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About

Bernd Jagla is a chemist turned bioinformatician currently working on a R/Shiny application for single-cell RNAseq data analysis called SCHNAPPs, as well as unsupervised cytometry data analysis concentrating on the application of self-organizing maps for high-dimensional cytometry data.

He received his Ph.D. in bioinformatics (department of Biology, Chemistry, and Pharmacy) from the Free University in Berlin, Germany in 1999. Before joining the Institut Pasteur, he worked for almost ten years in New York City, including as an associate research scientist in the Joint Centers for System Biology (Columbia University) and at the Columbia University Screening Center led by Dr. J.E. Rothman. He joined the Institut Pasteur in 2009 to take charge of the bioinformatic needs at the Transcriptome et Epigenome platform, focusing on Next Generation Sequencing. As of 2016, he is a member of the C3BI – HUB Team detached to the Human immunology center (CIH) and provides support for cytometry, next-generation sequencing, and microarray data analysis. His areas of interest include quality assurance and data analysis and visualization at the facility. He also has strong expertise in developing algorithms for function prediction from sequence data, image analysis, analysis of mass spectrometry data, workflow management systems. While at Pasteur he developed:

  • SCHNAPPs (Link)
  • Ideal4AdvIMM (Link)
  • KNIME extensions for Next Generation Sequencing (Link)
  • Post Alignment Visualization and Characterization of High-Throughput Sequencing Experiments (Link)
  • Post Alignment statistics of Illumina reads (Link)

 

Projects

CV

Professional experience

Since January 2016 Pasteur Institute, Paris, France. Biomarker Discovery Platform, UtechS CB Hub de Bioinformatique et Biostatistiques, C3BI. February 2009 – December 2015 Pasteur Institute, Paris, France. Bioinformatics Research Scientist at Transcriptome & Epigenome Platform. July 2006 – January 2009 Columbia University, New York, NY Associate Research Scientist at the Joint Centers for System Biology. July 2004 – June 2006 Columbia University, New York, NY Associate Research Scientist in the Genome Center / Molecular Library Screening Center Network January 2003 – July 2004 Memorial Sloan Kettering Cancer Center, New York, NY Associate Research Scientist in Functional Proteomics Project / JE Rothman laboratory. December 2001 – September 2002 Phase-It, Heidelberg, Germany Project leader, data-mining July 2002 – September 2002 Freelance consultant, Heidelberg, Germany October 1999 – September 2001 Memorial Sloan Kettering Cancer Center, New York, NY Postdoctoral Fellow, Laboratory of Dr. JE. Rothman January 1991 – January 1992 Technical University Munich, Germany Intern

Education

September 1999 Ph.D., Free University Berlin, Germany 1989 – 1995 Chemistry Diploma, Free University Berlin & Technical University Munich, Germany 1990 – 1991 Computer Science at Free University Berlin, Germany

Fellowships & Awards

2007 caBIG™ Embodying the Vision Award 1997 – 1999 DFG Fellowship of the Graduiertenkolleg: “Dynamic and evolution of macromolecular and cellular processes.” 

Publications

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