Silja Heilmann

Short presentation

CV

Education:

Degree awarded: Ph.D. Biophysics; August 2012.
Institution: Niels Bohr Institute (NBI), University of Copenhagen, Denmark

Degree awarded: M.S. in Biophysics; April 2009. Grade of M.S. Thesis: 12/12.
Institution: University of Copenhagen, Denmark

Degree awarded: B.Sc. Physics; July 2006.
Institution: University of Copenhagen, Denmark.

Employment:

Position: Postdoctoral researcher, Nov. 2015 - present, Semb lab, DanStem, Copenhagen University. 

Position: Research Scholar, Oct. 2012 – Oct. 2015, Xavier lab, MSKCC, New York. 

Position: Undergraduate researcher. Feb. 2007 – Jan. 2009. The office of Danish Science Communication, Copenhagen, Denmark.

Position: Undergraduate researcher. Jun. – Aug. 2006. Risø, Danish National Laboratory, Division of Plasma and Optics.

Short summary of research projects:

Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen: 
Image processing and image analysis of 3D microscopy images and movies of developing mouse pancreas. Computational Cellular Potts modeling of cellular sorting/dynamics during pancreas development using Python. 

White lab/Xavier lab, collaboration Memorial Sloan Kettering Cancer Center (MSKCC), New York: 
Fluorescence microscopy imaging of tumor growth and metastasis formation in transparent zebra fish. Development of theoretical and computational tools for extracting and analysing data from zebra fish images. Development of processing algorithms and computational infrastructure in MATLAB for handling the quantification of large amounts of images. Developing mathematical models of the cell population dynamics of the metastatic cascade.

Greenberg lab, University of Washington, Seattle:
Mathematical modeling of warfare between quorum sensing bacteria, (part of Ph.D. project).

Kerr lab, University of Washington, Seattle:
Spatial cellular automata modeling and mathematical modeling of cooperation in quorum sensing bacteria, (part of Ph.D. project).

CMOL, Niels Bohr Institute, University of Copenhagen:
Spatial cellular automata modeling and mathematical modeling focusing on questions regarding evolution and coexistence in phage-bacteria ecosystems. (Master thesis project continued into Ph.D. project).

Risø National Laboratory, Danish Polymer Centre:
Developing tracking software in MATLAB for determining trajectories of motile human Fibroblasts, (Undergraduate research project).

Risø National Laboratory, Division of Plasma and Optics:
Degradation of human growth hormone by ultraviolet irradiation, (Undergraduate research project).

Hvidovre Research Hospital:
Calibration of radio wave field in MRI scanning. (Bachelor thesis project).

Honors and Awards: 

• 2017-2019 The Danish Council for Independent Research, Medical Sciences, Postdoc Fellowship.
• 2016-2018 Lundbeck Foundation Postdoc Fellowship
• 2015 Presidents Innovator award. Awarded at the Society of Biomolecular Imaging and Informatics annual conference in Boston. 
• 2015 Cover paper in Cancer Research.
• 2012-2015 James S. MacDonnell Foundation Complex Systems Postdoctoral Fellowship Award
• 2014 Poster Prize at Center for Metastasis Research Inaugural Symposium, MSKCC. 
• 2013 Travel stipend awarded by OIST to participate in Okinawa Workshop on Frontiers in Integrative Biology. OIST, Okinawa, Japan.
• 2010 Cover paper in Journal of Virology
• 2007 Oticon Foundation Student Travel Grant.
• 2006 Erasmus Program Scholarship, monthly stipend.

Other scientific qualifications

Ad hoc reviewer: 
International Society of Microbial Ecology Journal (ISME), International Journal of Organic Evolution, Biofouling: The Journal Of Bioadhesion and Biofilm Research.

Teaching experience:

• Co-supervision of Computer Scence Master student. Project titled: "Segmenting tubular structures in pancreas using deep learning". Aug. 2017.
• Co-supervision of two undergraduate Computer science students. 3 month project concerning center line extraction in segmented pancreatic trees using a wavefront propagation method. Jan 2017. 
• Mentoring of student in the 2015 Medical Student Summer Research Fellowship Program via NCI funding at MSKCC. Project titled “Multicolor Time-lapse Imaging of Metastatic Melanoma in Zebrafish”. 
• Teaching assistant for the courses ‘Networks in Biological systems’ fall  2009 and ‘Biological Dynamics’ spring 2010 at Copenhagen University. 

Science popularization:

Editor and writer at the student run physics journal ‘Gamma’ 2007-2010 at the Niels Bohr Institute. 

Selected Talks at Meetings and Conferences:

• Second Annual Conference of the Society of Biomolecular Imaging & Informatics (SBI2), Boston, Ma, USA. Sep 2015. ‘Quantifying metastatic spread in a zebra fish melanoma model’. 
• MSKCC, USA, Research in Progress, Department of Immunology, Apr Mar. 142015. ’Quantifying metastatic spread/melanoma progression in a zebra fish melanoma model’. 
• NYU Langone Medical Center, NY Metropolitan Zebrafish Club imaging meeting. NYC USA. Nov. 2014. ‘Quantifying metastatic spread in a zebra fish melanoma model’.
• NBI, Denmark, Mini school / workshop on Signals and Space: Spatio-temporal patterns in simple bio-systems, Aug 2011.’A life on the edge’. 
• Friday Harbor Labs UW, USA, Kerr Lab Retreat, Jun 2011. ‘Cooperation in Quorum Sensing Bacteria’.
• Tokyo University, Japan, RCCSB symposium on cellular biophysics, Dec 2010. ‘A life on the edge’. 
• UW, Seattle, USA ShoKerr Meeting, Aug 2010. ‘A Tool for Exploring Quorum Sensing and the Evolution of Cooperation in Bacteria’.
• CMOL, NBI, Denmark. Small Systems Biology Meeting. Dragør, May 2010. ‘Life on the edge’. 
• Harvard Med. School Boston, UW Seattle, UCSF, USA. Visits at Depart. of Systems Biology Harvard (Kishony lab), Depart. of Biology UW (Kerr lab) Seattle and UCSF (Tang lab) SF. Feb - Mar 2010. ‘Survival of the mediocre killers’.
• Copenhagen University, Denmark. Star Lecture for 1'st year physics students, Nov 2009. ‘Biophysics at NBI’.

Selected Conferences, Workshops and Courses Abroad:

• Mechanical Forces in Development EMBL Heidelberg, Germany, 3 - 6 Jul 2019. (Poster presented).
• Computational Image Analysis in Cellular and Developmental Biology, course at MBL, Chicago University, Oct 2017. (Talk given). 
• Cell polarity and membrane dynamics, San Feliu de Guixols, Spain, June 2017. (Poster presented).
• Cell Polarity in Development, Division, and Disease, VT, USA June 2016. (Poster presented).
• Annual Zebrafish Disease Models Conference (ZDM8), Boston, Ma, USA Aug. 2015. (Poster presented).
• Compucell3D tissue modeling workshop, University of Indiana, Bloomington, In. USA. Aug. 2015
• Ohio State State UniversityUniversity, USA, Workshop: Ecology and Evolution of Cancer, the Mathematical Bioscience Institute, Sep. 2014. (Poster presented).
• Niels Bohr Institute, Copenhagen. Dynamics of Stem Cell Decisions, Aug. 2013. 
• UCSF, San Francisco, USA 2nd International Biennial Evolution and Cancer Conference, Jun. 2013. (Poster presented).
• OIST, Okinawa, Japan. Okinawa Workshop on Frontiers in Integrative Biology, May 2013. (Presentation of mini project and poster).
• IISc, Bangalore, India International Conference on Mathematical Biology, Jul. 2011. (Poster presented).
• ISME, Seattle, USA. 13th International Symposium on Microbial Ecology, USA, Aug. 2010.
• MGC, USA 17th Annual Microbial Genomics Conference. Rocky Gap, Oct. 2009. (Poster presented).
• Utrecht University, Netherlands. Six month spent at Utrecht University, Netherlands., Aug 2006 - Jan 2007. (Part of M.S. program).