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Ten simple rules for making a software tool workflow-ready
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- Journal Article
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FragGeneScanRs : faster gene prediction for short reads
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- Journal Article
- A1
- open access
Thunderstruck : the ACDC model of flexible sequences and rhythms in recurrent neural circuits
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The influence of unmeasured confounding on the MR Steiger approach
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Selection bias when inferring the effect direction in Mendelian randomization
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- Journal Article
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Obsessive-compulsive disorder is characterized by decreased Pavlovian influence on instrumental behavior
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- Journal Article
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Dynamic causal modelling shows a prominent role of local inhibition in alpha power modulation in higher visual cortex
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- Journal Article
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DG-Mapping : a novel software package for the analysis of any type of reentry and focal activation of simulated, experimental or clinical data of cardiac arrhythmia
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Patient-specific finite element analysis of heart failure and the impact of surgical intervention in pulmonary hypertension secondary to mitral valve disease
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- Journal Article
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SUBATOMIC : a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks
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- Journal Article
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Quantitative modeling identifies critical cell mechanics driving bile duct lumen formation
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- Journal Article
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CystiHuman : a model of human neurocysticercosis
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- Journal Article
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Forecasting time series in healthcare with Gaussian processes and Dynamic Time Warping based subset selection
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- Journal Article
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Food Enzyme Database (FEDA) : a web application gathering information about food enzyme preparations available on the European market
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- Journal Article
- A1
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Comment on ‘Hayai-annotation plants : an ultrafast and comprehensive functional gene annotation system in plants’ : the importance of taking the GO graph structure into account
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- Journal Article
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Radio-frequency exposure of the yellow fever mosquito (A. aegypti) from 2 to 240 GHz
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Biophysically realistic neural-network models of auditory neurons and synapses for neuroscience and machine-hearing applications
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- Miscellaneous
- open access
Ten simple rules for Global North researchers to stop perpetuating helicopter research in the Global South
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- Journal Article
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Closing the circle : current state and perspectives of circular RNA databases
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- Journal Article
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Double two-state opsin model with autonomous parameter inference
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- Journal Article
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Explainability in transformer models for functional genomics
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- Journal Article
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Directed graph mapping exceeds phase mapping in discriminating true and false rotors detected with a basket catheter in a complex in-silico excitation pattern
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- Journal Article
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Adaptive body area networks using kinematics and biosignals
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- Journal Article
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Segmentation of endothelial cells of the cornea from the distance map of confocal microscope images
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Caution against examining the role of reverse causality in Mendelian Randomization
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- Journal Article
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A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
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The structure of causal explanations in population biology
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- Journal Article
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DECONbench : a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification
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- Journal Article
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GABAC : an arithmetic coding solution for genomic data
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- Journal Article
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Transcriptome-wide association study of breast cancer risk by estrogen-receptor status
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- Journal Article
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Portable detection of apnea and hypopnea events using bio-impedance of the chest and deep learning
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- Journal Article
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PaSiT : a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing
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- Journal Article
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Learning generative state space models for active inference
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- Journal Article
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TinGa : fast and flexible trajectory inference with Growing Neural Gas
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- Journal Article
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Hierarchies of quantum chemical descriptors induced by statistical analyses of domain occupation number operators
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- Journal Article
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Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields
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- Journal Article
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Calibration of individual-based models to epidemiological data : a systematic review
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Unipept CLI 2.0 : adding support for visualizations and functional annotations
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- Journal Article
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Deciphering the morphology of motor evoked potentials
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- Journal Article
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High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing
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- Journal Article
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Pharmacoinformatic investigation of medicinal plants from East Africa
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- Journal Article
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BLAMM : BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs
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- Journal Article
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SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups
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- Journal Article
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SPsimSeq : semi-parametric simulation of bulk and single-cell RNA-sequencing data
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- Journal Article
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ToxDL : deep learning using primary structure and domain embeddings for assessing protein toxicity
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Logistic index for keratoconus detection and severity scoring (Logik)
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- Journal Article
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Noninvasive cardiac output and central systolic pressure from cuff-pressure and pulse wave velocity
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PPNID : a reference database and molecular identification pipeline for plant-parasitic nematodes
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Algebraic shortcuts for leave-one-out cross-validation in supervised network inference
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Phylogeny and sequence space : a combined approach to analyze the evolutionary trajectories of homologous proteins : the case study of aminodeoxychorismate synthase
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Conditional permutation importance revisited
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- Journal Article
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The role of actin protrusion dynamics in cell migration through a degradable viscoelastic extracellular matrix : insights from a computational model
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- Journal Article
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A novel approach for identifying and addressing case‐mix heterogeneity in individual participant data meta‐analysis
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- Journal Article
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Mixed impact of torsion on LV hemodynamics : a CFD study based on the Chimera technique
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A statistical approach to the identification of diploid cellular automata based on incomplete observations
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- Journal Article
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Illumina error correction near highly repetitive DNA regions improves de novo genome assembly
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- Journal Article
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wgd-simple command line tools for the analysis of ancient whole genome duplications
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- Journal Article
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Optimising orbit counting of arbitrary order by equation selection
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- Journal Article
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BrAPI : an application programming interface for plant breeding applications
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Left atrial appendage segmentation from 3D CCTA images for occluder placement procedure
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- Journal Article
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DoRes within CellMissy : dose-response analysis on cell migration and related data
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- Journal Article
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Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
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- Journal Article
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Learning to synchronize : how biological agents can couple neural task modules for dealing with the stability-plasticity dilemma
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- Journal Article
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Applications of next-generation sequencing technologies and computational tools in molecular evolution and aquatic animals conservation studies : a short review
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- Journal Article
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Large expert-curated database for benchmarking document similarity detection in biomedical literature search
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A broken promise : microbiome differential abundance methods do not control the false discovery rate
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- Journal Article
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Quantitative agent-based modeling reveals mechanical stress response of growing tumor spheroids is predictable over various growth conditions and cell lines
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Machine learning based brain tumour segmentation on limited data using local texture and abnormality
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- Journal Article
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Gearing up to handle the mosaic nature of life in the quest for orthologs
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- Journal Article
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Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations
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TISRover : ConvNets learn biologically relevant features for effective translation initiation site prediction
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- Journal Article
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Decoding steady-state visual evoked potentials from electrocorticography
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Identification of novel agonists and antagonists of the ecdysone receptor by virtual screening
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Stability analysis of the Michaelis-Menten approximation of a mixed mechanism of a phosphorylation system
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- Journal Article
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Core Hunter 3 : flexible core subset selection
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SpliceRover : interpretable convolutional neural networks for improved splice site prediction
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Computational deconvolution of transcriptomics data from mixed cell populations
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AQUa : an adaptive framework for compression of sequencing quality scores with random access functionality
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Assessment of methodologies to calculate intraventricular pressure differences in computational models and patients
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- Journal Article
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- open access
BrownieAligner : accurate alignment of Illumina sequencing data to de Bruijn graphs
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- Journal Article
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Dependence of excitability indices on membrane channel dynamics, myelin impedance, electrode location and stimulus waveforms in myelinated and unmyelinated fibre models
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Skeletonization method for vessel delineation of arteriovenous malformation
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- Journal Article
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High-throughput PCR assay design for targeted resequencing using primerXL
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- Journal Article
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decodeRNA-predicting non-coding RNA functions using guilt-by-association
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- Journal Article
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Local directional probability optimization for quantification of blurred gray/white matter junction in magnetic resonance image
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- Journal Article
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Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs
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AFRESh : an adaptive framework for compression of reads and assembled sequences with random access functionality
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sfinx : an R package for the elimination of false positives from affinity purification-mass spectrometry datasets
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- Journal Article
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Zipper plot : visualizing transcriptional activity of genomic regions
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A Cytoscape app for motif enumeration with ISMAGS
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- Journal Article
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MAPPI-DAT : data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform
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- Journal Article
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Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations
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- Journal Article
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OMSim : a simulator for optical map data
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- Journal Article
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Evaluation of the impact of Illumina error correction tools on de novo genome assembly
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PhyD3 : a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization
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- Journal Article
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Numerical modeling of percutaneous auricular vagus nerve stimulation : a realistic 3D model to evaluate sensitivity of neural activation to electrode position
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- Conference Paper
- C3
- open access
Assessing publication bias in coordinate-based meta-analysis techniques?
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- Journal Article
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Physiology-based regularization of the electrocardiographic inverse problem
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Details of regional particle deposition and airflow structures in a realistic model of human tracheobronchial airways : two-phase flow simulation
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- Journal Article
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- open access
Jabba: hybrid error correction for long sequencing reads
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- Journal Article
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Differential impact of local stiffening and narrowing on hemodynamics in repaired aortic coarctation: an FSI study
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BiDiFuse : a FIJI plugin for fusing bi-directionally recorded microscopic image volumes
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Mining balance disorders' data for the development of diagnostic decision support systems
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- Journal Article
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Random survival forests for predicting the bed occupancy in the intensive care unit
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- Journal Article
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A mathematical model of neonatal rat atrial monolayers with constitutively active acetylcholine-mediated K+ current
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- Journal Article
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Cell line name recognition in support of the identification of synthetic lethality in cancer from text
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- Journal Article
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Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks
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- Journal Article
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Evaluation of second-level inference in fMRI analysis
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Unipept web services for metaproteomics analysis
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A web application for sample size and power calculation in case-control microbiome studies
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- Journal Article
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- open access
Netter: re-ranking gene network inference predictions using structural network properties
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Simultaneous discovery of cancer subtypes and subtype features by molecular data integration
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- Journal Article
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Combining laboratory and mathematical models to infer mechanisms underlying kinetic changes in macrophage susceptibility to an RNA virus
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Positive unanimous voting algorithm for focal cortical dysplasia detection on magnetic resonance image
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The challenge of successive dynamic causal models
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Prospective power estimation for peak inference with the toolbox neuropower
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EVpedia: a community web portal for extracellular vesicles research
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The impact of initial evenness on biodiversity maintenance for a four-species in silico bacterial community
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- Journal Article
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QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles
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- Journal Article
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ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering
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VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering
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- Journal Article
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htsint: a Python library for sequencing pipelines that combines data through gene set generation
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- Journal Article
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RDML-Ninja and RDMLdb for standardized exchange of qPCR data
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- Journal Article
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An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
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- Journal Article
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The evolution of thermal performance can constrain dispersal during range shifting
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- Journal Article
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Halvade: scalable sequence analysis with MapReduce
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Combining femoral and acetabular parameters in femoroacetabular impingement : the omega surface
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- Journal Article
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Fishing for data and sorting the catch : assessing the data quality, completeness and fitness for use of data in marine biogeographic databases
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- Journal Article
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Suction power output and the inertial cost of rotating the neurocranium to generate suction in fish
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- Journal Article
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SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering
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- Journal Article
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BLSSpeller : exhaustive comparative discovery of conserved cis-regulatory elements
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- Journal Article
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A long fragment aligner called ALFALFA
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Vinamax: a macrospin simulation tool for magnetic nanoparticles
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vRNA structured population model for Hepatitis C Virus dynamics
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Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis
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- Journal Article
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Modeling mode choice behavior incorporating household and individual sociodemographics and travel attributes based on rough sets theory
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Objectifying facial expressivity assessment of Parkinson's patients : preliminary study
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unifiedWMWqPCR: the unified Wilcoxon–Mann–Whitney test for analyzing RT-qPCR data in R
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- Journal Article
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Isotropic non-white matter partial volume effects in constrained spherical deconvolution
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Heuristic reevaluation of the bacterial hypothesis of peptic ulcer disease in the 1950s
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- Journal Article
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A model reduction method for biochemical reaction networks
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- Journal Article
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Effect of global cardiac ischemia on human ventricular fibrillation : insights from a multi-scale mechanistic model of the human heart
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- Journal Article
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Impact of variance components on reliability of absolute quantification using digital PCR
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- Journal Article
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A general role for medial prefrontal cortex in event prediction
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MAGIC: access portal to a cross-platform gene expression compendium for maize
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- Miscellaneous
- open access
Big data and other challenges in the quest for orthologs
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- Journal Article
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A formal concept analysis approach to consensus clustering of multi-experiment expression data
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ASP-G: an ASP-based method for finding attractors in genetic regulatory networks
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- Journal Article
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miRBase Tracker : keeping track of microRNA annotation changes
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- Journal Article
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Active learning to understand infectious disease models and improve policy making
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- Journal Article
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A computational analysis of motor synergies by dynamic response decomposition
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- Miscellaneous
- open access
Editorial for the research topic: information-based methods for neuroimaging: analyzing structure, function and dynamics
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EPSILON: an eQTL prioritization framework using similarity measures derived from local networks
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essaMEM: finding maximal exact matches using enhanced sparse suffix arrays
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- Journal Article
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MACOP modular architecture with control primitives
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Omics derived networks in bacteria
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Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family
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PIUS: peptide identification by unbiased search
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CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays
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Bursts of vertex activation and epidemics in evolving networks
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- Journal Article
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An efficient algorithm to perform multiple testing in epistasis screening
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- Journal Article
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A robustness study of parametric and non-parametric tests in model-based multifactor dimensionality reduction for epistasis detection
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- Journal Article
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About dice, bouldering, and team empowerment: running the CompOmics group at VIB and Ghent University, Belgium
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- Journal Article
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MS²PIP: a tool for MS/MS peak intensity prediction
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- Journal Article
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Make the most of your samples : Bayes factor estimators for high-dimensional models of sequence evolution
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- Journal Article
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Analysis of initial cell spreading using mechanistic contact formulations for a deformable cell model
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- Journal Article
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Causal information approach to partial conditioning in multivariate data sets
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The effect of neural adaptation on population coding accuracy
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- Journal Article
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Toward community standards in the quest for orthologs
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MotifSuite: workflow for probabilistic motif detection and assessment
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- Journal Article
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Gauging triple stores with actual biological data
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- Journal Article
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Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling)
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- Journal Article
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Semantically linking molecular entities in literature through entity relationships
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- Journal Article
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Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model
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- Journal Article
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- open access
Core Hunter II : fast core subset selection based on multiple genetic diversity measures using Mixed Replica search
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Statistical interpretation of machine learning-based feature importance scores for biomarker discovery
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Travelling the world of gene-gene interactions
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- Journal Article
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U-Compare bio-event meta-service : compatible BioNLP event extraction services
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Reasoning with bio-ontologies: using relational closure rules to enable practical querying
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The use of semiparametric mixed models to analyze PamChip® peptide array data: an application to an oncology experiment
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- Journal Article
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Query-based biclustering of gene expression data using Probabilistic Relational Models
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- Journal Article
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A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
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Normative ethics does not need a foundation: it needs more science
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Effects of snout dimensions on the hydrodynamics of suction feeding in juvenile and adult seahorses
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Modelling gene and protein regulatory networks with answer set pogramming
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- Journal Article
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compomics-utilities: an open-source Java library for computational proteomics
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A greedy, graph-based algorithm for the alignment of multiple homologous gene lists
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CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks
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PiNGO: a cytoscape plugin to find candidate genes in biological networks
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An ensemble biclustering approach for querying gene expression compendia with experimental lists
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mbmdr : an R package for exploring gene-gene interactions associated with binary or quantitative traits
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- Journal Article
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- open access
DASS-GUI : a user interface for identification and analysis of significant patterns in non-sequential data
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Robust biomarker identification for cancer diagnosis with ensemble feature selection methods
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- Journal Article
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OLS Dialog : an open-source front end to the Ontology Lookup Service
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- Journal Article
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Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline
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- Journal Article
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From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification
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TAPIR, a web server for the prediction of plant microRNA targets, including target mimics
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- Journal Article
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Flexible network reconstruction from relational databases with Cytoscape and CytoSQL
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- Journal Article
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Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data
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- Journal Article
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Discriminative and informative features for biomolecular text mining with ensemble feature selection
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- Conference Paper
- C3
- open access
Integrating automated literature searches and text mining in biomarker discovery
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- Miscellaneous
- open access
Highlights of the BioTM 2010 workshop on advances in bio text mining
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- Conference Paper
- C3
- open access
Semantic integration of isolation habitat and location in StrainInfo
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- Journal Article
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ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules
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ViTraM: visualization of transcriptional modules
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An experimental and modelling exploration of the host-sanction hypothesis in legume-rhizobia mutualism
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Smoothing waves in array CGH tumor profiles
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Environmentally induced mechanical feedback in locomotion: frog performance as a model
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- Miscellaneous
- open access
Highlights from the 5(th) International Society for Computational Biology Student Council Symposium at the 17(th) Annual International Conference on Intelligent Systems for Molecular Biology and the 8(th) European Conference on Computational Biology: introduction
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- Journal Article
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Linguistic feature analysis for protein interaction extraction
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CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data
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- Journal Article
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- open access
BioGateway: a semantic systems biology tool for the life sciences
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Impact of antimicrobial usage on the transmission dynamics of antimicrobial resistant bacteria among pigs
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- Journal Article
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Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
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Module networks revisited: computational assessment and prioritization of model predictions
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Gene expression trends and protein features effectively complement each other in gene function prediction
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- Journal Article
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Impact of allelic dropout on evidential value of forensic DNA profiles
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- Journal Article
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Toward a gold standard for promoter prediction evaluation
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- Journal Article
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Evaluation of time profile reconstruction from complex two-color microarray designs
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- Journal Article
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MANTIS : a phylogenetic framework for multi-species genome comparisons
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ONTO-PERL: an API for supporting the development and analysis of bio-ontologies
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- Journal Article
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Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth
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- Journal Article
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Ontology design patterns for bio-ontologies: a case study on the cell cycle ontology
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FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA
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Analysis of a Gibbs sampler method for model-based clustering of gene expression data
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i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles
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- Journal Article
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ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
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TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers
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- Journal Article
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The Protein Identifier Cross-Referencing (PICR) service : reconciling protein identifiers across multiple source databases
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- Journal Article
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Joint mapping of genes and conditions via multidimensional unfolding analysis
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- Journal Article
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In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
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- Journal Article
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CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
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- Journal Article
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Validating module network learning algorithms using simulated data
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- Journal Article
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- open access
An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network
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Role of type-specific neuron properties in a spinal cord motor network