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Terkko 2005-2021
ECCB2020: the 19th European Conference on Computational Biology
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panRGP: a pangenome-based method to predict genomic islands and explore their diversity
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GRaSP: a graph-based residue neighborhood strategy to predict binding sites
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FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2
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MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants
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Exploring chromatin conformation and gene co-expression through graph embedding
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Feasible-metabolic-pathway-exploration technique using chemical latent space
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Ensembling graph attention networks for human microbe–drug association prediction
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A general near-exact k-mer counting method with low memory consumption enables de novo assembly of 106× human sequence data in 2.7 hours
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Adversarial deconfounding autoencoder for learning robust gene expression embeddings
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DeepCDR: a hybrid graph convolutional network for predicting cancer drug response
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CLPred: a sequence-based protein crystallization predictor using BLSTM neural network
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Conditional out-of-distribution generation for unpaired data using transfer VAE
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Supervised learning on phylogenetically distributed data
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Matrix (factorization) reloaded: flexible methods for imputing genetic interactions with cross-species and side information
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The effect of kinship in re-identification attacks against genomic data sharing beacons
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PathFinder: Bayesian inference of clone migration histories in cancer
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Probabilistic graphlets capture biological function in probabilistic molecular networks
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svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning
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Inferring signaling pathways with probabilistic programming
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Joint epitope selection and spacer design for string-of-beads vaccines
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APOD: accurate sequence-based predictor of disordered flexible linkers
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RAINFOREST: a random forest approach to predict treatment benefit in data from (failed) clinical drug trials
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FastSK: fast sequence analysis with gapped string kernels
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A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data
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Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated
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Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it
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New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics
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A neuro-evolution approach to infer a Boolean network from time-series gene expressions
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An efficient framework to identify key miRNA–mRNA regulatory modules in cancer
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SCHNEL: scalable clustering of high dimensional single-cell data
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Detecting evolutionary patterns of cancers using consensus trees
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Padhoc: a computational pipeline for pathway reconstruction on the fly
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SCIM: universal single-cell matching with unpaired feature sets
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DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs
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Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data
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PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection
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Geometricus represents protein structures as shape-mers derived from moment invariants
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Batch equalization with a generative adversarial network
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DriverGroup: a novel method for identifying driver gene groups
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Enhancing statistical power in temporal biomarker discovery through representative shapelet mining
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cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats
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Inference of gene regulatory networks based on nonlinear ordinary differential equations
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DeepAntigen: a novel method for neoantigen prioritization via 3D genome and deep sparse learning
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Rapid epistatic mixed-model association studies by controlling multiple polygenic effects
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Seqminer2: an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset
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AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata
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PAFway: pairwise associations between functional annotations in biological networks and pathways
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BYASE: a Python library for estimating gene and isoform level allele-specific expression
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