Michael Stromberg Email & Phone Number

San Diego, CA, US

Sevenoaks, GB

San Diego, CA, US

• Spearheaded the development and release of multiple Nirvana versions, incorporating new features, improved accuracy, and optimizations for performance.
• Improved core variant annotation speed by 2.4x
• Reduced HGVS issues by a remarkable 59% making Nirvana the most accurate variant annotator in the field.
• Conducted a comprehensive evaluation and comparison of six global oncology knowledge bases, including OncoKB, CKB, PierianDx, and three leading Chinese platforms, assessing data quality, accessibility.

San Diego, CA, US

• Successfully led the Nirvana team in developing and maintaining a core variant annotation platform for major Illumina products, such as DRAGEN, BaseSpace Variant Interpreter, TruSight Oncology, VeriSeq NIPT, and.
• Developed 10 Nirvana releases in a single year, with 7 containing an approved DHF for clinical IVD software.
• Architected and implemented the Nirvana annotation service into a scalable and cost-effective solution, capable of processing 10 million cases per year per AWS region.
• Established successful collaborations with several external commercial and academic partners.

San Diego, CA, US

• Developed Nirvana, a state-of-the-art variant annotator that is 30x faster than Illumina's previous annotator (IAS) and 235x faster than VEP, while providing nearly identical results on a single CPU. This innovation.
• Successfully managed the Genomic Algorithms Team, focusing on secondary analysis and developing algorithms for various medically-relevant products, contributing to Illumina's expansion in the clinical and diagnostic.
• Pioneered the adoption of best practices for maintaining agility in clinical software development, including code and design documentation, increased unit test code coverage, and modernized CI/CD processes.

San Diego, CA, US

• Enabled multi-node processing in the Isas secondary analysis pipeline, significantly reducing time-to-answer and making the platform more competitive.
• Developed the targeted RNA-Seq workflow, including the creation of a custom amplicon aligner and implementation of the DESeq algorithm in C#.
• Significantly boosted the metagenomics classification speed by an order of magnitude, while enhancing the accuracy and extending the classification sensitivity to the species level, and in certain cases, even to the.
• Actively participated in the Isas architecture group, refactoring core functionalities, and introducing independently-versioned plugin workflows, improving the overall performance and flexibility of the platform.

San Diego, CA, US

• Dramatically reduced the overall analysis time in the CASAVA 1.8 analysis pipeline by a third. This was achieved by developing a new tool that leveraged dynamic sampling of the read fragment length distribution.
• Designed and developed a 16S metagenomics classification program tailored specifically for the MiSeq platform. The program utilized a Naive Bayesian classifier, enabling it to accurately detect microorganisms down to.
• Conducted a comprehensive comparison of various aligners, including ELAND, BWA, SOAP, Bowtie, and iSAAC. The evaluation assessed speed, memory usage, accuracy, and usability, and involved researching alignment.
• Significantly reduced storage requirements for the CASAVA analysis pipeline by 60%, accomplished by updating it to produce and parse compressed export files.

Chestnut Hill, MA, US

• Developed MOSAIK, an ultra-fast, versatile NGS aligner supporting multiple sequencing technologies, including Roche 454, Illumina, AB SOLiD, Helicos, and Sanger capillary. Leveraging the Smith-Waterman algorithm.
• Overcame critical challenges in MOSAIK development, such as characterizing and compensating for sequencing technology-specific error modes and devising an accurate aligner error model to optimize mapping quality.
• Successfully implemented MOSAIK in over 250 labs worldwide by mid-July 2010, demonstrating its widespread utility and impact.
• Contributed to the 1000 Genomes Project's data analysis, by aligning and analyzing Roche 454 mate-pair reads and nearly six billion Illumina reads using MOSAIK. Employed our in-house variant caller, GigaBayes, for trio.

Cambridge, Massachusetts, US

• Engineered a Java-based software tool, Audacity, that analyzes confocal microscope image stacks to effectively characterize and track bacterial populations.
• Devised an ingenious strategy integrating pulse-coupled neural networks (PCNN) and axis of symmetry calculations, ensuring precise object segmentation and accurate dimension measurement.
• Leveraged the ImageJ API with Java and 3D deconvolution techniques, significantly enhancing image quality and resolution for advanced data analysis and research.

Solna, SE

• Designed and developed an innovative framework for simulating signal pathways in specified cell types, enabling a deeper understanding of cellular responses to various stimuli and targeted gene products.
• Integrated microarray data to accurately capture the current state of gene expression, serving as the foundation for pathway analysis and simulations.
• Successfully modeled and simulated the activation of specific receptors, such as the estrogen receptor (ER beta), and their subsequent signal pathways.Keywords: Computational modeling, Signal pathway simulation.

• As a consultant for the Swedish National Police in a child pornography case, employed expert computer forensics skills to develop a custom high-performance decryption tool, facilitating the decryption of a proprietary.
• Successfully extracted a critical password from the forensics data, which was instrumental in decrypting key evidence files, directly contributing to the dismantling of the ring.

• Co-founded Alecti Group, a consulting firm specializing in cutting-edge technology solutions for mainly the telecom and financial industries.
• Developing innovative micropayment solutions, enhancing financial transactions for clients.
• Provided expertise to banks and affiliates on building secure B2B applications, bolstering their operational security and efficiency.

• Successfully managed all media compression processes, including DVD production and real-time webcasts, ensuring high-quality output.
• Designed and optimized media compression pipelines and applications by fine-tuning MPEG-2 algorithm parameters, resulting in improved video quality.
• Boosted teleconferencing performance between the Royal Institute of Technology and Stanford University by delivering DVD-quality video on a dedicated high-bandwidth link.
• Developed load balancing software to enhance video streaming server scalability and prevent system overloads as viewer numbers increased.

• Created a 75th-anniversary trailer for SF, Sweden's premier cinema chain, and an immersive OMNIMAX solar system film for children.
• Applied expertise in particle animation systems to create engaging content for children's cartoons.
• Demonstrated proficiency in multiple 3D animation software, including Alias, Wavefront, Maya, and Softimage.

Ph.D., Computational Biology, Bioinformatics

Computer Science, Biomedical Engineering

Computer Engineering, Japanese

Education record