相关论文: From Protein Interactions to Functional Annotation…
Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps…
BACKGROUND: One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode of protein function assignment is mostly…
Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
We present a method that compares the protein interaction networks of two species to detect functionally similar (conserved) protein modules between them. The method is based on an algorithm we developed to identify matching subgraphs…
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments.…
What is the best way to match the nodes of two graphs? This graph alignment problem generalizes graph isomorphism and arises in applications from social network analysis to bioinformatics. Some solutions assume that auxiliary information on…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Predicting gene functions is a challenge for biologists in the post genomic era. Interactions among genes and their products compose networks that can be used to infer gene functions. Most previous studies adopt a linkage assumption, i.e.,…
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs…
Scarcity of high quality annotated images remains a limiting factor for training accurate image segmentation models. While more and more annotated datasets become publicly available, the number of samples in each individual database is…
Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
Parse graphs boost human pose estimation (HPE) by integrating context and hierarchies, yet prior work mostly focuses on single modality modeling, ignoring the potential of multimodal fusion. Notably, language offers rich HPE priors like…
A new method of hierarchical clustering of graph vertexes is suggested. In the method, the graph partition is determined with an equivalence relation satisfying a recursive definition stating that vertexes are equivalent if the vertexes…
Text alignment finds application in tasks such as citation recommendation and plagiarism detection. Existing alignment methods operate at a single, predefined level and cannot learn to align texts at, for example, sentence and document…
We introduce and study methods for inferring and learning from correspondences among neurons. The approach enables alignment of data from distinct multiunit studies of nervous systems. We show that the methods for inferring correspondences…
Recent studies reveal even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce…