Sint-Martens-Latem, Belgium, 20 September 2011 – The Board of Directors of Applied Maths has appointed Koen Janssens as CEO of Applied Maths. Koen Janssens holds a Master degree in Applied Economics and a Master of Science in Bioinformatics (Katholieke Universiteit Leuven). During the last seven years, he has been increasingly involved in the operational management of the company. In his new role as CEO, he will be supported by an Executive Committee, consisting of Paul Vauterin, Director of Software Development and Bruno Pot, Director of Business Development. Luc Vauterin, co-founder of Applied Maths, stepped down as CEO in June of this year but remains closely involved with Applied Maths as Scientific Advisor.

Stijn Spitaels, who assumed the position of CEO ad interim of Applied Maths on June 1st 2011, is now resuming his consultancy activities. The board wishes to thank Stijn Spitaels for his skilled assistance in the management transition and initiating a growth scenario for Applied Maths, aiming for the company to remain a world leader in bio-informatics solutions for academia, public health centers and industry.

“We are at the start of exciting new times”, said Koen Janssens. “Never before has the need been so high for ready-to-use bioinformatics solutions that can deal with the huge amount of genomics and meta-genomics data being generated today. Applied Maths is ready to face the bioinformatics challenges that new technological evolutions in biotechnology are bringing. I’m honoured to lead the team in this endeavour.”

Sint-Martens-Latem, Belgium, 15 July 2011 – Applied Maths NV today announces that it has released a new version of its flagship software suite BioNumerics that allows de novo assembly to be performed on next generation sequencing data. This new feature, available in version 6.6, consolidates the development of BioNumerics into a complete and fully integrated suite for preprocessing and analysis of NGS data.

The de novo assembly is available in BioNumerics’ new Power Assembler released in version 6.5 and is based on two open source third party tools: Velvet & Ray. Both applications are GPL-licensed, and have been revised to compile under Windows in 32 bit as well as 64 bit modes. Both assembly tools are complemented by an in-house developed greedy algorithm for final contig alignment. Additionally, several enhancements to the Power Assembler were included to relax the RAM requirements and to reduce calculation time of the assemblies. The assembler is designed to allow de novo assembly of full bacterial chromosomes on a regular desktop computer running a 64-bit Windows OS and having sufficient RAM.

To further increase the user-friendliness of the versatile pipeline design of the Power Assembler, project templates have been introduced. Predefined project templates are avaliable for the most commonly used workflows, thus allowing beginning users to easily start the analysis of their data. All parameters of a template can easily be accessed and changed at any time later to guarantee the maximal flexibility and performance of the tool. Project templates can be saved and shared between co-workers.

Sint-Martens-Latem, Belgium, 30 June 2011 – Scientists working at Applied Maths have published a research article that describes a global statistical framework to calculate the reliability of branches on trees or networks resulting from cluster analysis, and that allows the most probable trees to be produced from a set of degenerated solutions. The article, titled “A resampling strategy for reliable network construction”, has appeared in the May 2011 issue of Molecular Phylogenetics and Evolution (MPE 60: 273-286).

Cluster analysis of biological data, interpreting trees and assessing the reliability of branches has always been a central theme in the development of software at Applied Maths. The success of its software can be attributed for a large part to the availability of powerful clustering applications that are user-friendly, offer rich visualization and interpretation environments and allow clustering of the largest and most complex biological data sets. With the present article, describing algorithms that are implemented in the BioNumerics software, Applied Maths confirms its position as a pioneering and leading provider of powerful and user-friendly software for mining and clustering of biological data.

Luc Vauterin, Director of Science at Applied Maths: “With the emergence of new high-throughput techniques, turning data into information becomes a bottleneck, in spite of ever increasing computing power. Cluster analysis helps finding signals and structure in complex data sets of whatever source and nature. Clustering techniques have become increasingly popular in all branches of bioinformatics, ranging from phylogeny to drug discovery. Applied Maths’ mission is to provide scientists with powerful clustering tools that support reliable interpretation of the result.”

The full article can be downloaded from ScienceDirect.

Sint-Martens-Latem, Belgium, 10 June 2011 – Ruth Devenyns, Chairman of the board at Applied Maths, announces that Luc Vauterin has decided to step down as CEO, effective June 1, 2011, in order to focus more on the scientific development of the company and on supporting Applied Maths’ ever expanding customer base. With immediate effect, the CEO function is being assumed by Stijn Spitaels, a former consultant at McKinsey & Company.

Before joining Applied Maths, Stijn Spitaels has successively worked at Vandemoortele, a Belgian food group and as an Associate Partner at McKinsey, where he was serving clients in the food and pharmaceutical industries, mostly on the topic of growth development. Stijn holds degrees in economics, finance and business from Ghent University, the Vlerick School of Management and INSEAD.

Luc Vauterin is co-founder of Applied Maths and has been the driving force behind its development from a small software start-up into a global player in bioinformatics with BioNumerics as its flagship software suite. Thanks to Luc’s strong scientific background and business acumen, Applied Maths has built an impressive customer base spanning the whole globe, including leading institutions in microbiological research, healthcare and the food and biotech industries. Going forward, Luc will become Chief Scientific Officer at Applied Maths, focusing on the further scientific development of the BioNumerics software and continued client support.

Ruth Devenyns: “By combining outstanding scientific and entrepreneurial skills, Luc has been key to Applied Maths’ success since its foundation in 1992. We respect Luc’s decision and believe that his desire to focus on scientific development along with the introduction of Stijn’s professional experience with growth strategies and marketing will further strengthen the company both in terms of scientific achievements and market presence.”

Stijn Spitaels: “I am very excited to join this dynamic and successful company. Luc has done a tremendous job in building a great team, a strong BioNumerics brand and an impressive customer base and passes on a thriving company. I look forward to working with Luc and the team to guide Applied Maths into further growth.”

Sint-Martens-Latem, Belgium, 25 May 2011 – Applied Maths today announces that Bayer CropScience has decided to implement the BioNumerics platform globally for its plant breeding program. The choice for BioNumerics was incentivized by the software’s comprehensive databasing and analysis tools, enabling workers to deploy one uniform software platform for diverse projects and techniques. IT managers and bioinformaticians at Bayer CropScience greatly valued the flexible scripting possibilities using Python as an instrument to integrate the BioNumerics software with existing tools and realize automatic workflows for high-throughput data management.

Luc Vauterin, CEO at Applied Maths: “BioNumerics has an impressive track record in the academic and public health community, which is evidenced by thousands of scientific papers. The last years however, there is a growing interest for BioNumerics by the industry, especially the pharmaceutical, biotech and food industry. To close successful deals with major industrial players, a solid and reliable support and service base is equally important and mandatory as offering a well integrated and flexible software platform. We are pleased that Bayer CropScience has recognized the professional support from Applied Maths and we are committed to maintain our high level of support and strengthen it where possible.”

Sint-Martens-Latem, Belgium, 18 May 2011 – HIV researchers at CDC and across the globe are keeping close watch on the rapid mutations of HIV and its threat of resistance to current and novel therapies. In order to track variant, atypical and drug resistant HIV strains, smart systems are required that can rapidly process information from multiple sources into clear and reportable summarizations. Critical understanding of mutations in HIV is needed to allow physicians and public health policy makers to make treatment decisions and to create preventive measures.

With BioNumerics, Applied Maths delivers integrated solutions with a sustained commitment for implementing innovation in molecular and biomedical research and healthcare. The HIV Drug Resistance Analysis Plugin is a specialized application in BioNumerics, designed for the evaluation of antiretroviral drug resistance/susceptibility of HIV strains on gene sequences based on publicly available algorithms. The application allows users to automatically import and manage data, capture and analyze results and generate reports based on S-I-R mapping algorithms. In the framework of the US Global Health Initiative, the CDC will deploy BioNumerics and the HIV plugin for mutational analysis and monitoring of HIV drug resistance.

The HIV Drug Resistance Analysis plugin offers an expert system that allows users to co- evaluate and compare results generated from publicly available rule sets, including HIVDB (USA), Rega (Belgium) and ANRS (France). The application has a fully integrated and automated workflow starting from sequence assembly to final resistance reporting and is designed for professional high-throughput processing. Besides offering the advantage of integration and automation, the expert rule system provides a number of unique features that make it more flexible and powerful than any other system. The Decision Network empowering the expert rule system allows the user to import any publicly available algorithm and create, adapt and evaluate own expert rules. Furthermore, the system not only shows resistance/susceptibility results, but reports the particular rules that are triggered and the particular mutations that are responsible for the triggering. The full integration of all steps in the workflow, starting with assembly of raw sequences, allows the analyst to evaluate the data at all stages of the analysis, thus leading to the most reliable decisions.

Lem del Rosario, Director of North America Operations says, “Applied Maths is committed to strengthening public health surveillance systems and the choice of CDC to deploy our software for this challenging program is an endorsement of the intrinsic quality of our solutions and support. We will continue to work closely with researchers at CDC towards gaining insights into the molecular epidemiology of HIV.”

Sint-Martens-Latem, Belgium, 7 February 2011 – Applied Maths has entered into a partnership with 5 leading research and knowledge centers in the Netherlands to develop a methodology for the characterization of the genomic content of livestock-associated micro-organisms using the optical genome mapping technology. Optical mapping is a technology that rapidly generates high-resolution, ordered, whole genome restriction maps from single DNA molecules and is a valuable tool in understanding the genome organization, in facilitating de novo assembly, and as a portable high-resolution bacterial typing technique.

The collaborative project focuses on developing a highly sensitive and fast diagnostic detection test for surveillance and monitoring of livestock-associated-MRSA (methicellin-resistant Staphylococcus aureus). Reliable and quick identification and typing of infected farm animals and animal products will provide insight in the dissemination of this troublesome bacterium and prevent pathogens from entering and passing to the food chain.

Applied Maths will develop software to interpret and compare the optical maps from large numbers of bacterial isolates and infer evolutionary networks for population genetics on livestock and hospital associated MRSA.

The project is financially supported by the Dutch Food & Nutrition Delta Programme Phase 2 of the Ministry of Economic Affairs through the Dutch "Agentschap NL" and includes the following partners:

• PiEXT BV: a Dutch life sciences company that holds an exclusive license on the use of the Optical Mapping technology for developing diagnostic tests for pathogens, coordinator of the project,
• National Institute for Public Health and Environments (RIVM): a leading center of expertise in the fields of health, nutrition and environmental protection,
• VU University Medical Center: an internationally recognized reference laboratory for studying epidemiology and control of Staphylococcus aureus, and in particular MRSA,
• Applied Maths NV,
• Institute for Pig Genetics BV: supporting pig farmers in their efforts as breeding farms to improve health status and where possible eradicate diseases, and
• VION NV: the largest meat production company in Europe and the third largest in consumer foods in the Netherlands.

Sint-Martens-Latem, Belgium, 31 January 2011 – Applied Maths NV proudly announces that it has acquired a record number of new customers in 2010. The company now has an impressive customer base of over 2,300 unique organizations in 94 countries, including universities, governmental and non-profit research centers, food and quality inspection agencies, public health centers, hospitals and clinical research labs, pharmaceutical and biotech companies, food industry, etc.

Luc Vauterin, CEO at Applied Maths: “In the past our software has been especially recognized among the scientific community, which is evidenced by thousands of scientific papers published using BioNumerics and GelCompar. The last years, we are expanding our business with the BioNumerics platform towards the industry, and have closed major deals in the pharmaceutical and food industry. The comprehensive databasing and analysis capabilities of BioNumerics along with its flexible Python scripting environment, renders the software an excellent platform for enterprise-wide management of biodata. In response to the growing need for customized solutions from our industrial customers, we are expanding our sales and support force.”