subject area of

• A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana  Academic Article
• A comparison of match-only algorithms for the analysis of plasmodium falciparum oligonucleotide arrays  Academic Article
• A compass for stem-cell differentiation  Academic Article
• A correlation algorithm for the automated quantitative analysis of shotgun proteomics data  Academic Article
• A covering method for detecting genetic associations between rare variants and common phenotypes  Academic Article
• A density functional evaluation of an Fe(III)-Fe(IV) model diiron cluster: comparisons with ribonucleotide reductase intermediate X  Academic Article
• A highly informative snp linkage panel for human genetic studies  Academic Article
• A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry  Academic Article
• A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks  Academic Article
• A novel in silico approach to drug discovery via computational intelligence  Academic Article
• A novel method for finding tRNA genes  Academic Article
• A perspective on mechanisms of protein tetramer formation  Academic Article
• A population response analysis approach to assign class II HLA-epitope restrictions  Academic Article
• A quantitative analysis software tool for mass spectrometry-based proteomics  Academic Article
• A relational database for cryoem: Experience at one year and 50 000 images  Academic Article
• A robust hybrid between genetic algorithm and support vector machine for extracting an optimal feature gene subset  Academic Article
• A semiempirical free energy force field with charge-based desolvation  Academic Article
• A statistical approach to computer processing of cryo-electron microscope images: Virion classification and 3-d reconstruction  Academic Article
• A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum  Academic Article
• A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy  Academic Article
• A very large diversity space of synthetically accessible compounds for use with drug design programs  Academic Article
• APSY-NMR with proteins: practical aspects and backbone assignment  Academic Article
• ATP binding turns plant cryptochrome into an efficient natural photoswitch  Academic Article
• Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data  Academic Article
• Accurate scoring of non-uniform sampling schemes for quantitative NMR  Academic Article
• Ace: Automated ctf estimation  Academic Article
• Acute ischemic heart disease - cardiogenic shock complicating acute myocardial infarction: Predictors of death  Academic Article
• Adaptive partitioning QM/MM dynamics simulations for substrate uptake, product release, and solvent exchange  Academic Article
• Adult mouse brain gene expression patterns bear an embryologic imprint  Academic Article
• Advances in Analysis of Low Signal-to-Noise Images Link Dynamin and AP2 to the Functions of an Endocytic Checkpoint  Academic Article
• Advancing computational biology and bioinformatics research through open innovation competitions  Academic Article
• Aging-related differences in chondrocyte viscoelastic properties  Academic Article
• Air medical response to traumatic brain injury: a computer learning algorithm analysis  Academic Article
• Algorithm of myogenic differentiation in higher-order organisms  Academic Article
• Algorithms for automated DNA assembly  Academic Article
• Amnesia or retrieval deficit? Implications of a molecular approach to the question of reconsolidation  Academic Article
• An adjustable-threshold algorithm for the identification of objects in three-dimensional images  Academic Article
• An automated procedure for detecting protein folds from sub-nanometer resolution electron density  Academic Article
• An ensemble method for gene discovery based on DNA microarray data  Academic Article
• An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction  Academic Article
• Analysis of microtubule dynamic instability using a plus-end growth marker  Academic Article
• Artificial intelligence versus clinicians: systematic review of design, reporting standards, and claims of deep learning studies  Academic Article
• Assessment of sperm chemokinesis with exposure to jelly coats of sea urchin eggs and resact: a microfluidic experiment and numerical study  Academic Article
• AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading  Academic Article
• AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility  Academic Article
• Automated analysis of hypocotyl growth dynamics during shade avoidance in Arabidopsis  Academic Article
• Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra  Academic Article
• Automated conformational energy fitting for force-field development  Academic Article
• Automated identification of filaments in cryoelectron microscopy images  Academic Article
• Automated identification of functional dynamic contact networks from X-ray crystallography  Academic Article
• Automated peak picking and peak integration in macromolecular NMR spectra using autopsy  Academic Article
• Automated protein NMR structure determination in crude cell-extract  Academic Article
• Automated resonance assignment of proteins: 6d apsy-NMR  Academic Article
• Automated sequence-specific protein NMR assignment using the memetic algorithm match  Academic Article
• Automated structure refinement for a protein heterodimer complex using limited EPR spectroscopic data and a rigid-body docking algorithm: a three-dimensional model for an ankyrin-CDB3 complex  Academic Article
• Automated three-dimensional reconstruction of keyhole limpet hemocyanin type 1  Academic Article
• Automatic annotation of matrix-assisted laser desorption/ionization n-glycan spectra  Academic Article
• Automatic particle detection through efficient hough transforms  Academic Article
• Automatic particle selection: results of a comparative study  Academic Article
• Automatic quality assessment of peptide tandem mass spectra  Academic Article
• Automatic validation of phosphopeptide identifications from tandem mass spectra  Academic Article
• Automation in single-particle electron microscopy: connecting the pieces  Academic Article
• BCL::Align: sequence alignment and fold recognition with a custom scoring function online  Academic Article
• Balancing bond, nonbond, and go-like terms in coarse grain simulations of conformational dynamics  Academic Article
• Biochemistry. Integrative structural biology  Academic Article
• Biogenesis of the secretory granule: Chromogranin a coiled-coil structure results in unusual physical properties and suggests a mechanism for granule core condensation  Academic Article
• Biologically relevant molecular transducer with increased computing power and iterative abilities  Academic Article
• Building self-avoiding lattice models of proteins using a self-consistent field optimization  Academic Article
• CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma  Academic Article
• CTF Challenge: Result summary  Academic Article
• Cardiogenic shock complicating acute coronary syndromes  Academic Article
• Cell, isoform, and environment factors shape gradients and modulate chemotaxis  Academic Article
• Central limit theorem as an approximation for intensity-based scoring function  Academic Article
• Chaos and complexity - can it help us to understand mood and behavior  Academic Article
• Characterization of Fe(III) sequestration by an analog of the cytotoxic siderophore brasilibactin A: Implications for the iron transport mechanism in mycobacteria  Academic Article
• Chemogenomic profiling on a genomewide scale using reverse-engineered gene networks  Academic Article
• Cluster analysis of antigenic profiles of tumors: selection of number of clusters using Akaike's information criterion  Academic Article
• Clusters of bioactive compounds target dynamic endomembrane networks in vivo  Academic Article
• CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data  Academic Article
• Coarse-grained peptide modeling using a systematic multiscale approach  Academic Article
• Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search  Academic Article
• Combining h/d exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase  Academic Article
• Comparative analysis of haplotype association mapping algorithms  Academic Article
• Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold  Academic Article
• Computational analysis of crystallization trials  Academic Article
• Computational coevolution of antiviral drug resistance  Academic Article
• Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells  Academic Article
• Computational design of proteins targeting the conserved stem region of influenza hemagglutinin  Academic Article
• Computational prediction of N-linked glycosylation incorporating structural properties and patterns  Academic Article
• Computer vision's potential to improve health care  Academic Article
• Computer-assisted versus manual alignment in THA: a probabilistic approach to range of motion  Academic Article
• Consensus generation and variant detection by celera assembler  Academic Article
• Constructing lattice models of protein chains with side groups  Academic Article
• Contributions from hydration of carboxylate groups to the spectrum of water polypeptide proton proton overhauser effects in aqueous-solution  Academic Article
• Creep of trabecular bone from the human proximal tibia  Academic Article
• Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra  Academic Article
• Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates  Academic Article
• DFT calculations of comparative energetics and ENDOR/Mossbauer properties for two protonation states of the iron dimer cluster of ribonucleotide reductase intermediate X  Academic Article
• DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals  Academic Article
• DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics  Academic Article
• De novo computational design of retro-aldol enzymes  Academic Article
• Deconvolution of complex 1D NMR spectra using objective model selection  Academic Article
• Density functional study of a mu-1,1-carboxylate bridged Fe(III)-O-Fe(IV) model complex. 2. Comparison with ribonucleotide reductase intermediate X  Academic Article
• Detailed analysis of grid-based molecular docking: a case study of CDOCKER - A CHARMm-based MD docking algorithm  Academic Article
• Detecting genetic variation in microarray expression data  Academic Article
• Determination of binding affinities of triplex forming oligonucleotides using a fluorescent intercalator displacement (FID) assay  Academic Article
• Determination of monoclonality from sequential dilution assays  Academic Article
• Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes  Academic Article
• Development of a blood-based gene expression algorithm for assessment of obstructive coronary artery disease in non-diabetic patients  Academic Article
• Direct analysis of protein complexes using mass spectrometry  Academic Article
• Discovery of functional genomic motifs in viruses with ViReMa-a Virus Recombination Mapper-for analysis of next-generation sequencing data  Academic Article
• Distributed torsion angle grid search in high dimensions: A systematic approach to NMR structure determination  Academic Article
• Disubstituted 1-aryl-4-aminopiperidine library synthesis using computational drug design and high-throughput batch and flow technologies  Academic Article
• Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation  Academic Article
• Docking of 4-oxalocrotonate tautomerase substrates: implications for the catalytic mechanism  Academic Article
• Does contamination buildup limit throughput for automated cryoEM?  Academic Article
• Dosage optimization of treatments using population pharmacokinetic modeling and simulation  Academic Article
• Dynamics in cryo em reconstructions visualized with maximum-likelihood derived variance maps  Academic Article
• Easybound - a user-friendly approach to nonlinear regression analysis of binding data  Academic Article
• Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations  Academic Article
• Efficient computation of 3-dimensional protein structures in solution from nuclear-magnetic-resonance data using the program diana and the supporting programs caliba, habas and glomsa  Academic Article
• Efficient computation of patterned covariance-matrix mixed models in quantitative segregation analysis  Academic Article
• Electronically subtracting expression patterns from a mixed cell population  Academic Article
• Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins  Academic Article
• Encoding and processing of alphanumeric information by chemical mixtures  Academic Article
• Engineered DNA sequence syntax inspector  Academic Article
• Enhancing MALDI time-of-flight mass spectrometer performance through spectrum averaging  Academic Article
• Enrichment of regulatory signals in conserved non-coding genomic sequence  Academic Article
• Envelope: Interactive software for modeling and fitting complex isotope distributions  Academic Article
• Estimation of parameters for a mathematical model of growth hormone secretion  Academic Article
• Eugene: a domain specific language for specifying and constraining synthetic biological parts, devices, and systems  Academic Article
• Exact reduced-complexity maximum likelihood reconstruction of multiple 3-d objects from unlabeled unoriented 2-d projections and electron microscopy of viruses  Academic Article
• Expanding the scope of noninvasive prenatal testing: detection of fetal microdeletion syndromes  Academic Article
• Expanding the scope of noninvasive prenatal testing: detection of fetal microdeletion syndromes  Academic Article
• Experimental and DFT studies: novel structural modifications greatly enhance the solvent sensitivity of live cell imaging dyes  Academic Article
• Exploration of structural features of monomeric helical peptides designed with a genetic algorithm  Academic Article
• FUBAR: a fast, unconstrained Bayesian approximation for inferring selection  Academic Article
• Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE  Academic Article
• Fast docking on graphics processing units via Ray-Casting  Academic Article
• Fourier-ring descriptor to characterize rare circulating cells from images generated using immunofluorescence microscopy  Academic Article
• From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics  Academic Article
• GPCR stabilization using the bicelle-like architecture of mixed sterol-detergent micelles  Academic Article
• Games with a scientific purpose  Academic Article
• GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome  Academic Article
• Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?  Academic Article
• Glycan fingerprints: Calculating diversity in glycan libraries  Academic Article
• GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model  Academic Article
• HDX workbench: software for the analysis of H/D exchange MS data  Academic Article
• Haplotype-phased synthetic long reads from short-read sequencing  Academic Article
• Heterogeneity of functional groups in a metal-organic framework displays magic number ratios  Academic Article
• Hierarchical and multi-resolution representation of protein flexibility  Academic Article
• Hiers: Hierarchical scaffold clustering using topological chemical graphs  Academic Article
• High-throughput quantitative histological analysis of alzheimer's disease pathology using a confocal digital microscanner  Academic Article
• Highly selective Diels-Alder reactions of directly connected enyne dienophiles  Academic Article
• Human germline antibody gene segments encode polyspecific antibodies  Academic Article
• Human immunodeficiency virus type 1 elite neutralizers: Individuals with broad and potent neutralizing activity identified by using a high-throughput neutralization assay together with an analytical selection algorithm  Academic Article
• IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform  Academic Article
• Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data  Academic Article
• Identification of novel targets for miR-29a using miRNA proteomics  Academic Article
• Identification of rare cancer driver mutations by network reconstruction  Academic Article
• Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks  Academic Article
• Identifying differences in protein expression levels by spectral counting and feature selection  Academic Article
• Impact of ion trap tandem mass spectra variability on the identification of peptides  Academic Article
• Improved crystallographic structures using extensive combinatorial refinement  Academic Article
• Improving the TFold test for differential shotgun proteomics  Academic Article
• Improving the positional accuracy of the goniometer on the philips cm series tem  Academic Article
• In silico discovery of transcription regulatory elements in plasmodium falciparum  Academic Article
• In silico gene function prediction using ontology-based pattern identification  Academic Article
• In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses  Academic Article
• In vivo virus structures: Simultaneous classification, resolution enhancement, and noise reduction in whole-cell electron tomography  Academic Article
• Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure  Academic Article
• Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides  Academic Article
• Informatics and multiplexing of intact protein identification in bacteria and the archaea  Academic Article
• Infrared line shape of an alpha-carbon deuterium-labeled amino acid  Academic Article
• Inter-protein sequence co-evolution predicts known physical interactions in bacterial ribosomes and the trp operon  Academic Article
• Involvement of 5-ht3 receptors in the development and expression of methamphetamine-induced behavioral sensitization: 5-ht3a receptor channel and binding study  Academic Article
• Kinetic-analysis of the ca-2+-dependent, membrane-bound, macrophage phospholipase-a2 and the effects of arachidonic-acid  Academic Article
• Large-scale analysis of the yeast proteome by multidimensional protein identification technology  Academic Article
• Large-scate database searching using tandem mass spectra: looking up the answer in the back of the book  Academic Article
• Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy  Academic Article
• Letter to the editor: NMR structure determination of the hypothetical protein TM1290 from Thermotoga maritima using automated NOESY analysis  Academic Article
• Ligand-guided receptor optimization  Academic Article
• Likelihood-based classification of cryo-EM images using FREALIGN  Academic Article
• Limestone: high-throughput candidate phenotype generation via tensor factorization  Academic Article
• Liquid chromatography-fourier transform ion cyclotron resonance mass spectrometric characterization of protein kinase c phosphorylation  Academic Article
• Local quality assessment in homology models using statistical potentials and support vector machines  Academic Article
• Loop modeling: sampling, filtering, and scoring  Academic Article
• MDB: The metalloprotein database and browser at The Scripps Research Institute  Academic Article
• Magnetically assisted and accelerated self-assembly of strawberry-like nano/microparticles  Academic Article
• Measuring meals: Structure of prandial food and water intake of rats  Academic Article
• Metabolomic data streaming for biology-dependent data acquisition  Academic Article
• Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis  Academic Article
• Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database  Academic Article
• Microchip bioprocessor for integrated nanovolume sample purification and DNA sequencing  Academic Article
• Minimizing the risk of inappropriately administering thrombolytic therapy (thrombolysis and angioplasty in myocardial-infarction tami study-group)  Academic Article
• Molecular recognition and binding free energy calculations in drug development  Academic Article
• Monitoring jet engines and the health of people  Academic Article
• Multi-scale correlation structure of gene expression in the brain  Academic Article
• Multicenter validation of the diagnostic accuracy of a blood-based gene expression test for assessing obstructive coronary artery disease in nondiabetic patients  Academic Article
• Multiclass maximum-likelihood symmetry determination and motif reconstruction of 3-d helical objects from projection images for electron microscopy  Academic Article
• Multiple sequence assembly from reads alignable to a common reference genome  Academic Article
• Muscle synergies may improve optimization prediction of knee contact forces during walking  Academic Article
• Native atom types for knowledge-based potentials: application to binding energy prediction  Academic Article
• Networks link antigenic and receptor-binding sites of influenza hemagglutinin: Mechanistic insight into fitter strain propagation  Academic Article
• Non-invasive prenatal detection of trisomy 13 using a single nucleotide polymorphism- and informatics-based approach  Academic Article
• Nonstimulatory peptides contribute to antigen-induced CD8-T cell receptor interaction at the immunological synapse  Academic Article
• Novel computational methods for increasing pcr primer design effectiveness in directed sequencing  Academic Article
• Nuclear membrane proteins with potential disease links found by subtractive proteomics  Academic Article
• Numerical Matrices Method for nonlinear system identification and description of dynamics of biochemical reaction networks  Academic Article
• Optimod: An automated approach for constructing and optimizing initial models for single-particle electron microscopy  Academic Article
• Origin and correction of magnetic field inhomogeneity at the interface in biphasic NMR samples  Academic Article
• PDZ domain binding selectivity is optimized across the mouse proteome  Academic Article
• PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data  Academic Article
• PepExplorer: a similarity-driven tool for analyzing de novo sequencing results  Academic Article
• Peptide backbone sampling convergence with the adaptive biasing force algorithm  Academic Article
• Peptide mass maps: a highly informative approach to protein identification  Academic Article
• Periodic patterns of actin turnover in lamellipodia and lamellae of migrating epithelial cells analyzed by quantitative Fluorescent Speckle Microscopy  Academic Article
• Perspectives: protein synthesis. All you need is RNA  Academic Article
• Phoelix - a package for semiautomated helical reconstruction  Academic Article
• Population pharmacokinetics of atazanavir in patients with human immunodeficiency virus infection  Academic Article
• Population structure, admixture, and aging-related phenotypes in african american adults: The cardiovascular health study  Academic Article
• Posttranslational modifications in the CP43 subunit of photosystem II  Academic Article
• Potential beneficial metabolic interactions between tamoxifen and Isoflavones via cytochrome P450-mediated pathways in female rat liver microsomes  Academic Article
• Practical 4 '-phosphopantetheine active site discovery from proteomic samples  Academic Article
• Predicting molecular-interactions and inducible complementarity - fragment docking of fab-peptide complexes  Academic Article
• Predicting transcription factor synergism  Academic Article
• Predictors of cardiogenic shock after thrombolytic therapy for acute myocardial infarction  Academic Article
• Prestige centrality-based functional outlier detection in gene expression analysis  Academic Article
• ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity  Academic Article
• Probability of phenotypically detectable protein damage by ENU-induced mutations in the Mutagenetix database  Academic Article
• Probability-based validation of protein identifications using a modified SEQUEST algorithm  Academic Article
• Processing complex mixtures of intact proteins for direct analysis by mass spectrometry  Academic Article
• Prospective use of glycoprotein iib/iiia receptor blockers in the emergency department setting  Academic Article
• Protein NMR structure determination with automated noe assignment using the new software candid and the torsion angle dynamics algorithm dyana  Academic Article
• Protein NMR structure determination with automated noe-identification in the noesy spectra using the new software atnos  Academic Article
• Protein flexibility in virtual screening: the BACE-1 case study  Academic Article
• Protein identification using 2D-LC-MS/MS  Academic Article
• Protein structures in solution by nuclear-magnetic-resonance and distance geometry - the polypeptide fold of the basic pancreatic trypsin-inhibitor determined using 2 different algorithms, disgeo and disman  Academic Article
• Protein-protein docking with F(2)Dock 2.0 and GB-rerank  Academic Article
• Protein-protein interaction prediction by combined analysis of genomic and conservation information  Academic Article
• ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects  Academic Article
• Proteomic analysis of peptides tagged with dimedone and related probes  Academic Article
• Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae  Academic Article
• RNA origami  Academic Article
• RNAMotif, an RNA secondary structure definition and search algorithm  Academic Article
• Rapid, routine structure determination of macromolecular assemblies using electron microscopy: Current progress and further challenges  Academic Article
• Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 micron size X-ray synchrotron beam  Academic Article
• Real time surface reconstruction for moving molecular fragments  Academic Article
• Reciprocal space representations of helical objects and their projection images for helices constructed from motifs without spherical symmetry  Academic Article
• Regulatory networks define phenotypic classes of human stem cell lines  Academic Article
• Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery  Academic Article
• Replication dynamics of the yeast genome  Academic Article
• Revealing disease-associated pathways by network integration of untargeted metabolomics  Academic Article
• Robust scoring functions for protein-ligand interactions with quantum chemical charge models  Academic Article
• Robust single-particle tracking in live-cell time-lapse sequences  Academic Article
• Rosetta predictions in casp5: Successes, failures, and prospects for complete automation  Academic Article
• SDOCKER: A method utilizing existing X-ray structures to improve docking accuracy  Academic Article
• Search engine processor: filtering and organizing peptide spectrum matches  Academic Article
• Self-organizing neural networks bridge the biomolecular resolution gap  Academic Article
• Sequence and structure signatures of cancer mutation hotspots in protein kinases  Academic Article
• Sequence-specific NMR assignment of proteins by global fragment mapping with the program mapper  Academic Article
• Sequential nearest-neighbor effects on computed (13)Cα chemical shifts  Academic Article
• Shape complementarity of protein-protein complexes at multiple resolutions  Academic Article
• Short oligonucleotide probes containing g-stacks display abnormal binding affinity on affymetrix microarrays  Academic Article
• Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility  Academic Article
• Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq  Academic Article
• Single-mRNA counting using fluorescent in situ hybridization in budding yeast  Academic Article
• Single-nucleotide polymorphism-based noninvasive prenatal screening in a high-risk and low-risk cohort  Academic Article
• Site-directed combinatorial construction of chimaeric genes: general method for optimizing assembly of gene fragments  Academic Article
• Spreaders and sponges define metastasis in lung cancer: A Markov chain mathematical model  Academic Article
• Spreaders and sponges define metastasis in lung cancer: A markov chain mathematical model  Academic Article
• Stop the privatization of health data  Academic Article
• Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential  Academic Article
• Structure determination of the antp(c39- s) homeodomain from nuclear-magnetic-resonance data in solution using a novel strategy for the structure calculation with the programs diana, caliba, habas and glomsa  Academic Article
• Structure-based active site profiles for genome analysis and functional family subclassification  Academic Article
• Subject-specific knee joint geometry improves predictions of medial tibiofemoral contact forces  Academic Article
• Support for the open-artery hypothesis in survivors of acute myocardial infarction: Analysis of 11,228 patients treated with thrombolytic therapy  Academic Article
• Synergy of NMR, computation, and x-ray crystallography for structural biology  Academic Article
• Synthesis of isochrysohermidin-distamycin hybrids  Academic Article
• TagDock: an efficient rigid body docking algorithm for oligomeric protein complex model construction and experiment planning  Academic Article
• Tclust: A fast method for clustering genome-scale expression data  Academic Article
• The 2011 ABJS Nicolas Andry Award: 'Lab'-in-a-knee: in vivo knee forces, kinematics, and contact analysis  Academic Article
• The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis  Academic Article
• The DNA phosphate backbone is not involved in catalysis of the duocarmycin and CC-1065 DNA alkylation reaction  Academic Article
• The Ramachandran number: an order parameter for protein geometry  Academic Article
• The airborne metagenome in an indoor urban environment  Academic Article
• The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters  Academic Article
• The concordance index c and the mann-whitney parameter pr(x > y) with randomly censored data  Academic Article
• The fragile breakage versus random breakage models of chromosome evolution  Academic Article
• The impact of errors in copy number variation detection algorithms on association results  Academic Article
• The interdependence of protein surface-topography and bound water-molecules revealed by surface accessibility and fractal density measures  Academic Article
• The minnesota center for twin and family research genome-wide association study  Academic Article
• The origins of asymmetry in the folding transition states of protein L and protein G  Academic Article
• The parallelization of SPIDER on distributed-memory computers using MPI  Academic Article
• The reconstruction of helical particles with variable pitch  Academic Article
• The restoration of electron micrographs blurred by drift and rotation  Academic Article
• The sequence of the human genome  Academic Article
• The spectroscopic basis of fluorescence triple correlation spectroscopy  Academic Article
• TiMEx: a waiting time model for mutually exclusive cancer alterations  Academic Article
• Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network  Academic Article
• Torsion angle dynamics for NMR structure calculation with the new program dyana  Academic Article
• Toward objective evaluation of proteomic algorithms  Academic Article
• Towards precise classification of cancers based on robust gene functional expression profiles  Academic Article
• Transition to drug addiction: A negative reinforcement model based on an allostatic decrease in reward function  Academic Article
• Tyrosine hydroxylase, the rate-limiting enzyme in catecholamine biosynthesis - discovery of common human genetic variants governing transcription, autonomic activity, and blood pressure in vivo  Academic Article
• Ultrashort echo time magnetization transfer (UTE-MT) imaging of cortical bone  Academic Article
• Upgene: Application of a web-based DNA codon optimization algorithm  Academic Article
• Varid: A variation detection framework for color-space and letter-space platforms  Academic Article
• Virtual screening against acetylcholine binding protein  Academic Article
• Windex: A toolset for indexing helices  Academic Article
• XCMS2: Processing tandem mass spectrometry data for metabolite identification and structural characterization  Academic Article
• XDIA: improving on the label-free data-independent analysis  Academic Article
• Xcms: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification  Academic Article
• Xlandscape: The graphical display of word frequencies in sequences  Academic Article
• YADA: a tool for taking the most out of high-resolution spectra  Academic Article
• cellPACK: a virtual mesoscope to model and visualize structural systems biology  Academic Article
• ePMV embeds molecular modeling into professional animation software environments  Academic Article
• plusTipTracker: Quantitative image analysis software for the measurement of microtubule dynamics  Academic Article