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.