News | Uratim Ltd.

August 29, 2017: The Szigma Magazine of InfoRadio covered our result: Identifying Combinatorial Biomarkers by Association Rule Mining in the CAMD Alzheimer’s Database. News portals origo.hu and hirado.hu also reported it.

June 9, 2017: Our result: Brain Size Bias Compensated Graph-Theoretical Parameters are Also Better in Women’s Structural Connectomes was reported in the first channel of the Hungarian Television, in the Minden Tudas magazine.

June 3, 2017: A 25-minute broadcast on the metagenomic progress in today’s science was presented in “Mindenki Akadémiája” in the Hungarian Television.

March 6, 2017: The index.hu and origo.hu news portals reported on our results: The “Giant Virus Finder” Discovers an Abundance of Giant Viruses in the Antarctic Dry Valleys

November 11, 2016: The “Minden tudás” magazine of the first channel of the Hungarian Television M1, covered our result “Life without dUTPase“.

September 6, 2016: Origo.hu reported on our new publication: Parameterizable Consensus Connectomes from the Human Connectome Project: The Budapest Reference Connectome Server v3.0

July 29, 2016: The “Minden tudás” magazine of the first channel of the Hungarian Television M1, on our result (How to Direct the Edges of the Connectomes: Dynamics of the Consensus Connectomes and the Development of the Connections in the Human Brain) aired a block.

June 23, 2016: The Hungarian version of National Geographic and origo.hu reported on our new publication: Significant Differences Found in Short Nucleotide Sequences of Human Intestinal Metagenomes of Northern-European and Chinese Origin.

March 10, 2016: In its prime morning show “Ma Reggel”, Hungarian Televison Channel 1 (M1) aired an interview with Balázs Szalkai and Vince Grolmusz on their publication Nucleotide 9-mers Characterize the Type II Diabetic Gut Metagenome published in Genomics.

February 7, 2016: Radio Q aired an interview with Prof. Grolmusz, on the sex differences of the human connectomes (in Hungarian).

January 30, 2016: Our new article appeared: Csaba Kerepesi, Vince Grolmusz: Evaluating the Quantitative Capabilities of Metagenomic Analysis Software, Current Microbiology, First online: 30 January 2016, http://dx.doi.org/10.1007/s00284-016-0991-2

January 10, 2016: The prime Hungarian radio station, Kossuth Radio, in its science magazine “Szonda”, broadcasted an interview with Prof. Grolmusz and Csaba Kerepesi, on the discovery of giant viruses in the Kutch desert.

December 14, 2015: Our new paper appeared today: Csaba Kerepesi, Vince Grolmusz: Giant Viruses of the Kutch Desert Archives of Virology First online: 14 December 2015, doi: http://dx.doi.org/10.1007/s00705-015-2720-8

July 1, 2015: PLOS ONE published our result on the sex differences of the human connectomes: Balázs Szalkai, Bálint Varga, Vince Grolmusz: Theoretical Analysis Reveals: Women’s Brains are Better Connected than Men’s, PLoS One, 10(7): e0130045. doi:10.1371/journal.pone.0130045,

May 3, 2015: We have demonstrated that the nucleotide ninemers characterize the diabetic gut microbiome: arXiv preprint 1505.00476 (2015)

April 17, 2015: The first channel of the Hungarian state television in its morning show broadcasted a live interview with Balázs Szalkai and Prof. Grolmusz on the construction of the Budapest Reference Connectome Server.

March 18, 2015: We have found giant viruses in numerous biomes, including the the Antarctic dry valleys: arXiv preprint 1503.05575 (2015)

January 4, 2015: Our results on the deep graph-theoretic analysis of 96 brain graphs for sex differences appeared today: Balázs Szalkai, Bálint Varga, Vince Grolmusz: Graph Theoretical Analysis Reveals: Women’s Brains are Better Connected than Men’s, arXiv preprint arXiv:1501.00727

December 9, 2014: The second, upgraded version of the Budapest Reference Connectome Server is released. Its description appeared as a preprint: Balázs Szalkai, Csaba Kerepesi, Vince Grolmusz: The Budapest Reference Connectome Server v2.0, arXiv preprint arXiv:1412.3151,

October 10, 2014: Microbial Ecology published our new “methods” paper, describing the AmphoraVizu webserver of ours: Csaba Kerepesi, Balázs Szalkai, Vince Grolmusz: Visual analysis of the quantitative composition of metagenomic communities: the AmphoraVizu webserver

October 7, 2014: We have found the first evidence of the existence of the new, giant viruses in a desert environment; the preprint is available at: Csaba Kerepesi, Vince Grolmusz: Giant viruses of the Kutch desert; arXiv preprint arXiv 1410:1278,

August 15, 2014: Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics published today our new “methods” paper: Gábor Iván, Vince Grolmusz: Dimension reduction of clustering results in bioinformatics; 1844 (2014), pp. 2277-2283; DOI: 10.1016/j.bbapap.2014.08.015.

July 23, 2014: PLoS One published the Metagenomic Telescope: this is a novel method for discovering new functional annotations of human proteins through an innovative metagenomic view of diverse microorganisms in extreme environments.

April 10, 2014: Today the journal Gene published the paper describing our new, intuitive, multiple-choice protein-sequence search webserver.

January 22, 2014: Uratim with Prof. Grolmusz participated on the Horizon 2020 partnering meeting in Bratislava.

December 6, 2013: Uratim Ltd. today presented an application of an automatic combinatorial biomarker discovery tool in Alzheimer’s disease in Cornell University’s arXiv: arXiv 1312.1876. The reference is: Balazs Szalkai, Vince K Grolmusz, Vince I Grolmusz, CAMD Consortium: Identifying Combinatorial Biomarkers by Association Rule Mining in the CAMD Alzheimer’s Database; arXiv preprint arXiv:1312.1876 (2013).

October 12, 2013: Uratim Ltd. today presented an easy-to-use webserver implementation of the AMPHORA2 phylogenetic classification tool: the webserver is capable to assign phylogenetic classification to metagenomic data of clinical or environmental origin. The webserver is available at http://amphoranet.pitgroup.org.. Reference: Csaba Kerepesi, Daniel Banky, Vince Grolmusz: AmphoraNet: The Webserver Implementation of the AMPHORA2 Metagenomic Workflow Suite, Gene, 2014, Vol. 533 No. 2. pp. 538-540; http://dx.doi.org/10.1016/j.gene.2013.10.015.

September 8, 2013: Uratim Ltd. developed a general visualization method for the comparison of two classification schemes in bioinformatics. A large part of bioinformatics problems involves the comparison of two types of classifications (e.g., phylogenetic information with genetic information, or morbidity statistics with genetics clustering) such methods are of basic interest. Uratim connected the visualization algorithm to a dimension reduction solution based on the OPTICS clustering method. The result was published in Cornell University’s arXiv: arXiv 1309.1892.; the reference is: Gabor Ivan, Vince Grolmusz: Dimension reduction of clustering results in bioinformatics; arXiv preprint arXiv:1309.1892 (2013)

September 7, 2013: A publication on the SwissAlign webserver of Uratim Ltd. appeared in Cornell University’s arXiv: arXiv 1309.1895. The webserver is a lighting-fast implementation of the Smith-Waterman algorithm. The webserver is available at http://swissalign.pitgroup.org. Reference: Gabor Ivan, Daniel Banky, Vince Grolmusz: Fast and Exact Sequence Alignment with the Smith-Waterman Algorithm: The SwissAlign Webserver. arXiv preprint arXiv:1309.1895.

August 27, 2013: As a consequence of the pioneering data mining efforts of Uratim Ltd. in spatial protein structures, demonstarted earlier in works PMID:20014471,, PMID:19364497, PMID:18315842, or in PMID:20148971; today the journal Nucleic Acids Research published a work clarifying dUTPase enzyme mechanisms. Reference: Orsolya Barabas, Veronika Nemeth, Andrea Bodor, Andras Perczel, Edina Rosta, Zoltan Kele, Imre Zagyva, Zoltan Szabadka, Vince I Grolmusz, Matthias Wilmanns, Beata G Vertessy: Catalytic mechanism of ?-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling, Nucleic Acids Research, gkt756, published on August 27, 2013, doi: 10.1093/nar/gkt756

January 23, 2013: PLoS One published today our method of relativizing PageRank for finding low-degree, high importance nodes in networks. The method computes, the PageRank/vertex degree ratio for each node in the network; that ratio compensates low degree nodes for lower PageRanks; therefore we can identify low-degree and high importance nodes in networks. Reference: Daniel Banky, Gabor Ivan, Vince Grolmusz: Equal Opportunity for Low-Degree Network Nodes: A PageRank-Based Method for Protein Target Identification in Metabolic Graphs,PLoS ONE 8(1): e54204. doi:10.1371/journal.pone.0054204

September 4, 2012: Researchers from Uratim Ltd. have shown that the co-citation in networks is a reliable measure of vertex similarity. The result appeared today in Protein and Peptide Letters (Lilla Tothmeresz, Vince Grolmusz: Characterizing the Functional Similarity of Enzymes with high Co-Citation in Interaction Networks, Protein and Peptide Letters, 2012 Sep 4. [Epub ahead of print])

May 10, 2012: A researcher from Uratim Ltd. has clarified the relations between the PageRank of the vertices of undirected graphs (or networks) and the degrees of the vertices: the PageRank of the vertices of the undirected graphs are proportional to the degrees if and only if the PageRank is personalized with the degree distribution. The result appeared today in arXiv 1205.1960,

April 19, 2012: The Frigate docking program, developed by Uratim Ltd., found molecule hits against Mycobacterium tuberculosis, which were published today in Bioconjugate Chemistry, DOI: 10.1021/bc200221t .

December 31, 2011: Uratim Ltd. successfully completed the Nano-Mubiop EU FP7 project. The partners of URATIM in the NANO-MUBIOP project were the following institutions:

December 2, 2011: The Frigate molecular docking program, developed by Uratim Ltd., found new protein inhibitors, with the possibility of application in tuberculosis. The result appeared today in the journal PLoS ONE 6(12): e28428..

May 12, 2011: The Uratim Ltd., in cooperation with the Mathematical Institute of the Eötvös University, announced the public availability of the Erdős WebGraph Server at the web-graph.org web address today. The cooperative project makes large, constantly updated graphs accessible, describing the hyperlink structure of the World Wide Web. The webgraph is available for download for any interested researcher, without registration. The project pays tribute to Erdõs Pál (1913-1996), the world-famous Hungarian mathematician, a graph theory pioneer.

The Mathematical Institute of the Eötvös University (www.cs.elte.hu) is a prime mathematical research center in Hungary. It is involved for many decades in the study of large graphs and networks.

January 21, 2011: Uratim filed PCT patent applications for two new original drug molecules against tuberculosis.

January 12, 2011: Professor Grolmusz was interviewed by Julia Gimes on MR1 Kossuth Radio, on the use of on-line protein folding game foldit in protein science. The interview can be accessed here (in Hungarian).

December 12, 2010: The leading bioinformatics journal of Oxford University Press, Bioinformatics, publishes on-line the biological network analysis method of Uratim, based on Google’s PageRank algorithm. DOI: 10.1093/bioinformatics/btq680.

September 30, 2010: Uratim Ltd. successfully concluded the TB-INTER project, supported by the National Office for Research and Technology. The partners in the project were:

July 12, 2010: Daniel Banky presented a contribution on the new developments of our Nascent server, authored by Gabor Ivan, Daniel Banky, Vince Grolmusz, and titled: Refining the protein interaction network generated by NASCENT using sequence alignment, at the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA.
June 22, 2010: Mr. Gabor Ivan from Uratim presented a lecture at a Nanotech Conference and Expo at Anaheim, CA, on “Designing universal oligonucleotides for DNA/nanoparticle conjugates“.

April 26, 2010: Uratim Ltd. organized a conference on the fight of tuberculosis at the Institute of Enzymology. The programme of the conference can be found here. As a part of the public appearance of the conference, Radio magazine “Szonda” covered our project. Interviewer: Julia Gimes; broadcasted in May, 2010 on MR1 Kossuth Radio (in Hungarian).

January 11, 2010:
Uratim Ltd. releases the new version of its NASCENT tool. The new version is capable to predict much more protein-protein interactions, since it optionally uses the TrEMBL database of the UNIPROT. The default settings apply SwissProt. The new version of the tool is available at http://nascent.pitgroup.org for non-profit organizations.

August 27, 2009:
Prof. Grolmusz presented the network analysis tools , developed at Uratim Ltd., at the Annual Meeting of the Hungarian Biochemical Society at Budapest. The strictly mathematical method yielded clear-cut biological results in several applications.

July 3, 2009:
Uratim Ltd. concluded a very successful participation at the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) Stockholm, Sweden. The scientists of the company gave oral presentations on the WikiPDB, DECOMP and NASCENT web servers.

May 29, 2009:
Uratim Ltd. exhibited its HTP protein-ligand docking tools and protein-protein interaction network analysis capability at the Annual Meeting the Peptide Chemistry Committee of the Hungarian Academy of Sciences at Balatonszemes, Hungary 26th-28th May 2009.

April 20, 2009:
Uratim Ltd. releases its WikiPDB tool. WikiPDB provides a Wikipedia-like interface (an extension of the Mediawiki software) for modification of files deposited in the PDB (Protein Data Bank), and discussion between scientists doing research on the same structures. Our system detects syntax errors, provides an API for semantic error checking plug-ins, and keeps track of different versions. The server is available at http://wikipdb.org/ .

February 20, 2009:
Uratim Ltd. releases its ProtDict tool. ProtDict is a UniProt-based Protein dictionary, capable of finding UniProt entries based on AC numbers, SwissProt IDs, EC numbers, 3 types of gene names, and 100 different types of database cross references. The server is available at http://protdict.pitgroup.org/ .

February 1, 2009:
Uratim Ltd. released its DECOMP server. The server repairs and annotates source files in the Protein Data Bank. The server is available for non-profit organizations at http://decomp.pitgroup.org .

January 15, 2009:
Uratim Ltd. released its new NASCENT tool, for automatic prediction of protein-protein interaction networks for less researched species. The tool is available at http://nascent.pitgroup.org for non-profit organizations.

November 13-14, 2008:
Professor Grolmusz from Uratim Ltd. served as a panel member and rapporteur at the”Challenges for the Future” International Conference on HIV/AIDS, Malaria and Tuberculosis Research, organized by the European Commission (DG Research).

October 16, 2008:
Professor Grolmusz from Uratim Ltd. participated int the NANO-MUBIOP kick-off meeting in Florance, Italy. Uratim is one of the first Hungarian SME’s working in a new EU FP7 project.

September 13, 2008:
The “Delta” science magazine of the Hungarian State Television (MTV 1) broadcasted a report on our TB-INTERACTOME project.

August 6, 2008:
The European Commission signed the contract NANO-MUBIOP – Enhanced Sensitivity Nanotechnology-Based Multiplexed Bioassay Platform for Diagnostic Applications – a collaborative project funded under the European Union Seventh Framework Programme (FP7) that aims to develop a new bioassay technique applied to the detection of Human Papilloma Virus (HPV) responsible for cancer. In the three-year project, Uratim Ltd. performs mathematical modelling for the optimization of the nanotechnology processes.

The partners of URATIM in the NANO-MUBIOP project are the following institutions:

July 27, 2008:
In the Hungarian Radio channel 1 (MR1 Kossuth Radio) a report was aired about the TB-INTER project of ours, in the weekly science magazine “Szonda”.
The report is available on youtube.com (in Hungarian)

June 8, 2008:
URATIM Ltd. was invited to present the TB-INTERACTOME project at the 4th European Research and Innovation Exposititon (SERI) in Paris, France. The innovative research work of the project participants were highlighted in the printed and audio-visual materials circulated in the exposition. The Frigate docking algorithm and the new mathematical methods for the analysis of the protein interaction networks of the URATIM Ltd. attracted great interest in the Expo.