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BIOINFORMATICS EXPERTISE

Walter Pirovano (PhD) is the Director of the Bioinformatics department and a member of the BaseClear Management Team. He obtained his Master’s degree in (Molecular) Biology at the University of Milan. After an internship in the Bioinformatics group of Prof. Graziano Pesole, he went to Amsterdam for an exciting Ph.D. project on protein sequence analysis, under the supervision of Prof. Jaap Heringa and Dr. Anton Feenstra. The project resulted in high-impact publications addressing a series of different computational biology questions, including the identification of functional sites in protein subfamilies (Pirovano et al., 2006) and accurate sequence analysis and alignment of transmembrane proteins (Pirovano et al., 2008)..

Since 2009 Walter has been working at BaseClear, where his starting role as a Product Specialist Bioinformatics was to coordinate the analysis and management of NGS data. The following years saw a high growth rate for BaseClear, where the introduction of new sequencing services like PacBio and Oxford Nanopore Technologies lead to an increasing interest of customers in BaseClear’s complete solutions for microbial (meta)genome analyses. Accordingly, Walter took the next challenge and started building a strong bioinformatics team for assisting our customers with downstream data analysis and interpretation.

In the past years, BaseClear’s Bioinformatics team have created state-of-the-art software pipelines for genome assembly, annotation, comparative genomics, RNA-Seq (gene expression) analysis, metagenomics, and metatranscriptomics analysis. Some of the internally developed methods, such as SSPACE (Boetzer et al., 2011) and GapFiller (Boetzer and Pirovano, 2012), were met with an outstanding interest from the scientific community, and have been cited hundreds of times. In addition to the data analysis specialists, Walter’s team consists of excellent (bioinformatics) software specialists who are responsible for providing an optimal (cloud) IT infrastructure, front- and backend development of genome analysis portals (for an example see https://genome-explorer.com), database management, and implementation of lab-support software (such as the BaseClear LIMS sample tracking package).

BIOINFORMATICS TEAM 

Iris Kolder (PhD) works as a Senior Bioinformatician at BaseClear. After completing her Ph.D. at the Academic Medical Center (AMC) in Amsterdam, she took a Postdoc position at the Wellcome Trust Sanger institute in Cambridge. Next, Iris worked as a Senior Bioinformatician at Leiden University where she specialized in RNA-Seq expression analysis. Here, her work in human and animal studies resulted in high-impact publications (for a recent example, see Kolder et al., 2016). Iris joined BaseClear in May 2016, where she plays a key role in comparative genomics studies. Additionally, her experience in gene expression analysis makes her a central figure in the design and statistical analysis of RNA-Seq projects. Last but not least, Iris takes part in software development for downstream analysis of long-read sequencing projects, where the instruments of choice are the cutting edge Oxford Nanopore Technologies sequencers. 

Ali May (PhD) studied Biological Sciences & Bioengineering at Sabanci University in Istanbul. Next, he obtained a Master’s and a Ph.D. degree in Bioinformatics from the VU University in Amsterdam, where the latter was carried out in collaboration with the Academic Centre for Dentistry Amsterdam focusing on metagenomic and metatranscriptomic analysis of the oral microbiome. Of particular interest are his publications on the discovery of functional microbial subnetworks (May et al., 2016) that are linked to disease and gene expression analysis of infectious Candida albicans strains (Rajendran and May et al., 2017). Ali joined BaseClear in August 2016 as a Senior Bioinformatician and has been involved in genomic analysis projects with diverse biological questions, although he maintains a focus on metagenomics and metatranscriptomics applications. He is also responsible for the data management and downstream analyses of PacBio long-read sequencing projects.  

Marta ter Haar (MSc) started her academic career at the Hogeschool van Amsterdam where she obtained her Bachelor’s degree in Forensic Sciences. Next, she followed the Master’s program Bioinformatics and Systems Biology at the VU University in Amsterdam. In her internships, she had the opportunity to excel her skills in prestigious institutes such as the Netherlands Forensic Institute (NFI) and the Academic Centre of Dentistry in Amsterdam (ACTA). In 2015 she joined BaseClear where she works as a Bioinformatician on a variety of microbial genomics studies. Marta has a particular focus on genome annotation and microbial identification projects, but is also responsible for custom projects and software development. Finally, she is specialized in the implementation and maintenance of state-of-the-art IT infrastructures such as Docker containers. 

Marten Boetzer (MSc) studied Computer Science and Bioinformatics at Leiden University in a joint Master’s program with the Technical University of Delft. During his internship at BaseClear he designed the basis of “genome finishing” algorithms with the aim to improve draft assemblies using paired-end and matepair short read sequencing data. Subsequently in his role as Bioinformatician he further developed these algorithms into the SSPACE and GapFiller packages which resulted in a large commercial and scientific interest. This is reflected by an exponential growth in the number of assembly projects outsourced to BaseClear as well as the hundreds of citations the publications received. In the meanwhile Marten plays an important role in the development of state-of-the-art pipelines for microbial genome analysis which serve our clients in large scale analysis of microbial strain collections.

BIO-IT TEAM

Jonathan den Boer (MSc) received his Master’s degree in Computer Science – Bioinformatics in 2013 from Leiden University and the Technical University of Delft. As a master’s student, he had the opportunity to work in both academia and industry: one of his internships took place at the Leiden University Medical Center (LUMC) on PacBio long-read data analysis, while the second was done at BaseClear on de novo transcriptome analysis. Currently, Jonathan is working as a Bioinformatics Software Specialist in the Bio-IT team and is responsible for the coordination and development of cloud-based genome analysis platforms such as the Genome Explorer. The latter system is widely used by BaseClear customers to screen and mine microbial strain collections. Together with the other team members, he coordinates an array of projects that require large and complex IT infrastructures. Finally, Jonathan plays an pivotal role in the coordination and implementation of lab-support software, including BaseClear’s own laboratory in formation management system (LIMS) and Business Intelligence tools.

Benjamin Versteeg (MSc) obtained both his Bachelor’s and Master’s degree in Computer Science – Bioinformatics at Leiden University and the Technical University of Delft. One of the main topics he has focused during his internships has been the development of advanced web-based applications for comparative genomics. In addition, he has performed in-depth computational analyses to identify biologically interesting correlations between taxonomic profiles and metabolite concentrations. In his current role as a Bioinformatics Software Engineer, Benjamin is primarily responsible for the front- and back-end development of BaseClear’s OrderPortal, an online environment used for a range of processes starting from receiving orders to data release. Like Jonathan, he is involved in the design and implementation of projects that require a custom and complex IT infrastructure design among which BasePlaza, a suite of lab-support applications for internal usage. Finally, Benjamin supports the members of the analysis team by providing them with state-of-the-art IT solutions in their projects.

Hilde Stawski (MSc) obtained her Bachelor’s degree at Avans Hogeschool Breda, which included an internship on ancient DNA at the University of Lincoln (UK). Her next step in education was in the U.S., where she studied Forensic Biology (MSc) at Western Carolina University. Here, she specialized in human mitochondrial DNA analysis using next-generation sequencing. After working experiences as wet lab researcher and QA Specialist, she became a Software Consultant at Allshare as part of a service team that coordinated the analysis, design, development and (cross)testing of software to identify bugs and advise new functionalities.  At BaseClear, her main role is to develop lab-support software,with a focus on BaseClear’s LIMS sample tracking system. Importantly, she assists the Bioinformatics and Bio-IT teams in developing software through a professional lifecycle of design, development, testing and validation. 

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