Site: pubmed: Bioinformatics
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.
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.


