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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

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