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Vince Grolmusz

Publications and source records attributed to Vince Grolmusz.

52 records · Page 3Linked to original sources
arXiv2015

The "Giant Virus Finder" Discovers an Abundance of Giant Viruses in the Antarctic Dry Valleys

The first giant virus was identified in 2003 from a biofilm of an industrial water-cooling tower in England. Later, numerous new giant viruses were found in oceans and freshwater habitats, some of them having even 2,500 genes. We have demonstrated their very likely presence in four soil samples taken from the Kutch Desert (Gujarat, India). Here we describe a bioinformatics work-flow, called the "Giant Virus Finder" that is capable to discover the very likely presence of the genomes of giant viruses in metagenomic shotgun-sequenced datasets. The new tool is applied to numerous hot and cold desert soil samples as well as some tundra- and forest soils. We show that most of these samples contain giant viruses, and especially many were found in the Antarctic dry valleys. The results imply that giant viruses could be frequent not only in aqueous habitats, but in a wide spectrum of soils on our planet.

q-bio.GN↗
arXiv2015

Life without dUTPase

Fine-tuned regulation of the cellular nucleotide pools is indispensable for faithful replication of DNA. The genetic information is also safeguarded by DNA damage recognition and repair processes. Uracil is one of the most frequently occurring erroneous base in DNA; it can arise from cytosine deamination or thymine-replacing incorporation. Two enzyme families are primarily involved in keeping DNA uracil-free: dUTPases that prevent thymine-replacing incorporation and uracil-DNA glycosylases that excise uracil from DNA and initiate uracil-excision repair. Both dUTPase and the most efficient uracil-DNA glycosylase UNG is thought to be ubiquitous in free-living organisms. In the present work, we have systematically investigated the genotype of deposited fully sequenced bacterial and Archaeal genomes. Surprisingly, we have found that in contrast to the generally held opinion, a wide number of bacterial and Archaeal species lack the dUTPase gene(s). The dut- genotype is present in diverse bacterial phyla indicating that loss of this (or these) gene(s) has occurred multiple times during evolution. We have identified several survival strategies in lack of dUTPases: i) simultaneous lack or inhibition of UNG, ii) acquisition of a less dUTP-specific sanitizing nucleotide pyrophosphatase, and iii) supply of dUTPase from bacteriophages. Our data indicate that several unicellular microorganisms may efficiently cope with a dut- genotype potentially leading to an unusual uracil-enrichment in their genomic DNA.

q-bio.GN↗
arXiv2015

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 395 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. We have found that the frontal and the limbic lobes are more conservative, while the edges in the temporal and occipital lobes are more diverse. Interestingly, a "hybrid" conservative and diverse distribution was found in the paracentral lobule and the fusiform gyrus. Smaller cortical areas were also evaluated: precentral gyri were found to be more conservative, and the postcentral and the superior temporal gyri to be very diverse.

q-bio.NC↗
arXiv2015

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. Moderate changes were also detected in the microbial gene composition of the metagenomes of diabetic patients, but again, no specific gene was found that is present in disease-related and missing in healthy metagenome. However, these fine differences in microbial taxon- and gene composition are difficult to apply as quantitative biomarkers for diagnosing or predicting type II diabetes. In the present work we report some nucleotide 9-mers with significantly differing frequencies in diabetic and healthy intestinal flora. To our knowledge, it is the first time such short DNA fragments have been associated with T2D. The automated, quantitative analysis of the frequencies of short nucleotide sequences seems to be more feasible than accurate phylogenetic and functional analysis, and thus it might be a promising direction of diagnostic research.

q-bio.GN↗
arXiv2015

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. When scientists examine large networks of tens or hundreds of millions of vertices, only fast algorithms can be applied because of the size constraints. In the case of diffusion MRI-based structural human brain imaging, the effective vertex number of the connectomes, or brain graphs derived from the data is on the scale of several hundred today. That size facilitates applying strict mathematical graph algorithms even for some hard-to-compute (or NP-hard) quantities like vertex cover or balanced minimum cut. In the present work we have examined brain graphs, computed from the data of the Human Connectome Project, recorded from male and female subjects between ages 22 and 35. Significant differences were found between the male and female structural brain graphs: we show that the average female connectome has more edges, is a better expander graph, has larger minimal bisection width, and has more spanning trees than the average male connectome. Since the average female brain weights less than the brain of males, these properties show that the female brain is more "well-connected" or perhaps, more "efficient" in a sense than the brain of males.

q-bio.NC↗
arXiv2015

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 Ver. 2.0 (http://connectome.pitgroup.org) generates the common edges of the connectomes of 96 distinct cortexes, each with 1015 vertices, computed from 96 MRI data sets of the Human Connectome Project. The user may set numerous parameters for the identification and filtering of common edges, and the graphs are downloadable in both csv and GraphML formats; both formats carry the anatomical annotations of the vertices, generated by the Freesurfer program. The resulting consensus graph is also automatically visualized in a 3D rotating brain model on the website. The consensus graphs, generated with various parameter settings, can be used as reference connectomes based on different, independent MRI images, therefore they may serve as reduced-error, low-noise, robust graph representations of the human brain.

q-bio.NC↗
arXiv2014

Giant Viruses of the Kutch Desert

The Kutch desert (Great Rann of Kutch, Gujarat, India) is a unique ecosystem: in the larger part of the year it is a hot, salty desert that is flooded regularly in the Indian monsoon season. In the dry season, the crystallized salt deposits form the "white desert" in large regions. The first metagenomic analysis of the soil samples of Kutch was published in 2013, and the data was deposited in the NCBI Sequence Read Archive. The sequences were analyzed at the same time phylogenetically for prokaryotes, especially for bacterial taxa. In the present work, we are searching for the DNA sequences of the recently discovered giant viruses in the soil samples of the Kutch desert. Since most giant viruses were discovered in biofilms in industrial cooling towers, ocean water and freshwater ponds, we were surprised to find their DNA sequences in the soil samples of a seasonally very hot and arid, salty environment.

q-bio.GN↗
arXiv2013

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" become 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. Some servers support the formation of queries with regular expressions, but most of the users are unfamiliar with their syntax. Here we present an intuitive, easily applicable webserver, the Protein Sequence Analysis server, that allows the formation of multiple choice queries by simply drawing the residues to their positions; if more than one residue are drawn to the same position, then they will be nicely stacked on the user interface, indicating the multiple choice at he given position. This computer-game like interface is natural and intuitive, and the coloring of the residues makes possible to form queries requiring not just certain amino acids in the given positions, but also small nonpolar, negatively charged, hydrophobic, positively charged, or polar ones. The webserver is available at http://psa.pitgroup.org.

q-bio.GN↗
arXiv2013

Dimension reduction of clustering results in bioinformatics

OPTICS is a density-based clustering algorithm that performs well in a wide variety of applications. For a set of input objects, the algorithm creates a so-called reachability plot that can be either used to produce cluster membership assignments, or interpreted itself as an expressive two-dimensional representation of the density-based clustering structure of the input set, even if the input set is embedded in higher dimensions. The main focus of this work is a visualization method that can be used to assign colours to all entries of the input database, based on hierarchically represented a-priori knowledge available for each of these objects. Based on two different, bioinformatics-related applications we illustrate how the proposed method can be efficiently used to identify clusters with proven real-life relevance.

q-bio.QM↗
arXiv2013

Fast and Exact Sequence Alignment with the Smith-Waterman Algorithm: The SwissAlign Webserver

It is demonstrated earlier that the exact Smith-Waterman algorithm yields more accurate results than the members of the heuristic BLAST family of algorithms. Unfortunately, the Smith-Waterman algorithm is much slower than the BLAST and its clones. Here we present a technique and a webserver that uses the exact Smith-Waterman algorithm, and it is approximately as fast as the BLAST algorithm. The technique unites earlier methods of extensive preprocessing of the target sequence database, and CPU-specific coding of the Smith-Waterman algorithm. The SwissAlign webserver is available at the http://swissalign.pitgroup.org address.

q-bio.GN↗
arXiv2012

A Note on the PageRank of Undirected Graphs

The PageRank is a widely used scoring function of networks in general and of the World Wide Web graph in particular. The PageRank is defined for directed graphs, but in some special cases applications for undirected graphs occur. In the literature it is widely noted that the PageRank for undirected graphs are proportional to the degrees of the vertices of the graph. We prove that statement for a particular personalization vector in the definition of the PageRank, and we also show that in general, the PageRank of an undirected graph is not exactly proportional to the degree distribution of the graph: our main theorem gives an upper and a lower bound to the L_1 norm of the difference of the PageRank and the degree distribution vectors.

cs.DS↗
arXiv2003

High-density and Secure Data Transmission via Linear Combinations

Suppose that there are $n$ Senders and $n$ Receivers. Our goal is to send long messages from Sender $i$ to Receiver $i$ such that no other receiver can retrieve the message intended for Receiver $i$. The task can easily be completed using $n$ private channels between the pairs. Solutions, using one channel needs either encryption or switching elements for routing the messages to their addressee. The main result of the present work is a description of a network in which The Senders and the Receivers are connected with only $n^{o(1)}$ channels; the encoding and de-coding is nothing else just very fast linear combinations of the message-bits; and there are no switching or routing-elements in the network, just linear combinations are computed, with fixed connections (channels or wires). In the proofs we do not use {\em any} unproven cryptographical or complexity theoretical assumptions.

cs.CC↗
arXiv2003

Defying Dimensions Mod 6

We show that a certain representation of the matrix-product can be computed with $n^{o(1)}$ multiplications. We also show, that siumilar representations of matrices can be compressed enormously.

cs.CC↗
arXiv2003

Hyperdense Coding Modulo 6 with Filter-Machines

We show how one can encode $n$ bits with $n^{o(1)}$ ``wave-bits'' using still hypothetical filter-machines (here $o(1)$ denotes a positive quantity which goes to 0 as $n$ goes to infity). Our present result - in a completely different computational model - significantly improves on the quantum superdense-coding breakthrough of Bennet and Wiesner (1992) which encoded $n$ bits by $\lceil{n/2}\rceil$ quantum-bits. We also show that our earlier algorithm (Tech. Rep. TR03-001, ECCC, See ftp://ftp.eccc.uni-trier.de/pub/eccc/reports/2003/TR03-001/index.html) which used $n^{o(1)}$ muliplication for computing a representation of the dot-product of two $n$-bit sequences modulo 6, and, similarly, an algorithm for computing a representation of the multiplication of two $n\times n$ matrices with $n^{2+o(1)}$ multiplications can be turned to algorithms computing the exact dot-product or the exact matrix-product with the same number of multiplications with filter-machines. With classical computation, computing the dot-product needs $Ω(n)$ multiplications and the best known algorithm for matrix multiplication (D. Coppersmith and S. Winograd, Matrix multiplication via arithmetic progressions, J. Symbolic Comput., 9(3):251--280, 1990) uses $n^{2.376}$ multiplications.

cs.CC↗
arXiv2002

Computing Elementary Symmetric Polynomials with a Sublinear Number of Multiplications

Elementary symmetric polynomials $S_n^k$ are used as a benchmark for the bounded-depth arithmetic circuit model of computation. In this work we prove that $S_n^k$ modulo composite numbers $m=p_1p_2$ can be computed with much fewer multiplications than over any field, if the coefficients of monomials $x_{i_1}x_{i_2}... x_{i_k}$ are allowed to be 1 either mod $p_1$ or mod $p_2$ but not necessarily both. More exactly, we prove that for any constant $k$ such a representation of $S_n^k$ can be computed modulo $p_1p_2$ using only $\exp(O(\sqrt{\log n}\log\log n))$ multiplications on the most restricted depth-3 arithmetic circuits, for $\min({p_1,p_2})>k!$. Moreover, the number of multiplications remain sublinear while $k=O(\log\log n).$ In contrast, the well-known Graham-Pollack bound yields an $n-1$ lower bound for the number of multiplications even for the exact computation (not the representation) of $S_n^2$. Our results generalize for other non-prime power composite moduli as well. The proof uses the famous BBR-polynomial of Barrington, Beigel and Rudich.

cs.CC↗