual information from Hidden Markov Models. 
  • Computation of steady-state probability distributions in stochastic models of cellular networks. 
  • Computational Causal Modeling of the Dynamic Biomarker Cascade in Alzheimer's Disease. 
  • Computational analysis of core promoters in the Drosophila genome. 
  • Computational and experimental identification of novel human imprinted genes. 
  • Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5. 
  • Computational inference of neural information flow networks. 
  • Computing and graphing probability values of pearson distributions: a SAS/IML macro. 
  • Computing van der Waals energies in the context of the rotamer approximation. 
  • Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom. 
  • Constructal law: pleasure, golden ratio, animal locomotion and the design of pedestrian evacuation: comment on "The emergence of design in pedestrian dynamics: locomotion, self-organization, walking paths and the constructal law" by A. Miguel. 
  • Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica. 
  • Cooperation between Polycomb and androgen receptor during oncogenic transformation 
  • Coordinated posttranscriptional mRNA population dynamics during T-cell activation. 
  • Coping with viral diversity in HIV vaccine design: A response to Nickle et al. [1] 
  • Coping with viral diversity in HIV vaccine design: a response to Nickle et al. 
  • Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. 
  • Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. 
  • Correction to: DNA copy number evolution in Drosophila cell lines. 
  • Correction to: Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling. 
  • Correction: Bang-Bang Control of Feeding: Role of Hypothalamic and Satiety Signals 
  • Corrigendum: Detecting differential copy number variation between groups of samples. 
  • Coupling spatial segregation with synthetic circuits to control bacterial survival. 
  • Cover Image, Volume 84, Issue 9 
  • Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR. 
  • Crystal structure of YbaK protein fromHaemophilus influenzae (HI1434) at 1.8 ? resolution: Functional implications 
  • Crystal structure of Yeco fromHaemophilus influenzae (HI0319) reveals a methyltransferase fold and a boundS-adenosylhomocysteine 
  • Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis. 
  • Crystallization of a fragment of human fibronectin: introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine. 
  • Crystallization of the purine salvage enzyme adenine phosphoribosyltransferase. 
  • Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences. 
  • Culture and the Constructal-Law evolution of the human and machine species: comment on "An evolutionary framework for cultural change: selectionism versus communal exchange" by L. Gabora. 
  • Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. 
  • DIG--a system for gene annotation and functional discovery. 
  • DNA copy number evolution in Drosophila cell lines. 
  • DNA replication and transcription programs respond to the same chromatin cues. 
  • DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. 
  • DOOR: a prokaryotic operon database for genome analyses and functional inference 
  • DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages. 
  • Dating branches on the tree of life using DNA. 
  • De Novo Transcriptome Assembly and Development of Novel Microsatellite Markers for the Traditional Chinese Medicinal Herb, Veratrilla baillonii Franch (Gentianaceae). 
  • De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. 
  • Decentralized resource allocation to control an epidemic: a game theoretic approach. 
  • Deciphering the molecular machinery of stem cells: a look at the neoblast gene expression profile. 
  • Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. 
  • Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans. 
  • Dependence of paracentric inversion rate on tract length. 
  • Dependent competing risks: a stochastic process model. 
  • Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. 
  • Design and implementation of high-throughput RNAi screens in cultured Drosophila cells. 
  • Design in nature, thermodynamics, and the constructal law: comment on "Life, hierarchy, and the thermodynamic machinery of planet Earth" by A. Kleidon. 
  • Detecting differential copy number variation between groups of samples. 
  • Detecting differential growth of microbial populations with Gaussian process regression. 
  • Detecting separate time scales in genetic expression data. 
  • Detection and identification of bacteria using antibiotic susceptibility and a multi-array electrochemical sensor with pattern recognition. 
  • Detection of hormesis effect in longevity: simulation approach for heterogeneous population. 
  • Developing a synthetic psychosocial stress measure and harmonizing CVD-risk data: a way forward to GxE meta- and mega-analyses. 
  • Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs. 
  • Development of human protein reference database as an initial platform for approaching systems biology in humans. 
  • Developmental control of gene copy number by repression of replication initiation and fork progression. 
  • Developmental control of the DNA replication and transcription programs. 
  • Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. 
  • Different methods of sample preparation influence sensitivity of Mycobacterium tuberculosis and Borrelia burgdorferi PCR. 
  • Different methods of sample preparation influence sensitivity of mycobacterium tuberculosis and borrelia burgdorferi PCR 
  • Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. 
  • Differential pathlength factor for diffuse photon scattering through tissue by a pulse-response method. 
  • Differentially labeled mutant oligonucleotides for analysis of protein-DNA interactions. 
  • Digital atlasing and standardization in the mouse brain. 
  • Digital image analysis for rapid quantification of total RNA and cDNA for SMART-PCR. 
  • Direct electrochemistry of hemoglobin in egg-phosphatidylcholine films and its catalysis to H(2)O(2). 
  • Directed differentiation of human induced pluripotent stem cells into mature kidney podocytes and establishment of a Glomerulus Chip. 
  • Dissecting the regulatory architecture of gene expression QTLs. 
  • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. 
  • Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy. 
  • Distinguishing direct versus indirect transcription factor-DNA interactions. 
  • Distributed solute and water reabsorption in a central core model of the renal medulla. 
  • Does an offer for a free on-line continuing medical education (CME) activity increase physician survey response rate? A randomized trial. 
  • Domain prediction with probabilistic directional context. 
  • Domain-oriented edge-based alignment of protein interaction networks. 
  • Drivers of Inter-individual Variation in Dengue Viral Load Dynamics. 
  • Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. 
  • Drug detoxification dynamics explain the postantibiotic effect. 
  • Dynamic DNA methylation across diverse human cell lines and tissues. 
  • Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. 
  • EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. 
  • Ecohydrology of agroecosystems: quantitative approaches towards sustainable irrigation. 
  • Effect of dimensionality on Lotka-Volterra predator-prey dynamics: Individual based simulation results 
  • Effect of pegloticase on renal function in patients with chronic kidney disease: a post hoc subgroup analysis of 2 randomized, placebo-controlled, phase 3 clinical trials. 
  • Effect of tubular inhomogeneities on filter properties of thick ascending limb of Henle's loop. Mathematical Biosciences 209(2): 564-592, 2007 
  • Effect of tubular inhomogeneities on filter properties of thick ascending limb of Henle's loop. 
  • Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin. 
  • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. 
  • Effects of serelaxin in subgroups of patients with acute heart failure: Results fromRELAX-AHF 
  • Efficiency, selectivity, and robustness of nucleocytoplasmic transport. 
  • Efficiency, selectivity, and robustness of nucleocytoplasmic transport. 
  • Efficient decoding algorithms for generalized hidden Markov model gene finders 
  • Efficient estimation of grouped survival models. 
  • Efficient implementation of a generalized pair hidden Markov model for comparative gene finding 
  • Embracing the complexity of genomic data for personalized medicine. 
  • Emotion and autobiographical memory: considerations from posttraumatic stress disorder. 
  • Enabling functional genomics with genome engineering. 
  • Encoding of naturalistic stimuli by local field potential spectra in networks of excitatory and inhibitory neurons. 
  • Engineering key components in a synthetic eukaryotic signal transduction pathway. 
  • Enhancement of transport selectivity through nano-channels by non-specific competition. 
  • Enhancement of transport selectivity through nano-channels by non-specific competition. 
  • Epigenetic assimilation in the aging human brain. 
  • Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer. 
  • Erratum to: Host lifestyle affects human microbiota on daily timescales. 
  • Erratum: A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat (Genome Research (1999) 9, (AP1-AP8)) 
  • Erratum: Applications of a rat multiple tissue gene expression data set (Genome Research (2004) vol. 14 (742-749)) 
  • Erratum: Bayesian analysis of signaling networks embryonic stem cell fate decisions (Bioinformatics (2005) vol. 21 (741-753)) 
  • Erratum: Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets (Genome Research (2012) 22 (386-397)) 
  • Erratum: RIP-Chip: The isolation and identification of mRNAs, microRNAS and protein components of ribonucleoprotein complexes from cell extracts (Nature Protocols (2006) vol. 1 (302-307) 10.1038/nprot.2006.47) 
  • Ertapenem for treatment of osteomyelitis: a case series. 
  • Escape from homeostasis. 
  • Establishing reporting standards for metabolomic and metabonomic studies: a call for participation. 
  • Estimating Tumor Growth Rates In Vivo. 
  • Estimating genomic coexpression networks using first-order conditional independence. 
  • Estimating relative changes of metabolic fluxes. 
  • Estimating the Probability of Polyreactive Antibodies 4E10 and 2F5 Disabling a gp41 Trimer after T Cell-HIV Adhesion 
  • Estimating the probability of polyreactive antibodies 4E10 and 2F5 disabling a gp41 trimer after T cell-HIV adhesion. 
  • Estimation and prediction with HIV-treatment interruption data. 
  • Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping 
  • Ethical challenges in genotype-driven research recruitment. 
  • Evaluating Spatial Interaction Models for Regional Mobility in Sub-Saharan Africa. 
  • Evaluating cell-surface expression and measuring activation of mammalian odorant receptors in heterologous cells. 
  • Evaluating functional network inference using simulations of complex biological systems. 
  • Evaluating the quality of NMR structures by local density of protons. 
  • Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes. 
  • Evaluation of EEG features in decoding individual finger movements from one hand. 
  • Evaluation of multiple models to distinguish closely related forms of disease using DNA microarray data: an application to multiple myeloma. 
  • Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. 
  • Evidence-ranked motif identification. 
  • Evolution of dispersal distance. 
  • Evolutionary design on a budget: robustness and optimality of bacteriophage T7. 
  • Existence and uniqueness of solutions to a mathematical model of the urine concentrating mechanism 
  • Expanding the diversity of DNA base modifications with N⁶-methyldeoxyadenosine. 
  • Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans. 
  • Explant culture of adult zebrafish hearts for epicardial regeneration studies. 
  • Explicit equilibrium modeling of transcription-factor binding and gene regulation. 
  • Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. 
  • Expressed sequence tag analysis in Cycas, the most primitive living seed plant. 
  • Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster. 
  • Extending assembly of short DNA sequences to handle error. 
  • Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: Environmental covariates, gene-gene and gene-environment interaction 
  • Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: environmental covariates, gene-gene and gene-environment interaction. 
  • Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. 
  • Extrapolating weak selection in evolutionary games. 
  • Extrema-weighted feature extraction for functional data. 
  • F-Seq: a feature density estimator for high-throughput sequence tags. 
  • Fabrication of an autoclavable one-way valve for venting fermentation gases. 
  • Familial and sporadic idiopathic pulmonary fibrosis: making the diagnosis from peripheral blood. 
  • Fast ion-exchange membrane purification of a microsomal protein. 
  • Fast molecular shape matching using contact maps. 
  • Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons. 
  • Feedback-mediated dynamics in a model of coupled nephrons with compliant thick ascending limbs. 
  • Feedback-mediated dynamics in two coupled nephrons. 
  • Femtomolar sensitivity using a channel-etched thin film waveguide fluoroimmunosensor. 
  • Field-induced forces at dielectric interfaces as a possible mechanism of RF hearing effects. 
  • First somatic mutation of E2F1 in a critical DNA binding residue discovered in well-differentiated papillary mesothelioma of the peritoneum. 
  • Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. 
  • Flow: Statistics, visualization and informatics for flow cytometry. 
  • Fluorescence in situ hybridization method for measuring transfection efficiency. 
  • Freedom and evolution in the dynamics of social systems. 
  • From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. 
  • From spiking neuron models to linear-nonlinear models. 
  • From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase. 
  • Fully printed prothrombin time sensor for point-of-care testing. 
  • Functional Annotation Signatures of Disease Susceptibility Loci Improve SNP Association Analysis 
  • Functional analysis of novel SNPs and mutations in human and mouse genomes. 
  • Functional annotation signatures of disease susceptibility loci improve SNP association analysis 
  • GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. 
  • Gene expression and adaptive noncoding changes during human evolution. 
  • Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation 
  • Gene expression throughout a vertebrate's embryogenesis. 
  • Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. 
  • Gene selection using iterative feature elimination random forests for survival outcomes. 
  • Gene-expression profiling of the response of peripheral blood mononuclear cells and melanoma metastases to systemic IL-2 administration. 
  • Generation and customization of biosynthetic excitable tissues for electrophysiological studies and cell-based therapies. 
  • Generation of orthotopic and heterotopic human pancreatic cancer xenografts in immunodeficient mice. 
  • Genetic engineering of a single-chain antibody fragment for surface immobilization in an optical biosensor. 
  • Genetic network identification using convex programming. 
  • Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies. 
  • Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner. 
  • Genome accessibility is widely preserved and locally modulated during mitosis. 
  • Genome annotation assessment in Drosophila melanogaster. 
  • Genome editing: the end of the beginning. 
  • Genome mapping by fluorescent fingerprinting. 
  • Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. 
  • Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. 
  • Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors. 
  • Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. 
  • Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. 
  • Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). 
  • Genome-wide prediction of imprinted murine genes. 
  • Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. 
  • Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. 
  • Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. 
  • Genomic and physiological responses to strong selective pressure during late organogenesis: few gene expression changes found despite striking morphological differences. 
  • Genomic approaches for understanding the genetics of complex disease. 
  • Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. 
  • Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. 
  • Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae. 
  • Genomic resources for the endangered Hawaiian honeycreepers. 
  • Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. 
  • Genomic sweeping for hypermethylated genes. 
  • Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles. 
  • Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. 
  • Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. 
  • Gradient lasso for Cox proportional hazards model. 
  • HPV clearance and the neglected role of stochasticity. 
  • Hans J. Bremermann: a pioneer in mathematical biology. 
  • Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal. 
  • Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. 
  • Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. 
  • Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies. 
  • Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples. 
  • High heritability of metabolomic profiles in families burdened with premature cardiovascular disease. 
  • High prevalence of hypertension and cardiovascular disease risk factors among medical students at Makerere University College of Health Sciences, Kampala, Uganda. 
  • High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer. 
  • High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. 
  • High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. 
  • High-resolution mapping of open chromatin in the rice genome. 
  • High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family. 
  • High-throughput genotyping with single nucleotide polymorphisms. 
  • High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. 
  • High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype. 
  • Highly active zinc-finger nucleases by extended modular assembly. 
  • Homeostasis despite instability. 
  • Homeostatic mechanisms in dopamine synthesis and release: a mathematical model. 
  • Host lifestyle affects human microbiota on daily timescales. 
  • How accurately can we control the FDR in analyzing microarray data? 
  • Human and mouse alpha-synuclein genes: comparative genomic sequence analysis and identification of a novel gene regulatory element. 
  • Human evolution is biological & technological evolution. 
  • Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing. 
  • Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. 
  • Human sterile alpha motif domain 9, a novel gene identified as down-regulated in aggressive fibromatosis, is absent in the mouse. 
  • Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain. 
  • Hydrogen peroxide biosensor based on microperoxidase-11 entrapped in lipid membrane. 
  • IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. 
  • IN SILICO PHENOTYPIC SCREENING METHOD OF MUTANTS BASED ON STATISTICAL MODELING OF GENETICALLY MIXED SAMPLES 
  • Identification and isolation of differentially expressed genes from very small tissue samples. 
  • Identification and utilization of arbitrary correlations in models of recombination signal sequences. 
  • Identification of co-regulated transcripts affecting male body size in Drosophila. 
  • Identification of host-induced pathogen genes by differential fluorescence induction reporter systems. 
  • Identification of key concepts in biomedical literature using a modified Markov heuristic 
  • Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. 
  • Identification of osteopontin-dependent signaling pathways in a mouse model of human breast cancer. 
  • Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals. 
  • Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral. 
  • Identifying determinants of persistent MRSA bacteremia using mathematical modeling. 
  • Identifying potential tumor markers and antigens by database mining and rapid expression screening. 
  • Impact of maternal breast cancer on school-aged children in Saudi Arabia. 
  • Importance sampling for the infinite sites model. 
  • Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. 
  • Improved transcript isoform discovery using ORF graphs. 
  • Improving peptide-MHC class I binding prediction for unbalanced datasets. 
  • Improving the modeling of disease data from the government surveillance system: a case study on malaria in the Brazilian Amazon. 
  • In silico experimentation with a model of hepatic mitochondrial folate metabolism. 
  • In vivo optical molecular imaging and analysis in mice using dorsal window chamber models applied to hypoxia, vasculature and fluorescent reporters. 
  • In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors. 
  • Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models. 
  • Infectious pathogen detection arrays: viral detection in cell lines and postmortem brain tissue. 
  • Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. 
  • Informative priors based on transcription factor structural class improve de novo motif discovery. 
  • Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. 
  • Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. 
  • Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. 
  • Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. 
  • Integrating statistical pair potentials into protein complex prediction. 
  • Integrative Pathway Analysis Using Graph-Based Learning with Applications to TCGA Colon and Ovarian Data. 
  • Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility. 
  • Integrative pathway analysis using Graph-Based learning with applications to TCGA colon and ovarian data 
  • Interpolated markov chains for eukaryotic promoter recognition. 
  • Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data. 
  • Joint eQTL assessment of whole blood and dura mater tissue from individuals with Chiari type I malformation. 
  • Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. 
  • Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage 
  • Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage. 
  • Kilohertz waveforms optimized to produce closed-state Na+ channel inactivation eliminate onset response in nerve conduction block. 
  • KinImmerse: Macromolecular VR for NMR ensembles. 
  • Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. 
  • Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers. 
  • Latent goal models for dynamic strategic interaction. 
  • Learning phenotype densities conditional on many interacting predictors. 
  • Learning protein-DNA interaction landscapes by integrating experimental data through computational models. 
  • Less is more: compact genomes pay dividends. 
  • Lessons learned through piloting a community-based SMS referral system for common mental health disorders used by female community health volunteers in rural Nepal. 
  • Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. 
  • Leveraging prior information to detect causal variants via multi-variant regression. 
  • Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling. 
  • Lift and Drag Acting on the Shell of the American Horseshoe Crab (Limulus polyphemus). 
  • Linear algebraic transformations of the bidomain equations: implications for numerical methods. 
  • Linear latent structure analysis and modelling of multiple categorical variables 
  • Lipid membrane immobilized horseradish peroxidase biosensor for amperometric determination of hydrogen peroxide. 
  • Live-cell confocal microscopy and quantitative 4D image analysis of anchor-cell invasion through the basement membrane in Caenorhabditis elegans. 
  • Localized delivery of DNA to the cells by viral collagen-loaded silica colloidal crystals. 
  • Low frequency of paleoviral infiltration across the avian phylogeny. 
  • MAGI: a Node. js web service for fast MicroRNA-Seq Analysis in a GPU Infrastructure 
  • MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. 
  • MPDA: microarray pooled DNA analyzer. 
  • Magellan: a web based system for the integrated analysis of heterogeneous biological data and annotations; application to DNA copy number and expression data in ovarian cancer. 
  • Magnetic separation to concentrate the estrogen receptor from adipose tissue for western analysis. 
  • Making sense of microarrays. 
  • Managing Multi-center Flow Cytometry Data for Immune Monitoring. 
  • Mapping eQTL by leveraging multiple tissues and DNA methylation. 
  • Mapping nucleosome positions using DNase-seq. 
  • Mapping the complexity of transcription control in higher eukaryotes. 
  • Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. 
  • Matching isotopic distributions from metabolically labeled samples. 
  • Mathematical analysis of the regulation of competing methyltransferases. 
  • Mathematical model insights into arsenic detoxification 
  • Mathematical model insights into arsenic detoxification. 
  • Mathematical modeling of perifusion cell culture experiments on GnRH signaling. 
  • Mathematical modeling of the Phoenix Rising pathway. 
  • Mathematical modeling of the effects of glutathione on arsenic methylation. 
  • Maximization of signal derived from cDNA microarrays. 
  • Maximum urine concentrating capability in a mathematical model of the inner medulla of the rat kidney. 
  • Medical cost trajectories and onsets of cancer and noncancer diseases in US elderly population. 
  • Medical student opinions on character development in medical education: a national survey. 
  • Memory capacity of networks with stochastic binary synapses. 
  • Memory maintenance in synapses with calcium-based plasticity in the presence of background activity. 
  • Mesoscopic hydrogel molding to control the 3D geometry of bioartificial muscle tissues. 
  • Metabolic pattern formation in the tumor microenvironment. 
  • Metabolic rewiring drives resistance to targeted cancer therapy. 
  • Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results. 
  • Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data. 
  • Metaprotein expression modeling for label-free quantitative proteomics. 
  • Methods for generating and colonizing gnotobiotic zebrafish. 
  • Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group. 
  • Methods for the purification and direct transformation of epithelial progenitor cells from primary human prostate 
  • Micro flow bio-molecular computation. 
  • Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. 
  • Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha. 
  • Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study. 
  • Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study 
  • Mining the Gene Wiki for functional genomic knowledge. 
  • Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data. 
  • Mlcoalsim: multilocus coalescent simulations. 
  • Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies. 
  • Modeling biological systems using Dynetica--a simulator of dynamic networks. 
  • Modeling cancer progression via pathway dependencies. 
  • Modeling endocrine control of the pituitary-ovarian axis: androgenic influence and chaotic dynamics. 
  • Modeling hepatitis C virus protein and p53 interactions in hepatocytes: Implications for carcinogenesis. 
  • Modeling longitudinal data on health aging and life span 
  • Modeling mutant phenotypes and oscillatory dynamics in the Saccharomyces cerevisiae cAMP-PKA pathway. 
  • Modeling the biochemical differences between rabbit muscle and human liver phosphorylase. 
  • Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. 
  • Modelling regulatory pathways in E. coli from time series expression profiles. 
  • Modification of a cylindrical bidomain model for cardiac tissue. 
  • Modulation of network excitability by persistent activity: how working memory affects the response to incoming stimuli. 
  • Molprobity's ultimate rotamer-library distributions for model validation. 
  • Monitoring protein conformational changes and dynamics using stable-isotope labeling and mass spectrometry. 
  • Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. 
  • Multiple testing for gene sets from microarray experiments. 
  • Multistable dynamics mediated by tubuloglomerular feedback in a model of coupled nephrons. 
  • Myocardial infarction and intramyocardial injection models in swine. 
  • Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair. 
  • Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork. 
  • Network-based SNP meta-analysis identifies joint and disjoint genetic features across common human diseases. 
  • Neuron's eye view: Inferring features of complex stimuli from neural responses. 
  • Neuroprosthetic Decoder Training as Imitation Learning. 
  • New stochastic carcinogenesis model with covariates: an approach involving intracellular barrier mechanisms. 
  • New techniques for DNA sequence classification. 
  • Next generation distributed computing for cancer research. 
  • Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications. 
  • Noise reduction by diffusional dissipation in a minimal quorum sensing motif. 
  • Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. 
  • Norepinephrine transport-mediated gene expression in noradrenergic neurogenesis. 
  • Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation. 
  • Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping. 
  • Numerical simulation of propagating concentration profiles in renal tubules. 
  • Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans. 
  • Observation of dually decoded regions of the human genome using ribosome profiling data. 
  • On the maternal transmission of immunity: A ‘molecular attention’ hypothesis 
  • OntologyWidget - a reusable, embeddable widget for easily locating ontology terms. 
  • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. 
  • Open source tools and toolkits for bioinformatics: significance, and where are we? 
  • Optical aberrations and objective choice in multicolor confocal microscopy. 
  • Optimal properties of analog perceptrons with excitatory weights. 
  • Optimal tuning of bacterial sensing potential. 
  • Optimized mixed Markov models for motif identification. 
  • Optimized regimen for expression of heat-inducible Cre in mice. 
  • Ordinary Differential Equation Models for Adoptive Immunotherapy. 
  • Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse. 
  • Origin of bistability underlying mammalian cell cycle entry. 
  • PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. 
  • Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression. 
  • Parametric modeling of cellular state transitions as measured with flow cytometry. 
  • Parametric modeling of cellular state transitions as measured with flow cytometry. 
  • Pathway analysis using random forests classification and regression. 
  • Pathway analysis using random forests with bivariate node-split for survival outcomes 
  • Pathway analysis using random forests with bivariate node-split for survival outcomes. 
  • Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. 
  • Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. 
  • Phenotypic signatures arising from unbalanced bacterial growth. 
  • Phylogenetic footprint analysis of IGF2 in extant mammals. 
  • Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. 
  • Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. 
  • Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. 
  • Polarized monocyte response to cytokine stimulation. 
  • Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans. 
  • Post-translational regulation enables robust p53 regulation. 
  • Predicting HLA genotypes using unphased and flanking single-nucleotide polymorphisms in Han Chinese population. 
  • Predicting cell-type-specific gene expression from regions of open chromatin. 
  • Predicting gene structure changes resulting from genetic variants via exon definition features. 
  • Prediction and uncertainty in the analysis of gene expression profiles 
  • Prediction and uncertainty in the analysis of gene expression profiles. 
  • Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features. 
  • Prediction of a time-to-event trait using genome wide SNP data. 
  • Preparation of N-succinimidyl 3-[*I]iodobenzoate: an agent for the indirect radioiodination of proteins. 
  • Prevalence and correlates of proteinuria in Kampala, Uganda: a cross-sectional pilot study. 
  • Prevalence and risk factors associated with self-reported carpal tunnel syndrome (CTS) among office workers in Kuwait. 
  • Prevalence of transcription promoters within archaeal operons and coding sequences. 
  • Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. 
  • Principles of microRNA regulation of a human cellular signaling network. 
  • Principles that govern competition or co-existence in Rho-GTPase driven polarization. 
  • Probabilistic fluorescence-based synapse detection. 
  • Probabilistic modelling for estimating gas kinetics and decompression sickness risk in pigs during H2 biochemical decompression. 
  • Processing Oscillatory Signals by Incoherent Feedforward Loops. 
  • Programming stress-induced altruistic death in engineered bacteria. 
  • Projected t-SNE for batch correction. 
  • Promoter prediction on a genomic scale--the Adh experience. 
  • Propagation of fluctuations in biochemical systems, I: linear SSC networks. 
  • Propagation of fluctuations in biochemical systems, II: Nonlinear chains. 
  • Properties of overlapping genes are conserved across microbial genomes. 
  • Prospective health care: the second transformation of medicine. 
  • Protein loop closure using orientational restraints from NMR data. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Pulling the genome in opposite directions to dissect gene networks. 
  • Putative biomarkers for predicting tumor sample purity based on gene expression data. 
  • Pyruvate aldolases in chiral carbon-carbon bond formation. 
  • Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. 
  • Quantification of transcription factor expression from Arabidopsis images. 
  • Quantifying gene expression: the importance of being subtle 
  • Quantum dots-bienzyme hybrid system for the sensitive determination of glucose. 
  • Quantum mechanics simulation of protein dynamics on long timescale. 
  • R/BHC: fast Bayesian hierarchical clustering for microarray data. 
  • RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. 
  • RNA-Seq optimization with eQTL gold standards. 
  • RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L. 
  • RNA: An Expanding View of Function and Evolution. 
  • RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. 
  • Race and sex differences in small-molecule metabolites and metabolic hormones in overweight and obese adults. 
  • Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex. 
  • Random forests for genetic association studies. 
  • Rank order metrics for quantifying the association of sequence features with gene regulation. 
  • Rapid 16S ribosomal DNA sequencing from a single colony without DNA extraction or purification. 
  • Rapid purification of microtubule motor domain proteins expressed in bacteria. 
  • Recognition of unknown conserved alternatively spliced exons. 
  • Reconstructing spatiotemporal gene expression data from partial observations. 
  • Reconstructing the temporal ordering of biological samples using microarray data. 
  • Reconstruction of cell population dynamics using CFSE. 
  • Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. 
  • Refined localization of the cerebral cavernous malformation gene (CCM1) to a 4-cM interval of chromosome 7q contained in a well-defined YAC contig. 
  • Regression analysis of multiple protein structures 
  • Regression analysis of multiple protein structures. 
  • Regulation of signal duration and the statistical dynamics of kinase activation by scaffold proteins. 
  • Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network. 
  • Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. 
  • Reliability of transcriptional cycles and the yeast cell-cycle oscillator 
  • Reliability of transcriptional cycles and the yeast cell-cycle oscillator. 
  • Removable cranial windows for long-term imaging in awake mice. 
  • Repeated phenotypic changes highlight molecular targets of convergent evolution. 
  • Response nonlinearities in networks of spiking neurons. 
  • Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. 
  • Risk of dislocation using large- vs. small-diameter femoral heads in total hip arthroplasty 
  • Risk of dislocation using large- vs. small-diameter femoral heads in total hip arthroplasty. 
  • Robust test method for time-course microarray experiments. 
  • Robustness of MetaNet graph models: predicting control of urea production in humans. 
  • SAQC: SNP array quality control. 
  • SGP-1: prediction and validation of homologous genes based on sequence alignments. 
  • SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. 
  • SNP selection in genome-wide association studies via penalized support vector machine with MAX test. 
  • SNPs in Multi-species Conserved Sequences (MCS) as useful markers in association studies: a practical approach. 
  • SNPselector: a web tool for selecting SNPs for genetic association studies. 
  • SNiPA: an interactive, genetic variant-centered annotation browser. 
  • STDP in a bistable synapse model based on CaMKII and associated signaling pathways. 
  • SVA: software for annotating and visualizing sequenced human genomes. 
  • SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data. 
  • Sample size calculation for microarray experiments with blocked one-way design. 
  • Sample size for FDR-control in microarray data analysis. 
  • Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. 
  • Search for organising principles: understanding in systems biology. 
  • Security Assessment of Cyberphysical Digital Microfluidic Biochips. 
  • Segregation and mixing in degenerate diffusion in population dynamics 
  • Selection and validation of endogenous reference genes using a high throughput approach. 
  • Selection of optimal reference genes for normalization in quantitative RT-PCR. 
  • Self monitoring of blood glucose - A survey of diabetes UK members with type 2 diabetes who use SMBG 
  • Sensing and integration of Erk and PI3K signals by Myc. 
  • Sensitive DNA detection and SNP discrimination using ultrabright SERS nanorattles and magnetic beads for malaria diagnostics. 
  • Sequence features of DNA binding sites reveal structural class of associated transcription factor. 
  • Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. 
  • Sequence specificity incompletely defines the genome-wide occupancy of Myc. 
  • Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. 
  • Sequential gene profiling of basal cell carcinomas treated with imiquimod in a placebo-controlled study defines the requirements for tissue rejection. 
  • Serial dilution curve: a new method for analysis of reverse phase protein array data. 
  • Serotonin synthesis, release and reuptake in terminals: a mathematical model. 
  • Sex differences in hepatic one-carbon metabolism. 
  • SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. 
  • Signal duration and the time scale dependence of signal integration in biochemical pathways. 
  • Simple models of genomic variation in human SNP density. 
  • Simulation of aggregation in Dictyostelium using the Cell Programming Language. 
  • Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. 
  • Single-cell imaging of human cancer xenografts using adult immunodeficient zebrafish. 
  • Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo. 
  • Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning. 
  • Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. 
  • SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization. 
  • Spatial Measures of Genetic Heterogeneity During Carcinogenesis. 
  • Spatial Moran models, II: cancer initiation in spatially structured tissue. 
  • Spatial preferences of microRNA targets in 3' untranslated regions. 
  • SplicerAV: a tool for mining microarray expression data for changes in RNA processing. 
  • Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. 
  • Stability selection for regression-based models of transcription factor-DNA binding specificity. 
  • Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling. 
  • Stakeholder Perspectives on Public Health Genomics Applications for Sickle Cell Disease: A Methodology for a Human Heredity and Health in Africa (H3Africa) Qualitative Research Study 
  • Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. 
  • Statistical analysis of RNA backbone. 
  • Statistical analysis of antigen receptor spectratype data. 
  • Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. 
  • Statistical characterization of protein ensembles. 
  • Statistical estimation of statistical mechanical models: helix-coil theory and peptide helicity prediction. 
  • Stochastic model for analysis of longitudinal data on aging and mortality. 
  • Storage of correlated patterns in standard and bistable Purkinje cell models. 
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. 
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. 
  • Stratified pathway analysis to identify gene sets associated with oral contraceptive use and breast cancer. 
  • Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation. 
  • Structural adaptation and heterogeneity of normal and tumor microvascular networks. 
  • Structural analysis, identification, and design of calcium-binding sites in proteins. 
  • Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes. 
  • Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin. 
  • Structure of 2C-methyl-D-erythrol-2,4-cyclodiphosphate synthase from Haemophilus influenzae: activation by conformational transition. 
  • Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot. 
  • Structure validation by Calpha geometry: phi,psi and Cbeta deviation. 
  • Structure-based classification of 45 FK506-binding proteins. 
  • Studying health histories of cancer: a new model connecting cancer incidence and survival. 
  • Substrate recognition by the EcoRI endonuclease. 
  • Surface engineering for efficient capture of circulating tumor cells in renal cell carcinoma: From nanoscale analysis to clinical application. 
  • Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. 
  • Synchronous luminescence: a new detection technique for multiple fluorescent probes used for DNA sequencing. 
  • Synthesis of N-succinimidyl 4-[18F]fluorobenzoate, an agent for labeling proteins and peptides with 18F. 
  • Synthesis of N-succinimidyl 4-guanidinomethyl-3-[*I]iodobenzoate: a radio-iodination agent for labeling internalizing proteins and peptides. 
  • Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions. 
  • Systematic solution to homo-oligomeric structures determined by NMR. 
  • T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. 
  • Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). 
  • Target domain definition and classification in CASP8. 
  • Taste and pheromone perception in mammals and flies. 
  • Temporal control of self-organized pattern formation without morphogen gradients in bacteria. 
  • Ten Simple Rules for Effective Statistical Practice. 
  • Tension and robustness in multitasking cellular networks. 
  • The Software Section. 
  • The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. 
  • The 2006 NESCent Phyloinformatics Hackathon: A Field Report. 
  • The 2015 Bioinformatics Open Source Conference (BOSC 2015). 
  • The Bioinformatics Open Source Conference (BOSC) 2013. 
  • The Bioperl toolkit: Perl modules for the life sciences. 
  • The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. 
  • The LabBase system for data management in large scale biology research laboratories. 
  • The Local Edge Machine: inference of dynamic models of gene regulation. 
  • The MetJ regulon in gammaproteobacteria determined by comparative genomics methods. 
  • The Multiscale Systems Immunology project: software for cell-based immunological simulation. 
  • The Nubeam reference-free approach to analyze metagenomic sequencing reads. 
  • The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon. 
  • The STEDMAN project: biophysical, biochemical and metabolic effects of a behavioral weight loss intervention during weight loss, maintenance, and regain. 
  • The Sox10(Dom) mouse: modeling the genetic variation of Waardenburg-Shah (WS4) syndrome. 
  • The anatomy of microbial cell state transitions in response to oxygen. 
  • The biochemistry of acetaminophen hepatotoxicity and rescue: a mathematical model. 
  • The birth of the Epitranscriptome: deciphering the function of RNA modifications. 
  • The cis-Pro touch-turn: a rare motif preferred at functional sites. 
  • The constructal law and the evolution of design in nature. 
  • The constructal law makes biology and economics be like physics. Reply to comments on "The constructal law and the evolution of design in nature" 
  • The constructal unification of biological and geophysical design. 
  • The cyclophilins. 
  • The dynamics of T-cell receptor repertoire diversity following thymus transplantation for DiGeorge anomaly. 
  • The effect of polar lipids on tear film dynamics. 
  • The effect of the organisms' body size and energy reserves in models for population dynamics 
  • The effects of health histories on stochastic process models of aging and mortality. 
  • The electrical conductivity of phospholipid films as an iodine-sensing mechanism. 
  • The evolutionary dynamics of alpha-satellite. 
  • The evolutionary forest algorithm. 
  • The histone deacetylase inhibitor trichostatin a decreases lymphangiogenesis by inducing apoptosis and cell cycle arrest via p21-dependent pathways 
  • The human olfactory transcriptome. 
  • The influence of a consumer-wearable activity tracker on sedentary time and prolonged sedentary bouts: secondary analysis of a randomized controlled trial. 
  • The inoculum effect and band-pass bacterial response to periodic antibiotic treatment. 
  • The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. 
  • The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. 
  • The location of olfactory receptors within olfactory epithelium is independent of odorant volatility and solubility. 
  • The origins and genomic diversity of American Civil War Era smallpox vaccine strains. 
  • The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. 
  • The penultimate rotamer library. 
  • The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. 
  • The quadratic hazard model for analyzing longitudinal data on aging, health, and the life span. 
  • The role of local backrub motions in evolved and designed mutations. 
  • The statistics of bulk segregant analysis using next generation sequencing. 
  • The surface of beta-sheet proteins contains amphiphilic regions which may provide clues about protein folding. 
  • The transport of organelles in axons 
  • The use of an inexpensive processing aid device (the Mouse PAD) to facilitate rodent tissue banking. 
  • The uses of green fluorescent protein in prokaryotes. 
  • The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms. 
  • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage 
  • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. 
  • Theoretical and practical advances in genome halving. 
  • Thermodynamic analysis of protein-ligand binding interactions in complex biological mixtures using the stability of proteins from rates of oxidation. 
  • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders 
  • Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation. 
  • Transcriptomic profiles of aging in purified human immune cells. 
  • Translational Bioinformatics: Past, Present, and Future. 
  • Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. 
  • Transversions have larger regulatory effects than transitions. 
  • UV absorption complicates PCR decontamination. 
  • Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation. 
  • Unmasking a role for sex chromosomes in gene silencing. 
  • Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist. 
  • Unsupervised Bayesian linear unmixing of gene expression microarrays. 
  • Using context to improve protein domain identification. 
  • Using dynamic programming to create isotopic distribution maps from mass spectra. 
  • Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients. 
  • Visualization of cortical, subcortical and deep brain neural circuit dynamics during naturalistic mammalian behavior with head-mounted microscopes and chronically implanted lenses. 
  • Wavelet variations on the Shannon sampling theorem. 
  • WebGLORE: a web service for Grid LOgistic REgression. 
  • What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). 
  • Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. 
  • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. 
  • Whole-genome reconstruction and mutational signatures in gastric cancer. 
  • X-ray structure of Arabidopsis At1g77680, 12-oxophytodienoate reductase isoform 1. 
  • YbiV from Escherichia coli K12 is a HAD phosphatase. 
  • ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. 
  • ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. 
  • bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens. 
  • chngpt: threshold regression model estimation and inference. 
  • cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. 
  • fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies. 
  • lambda RNA internal standards quantify sensitivity and amplification efficiency of mammalian gene expression profiling. 
  • lumi: a pipeline for processing Illumina microarray. 
  • meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays. 
  • miR-27b shapes the presynaptic transcriptome and influences neurotransmission by silencing the polycomb group protein Bmi1. 
  • nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. 
  • permGPU: Using graphics processing units in RNA microarray association studies. 
  • rqt: an R package for gene-level meta-analysis. 
  • stpm: an R package for stochastic process model. 
• 

  Keywords of People

  • Arnold, Matthias, Adjunct Assistant Professor in the Department of Psychiatry and Behavioral Sciences, Psychiatry & Behavioral Sciences, Behavioral Medicine
  • Bhavsar, Nrupen, Assistant Professor in Medicine, Duke Science & Society
  • Kibbe, Warren Alden, Professor in Biostatistics and Bioinformatics, Biostatistics & Bioinformatics
  • Mangan, Riley, Student, Basic Science Departments
  • Schickling, Brandon, Postdoctoral Scholar, Medicine, Cardiology
  • Tchapyjnikov, Dmitry, Assistant Professor of Pediatrics, Pediatrics, Neurology
  • Tenenbaum, Jessica Dale, Assistant Professor of Biostatistics & Bioinformatics, Duke Science & Society
  • Wu, Qingrong, Professor of Radiation Oncology, Radiation Oncology
  • Yin, Fang-Fang, Professor in Radiation Oncology, Radiation Oncology