Detecting transposable elements with less a priori
An Integrated Approach for the Storage, Exploration, and Analysis of Microarray Gene
Expression Data.
Ligand Binding with OBPRM and Haptic Input.
A Vector Algorithm for Approximate String Matching with Arbitrary Weighted Distances.
Mapping isochores by entropic segmentation of long genome sequences.
Finding "Important" Sites in Protein Sequences
Information transmission along DNA
Simplified partial digest method for DNA restriction maps construction
Gene expression in human heart failure: Microarray analysis of dilated cardiomyopathy
The human cardiac gene expression knowledgebase.
Structured query fragment analysis.
A structured query fragment analysis database
Bioinformatics as an inexpensive vector for introducing modern biological concepts into the american high school curriculum
Heuristic for Genome Rearrangements in Multi-Chromosomal Species
Flexible protein docking oriented to the inference of structural characteristics
involved in molecular recognition
A hierarchical object-relation knowledge base for identifying ABC transporters
pH-dependent electrostatics of class C Beta-Lactamase (Enterobacter cloacae): Tyrosyl ionizations.
Framework annotation of the human genome by CRASA
XBase: an open source gene expression database project
Modeling Protein Secondary Structure by Combination of Dependent Experts
ATGC: Another Tool for Genome Comparison
A Novel Heuristic Algorithm For Identifying Sets of Genetic Markers In Transcriptional Profiling Data
Cross linking entropic evaluation in RNA secondary structure free energy calculations
Approximation Algorithms for Distinguishing String Selection Problems
A Linear-Time Algorithm for Solving the Molecular Distance Geometry Problem
Use of genomic signature to detect horizontal DNA transfers
Benchmarks for Protein Structure Prediction
High throughput subcloning of complete protein coding open reading frames (ORF)
Visualization of Biodegradation Pathways in the UM-BBD
Reconstructing an ancestral genome by reversals and multiple gene duplication
Using Conditional Entropy to Investigate Genetic Networks
Practical Algorithms for Universal DNA Primer Design:
An Exercise in Algorithm Engineering
Protein side-chain flexibility upon point mutations: Deriving the upper limit of
predictive accuracy from PDB files
Reconstructing Phylogenetic Trees Based on Ribosomal RNA Secondary Structures
Branch-and-Bound Reconstruction of Ancestral Sequences
Arguments for measuring the metabolome in functional genomics research
Using correlation matrices in the comparative analysis of immunoglobulin chains
Computational Analysis of DNAZymes
Tree-based method to identify protein functional domains: Case study of
primer utilization by reverse transcriptase
Enantioselectivity of Pseudomonas cepacia lipase and mutants towards
primary alcohols: Prediction by an in silico assay
Molecular Modeling of Interactions of no-Peptide Antagonist OPC-31360 with
the Human Vasopresin V2 Receptor
Bioinformatic analysis of gene expression patterns suggests chemokine
autocrine loops in lymphomas and leukemias
Evaluating an algorithm for parameterized Minimum Quartet Inconsistency
Identifying Target Sites for Cooperatively Binding Factors
A novel computational approach to protein identification
Invariants for the General Model
Protein Identification by Epitope Recognition
A computational approach to condition-based promoter characterization in
S.c. based on genome-wide expression and binding profiles
Translation Initiation Site Prediction on full length and partial cDNA's
using Artificial Neural Networks
The Atlas Whole-Genome Assembler
A BioKnowledge(TM Library for Rapid Assessment of the Function of Novel Human Genes
Rare gene expression patterns discovered by hierarchical clustering from
microarray data
Effective dimensionality of expression data from development of rat central nervous system
Mining The Putative Functional Sites Using Repetitive Elements
Predicting Splice Variant from DNA Chip Expression Data
Automated analysis of three-dimensional protein structures from NOESY data
using AutoStructure
Data preprocessing and quality control for DNA array expression profiling experiments
Possible negative effects of reference mRNA sample in cDNA microarrays
RNA Evolution and Molecular Phylogenetics
Distribution Analysis of 5’ Splice Site-Like Sequences in human mRNA Precursors
Integration of biological databases: the example of InterPro
Evolving Fuzzy Neural Networks for Knowledge Discovery from Gene Expression
Data - a Case Study
A decision tree classifier of promoters based on composite modules of TF binding sites
Statistical Inference for Gene Expression Microarray Data Analysis
New computational tools for analyzing and searching gene expression data
derived from TaqMan real-time PCR.
New selenocysteine-containing proteins identified with a program that searches for
an mRNA structural element
Structural commonality in protein binding sites for ATP
Informative Descriptors of Non-Local Residue Environments in Protein Structures
The DBRF Method for Inferring a Gene Network from Steady-State Gene Expression Data
Modifying Standard Bioinformatics Analysis Tools For Use On High Performance
Computational Platforms
A Fast Procedure for Estimating Missing Distances in Incomplete Matrices
Prior to Phylogenetic Analysis
Insights from a structural genomics approach
Exploratory data analysis and the visualization of extremely large sequence data sets
The Degenerate Primer Selection Problem
Sequencing by Hybridization - A Simulation Study of Performance on Genomic Sequences
Genome-wide Motif Scanning
SOAP, a Program for Cleaning Multiple Alignments from Unstable Blocks
Clustering Protein Sequences by Parallel Mining Non-positional k-tuple Matches
Comparison of the dynamics of substrate access channels in three bacterial
cytochrome P450 proteins reveals different opening mechanisms and a new functional
role for a buried arginine
NCBI~Rs LocusLink: data integration to facilitate navigation within and
between several model organisms
T-REX - software for reconstructing phylogenetic trees and reticulation networks.
The multiple regression on distance matrices as a comparative method
Regulations of the transcriptome adaptations to cellular environment:
the yeast multidrug resistance phenomenon
fprotml: Protein Analysis Using Maximum Likelihood
Genomic Object Net: Hybrid Petri Net for Describing Biological Systems
Specificity of SAF-A and lamin B binding in vitro correlates with the satellite
DNA bending state
Identification of Retroid Agents in the Human Genome
Ligand-Protein Docking Using a Two Stage Algorithm: 1. Rapid Determination of
Binding Site and Approximate Ligand Position
Microarray spot reading: SpotView
Structural analysis of conserved base-pairs in protein-DNA complexes
Visualization of features in flat file by use of DDBJ-XML
An Alternative Approach to Investigating Sequence-Structure Relationships in Proteins
TM: A Transmembrane-Specific Scoring Matrix
SSPDP: A Novel method to Predict Secondary Structure from Amino Acid Sequences
Population Boom: An Improved Genetic Algorithm
Statistical and Numerical Analysis of Genotypes and Haplotypes
Novel method for template identification for globular proteins using
sequence profiles and predicted secondary structure
Variability in large-scale gene expression data
Analysis of Learning-Related Changes in Gene Expression
Using Nylon Membrane {cDNA} Microarrays
AVID and VISTA: Comparative Genomics Tools for Biological Discovery
Methodologies for Constructing and Training Large Hierarchical Hidden Markov Models
for Sequence Analysis
Comparative analysis of genes involved in regulating the chromatin environment in the genome
of the model plant - Arabidopsis thaliana
New Fur-regulated Systems in Gamma-Proteobacteria
A model of structurally constrained protein evolution
Unifying Genomics and Proteomics in whole Genomes and Chromosomes
APES - Automated Processing and Extraction of Sequences
Software to Predict MicroArray Hybridization: ACROSS
A test for positive Darwinian selection
Improved Discrimination in Bayesian Profile Searching using Biconditional Residue
Background Frequencies
Cellular Signal Regulation by Endocytic Trafficking
The Fidelity of the Universal DNA Chip
Genome-wide identification of horizontal gene transfer events using Bayesian statistics
Short inversions and conserved gene clusters
A Probabilistic Model for Generating Hypotheses using Gene Expression
An Integrated Data Management System for Microbial Genome Projects
Predicting phosphopeptide selectivity of SH2 domains
RAKE: Accurate automated annotation of the human genome based on SCOP
domain-derived hidden Markov models
DNA Mutation Bias vs. Selection in Mitochondrial Proteins
Leveraging Genomic Research with the Biomedical Literature
Approximate P-values for Local Sequence Alignments: Numerical Studies
Automatic RNA secondary structure prediction with the comparative approach
A new objective function for multiple sequence alignments
Cataloguing Candidate Elements involved in Transcriptional Regulation in the
Caenorhabditis elegans Genome
Is co-substitution a general process associated with the preservation
of protein structure?
Computer simulations suggest an early form of instability in
irradiated human lymphocytes
Comparison of nucleotide, codon, and amino acid substitution
models in evolutionary distance estimation
Clustering Method for Repeat Analysis of DNA Sequences
Exploring Functional Divergence from Sequence Evolution
Functional Classification of Proteins by Hierarchical Categorization of Pfam Models
RNAML: An XML Format for RNA Data-Exchange
Genetic Variation Study with Integrated KEGG Pathway Data
Using Physicochemical Properties in Alignment of Multiple Protein Sequences
Simulation and evaluation of complex hybridisation experiments
A Greedy Algorithm for Optimal Recombination
Finding Tandem Repeats Online in Genome Sequences
Integration System of SNP Genotyping for Association Study in Millennium Project
Classifying multiple tumor types with gene expression data
Mesoscopic order in supercoiled DNA solutions
Multivalent Ion - DNA Interaction
InterProScan - an integration tool for the signature-recognition methods in InterPro
Efficiently Maintaining Molecular Conformations Using Local Frames