SCARF: a biomedical association rule finding webserver.

The analysis of enormous datasets with missing data entries is a standard task in biological and medical data processing. Large-scale, multi-institution clinical studies are the typical examples of such datasets. These sets make possible the search for multi-parametric relations since from the plenty of the data one is likely to find a satisfying number of subjects with the required parameter ensembles.

The Graph of Our Mind.

Graph theory in the last two decades penetrated sociology, molecular biology, genetics, chemistry, computer engineering, and numerous other fields of science. One of the more recent areas of its applications is the study of the connections of the human brain. By the development of diffusion magnetic resonance imaging (diffusion MRI), it is possible today to map the connections between the 1-1.

High-resolution directed human connectomes and the Consensus Connectome Dynamics.

Here we show a method of directing the edges of the connectomes, prepared from HARDI datasets from the human brain. Before the present work, no high-definition directed braingraphs were published, because the tractography methods in use are not capable of assigning directions to the neural tracts discovered. Previous work on the functional connectomes applied low-resolution functional MRI-detected statistical causality for the assignment of directions of connectomes of typically several dozens of vertices.

Comparing advanced graph-theoretical parameters of the connectomes of the lobes of the human brain.

Deep, classical graph-theoretical parameters, like the size of the minimum vertex cover, the chromatic number, or the eigengap of the adjacency matrix of the graph were studied widely by mathematicians in the last century. Most researchers today study much simpler parameters of braingraphs or connectomes which were defined in the last twenty years for enormous networks-like the graph of the World Wide Web-with hundreds of millions of nodes. Since the connectomes, describing the connections of the human brain, typically contain several hundred vertices today, one can compute and analyze the much deeper, harder-to-compute classical graph parameters for these, relatively small graphs of the brain.

Mapping correlations of psychological and structural connectome properties of the dataset of the human connectome project with the maximum spanning tree method.

Genome-wide association studies (GWAS) opened new horizons in genomics and medicine by discovering novel genetic factors in numerous health conditions. The analogous analysis of the correlations of large quantities of psychological and brain imaging measures may yield similarly striking results in the brain science. Smith et al.

MetaHMM: A webserver for identifying novel genes with specified functions in metagenomic samples.

The fast and affordable sequencing of large clinical and environmental metagenomic datasets opens up new horizons in medical and biotechnological applications. It is believed that today we have described only about 1% of the microorganisms on the Earth, therefore, metagenomic analysis mostly deals with unknown species in the samples. Microbial communities in extreme environments may contain genes with high biotechnological potential, and clinical metagenomes, related to diseases, may uncover still unknown pathogens and pathological mechanisms in known diseases.

The dorsal striatum and the dynamics of the consensus connectomes in the frontal lobe of the human brain.

In the applications of the graph theory, it is unusual that one considers numerous, pairwise different graphs on the very same set of vertices. In the case of human braingraphs or connectomes, however, this is the standard situation: the nodes correspond to anatomically identified cerebral regions, and two vertices are connected by an edge if a diffusion MRI-based workflow identifies a fiber of axons, running between the two regions, corresponding to the two vertices. Therefore, if we examine the braingraphs of n subjects, then we have n graphs on the very same, anatomically identified vertex set.

SECLAF: a webserver and deep neural network design tool for hierarchical biological sequence classification.

Summary: Artificial intelligence tools are gaining more and more ground each year in bioinformatics. Learning algorithms can be taught for specific tasks by using the existing enormous biological databases, and the resulting models can be used for the high-quality classification of novel, un-categorized data in numerous areas, including biological sequence analysis. Here, we introduce SECLAF, a webserver that uses deep neural networks for hierarchical biological sequence classification.

The Robustness and the Doubly-Preferential Attachment Simulation of the Consensus Connectome Dynamics of the Human Brain.

Consensus Connectome Dynamics (CCD) is a remarkable phenomenon of the human connectomes (braingraphs) that was discovered by continuously decreasing the minimum confidence-parameter at the graphical interface of the Budapest Reference Connectome Server, which depicts the cerebral connections of n = 418 subjects with a frequency-parameter k: For any k = 1, 2, …, n one can view the graph of the edges that are present in at least k connectomes. If parameter k is decreased one-by-one from k = n through k = 1 then more and more edges appear in the graph, since the inclusion condition is relaxed. The surprising observation is that the appearance of the edges is far from random: it resembles a growing, complex structure.

The braingraph.org database of high resolution structural connectomes and the brain graph tools.

Based on the data of the NIH-funded Human Connectome Project, we have computed structural connectomes of 426 human subjects in five different resolutions of 83, 129, 234, 463 and 1015 nodes and several edge weights. The graphs are given in anatomically annotated GraphML format that facilitates better further processing and visualization. For 96 subjects, the anatomically classified sub-graphs can also be accessed, formed from the vertices corresponding to distinct lobes or even smaller regions of interests of the brain.

Comparative connectomics: Mapping the inter-individual variability of connections within the regions of the human brain.

The human braingraph, or connectome is a description of the connections of the brain: the nodes of the graph correspond to small areas of the gray matter, and two nodes are connected by an edge if a diffusion MRI-based workflow finds fibers between those brain areas. We have constructed 1015-vertex graphs from the diffusion MRI brain images of 392 human subjects and compared the individual graphs with respect to several different areas of the brain. The inter-individual variability of the graphs within different brain regions was discovered and described.

Identifying combinatorial biomarkers by association rule mining in the CAMD Alzheimer's database.

The concept of combinatorial biomarkers was conceived when it was noticed that simple biomarkers are often inadequate for recognizing and characterizing complex diseases. Here we present an algorithmic search method for complex biomarkers which may predict or indicate Alzheimer's disease (AD) and other kinds of dementia. We show that our method is universal since it can describe any Boolean function for biomarker discovery.

Near perfect protein multi-label classification with deep neural networks.

Biological sequences can be considered as data items of high-, non-fixed dimensions, corresponding to the length of those sequences. The comparison and the classification of biological sequences in their relations to large databases are important areas of research today. Artificial neural networks (ANNs) have gained a well-deserved popularity among machine learning tools upon their recent successful applications in image- and sound processing and classification problems.

Parameterizable consensus connectomes from the Human Connectome Project: the Budapest Reference Connectome Server v3.0.

Connections of the living human brain, on a macroscopic scale, can be mapped by a diffusion MR imaging based workflow. Since the same anatomic regions can be corresponded between distinct brains, one can compare the presence or the absence of the edges, connecting the very same two anatomic regions, among multiple cortices. Previously, we have constructed the consensus braingraphs on 1015 vertices first in five, then in 96 subjects in the Budapest Reference Connectome Server v1.

How to Direct the Edges of the Connectomes: Dynamics of the Consensus Connectomes and the Development of the Connections in the Human Brain.

The human braingraph or the connectome is the object of an intensive research today. The advantage of the graph-approach to brain science is that the rich structures, algorithms and definitions of graph theory can be applied to the anatomical networks of the connections of the human brain. In these graphs, the vertices correspond to the small (1-1.

Significant differences found in short nucleotide sequences of human intestinal metagenomes of Northern-European and Chinese Origin.

Background: Metagenomic analysis of environmental and clinical samples is gaining considerable importance in today's literature. Changes in the composition of the intestinal microbial communities, relative to the healthy control, are reported in numerous conditions.

Methods: We have carefully analyzed the frequencies of the short nucleotide sequences in the metagenomes of two different enterotypes; namely of Chinese and European origins.

Nucleotide 9-mers characterize the type II diabetic gut metagenome.

Discoveries of new biomarkers for frequently occurring diseases are of special importance in today's medicine. While fully developed type II diabetes (T2D) can be detected easily, the early identification of high risk individuals is an area of interest in T2D, too. Metagenomic analysis of the human bacterial flora has shown subtle changes in diabetic patients, but no specific microbes are known to cause or promote the disease.

Graph Theoretical Analysis Reveals: Women's Brains Are Better Connected than Men's.

Deep graph-theoretic ideas in the context with the graph of the World Wide Web led to the definition of Google's PageRank and the subsequent rise of the most popular search engine to date. Brain graphs, or connectomes, are being widely explored today. We believe that non-trivial graph theoretic concepts, similarly as it happened in the case of the World Wide Web, will lead to discoveries enlightening the structural and also the functional details of the animal and human brains.

The Budapest Reference Connectome Server v2.0.

The connectomes of different human brains are pairwise distinct: we cannot talk about an abstract "graph of the brain". Two typical connectomes, however, have quite a few common graph edges that may describe the same connections between the same cortical areas. The Budapest Reference Connectome Server v2.

Visual analysis of the quantitative composition of metagenomic communities: the AmphoraVizu webserver.

Low-cost DNA sequencing methods have given rise to an enormous development of metagenomics in the past few years. One basic--and difficult--task is the phylogenetic annotation of the metagenomic samples studied. The difficulty comes from the fact that the typical environmental sample contains hundreds of unknown and still uncharacterized microorganisms.

The metagenomic telescope.

Next generation sequencing technologies led to the discovery of numerous new microbe species in diverse environmental samples. Some of the new species contain genes never encountered before. Some of these genes encode proteins with novel functions, and some of these genes encode proteins that perform some well-known function in a novel way.

An intuitive graphical webserver for multiple-choice protein sequence search.

Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" becomes a verb, describing the act of performing sequence search and alignment. However, if one needs to search for sequences that contain, for example, two hydrophobic and three polar residues at five given positions, the query formation on the most frequently used webservers will be difficult.