Site: pubmed: Bioinformatics

• AQUA: Automated quality improvement for multiple sequence alignments.

Site: pubmed: BMC Bioinformatics

• Prediction of protein binding sites in protein structures using hidden Markov support vector machine.
• An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

Site: pubmed: PLoS Comp. Biol.

• Discovery and annotation of functional chromatin signatures in the human genome.

Site: Journal of Computational Biology - Table of Contents

• Computation of Rank and Select Functions on Hierarchical Binary String and Its Application to Genome Mapping Problems for Short-Read DNA Sequences
• Survival Prediction and Gene Identification with Penalized Global AUC Maximization
• Parallel GPU Implementation of Iterative PCA Algorithms
• On the Parameterized Complexity of Pooling Design
• BCL::Contact?Low Confidence Fold Recognition Hits Boost Protein Contact Prediction and De Novo Structure Determination
• Data Structures for Parsimony Correlation and Biosequence Co-Evolution
• RECOMB?Comparative Genomics Special Issue
• Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes
• DCJ Path Formulation for Genome Transformations which Include Insertions, Deletions, and Duplications
• Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results
• Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny
• A Fast and Exact Algorithm for the Median of Three Problem: A Graph Decomposition Approach
• Gene Team Tree: A Hierarchical Representation of Gene Teams for All Gap Lengths
• Space of Gene/Species Trees Reconciliations and Parsimonious Models
• All Human-Specific Gene Losses Are Present in the Genome as Pseudogenes
• The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution
• Sorting Cancer Karyotypes by Elementary Operations
• A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses
• Genetic Map Refinement Using a Comparative Genomic Approach
• Estimating Mutation Distances from Unaligned Genomes

Site: EURASIP Journal on Bioinformatics and Systems Biology

• Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks
• Stochastic Simulation of Delay-Induced Circadian Rhythms in Drosophila
• Network Structure and Biological Function: Reconstruction, Modeling, and Statistical Approaches
• Reverse Engineering of Gene Regulatory Networks: A Comparative Study
• Modelling Transcriptional Regulation with a Mixture of Factor Analyzers and Variational Bayesian Expectation Maximization
• Applications of Signal Processing Techniques to Bioinformatics, Genomics, and Proteomics
• Clustering of Gene Expression Data Based on Shape Similarity
• Is Bagging Effective in the Classification of Small-Sample Genomic and Proteomic Data?
• Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge
• Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited
• Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints
• A Hybrid Technique for the Periodicity Characterization of Genomic Sequence Data
• Spectral Preprocessing for Clustering Time-Series Gene Expressions
• Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data
• Functional Classification of Genome-Scale Metabolic Networks
• Adaptive Dynamics of Regulatory Networks: Size Matters
• How to Improve Postgenomic Knowledge Discovery Using Imputation
• Transition Dependency: A Gene-Gene Interaction Measure for Times Series Microarray Data
• Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks
• Assessing the Exceptionality of Coloured Motifs in Networks
• Compressive Sensing DNA Microarrays
• On the Impact of Entropy Estimation on Transcriptional Regulatory Network Inference Based on Mutual Information
• A Bayesian Network View on Nested Effects Models
• The Impact of Time Delays on the Robustness of Biological Oscillators and the Effect of Bifurcations on the Inverse Problem
• Origins of Stochasticity and Burstiness in High-Dimensional Biochemical Networks
• Towards Systems Biology of Heterosis: A Hypothesis about Molecular Network Structure Applied for the Arabidopsis Metabolome
• Integrating Biosystem Models Using Waveform Relaxation
• Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks
• Using Temporal Correlation in Factor Analysis for Reconstructing Transcription Factor Activities
• Inference of Boolean Networks Using Sensitivity Regularization

Site: pubmed: Nature Biotechnology

• Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde.
• High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.
• A recombinant polypeptide extends the in vivo half-life of peptides and proteins in a tunable manner.

Site: pubmed: Nature

• A letter from the past.
• Dynamic activation of an allosteric regulatory protein.
• Signal peptides are allosteric activators of the protein translocase.
• Systems-level dynamic analyses of fate change in murine embryonic stem cells.
• Frequency of gamma oscillations routes flow of information in the hippocampus.
• Reconstruction of the history of anthropogenic CO(2) concentrations in the ocean.
• Evidence for warmer interglacials in East Antarctic ice cores.
• Ultraflat graphene.
• Coexistence of Fermi arcs and Fermi pockets in a high-T(c) copper oxide superconductor.
• Human genetics illuminates the paths to metabolic disease.
• Light and shadow from distant worlds.
• Malaria: Evolution in vector control.
• Chemical physics: Guiding light.
• Epigenomics: Methylation matters.
• 50 & 100 years ago.
• Palaeoclimate: Kink in the thermometer.
• Evolutionary biology: Why reproduction often takes two.
• Structural biology: New beginnings for transcription.
• Astrophysics: Burst of support for relativity.
• In Retrospect: The earliest picture of evolution?
• Corrections.
• Q&A: Bird behaviour, Darwin and dance.
• Log of life beneath the waves.
• Bonds forged on the high seas.
• Global Darwin: Multicultural mergers.
• A call to the custodians of deep time.
• Let the locals lead.
• A force to fight global warming.
• Boreal forests' carbon stores need better management.
• Legal and practical pitfalls in making use of patents.
• Water should take centre stage at climate talks.
• Sensible measures to guard India's groundwater supply.
• World view: Experts and democracy.
• Biodiversity: On the origin of bar codes.
• Biodiversity: Putting a price on nature.
• Biodiversity: Biodiversity's bright spot.
• Fresh hope for German stem-cell patent case.
• Growth in R&D investment holding up.
• Efforts to sustain biodiversity fall short.
• Muon collider gains momentum.
• Plant genetics database at risk as funds run dry.
• Japanese science faces deep cuts.
• News briefing: 19 November 2009.
• Nanobiotechnology: Magnetic tumour cells.
• Marine ecology: Speedy sponge.
• Planetary science: Cracking Martian ice.
• Regenerative biology: Brainy stem cells.
• Journal club.
• Biodiversity: Weird worms.
• Geology: Impact ironed out.
• Agriculture: Mixed manure message.
• Microscopy: Cell close-up.
• Cancer biology: Gene highs and lows.
• Palaeontology: Hot-blooded dinosaurs.
• Access denied?
• The entangled bank unravels.
• Abstractions.
• Making the paper: Samar Khatiwala.
• From the blogosphere.
• In vitro reconstitution of an abscisic acid signalling pathway.
• Coordinating DNA replication by means of priming loop and differential synthesis rate.
• Transport mechanism of a bacterial homologue of glutamate transporters.

Site: pubmed: Science

• Hemagglutinin receptor binding avidity drives influenza A virus antigenic drift.
• Quantifying the impact of immune escape on transmission dynamics of influenza.
• Improved attribution of climate forcing to emissions.
• A late Archean sulfidic sea stimulated by early oxidative weathering of the continents.
• 4D nanoscale diffraction observed by convergent-beam ultrafast electron microscopy.
• Synergic sedation of sensitive anions: alkali-mediated zincation of cyclic ethers and ethene.
• High-temperature superconductivity in a single copper-oxygen plane.
• Intergenerational wealth transmission and the dynamics of inequality in small-scale societies.
• 10-GHz self-referenced optical frequency comb.
• Economics. Foundations of societal inequality.
• Cell biology. An ancient gauge for iron.
• Climate change. Clean air for megacities.
• Chemistry. The basics of zinc activation.
• Atmospheric science. Clean the air, heat the planet?
• Science and regulation. The electronics revolution: from e-wonderland to e-wasteland.
• Nutrient imbalances: follow the waste.
• Nutrient imbalances: pollution remains.
• Too sanitary for vultures.
• Underestimating energy.
• Climate change. Hot, flat, crowded--and preparing for the worst.
• Profile: Chewang Norphel. Glacier man.
• 2009 Nobels: break or breakthrough for women? Interview by Jeffrey Mervis and Kate Travis.
• Paleoanthropology. Signs of early Homo sapiens in China?
• U.S. STEM work force. Study finds science pipeline strong, but losing top students.
• U.S. STEM education. Obama's science advisers look at reform of schools.
• HIV/AIDS research. Beyond Thailand: making sense of a qualified AIDS vaccine "success".
• Energy research. DOE gives $151 million to 'out-of-box' research.
• Scientific misconduct. Hwang convicted but dodges jail; stem cell research has moved on.
• Scientific misconduct. Timeline of events.
• Beyond climate science.
• Complete reconstitution of a highly reducing iterative polyketide synthase.
• Pathogenesis of chytridiomycosis, a cause of catastrophic amphibian declines.
• Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones.
• A Cdc20-APC ubiquitin signaling pathway regulates presynaptic differentiation.
• Carbenes as catalysts for transformations of organometallic iron complexes.
• Isolation of a C5-deprotonated imidazolium, a crystalline "abnormal" N-heterocyclic carbene.
• Characterization of a rhodium(I) sigma-methane complex in solution.
• Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila.
• Smallest algae thrive as the Arctic Ocean freshens.
• Lab experiments are a major source of knowledge in the social sciences.
• Molecular biology. Rejoice--RNAi for yeast.
• Chemistry. Carbenes in action.
• Physics. Glimpsing the weak magnetic field of light.
• Climate change. Fixing a critical climate accounting error.
• Climate change. Parallel pursuit of near-term and long-term climate mitigation.
• Focus on enhancing phytochemical content.
• Stay tuned for multimedia browsing.
• The antidote to bias in research.
• Defending freedom in Iran's universities.
• Restructure conflicting grant incentives.
• Behavioral ecology. Sex and social structure.
• Green energy. The promise of drought-tolerant corn.
• Green energy. Another biofuels drawback: the demand for irrigation.
• Astronomy. The colossus of Europe.
• Astronomy. Race for the heavens.
• Archaeology. Archaeologists alarmed by Turkey's proposed dig rules.
• Science in society. Hong Kong's Darwin defenders declare victory in teaching fracas.
• China. Scientists line up against dam that would alter protected wetlands.
• Amphibian decline. Life and death play out on the skins of frogs.
• Conservation biology. Research wolves of Yellowstone killed in hunt.
• Europe rethinks education.

Site: pubmed: PNAS

• The polychromatic Helitron landscape of the maize genome.
• Distribution, diversity, evolution, and survival of Helitrons in the maize genome.
• A cornucopia of Helitrons shapes the maize genome.
• Amyloid-{beta}42 signals tau hyperphosphorylation and compromises neuronal viability by disrupting alkylacylglycerophosphocholine metabolism.
• Subcellular localization of marine bacterial alkaline phosphatases.
• Cerebral and spinal modulation of pain by emotions.
• Regulation of hematopoiesis by the K63-specific ubiquitin-conjugating enzyme Ubc13.
• Lethal factor unfolding is the most force-dependent step of anthrax toxin translocation.
• Trypsin is a multifunctional factor in spermatogenesis.
• Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries.
• The synaptic proteins neurexins and neuroligins are widely expressed in the vascular system and contribute to its functions.
• Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction.
• Selective N-acylethanolamine-hydrolyzing acid amidase inhibition reveals a key role for endogenous palmitoylethanolamide in inflammation.
• Live imaging of rapid chromosome movements in meiotic prophase I in maize.
• A different mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by tepraloxydim.
• Clonal expansions in ulcerative colitis identify patients with neoplasia.
• Ubiquitous internal gene duplication and intron creation in eukaryotes.
• Inward-facing conformation of glutamate transporters as revealed by their inverted-topology structural repeats.
• Gaining ligand selectivity in thyroid hormone receptors via entropy.
• Phase-dependent neuronal coding of objects in short-term memory.
• Atg9a controls dsDNA-driven dynamic translocation of STING and the innate immune response.
• A progeria mutation reveals functions for lamin A in nuclear assembly, architecture, and chromosome organization.

Site: pubmed: In silico biology

• Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies.
• Empowering spot detection in 2DE images by wavelet denoising.
• Determinants for psychrophilic and thermophilic features of metallopeptidases of the M4 family.
• Remote homology detection using a kernel method that combines sequence and secondary-structure similarity scores.
• Numerical characterization of protein sequences and application to voltage-gated sodium channel alpha subunit phylogeny.
• Classification of information fusion methods in systems biology.
• Gene set enrichment analyses revealed differences in gene expression patterns between males and females.