Previous "Picks of the Week"
20 Jan 2007
- TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
- Translating microarray data for diagnostic testing in childhood leukaemia
- Phosphoproteome analysis of the human mitotic spindle
- Proteomics of early zebrafish embryos
- The Science of Soy: What Do We Really Know?
- ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants
- ORENZA: a web resource for studying ORphan ENZyme activities
27 Jan 2007
- A subset of Arabidopsis AP2 transcription factors mediates cytokinin responses in concert with a two-component pathway
- A DNA transfection system for generation of influenza A virus from eight plasmids
- ForestTreeDB: a database dedicated to the mining of tree transcriptomes
- Biodegradation of Aromatic Compounds by Escherichia coli
- Invader Plus Method Detects Herpes Simplex Virus in Cerebrospinal Fluid and Simultaneously Differentiates Types 1 and 2
- Transcriptome Analysis Reveals a Critical Role of CHS7 and CHS8 Genes for Isoflavonoid Synthesis in Soybean Seeds
- The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
4 Feb 2007
- Organ-Specific Expression of Glutathione S-Transferases and the Efficacy of Herbicide Safeners in Arabidopsis
- Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system
- High magnetic field induced changes of gene expression in arabidopsis
- ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
- Functional erythroid promoters created by interaction of the transcription factor GATA-1 with CACCC and AP-1/NFE-2 elements
- Methylation of coding region alone inhibits gene expression in plant protoplasts
- Cytokinesis in Prokaryotes and Eukaryotes: Common Principles and Different Solutions
11 Feb 2007
- Nuclear Dynamics in Arabidopsis thaliana
- Evolving Strategies for the Incorporation of Bioinformatics Within the Undergraduate Cell Biology Curriculum
- What makes species unique? The contribution of proteins with obscure features
- Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR
- cis-acting DNA elements responsive to gibberellin and its antagonist abscisic acid
- Prokaryotes: The unseen majority
- Expressing functional siRNAs in mammalian cells using convergent transcription
- Computer Simulations Improve University Instructional Laboratories
- Atlas – a data warehouse for integrative bioinformatics
- Bioinformatics Education—Perspectives and Challenges
- A library-based bioinformatics services program
- The European Bioinformatics Institute's data resources
- New journal: Algorithms for Molecular Biology
- iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website
18 Feb 2007
- Transposon diversity in Arabidopsis thaliana
- FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
- Improving the use of clinical databases
- Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease-prepared short interfering RNA
- Functional binding of the "TATA" box binding component of transcription factor TFIID to the -30 region of TATA-less promoters
- Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures
- Caenorhabditis elegans embryonic axial patterning requires two recently discovered posterior-group Hox genes
- The Use of Gene Expression Analysis and Proteomic Databases in The Development of a Screening System To Determine The Value of Natural Medicinal Products
- Abstract shapes of RNA
- WU-Blast2 server at the European Bioinformatics Institute
- BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data
- AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
- Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser
- ArrayQuest: a web resource for the analysis of DNA microarray data
25 Feb 2007
- Similar behaviour of single-strand and double-strand siRNAs suggests they act through a common RNAi pathway
- A Survey of Essential Gene Function in the Yeast Cell Division Cycle
- Stable and efficient gene transfer into the retina using an HIV-based lentiviral vector
- A perspective on microarrays: current applications, pitfalls, and potential uses
- Protein length in eukaryotic and prokaryotic proteomes
- Hepatic glucokinase promoter polymorphism is associated with hepatic insulin resistance in Asian Indians
- A novel approach for the identification of protein–protein interaction with integral membrane proteins
- APID: Agile Protein Interaction DataAnalyzer
- The Use of Gene Expression Analysis and Proteomic Databases in The Development of a Screening System To Determine The Value of Natural Medicinal Products
- An informatics model for tissue banks – Lessons learned from the Cooperative Prostate Cancer Tissue Resource
- G2D: a tool for mining genes associated with disease
- Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine?
- BIBI, a Bioinformatics Bacterial Identification Tool
- The Protein Data Bank
4 Mar 2007
- The Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance
- Bioconductor: open software development for computational biology and bioinformatics
- PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results
- Caenorhabditis elegans DYF-2, an Orthologue of Human WDR19, Is a Component of the Intraflagellar Transport Machinery in Sensory Cilia
- A perspective on microarrays: current applications, pitfalls, and potential uses
- Autoantibody profiling for the study and treatment of autoimmune disease
- Development and evaluation of evidence-based nursing (EBN) filters and related databases
- Delayed impact: ISI's citation tracking choices are keeping scientists in the dark
- MuTrack: a genome analysis system for large-scale mutagenesis in the mouse
- Relational Databases: A Transparent Framework for Encouraging Biology Students To Think Informatically
- libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny
- Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress
- MaGe: a microbial genome annotation system supported by synteny results
- Training the Next Generation of Informaticians: The Impact of “BISTI” and Bioinformatics—A Report from the American College of Medical Informatics
11 Mar 2007
- JACQUES BANCHEREAU, PHD: a conversation with Michael Ramsay, MD, president of Baylor Research Institute
- Immunome Research
- A success story: HIV prevention for injection drug users in Rhode Island
- CED: a conformational epitope database
- AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data
- Molecular Biology: The Shape of Food Allergenicity
- New frontiers in immunology
- IMGT, the international ImMunoGeneTics information system
- dbPTM: an information repository of protein post-translational modification
- The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes
- Biological Databases for Plant Research
- Large scale hierarchical clustering of protein sequences
- Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow
- DWARF – a data warehouse system for analyzing protein families
18 Mar 2007
- Nanotechnology and the Developing World
- Emulating biology: Building nanostructures from the bottom up
- The Flexibility of DNA Double Crossover Molecules
- Waiter, there's a nanobot in my martini
- Nanoparticles: Health Effects—Pros and Cons
- How Should Society Approach the Real and Potential Risks Posed by New Technologies?
- Nature's Nanotechnologists: Unveiling the Secrets of Diatoms
- TOPAAS, a Tomato and Potato Assembly Assistance System for Selection and Finishing of Bacterial Artificial Chromosomes
- PRESTA: associating promoter sequences with information on gene expression
- A knowledge discovery object model API for Java
- The Bioperl Toolkit: Perl Modules for the Life Sciences
- MetaCyc: a multiorganism database of metabolic pathways and enzymes
- STEM: a tool for the analysis of short time series gene expression data
- Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
25 Mar 2007
- Essential Roles for Caenorhabditis elegans Lamin Gene in Nuclear Organization, Cell Cycle Progression, and Spatial Organization of Nuclear Pore Complexes
- Genetically targeted cell disruption in Caenorhabditis elegans
- Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA
- A power law for cells
- Genes that control a temperature-compensated ultradian clock in Caenorhabditis elegans
- Alteration of Caenorhabditis elegans gene expression by targeted transformation
- The evolutionary position of nematodes
- A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis
- DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches
- Software and methods for oligonucleotide and cDNA array data analysis
- A computational approach for identifying pseudogenes in the ENCODE regions
- Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance
- Proposed methods for testing and selecting the ERCC external RNA controls
- Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
1 Apr 2007
- Functional analysis of oxidative stress-activated mitogen-activated protein kinase cascade in plants
- Random GFP?cDNA fusions enable visualization of subcellular structures in cells of Arabidopsis at a high frequency
- The violaxanthin cycle protects plants from photooxidative damage by more than one mechanism
- Transposon diversity in Arabidopsis thaliana
- The Cellular Level of PR500, a Protein Complex Related to the 19S Regulatory Particle of the Proteasome, Is Regulated in Response to Stresses in Plants
- Apyrase Functions in Plant Phosphate Nutrition and Mobilizes Phosphate from Extracellular ATP
- Protein-coding genes are epigenetically regulated in Arabidopsis polyploids
- VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines
- Tumor microenvironments, the immune system and cancer survival
- SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites
- Computationally Identifying Novel NF-kappaB-Regulated Immune Genes in the Human Genome
- Farm animal genomics and informatics: an update
- The emergence and diffusion of DNA microarray technology
- Evolution and evolvability of proteins in the laboratory
8 Apr 2007
- Use of cDNA subtraction and RNA interference screens in combination reveals genes required for germ-line development in Caenorhabditis elegans
- A RHO GTPase-mediated pathway is required during P cell migration in Caenorhabditis elegans
- RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans
- SKIP is an indispensable factor for Caenorhabditis elegans development
- High-throughput reverse genetics: RNAi screens in Caenorhabditis elegans
- Involvement of fatty acid pathways and cortical interaction of the pronuclear complex in Caenorhabditis elegans embryonic polarity
- BIR-1, a Caenorhabditis elegans homologue of Survivin, regulates transcription and development
- The Distributed Annotation System
- GeneClinics:
A Hybrid Text/Data Electronic Publishing Model Using XML Applied to Clinical Genetic Testing
- GEM:
A Proposal for a More Comprehensive Guideline Document Model Using XML
- ORFer – retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files
- Apollo: a sequence annotation editor
- DNA Data Bank of Japan (DDBJ) in XML
- An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results
15 Apr 2007
- Impact of Transcriptional Properties on Essentiality and Evolutionary Rate
- Temporal Estimates of Effective Population Size in Species With Overlapping Generations
- Molecular Insights into Human Brain Evolution
- Ancient DNA Comes of Age
- Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics
- Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism
- GeneSeer: A sage for gene names and genomic resources
- Web-based access to mouse models of human cancers: the Mouse Tumor Biology (MTB) Database
- Is 'big biology' a commercial enterprise?
- The Mouse Genome Database (MGD): integrating biology with the genome
- Dry work in a wet world: computation in systems biology
- It's All GO for Plant Scientists
- From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research
- Genome informatics for data-driven biology
22 Apr 2007
- Secretion of glutathione S-transferase isoforms in the seminiferous tubular fluid, tissue distribution and sex steroid binding by rat GSTM1
- A Peroxisomal Glutathione Transferase of Saccharomyces cerevisiae Is Functionally Related to Sulfur Amino Acid Metabolism
- Plant glutathione transferases
- The Anopheles gambiae glutathione transferase supergene family: annotation, phylogeny and expression profiles
- Glutathione S-Transferase Isoenzymes from Streptomyces griseus
- Isolation and Characterization of Glutathione S-Transferase Isozymes from Sorghum
- Mammalian class Sigma glutathione S-transferases: catalytic properties and tissue-specific expression of human and rat GSH-dependent prostaglandin D2 synthases
- Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
- Perl Programming for Biologists
- Review on ''Bioinformatics, Biocomputing and Perl'' by Michael Moorhouse and Paul Barry
- POSA: Perl Objects for DNA Sequencing Data Analysis
- SeqHound: biological sequence and structure database as a platform for bioinformatics research
- A computational investigation of kinetoplastid trans-splicing
- LOCnet and LOCtarget: sub-cellular localization for structural genomics targets
29 Apr 2007
- DAVID: Database for Annotation, Visualization, and Integrated Discovery
- GERMINATE. A Generic Database for Integrating Genotypic and Phenotypic Information for Plant Genetic Resource Collections
- CR-EST: a resource for crop ESTs
- PlantGDB, plant genome database and analysis tools
- SUBA: the Arabidopsis Subcellular Database
- VIPERdb: a relational database for structural virology
- Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system
- Octamer-primed sequencing technology: effects of dNTP supplementation
- Primer-design for multiplexed genotyping
- RTPrimerDB: the Real-Time PCR primer and probe database
- DePIE: Designing Primers for Protein Interaction Experiments
- SNPbox: web-based high-throughput primer design from gene to genome
- SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms
- Use of GC Clamps in DHPLC Mutation Scanning
24 June 2007
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- T-cell responses to minor histocompatibility antigens
- Phenotypic diversity of the CD45 antigen and its relationship to function
- Antibodies Enhance Interaction of Vibrio cholerae with Intestinal M-Like Cells
- Accelerated development of IgG autoantibodies and autoimmune disease in the absence of secreted IgM
- Immunization against Alzheimer's beta-amyloid plaques via EFRH phage administration
- Stimulation of HIV-1-neutralizing antibodies in simian HIV-IIIB-infected macaques
- Production of secretory immunoglobulin A by a single mammalian cell
- BioWMS: a web-based Workflow Management System for bioinformatics
- Biowep: a workflow enactment portal for bioinformatics applications
- IDR: the ImmunoDeficiency Resource
- Design and implementation of microarray gene expression markup language (MAGE-ML)
- A markup language for electrocardiogram data acquisition and analysis (ecgML)
- Classifying the precancers: A metadata approach
- SCMD: Saccharomyces cerevisiae Morphological Database
1 July 2007
- Embryonic stem cells and somatic cells differ in mutation frequency and type
- Directed neuronal differentiation of human embryonic stem cells
- The new stem cell biology: something for everyone
- In vitro differentiation of embryonic stem cells into lymphocyte precursors able to generate T and B lymphocytes in vivo
- SDF-1 tells stem cells to mind their P's and Z's
- Skeletal muscle stem cells
- Differentiation of human embryonic stem cells on three-dimensional polymer scaffolds
- FOUNTAIN: A JAVA open-source package to assist large sequencing projects
- The Universal Protein Resource (UniProt)
- tacg – a grep for DNA
- CpG Island Mapping by Epigenome Prediction
- PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories
- Validating module network learning algorithms using simulated data
- Deductive Biocomputing
8 July 2007
- Retroviral Expression in Embryonic Stem Cells and Hematopoietic Stem Cells
- Correction of canine X-linked severe combined immunodeficiency by in vivo retroviral gene therapy
- Viral-mediated gene therapy for the muscular dystrophies: Successes, limitations and recent advances
- Gene therapy for the hemoglobin disorders: Past, present, and future
- Hematopoietic stem cell gene therapy: selecting only the best
- Cellular immunotherapy for cancer
- Duchenne muscular dystrophy and dystrophin: pathogenesis and opportunities for treatment
- Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
- PipeOnline 2.0: automated EST processing and functional data sorting
- The TIGR Maize Database
- Database resources of the National Center for Biotechnology Information
- Plant Genome Resources at the National Center for Biotechnology Information
- Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA
- The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
8 September 2007
- Cis-acting regulatory elements controlling temporal and organ-specific activity of nopaline synthase promoter
- Attempts to Detect Agrobacterium tumefaciens DNA in Crown-Gall Tumor Tissue
- ChvD, a Chromosomally Encoded ATP-Binding Cassette Transporter-Homologous Protein Involved in Regulation of Virulence Gene Expression in Agrobacterium tumefaciens
- The chvH Locus of Agrobacterium Encodes a Homologue of an Elongation Factor Involved in Protein Synthesis
- Agrobacterium tumefaciens and the Plant: The David and Goliath of Modern Genetics
- Agrobacterium tumefaciens T-complex transport apparatus: a paradigm for a new family of multifunctional transporters in eubacteria
- Temperature affects the T-DNA transfer machinery of Agrobacterium tumefaciens
- Primer3Plus, an enhanced web interface to Primer3
- ORFer – retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files
- NeuroTerrain – a client-server system for browsing 3D biomedical image data sets
- BIOZON: a system for unification, management and analysis of heterogeneous biological data
- maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
- GeneTools – application for functional annotation and statistical hypothesis testing
- BioInfer: a corpus for information extraction in the biomedical domain
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