Site: PubMed: Bioinformatics
- An Unsupervised Conditional Random Fields Approach for Clustering Gene Expression Time Series.
- MULTI-DIMENSIONAL CLASSIFICATION of BIOMEDICAL TEXT: Toward Automated, Practical Provision of High-Utility Text to Diverse Users.
- Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores.
- Eigen-R2 for Dissecting Variation in High-dimensional Studies.
- Local Coherence in Genetic Interaction Patterns Reveals Prevalent Functional Versatility.
- siDRM: an effective and generally applicable online siRNA design tool.
- cneViewer: A Database of Conserved Noncoding Elements for Studies of Tissue-Specific Gene Regulation.
- Seeder: Discriminative Seeding DNA Motif Discovery.
- Empirical profile mixture models for phylogenetic reconstruction.
- Novel Pathway Compendium Analysis Elucidates Mechanism of Pro-Angiogenic Synthetic Small Molecule.
- Analyzing Gene Perturbation Screens With Nested Effects Models in R and Bioconductor.
Site: PubMed: BMC Bioinformatics
- A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time.
- AccPbFRET: an ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images.
Site: PubMed: PLoS Comp. Biol.
- Coordinate regulation of G protein signaling via dynamic interactions of receptor and GAP.
- Regulatory control and the costs and benefits of biochemical noise.
- Classifying RNA-binding proteins based on electrostatic properties.
Site: Journal of Computational Biology - Table of Contents
- Preface
- Efficient Enumeration of Phylogenetically Informative Substrings
- Efficiently Computing the Robinson-Foulds Metric
- Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction
- Assessing Significance of Connectivity and Conservation in Protein Interaction Networks
- Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics
- Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination
- The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs
- Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length
- Simulating Protein Motions with Rigidity Analysis
- A Study of Accessible Motifs and RNA Folding Complexity
Site: EURASIP Journal on Bioinformatics and Systems Biology
- Using Temporal Correlation in Factor Analysis for Reconstructing Transcription Factor Activities
- Inference of Boolean Networks Using Sensitivity Regularization
- Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study
- Gene Regulatory Network Reconstruction Using Conditional Mutual Information
- Recovering Genetic Regulatory Networks from Chromatin Immunoprecipitation and Steady-State Microarray Data
- Optimal Constrained Stationary Intervention in Gene Regulatory Networks
- A Time-Series-Based Feature Extraction Approach for Prediction of Protein Structural Class
- Which Is Better: Holdout or Full-Sample Classifier Design?
- Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays
- Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text
- Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length
- Information Theoretic Methods for Bioinformatics
- IκB, NF-κB Regulation Model: Simulation Analysis of Small Number of Molecules
- NML Computation Algorithms for Tree-Structured Multinomial Bayesian Networks
- Aligning Sequences by Minimum Description Length
- Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information
- Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use
- Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates
- Question Processing and Clustering in INDOC: A Biomedical Question Answering System
- Compressing Proteomes: The Relevance of Medium Range Correlations
- MicroRNA Target Detection and Analysis for Genes Related to Breast Cancer Using MDLcompress
- Decorrelation of the True and Estimated Classifier Errors in High-Dimensional Settings
- Genome-Wide Analysis of Intergenic Regions of Mycobacterium tuberculosis H37Rv Using Affymetrix GeneChips
- A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification
- Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells
- Genetic Regulatory Networks
- Gene Systems Network Inferred from Expression Profiles in Hepatocellular Carcinogenesis by Graphical Gaussian Model
- Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria
- Gene Selection for Multiclass Prediction by Weighted Fisher Criterion
- Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization
Site: PubMed: Nature Biotechnology
- Network-based prediction of human tissue-specific metabolism.
- High-resolution metagenomics targets specific functional types in complex microbial communities.
- Predicting PDZ domain-peptide interactions from primary sequences.
Site: PubMed: Nature
- All of me.
- New role of bone morphogenetic protein 7 in brown adipogenesis and energy expenditure.
- Self-destructive cooperation mediated by phenotypic noise.
- Effect of phase transitions on compressional-wave velocities in the Earth's mantle.
- Selective oxidation with dioxygen by gold nanoparticle catalysts derived from 55-atom clusters.
- Doping a semiconductor to create an unconventional metal.
- Heterogeneous chemistry in the atmosphere of Mars.
- Magnetic support of the optical emission line filaments in NGC 1275.
- PRDM16 controls a brown fat/skeletal muscle switch.
- The Trichoplax genome and the nature of placozoans.
- Obituary: yoji totsuka (1942-2008).
- Archaeology: An oasis in time.
- Biogeochemistry: Who lives in the sea floor?
- Materials science: A metal left spinning.
- 50 & 100 years ago.
- Physiology: Mutant flies lack magnetic sense.
- Chemistry: Precious little catalyst.
- Developmental biology: Neither fat nor flesh.
- Exhibition digs deep to save our soils.
- A potter round Darwin's patch.
- Microbial fuels for the future.
- Flat Earth and amazons.
- Innovation policy: not just a jumbo shrimp.
- The human face of a difficult, heroic, passionate scientist.
- Micromanaging ideas risks impeding flow of potential benefits.
- Open debate could slow flu vaccine production.
- A possible way out of the impact-factor game.
- IVF: tight regulation may not be suitable for all cultures.
- IVF: stars may have to consider the risk of stolen parenthood.
- Neuroscience: The great squid hunt.
- Volcanology: Fire and life.
- Leak leaves Antarctic observatory blinded.
- New species of robin found in Gabon.
- Plans for the largest ever solar-power plants.
- Science illustration course draws to an end.
- US ocean agency upgrades its research fleet.
- Correction.
- Computer experts blast ruling to gag students.
- Bell Labs bottoms out.
- Whatever floats your boat.
- Unproven stem-cell therapy ban.
- Botany: Biofuel heir apparent?
- A biophysicist marvels at the idea of grabbing microscopic particles with light by tweaking its phase.
- Animal behaviour: Crowd control.
- Immunology: The power of tick spit.
- Biophysics: Mob rule.
- Climate indicators: Early birds.
- Atmospheric chemistry: Attacked from within.
- Fluid dynamics: Slip and slide.
- Microbiology: Running on arsenic.
- Electrophysiology: On the pulse.
- Animal behaviour: Don't you step on my ...
- A case for nurture.
- Case not closed.
- Scandalous behaviour.
- Making the paper: Andrew Fabian.
- Abstractions.
- From the blogosphere.
Site: PubMed: Science
- Science Podcast.
- Automatic mental associations predict future choices of undecided decision-makers.
- Control of the reversibility of cellular quiescence by the transcriptional repressor HES1.
- Grueneberg ganglion cells mediate alarm pheromone detection in mice.
- Heterochromatin integrity affects chromosome reorganization after centromere dysfunction.
- Epigenetic reprogramming by adenovirus e1a.
- Adenovirus small e1a alters global patterns of histone modification.
- Variability and robustness in T cell activation from regulated heterogeneity in protein levels.
- Targeting QseC signaling and virulence for antibiotic development.
- The global atmospheric circulation on moist isentropes.
- A stable silicon(0) compound with a Si=Si double bond.
- Observation of atomic diffusion at twin-modified grain boundaries in copper.
- Quantum gas of deeply bound ground state molecules.
- Star formation around supermassive black holes.
- The geological evolution of the Tibetan Plateau.
- Plant science. Using tobacco to treat cancer.
- Ecology. A matter of timing.
- Chemistry. Soluble allotropes of main-group elements.
- Developmental biology. How now, brown fat?
- Astronomy. Stars in the making.
- Psychology. The unseen mind.
- Ecology. Toward a global biodiversity observing system.
- The carrageenan diet: not recommended.
- Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry".
- Taking responsibility for scientific discourse.
- High-profile journals not worth the trouble.
- An editor's checklist.
- Nanotechnology. Can high-speed tests sort out which nanomaterials are safe?
- Cultural heritage. Shielding a Buddhist shrine from the howling desert sands.
- Climate science. Turbulent times for climate model.
- U.S. higher education. Departments scramble to find math education faculty.
- Endangered species. New regulation would lessen influence of fish and wildlife experts.
- Genomics. 'Simple' animal's genome proves unexpectedly complex.
- Tectonics. Pumping up the Tibetan Plateau from the far Pacific Ocean.
- Anthrax investigation. Six anthrax science questions the FBI has yet to answer.
- Anthrax investigation. FBI discusses microbial forensics--but key questions remain unanswered.
- Science and security, again.
- High-Quality Binary Protein Interaction Map of the Yeast Interactome Network.
- Chemokine Signaling Controls Endodermal Migration During Zebrafish Gastrulation.
- Coupled Superconducting and Magnetic Order in CeCoIn5.
- Quantum Communication with Zero-Capacity Channels.
Site: PubMed: PNAS
- From the Cover: Neutralization of HIV-1 by redirection of natural antibodies.
- Structure of apolipoprotein A-I in spherical high density lipoproteins of different sizes.
- Interleukin-6 regulates pancreatic {alpha}-cell mass expansion.
- Inaugural Article: Dissecting the roles of MuB in Mu transposition: ATP regulation of DNA binding is not essential for target delivery.
- Endogenous oxidative stress produces diversity and adaptability in biofilm communities.
- Stress resistance and signal fidelity independent of nuclear MAPK function.
- Localizing organomercury uptake and accumulation in zebrafish larvae at the tissue and cellular level.
- Mass spectrometry-based discovery of circadian peptides.
- Beyond tumor necrosis factor receptor: TRADD signaling in toll-like receptors.
- Engineering graded tissue interfaces.
- Transmembrane domain length of viral K+ channels is a signal for mitochondria targeting.
- Mutant dynein (Loa) triggers proprioceptive axon loss that extends survival only in the SOD1 ALS model with highest motor neuron death.
- Interaction between connexin35 and zonula occludens-1 and its potential role in the regulation of electrical synapses.
- From the Cover: Opposing plant community responses to warming with and without herbivores.
- The H19 locus acts in vivo as a tumor suppressor.
- Nucleus accumbens AGS3 expression drives ethanol seeking through G{beta}{gamma}.
- Alfalfa benefits from Medicago truncatula: The RCT1 gene from M. truncatula confers broad-spectrum resistance to anthracnose in alfalfa.
- Information flow and optimization in transcriptional regulation.
- Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations.
- In vivo studies fail to reveal a role for IL-4 or STAT6 signaling in Th2 lymphocyte differentiation.
- Methionine oxidation impairs reverse cholesterol transport by apolipoprotein A-I.
- Molecular basis of the interaction between the antiapoptotic Bcl-2 family proteins and the proapoptotic protein ASPP2.
- Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice.
- Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks.
- Erythromycin derivatives inhibit HIV-1 replication in macrophages through modulation of MAPK activity to induce small isoforms of C/EBP{beta}.
- Molecular basis for the autoregulation of the protein acetyl transferase Rtt109.
- Late-surviving megafauna in Tasmania, Australia, implicate human involvement in their extinction.
- Netrin-4 inhibits angiogenesis via binding to neogenin and recruitment of Unc5B.
- Highly efficient differentiation of hESCs to functional hepatic endoderm requires ActivinA and Wnt3a signaling.
- Transcriptional profiling of endogenous germ layer precursor cells identifies dusp4 as an essential gene in zebrafish endoderm specification.
- Object continuity enhances selective auditory attention.
- The Kv channel blocker 4-aminopyridine enhances Ag+ uptake: a scanning electrochemical microscopy study of single living cells.
- Resolving voltage-dependent structural changes of a membrane photoreceptor by surface-enhanced IR difference spectroscopy.
- Brk is coamplified with ErbB2 to promote proliferation in breast cancer.
- An engineered selenocysteine defines a unique class of antibody derivatives.
- TRPV4 channel participates in receptor-operated calcium entry and ciliary beat frequency regulation in mouse airway epithelial cells.
Site: PubMed: In silico biology
- HBAT: a complete package for analysing strong and weak hydrogen bonds in macromolecular crystal structures.
- CGHsweep: an algorithm for analyzing chromosomal aberrations in genome using aCGH profiles.
- Cell system ontology: representation for modeling, visualizing, and simulating biological pathways.
- Self-alignments to detect mutually exclusive exon usage.
- Identification of novel genomic islands associated with small RNAs.
- PREDICTOR: a web-based tool for the prediction of atomic structure from sequence for double helical DNA with up to 150 base pairs.
- Structural considerations for designing adenosine analogs as selective inhibitors of Trichomonas sp. glyceraldehyde-3- phosphate dehydrogenase.
- The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation.
- Cell interaction knowledgebase: an online database for innate immune cells, cytokines and chemokines.
- Prediction of ubiquitin proteins using artificial neural networks, hidden markov model and support vector machines.


