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CV 2013 Pavel Tomancak
Pavel Tomancak
Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
Pfotenhauerstrasse 108
D-01307 Dresden
Germany
Tel.: +49 351 210 2670
Email: [email protected] Homepage: http://www.mpi-cbg.de/research/research-groups/pavel-tomancak/research.html
Twitter: @PavelTomancak
BIOGRAPHICAL DATA
Born 27 March 1972, Frydek-Mistek, Czechoslovakia
Citizen of Czech Republic
single
EDUCATION
University of Heidelberg, Heidelberg, Germany, 1995-1999
Ph.D. in Developmental Biology, 1999,
Masaryk University, Brno, Czech Republic, 1990-1995
Mgr. in Natural Sciences, specializing in Molecular Biology and Genetics, 1995
FELLOWSHIPS AND AWARDS
ERC Starting grant 2010-2015
HFSP Young Investigator grant 2012-2015
HFSP Young Investigator grant 2008-2012
European Molecular Biology Laboratory predoctoral fellowship, 1995-1999
Masaryk University, Dean of faculty of Science Award, 1995
RESEARCH EXPERIENCE
Independent Research: Senior Permanent Research Group Leader, Max-Planck Institute of Molecular
Cell Biology and Genetics, Dresden, Germany, 2013-present
“Patterns of gene expression in development and evolution”
Research Group Leader, Max-Planck Institute of Molecular Cell Biology and
Genetics, Dresden, Germany, 2005-2013
“Patterns of gene expression in animal development”
Postdoctoral Research: Assistant Researcher at Dr. Gerald M. Rubin's laboratory
HHMI/Department of Molecular and Cell Biology,
University of California, Berkeley, 2002-2005
“Large scale Drosophila in situ projects”
Doctoral Research: EMBL, Heidelberg, Germany, 1995-1999 (Research advisor Dr. Anne Ephrussi)
“Establishment of polarity in Drosophila oocyte.”
CV 2013 Pavel Tomancak
Undergraduate Research: Masaryk University, Brno, Czech Republic, 1994-1995 (Research advisor Dr. Ing. Karel Chroust)
“Construction of transgenic Drosophila melanogaster carrying human genes for metabolizing
enzymes.”
RESEARCH RELATED ACTIVITIES
Conference Organization: EMBO course on Light Sheet Microscopy MPI-CBG Dresden, Germany, 18th -
28th August 2014
Bioimage Informatics 2012 MPI-CBG Dresden, Germany, 16th – 19th September
2012
Evolution and Development of Integrated Phenotype, International Congress of
Entomology, Daegu , South Korea, August 19th – 25th 2012
Image Analysis in Living Systems Workshop at the LeadNet meeting of the Max
Planck Society, May 8th 2012
Next Generation Resources plenary session at the 22nd European Drosophila
Research Conference in Lisbon, Portugal, September 21 - 24th 2011
Workshop on Image Analysis for Drosophila research at the 51st Annual
Drosophila Research Conference in Washington, April 7th - 11th 2010
Trilateral Workshop for young scientists from Czech Republic, Poland and
Germany on “Optical Techniques in Cell and Developmental Biology”, Dresden,
November 29th - December 1st 2009
The First Light Sheet based Fluorescence Microscopy Workshop
MPI-CBG, Dresden, September 24th - 25th 2009
Grant Reviewing: Welcome Trust, German-Israeli Foundation, NSF, DFG, Research Council KU
Leuven
Journal Reviewing: Nature Methods, Cell, Genome Biology, Nature Biotechnology, Developmental
Biology, Bioinformatics, BMC, PLoS Genetics, Journal of Microscopy, Bioessays,
PLoS One, JoVE
Editorial boards: BMC Bioinformatics, Gene
Recent invited talks at international meetings
Structured Illumination: Biomedical Applications and Future Developments, Oxford, October 2013
European Drosophila Research Conference, Barcelona, October 2013
European Bioimage Analysis Symposium, Barcelona, October 2013
Seeing is believing, EMBL Heidelberg, October 2013
5th EMBO meeting, Amsterdam, September 2013
15th Annual Meeting for the Society of Evolutionary Biology, Tsukuba, August 2013
Manipulation of Drosophila Genome, Janelia Farm, March 2013
BioTec Forum, Dresden, December 2012
Imaging in Cell Biology: Where Next, Cumberland Lodge, Windsor, October 2012
French Drosophila meeting, Clermont-Ferrand, September 2012
24th Entomological Congress, Daegu, South Korea, August 2012
The molecular and developmental biology of Drosophila, Kolymbari, Crete, June 2012
12th European Light Microscopy Initiative (ELMI) Meeting, Leuven, June 2012
ESF/EMBO Conference on Systems Biology of Drosophila development, Pultusk/Poland, May 2012
CV 2013 Pavel Tomancak
The 30th Pattern Recognition and Computer Vision Colloquium, Prague, April 2012
EMBO Practical Course on Microscopy, Johannesburgh, November 2011
DIPP Vision Talk, Dresden, September 2011
European Drosophila Reseacrh Conference, Lisbon, September 2011
Bioimage Informatics II Janelia Farm Research Campus, September 2011
INSERM workshop Emerging tools in quantitative fluorescence microscopy for systems biology,
Lisbon, September 2011
EMBO practical course on Drosophila, Lisbon, March 2011
Automated Imaging and High Throughput Phenotyping, CSHL, December 2010
The molecular and developmental biology of Drosophila, Kolymbari, Crete, June 2010
Open Microscopy Environment (OME) User’s meeting, Paris, June 2010
VizBi Visualization of Biological Data, EMBL, March 2010
Trilateral Workshop Dresden, December 2009
European Drosophila Research Conference, Nice, November 2009
The First Light Sheet based Fluorescence Microscopy Workshop, Dresden, September 2009
BioImage Informatics, Janelia Farm Research Campus, 2009
What Can Computer Vision Do for Neuroscience and Vice Versa? Janelia Farm Research Campus 2008
ISBI, Paris, France, 2008
Trilateral MPI Workshop on Regulation of gene expression in Prague, 2007
Cytokinematics in Hradec Kralove, Czech Republic, 2006
Recent invited talks at Universities and Academic Institutes
2013 Dec 17th University of Ostrava, Ostrava, invited by Marek Elias
2013 Nov 21st Advanced Techniques Day: Lightsheet microscopy, Prague, invited by Karel Drbal
2013 Nov 12th BIOCEV day, Prague, invited by Pavel Martasek
2013 Sep 17th Einstein College of Medicine, New York, invited by Rob Singer
2013 Sep 12th University of Wisconsin, Madison, invited by Kevin Eliceiri
2013 May 8th Leibnitz Institute for Neurobiology, Magdeburg, invited by Rainer Pielot
2013 Apr 10th Stowers Institute, Kansas City, invited by Julia Zeitlinger
2013 Mar 20th Janelia Farm Research Campus, invited by Albert Cardona
2013 Feb 5th College of Life Sciences, Dundee, invited by Mike Ferguson & Jason Swedlow
2012 Dec 17th Centrum for Organismal Studies Heidelberg, invited by Steffen Lemke
2012 Dec 13th ZMBH Heidelberg, invited by Bruce Edgar
2012 Nov 19th Department of Molecular Genetics, University of Toronto, invited by Howard Lipshitz
2012 Nov 8th, Department of Genetics, University of Cambridge, invited by Boris Adryan
2012 Nov 1st ETH Zurich Institute of Biochemistry, invited by Yves Barral
2012 July 3rd IMBB Heraklion, Crete, invited by Michaelis Averof
2012 June 12th VIB Leuven, invited by Bassem Hassan
2012 Feb 13th MPI for Developmental Biology, invited by Gaspar Jekely
2012 Feb 23rd UMC St Radboud, Nijmegen, invited by Annette Schenck
2012 Jan 20th Institute Curie, Paris, invited by Emmanuel Farge
2012 Jan 19th Institute Pasteur, Paris, invited by Jost Enninga
2012 Jan 9th Institute of Entomology, Ceske Budejovice, invited by Tomas Dolezal
2011 Dec 2nd CADB Madrid, invited by Acaimo Gonzalez Reyes
2011 Nov 4th CRG, Barcelona, invited by Yogi Jaeger
2011 Nov 3rd IRB, Barcelona, invited by Marco Milan
2011 Oct 13th Universite Paul Sabatier, Toulouse, invited by Alain Vincent
2011 June 20th MPI for Molecular Genetics Berlin, invited by S. Meijsing
CV 2013 Pavel Tomancak
2011 June 9th IRCM Montreal, invited by Eric Lecuyer
2011 May 23th IST, Vienna, invited by Carl-Phillip Heisenberg
2011 Apr 26th Institute of Molecular Genetics Prague, invited by Vaclav Horejsi
2011 Apr 18th Faculty of Life Science, University of Manchester, invited by Casey Bergman
2011 Feb 4th LOCI, University of Madison, invited by Kevin Eliceiri
2010 Dec 2nd The Donnelly Centre, University of Toronto, invited by Henry Krause
2010 October 19th Dept. of Cell Biology, Charles University in Prague, invited by Marian Novotny
2010 May 17th SFB610, Halle, invited by Gunter Reuter
2010 March 19th EMBL Heidelberg, invited by Francesca Peri
2009 August 12th Institute of Molecular Genetics, Prague, invited by Peter Sebo
2009 June 23rd EPFL, Lausanne, invited by Bruno Lemaitre
2009 June 22nd University of Geneva, invited by Marcos Gonzales-Gaitan
2009 June 16th IMP/IMBA, Wienna, invited by Alexander Stark
2008 December 15th EMBL, Heidelberg, invited by Anne Ephrussi
2008 October 14th MPI for Neurobiology in Martinsried, invited by Ilona Kadow
2008 April 18th IBDML, Marseille, invited by Nicolas Gompel
2008 April 11th Tokyo Metropolitan University, Japan, invited by Toshiro Aigaki
2007 July 10th A*STAR Bioinformatics Institute, invited by Martin Wasser
2006 April 27th MRC Laboratory of Molecular Biology, Cambridge invited by Sarah Teichmann
CV 2013 Pavel Tomancak
OPEN ACCESS ACTIVITIES
Resource
name Description Website
APOGEE Atlas of patterns of gene expression in Drosophila
embryogenesis. A widely used database of gene expression
patterns that I established.
http://www.fruitfly.org
Fly-FISH
Atlas of patterns of RNA localization in Drosophila
embryogenesis. A database companion to Cell paper
established in collaboration with Eric Lecuyer and Henry
Krause.
http://fly-
fish.ccbr.utoronto.ca
Disc-pattern
database
Atlas of patterns of genes expression in Drosophila
imaginal discs. Data collection finished, analysis in
progress.
upcoming
Ovary-FISH Atlas of patterns of RNA localization in the Drosophila
ovary. Data collection in progress. upcoming
Transgeneome
&
FLY2K
Online resource for genomic fosmid libraries for D.
melanogaster and D. pseudoobscura and an online voting
system for the community to prioritize gene tagging with
fluorescent proteins aiming at generating genome-wide
collection of tagged fosmid transgenes.
http://transgeneome.mpi-
cbg.de
Fiji (Fiji Is Just
ImageJ)
A wiki for powerfull ImageJ distribution called Fiji, which
focuses on image registration and segmentation. I publish
all my image analysis projects under Fiji, fully open source,
documented and USABLE. We organize a community of
talented Fiji developers and host the source code
management repository of the project.
http://fiji.sc
SPIM Wiki A wiki collecting information about annual Light Sheet
based Fluorescence Microscopy workshop iniated by
Pavel Tomancak and Emmanuel Reynaud
http://spim.mpi-cbg.de
OpenSPIM
A wiki presenting information on how to build and use an
simple, cost-effective version of SPIM microscope.
Combining the ideas of Open Hardware and Software to
empower biological research.
http://openspim.org
FUNDING
Current funding
MPG MPI-CBG Senior Permanent Research Group Leader Block Funding
09/2013 - present Salaries for myself, a technician, 2 post-docs and 2 PhD students;
Consumables of 75,000 Euro/y and 40,000 Euro/y facility budget
This represents the core funding for my group provided by the Max Planck Society through my permanent appointment at
the MPI-CBG.
ERC Quantitative Analysis of the Hourglass Model of Evolution of Development
09/2010 - 09/2015 1.500.000 Euro
CV 2013 Pavel Tomancak
An ERC Starting Grant that extends the analysis of the hourglass model of development initiated under HFSP.
HFSP Quantitative modeling of expression pattern evolution in insect development
RENEWAL_APP
~09/2012 - 09/2015 ~ 100.000 Euro/y
A joint application with Dr. Uwe Ohler (Duke) and Dr. Casey Bergman (University of Manchester) to study the
divergence of gene expression patterns with respect to the hourglass model of morphological evolution. This is the first
time in the history of HFSP that a grant has been renewed.
FP7 GENCODYS: Genetic and Epigenetic Networks in Cognitive Disfunction
01/2010 - 01/2015 ~ 200.000 Euro per year (including 1 postdoc, 1 student)
This large EU network project, of which I am one of the 12 partners, aims to understand the molecular basis of cognitive
disorders by combining various functional genomics approaches in invertebrate and vertebrate model systems with clinical
studies. My role is to generate and study large collection of tagged fosmid transgenes for Drosophila orthologs of genes
implicated in human mental retardation.
MPG Innovation Fund
of the President A reverse genetic toolkit for systematic study of gene function and protein localization in
Drosophila.
03/2011 - 03/2014 1.700.000 Euro total award
A systematic effort to generate tagged genomic fosmid transgenes for all genes in the Drosophila genome. These reagents
will enable both, visualization of the tissue specificity and sub-cellular localization of proteins throughout Drosophila life-
cycle and purification of protein-protein or protein-DNA complexes, in a tissue-specific manner. A consortium of 4
participating MPG groups. Majority of the funding goes to Dresden where the resources will be generated.
BMBF Collective organization of cells and tissues: Systems biology of tissue size and shape.
2012 - 2015 1.200.000 Euro total award
A joint grant of 10 MPI-CBG group leaders designed to seed and support the newly established Center for Systems
Biology in Dresden.
Past
MPG MPI-CBG Junior Research Group Leader Block Funding
09/2005 - 08/2013 Salaries for myself, a technician, post-doc and pre-doctoral student;
Consumables of 60,000 Euro/y and 33,000 Euro/y facility budget
This represents the core funding for my group provided by the Max Planck Society through my permanent appointment at
the MPI-CBG.
HFSP Quantitative modeling of expression pattern evolution in insect development
09/2008 - 03/2012 ~ 100.000 Euro/y
A joint application with Dr. Uwe Ohler (Duke) and Dr. Casey Bergman (University of Manchester) to study the
divergence of gene expression patterns with respect to the hourglass model of morphological evolution.
CV 2013 Pavel Tomancak
DFG Genome-wide analysis of gene expression in imaginal discs of Drosophila melanogaster
01/2007 - 01/2010 ~ 12 000 Euro/y + one technician and two HiWis
A joint application with Christian Dahmann to map the patterns of gene expression in larval imaginal discs using RNA in
situ probes previously employed in similar survey in the fly embryo.
Supervision of PhD students and post-docs
PhD thesis completed under my guidance
Stephan Saalfeld Automatic inter-slice registration of tiled Transmission Electron Microscopy (TEM)
images, TU Dresden Faculty of Computer Science (2013), magna cum laude, subsequently Lab Head at
the Janelia Farm Research Campus
Stephan Preibisch Reconstruction of Multi-View Microscopic Acquisitions TU Dresden Faculty of
Computer Science, (2011) suma cum laude, subsequently HFSP funded post-doctoral fellow with Rob
Singer/Eugene Myers (Janelia Farm/MPI-CBG)
Radoslaw Kamil Ejsmont Toolkit for high-througput gene engineering in Drosophila TU Dresden
Faculty of Biology, (2011) magna cum laude, subsequently EMBO funded post-doctoral fellow with
Bassem Hassan (KU Leuven)
Jastrzebowska, Karolina Evolution of gene expression regulation during embryonic development of
Drosophila species TU Dresden Faculty of Biology, (2010) magna cum laude, subsequently post-
doctoral fellow with Ilan Davis (Oxford University)
Arunachalan, Manonmani Computational discovery of cis-regulatory elements in multiple Drosophila
species TU Dresden Faculty of Biology, (2009) magna cum laude, subsequently postdoctoral fellow with
Uwe Ohler (Duke University)
Other thesis completed under my guidance
Christopher Todd (undergraduate student) Sequence Heterochrony within populations University of
York under the ‘Year in Europe’ program.
Michael Weber Interspecimen registration of long-term, time-lapse selective plane illumination
microscopy recordings of Drosophila melanogaster embryogenesis TU Dresden (2010), subsequently
PhD with Jan Huisken (MPI-CBG)
Radostina Izhakarowa Dual color RNA in situ analysis of gene expression during Drosophila
embryogenesis TU Dresden, (2006)
Currently supervising
Helena Jambor, Ivana Viktorinova (maternity leave), Tobias Pietszch, Tassos Pavlopoulos (FP7
Marie-Curie fellowship), Monika Zuberova (FP7 Marie-Curie fellowship maternity leave), Mette
Handberg-Thorsager (post-docs)
Melek Asli Kayserili, Vineeth Surendranath (DIGGS-BB fellowship), Christopher Schmied,
Akanksha Jain (PhD students)
Pavel Mejstrik, Peter Pitrone (technicians)
Post-docs who completed their post-doctoral studies in my group
Alex Kalinka 2009-2013 funded by HFSP, subsequently Research Group Leader at Institute of
Population Genetics, University of Veterinary Medicine Vienna
CV 2013 Pavel Tomancak
Tassos Pavlopoulos 2012-2013 funded by FP7 Marie-Curie fellowship, subsequently Research Fellow
at the Janelia Farm Research Campus
Teaching experience
PhD training within The International Max Planck Research School for Molecular Cell Biology and
Bioengineering, 2 weeks per year since 2005, plus lectures.
SPIMmage processing tutorial at the 5th Light Sheet Fluorescence Microscopy Worskhop, Thornwood,
NY, September 12th 2013
Hellenic Pasteur Institute regional course “Digital image processing/analysis tools in Light
Microscopy: From the basics and beyond”, Athens Greece, June 10-17th 2013
EMBO Course “Imaging Infection and Immunity” Pretoria, South Africa, Mar 20-30th 2013
Wellcome Trust course “Drosophila Genetics and Genomics” Cambridge, UK, 12-20th August 2012
EMBO Course “Drosophila Techniques”, Lisbon, Portugal 11-28th of March 2011
EMBO Course “Imaging Infection: from single molecules to animals”, Pretoria, South Africa, Nov 2-
13th 2011
BIOTEC Dresden Master Course „Drosophila as a model system“ 2007-2011, 2013
Organization of hackathons that involves teaching activities
Fiji/ImageJ2 hackathon Dresden 10th – 19th December 2011
ImageJ2 hackathon Madison Wisconsin 27th January – 11th February 2011
Fiji hackathon EMBL 15th – 27th March 2010
Fiji hackathon Dresden 22nd March – 4 April 2009
Fiji hackathon Dresden 21st – 30th April 2008
Responsibilities and Committees at the MPI-CBG
Evaluating PhD applications from Czech Republic and Bulgaria, Romania, Moldova
Thursday Seminar Committee 2010-2011
Organization of parties and shows, exemplary attendance of beer hours, “acting” and generally making a
fool of oneself for the amusement of colleagues
CV 2013 Pavel Tomancak
PUBLICATIONS
Citation data from Google Scholar as of 29.04.2013, h-index = 22, i-10 index 28. Total number of citations 3599.
PUBLICATIONS DURING INDEPENDENT RESEARCH PERIOD: 2005 - present
1. Preibisch S., Amat F., Stamataki E., Sarov M., Myers E., Tomancak P. (2013) Efficient bayesian multi-
view deconvolution manuscript under revision at Nature Methods, http://arxiv.org/abs/1308.0730
2. Heyn P., Kircher M., Dahl A., Kelso J., Tomancak P., Kalinka A.T., Neugebauer K.M. (2013) The
earliest transcribed zygotic genes are short, newly evolved and different across species Cell Reports,
in press, co-corresponding author
3. Pitrone P., Schindelin J., Stuyvenberg L., Preibisch S., Weber M., Eliceiri K.W., Huisken J., Tomancak P.
(2013) OpenSPIM - an open access platform for light sheet microscopy Nature Methods, 10, 598–599
see also http://arxiv.org/abs/1302.1987 (2 citations)
Mentioned in Nature Methods editorial (2013) Sharing blueprints for better research Nature Methods
10, 591 and Nature Methods Methagora blog “Promoting shared hardware designs”, featured in HFSP
newsletter Sep 2013
4. Lewitus E., Kelava I., Kalinka A.T., Tomancak P., Huttner W.B. (2013) An Adaptive Threshold in
Mammalian Neocortical Evolution http://arxiv.org/abs/1304.5412
5. Kayserili M.A., Gerrard D., Tomancak P., Kalinka A. (2012) An excess of gene expression divergence
on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis PLoS
Genetics 8(12) http://arxiv.org/abs/1209.0968v1corresponding author (1 citation)
6. Pietszch T., Preibisch S., Tomancak P., Saalfeld S. (2012) Imglib2: Generic Image Processing in Java
Bioinformatics 28(22): 3009-3011 (6 citation)
7. Saalfeld S., Fetter R., Cardona A., Tomancak P. (2012) Elastic Volume
Reconstruction from Series of Ultra-thin Microscopy Sections Nature Methods
9(7), 717-720 (14 citations)
8. Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Preibisch S.,
Rueden C., Saalfeld S., Schmid B., Tinevez J., Hartenstein V., Eliceiri K., Tomancak
P., Cardona A. (2012) Fiji - an open source platform for biological image Nature
Methods 9(7), 676-682 corresponding author (383 citations)
9. Cardona A., Saalfeld S., Schindelin J., Arganda-Carreras I., Preibisch S., Longair M., Tomancak P.,
Hartenstein V., Douglas R.J. (2012) TrakEM2 software for neural circuit reconstruction. PLoS ONE
7(6):38011 (36 citation)
10. Kalinka A.T., Tomancak P. (2012) The evolution of early animal embryos: conservation or
divergence? Trends in Ecology and Evolution 27(7), 385-393 (9 citation)
11. Kelava I., Reillo, I., Murayama A.Y., Kalinka A. T., Stenzel D., Tomancak P., Matsuzaki F., Lebrand C.,
Sasaki E., Schwamborn J.C., Okano H., Huttner W.B., Borrell V. (2012) Abundant Occurrence of
Basal Radial Glia in the Subventricular Zone of Embryonic Neocortex of a Lissencephalic Primate,
the Common Marmoset Callithrix jacchus Cereb. Cortex, 22(2), 469-481 (32 citations)
12. Mohammad S.U., Lee H.K., Preibisch S., Tomancak, P. (2011) Restoring uneven illumination in
selective plane illumination microscopy images. Microscopy and Microanalysis Jun 20:1-7.
CV 2013 Pavel Tomancak
13. Kalinka A.T., Tomancak P. (2011) linkcomm: an R package for the generation, visualization, and
analysis of link communities in networks of arbitrary size and type. Bioinformatics 27(14) 2011-2012
(22 citations)
14. Kalinka A.T., Varga K.M., Gerrard D.T., Preibisch S., Jarrells J., Corcoran D., Ohler
U., Bergman C.M., Tomancak P. (2010) Gene expression divergence recapitulates
the developmental hourglass model Nature 468, 811–814 cover story (83 citations)
Highlighted in:
Prud'homme B, Gompel N. (2010) Evolutionary biology: Genomic hourglass. Nature
468:768-9
Casci T. (2010) Development: Hourglass theory gets molecular approval. Nat Rev Genet.
2010
Faculty of 1000: 2011. F1000.com/7774958 (FFa 8)
International Press: Frankfurter Allgemeine Zeitung, Discovery News, MSNBC; Evolution blogs: Pharyngula,
Panda’s thumb, Why Evolution Is True; Czech newspapers: iDnes, Literarni Noviny, 21 stoleti
15. Cardona A., Saalfeld S., Preibisch S., Schmid B., Cheng A., Pulokas J., Tomancak P., Hartenstein V.
(2010) An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-
assisted serial section electron microscopy. PLoS Biology 8(10): e1000502 (83 citation)
Highlighted in:
News in Brief : Mapping microcircuitry in the fly brain Nature Methods 2010 7(12): 949
16. Manonmani A., Karthik J., Tomancak P., Ohler U. (2010) An alignment-free method to identify
candidate orthologous enhancers in multiple Drosophila genomes. Bioinformatics 26 (17): 2109-
2115. corresponding author (5 citations)
17. Preibisch S., Saalfeld S., Schindelin J., Tomancak P. (2010) Software for bead-based registration of
selective plane illumination microscopy data. Nature Methods 7:418-419 (64 citations)
18. Saalfeld S., Cardona A., Hartenstein, V., Tomancak P. (2010) As-rigid-as-possible 2d-mosaicking and
3d-registration of large serial section TEM datasets. Bioinformatics 26 (12): i57-i63, ISMB
Proceedings paper (25 citations)
19. Langer C.C.H., Ejsmont R.K., Schönbauer C., Schnorrer F., Tomancak P. (2010) In vivo RNAi Rescue
in Drosophila melanogaster with Genomic Transgenes from Drosophila pseudoobscura. PLoS One
5(1) e8928 (17 citation)
20. Rach E.A., Yuan H.Y., Majoros W.H., Tomancak P., Ohler U. (2009) Motif composition, conservation
and condition-specificity of single and alternative transcription start sites in the Drosophila
genome. Genome Biol. 2009;10(7):R73 (27 citations)
21. Ejsmont R.K., Sarov M., Winkler S., Lipinski K., Tomancak P. (2009) A toolkit for
high-throughput, cross-species gene engineering in Drosophila. Nature Methods
Jun; 6(6):435-7 cover story (46 citations)
22. Saalfeld S., Cardona A., Hartenstein V., Tomancak P. (2009) CATMAID:
Collaborative Annotation Toolkit for Massive Amounts of Image Data.
Bioinformatics Aug 1;25(15):1984-6 (25 citations)
23. Preibisch S., Saalfeld S., Tomancak P. (2009) Globally optimal stitching of tiled 3D
microscopic image acquisitions. Bioinformatics Jun 1;25(11):1463-5 (119 citations)
24. Quijano C., Tomancak P., Lopez-Marti J., Suyama M., Bork P., Milan M., Torrents D., Manzanares M.
(2008) Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.
Genome Biol. 9(12):R176. (10 citation)
CV 2013 Pavel Tomancak
25. Lécuyer E., Yoshida H., Parthasarathy N., Alm C., Babak T., Cerovina T., Hughes T.R., Tomancak P.,
Krause H.M. (2007) Global analysis of mRNA localization reveals a prominent role in organizing
cellular architecture and function. Cell Oct 5;131(1):174-87 cover story (348
citations)
Highlighted in:
Faculty of 1000: 2008. F1000.com/1092213 (FFa 22)
Selected by Nature as Research Highlight of 2007
26. Magalhães T.R., Palmer J, Tomancak P, Pollard K.S. (2007) Transcriptional
control in embryonic Drosophila midline guidance assessed through a whole
genome approach. BMC Neurosci. Jul 31;8:59. (6 citations)
CONFERENCE PROCEEDINGS PAPERS
27. Preibisch S., Tomancak P., Saalfeld S. (2010) Into Imglib – Generic Image Processing in Java In
Proceedings of the ImageJ User and Developer Conference (3 citation)
28. Preibisch S., Saalfeld S., Rohlfing T., Tomancak P. (2009) Bead-based mosaicing of single plane
illumination microscopy images using geometric local descriptor matching Proceedings of SPIE,
SPIE, Bellingham, no. 72592S, pp. 1-10 (12 citations)
29. Preibisch S., Ejsmont R.K., Rohlfing T., Tomancak P. (2008) Towards digital representation of
Drosophila embryogenesis 5th IEEE International Symposium on Biomedical Imaging: From Nano to
Macro, IEEE Service Center, Piscataway, pp. 324-327, peer reviewed (4 citations)
30. Preibisch S., Rohlfing T., Hasak M.P., Tomancak P. (2008) Mosaicing of Single Plane Illumination
Microscopy Images Using Groupwise Registration and Fast Content-Based Image Fusion Proceedings of SPIE Medical Imaging 2008: Image Processing, SPIE, Bellingham, Wash., pp. 69140E-1-
69140E-8 (10 citations)
31. Saalfeld S., Tomancak P. (2008) Automatic landmark correspondence detection for ImageJ In
Proceedings of the ImageJ User and Developer Conference, 128–133, Luxembourg (2 citations)
32. Preibisch S., Saalfeld S., Tomancak P. (2008) Fast stitching of large 3d biological datasets In
Proceedings of the ImageJ User and Developer Conference, 134–139, Luxembourg (2 citation)
REVIEWS AND COMMENTARIES
33. Eliceiri K. V., Berthold M. R., Goldberg I. G., Ibanez L., Manjunath B. S., Martone M. E., Murphy R. F.,
Peng H., Plant A. L., Roysam B., Stuurmann N., Swedlow J.R., Tomancak P., Carpenter A. E. (2012)
Biological Imaging Software Tools Nature Methods 9(7), 697-710 (46 citations)
34. Cardona A., Tomancak P. (2012) Current challenges in open-source bioimage informatics Nature
Methods 9(7), 661-665 (15 citation)
35. Reynaud E., Tomancak P. (2010) The First Light Sheet Based Fluorescence Microscopy Workshop.
Biotechnology Journal Aug;5(8):798-804 (7 citations)
36. Tomancak P., Ohler U. (2010) Mapping the complexity of transcription control in higher eukaryotes
Genome Biol., 11, no. 4 (2 citation)
37. Walter T., Shattuck D.W., Baldock R., Bastin M., Carpenter A.E., Duce S., Ellenberg J., Fraser A.,
Hamilton N., Pieper S., Ragan M.A., Schneider J., Tomancak P., Hériché J-K. (2010) Visualization of
image data from cells to organisms. Nature Methods 7, S26 - S41 (122 citations)
CV 2013 Pavel Tomancak
38. Cardona A., Saalfeld S., Tomancak P., Hartenstein V. (2009) Drosophila Brain Development: Closing
the Gap between a Macroarchitectural and Microarchitectural Approach. Cold Spring Harb Symp
Quant Biol. Dec 22 (5 citations)
39. Lécuyer E., Tomancak P. (2008) Mapping the gene expression universe. Curr Opin Genet Dev.
Dec;18(6):506-12. (13 citations)
BOOK CHAPTERS
40. Ejsmont R.K., Bogdanzaliewa M., Lipinski K.A., Tomancak P. (2011) Production of fosmid genomic
libraries optimized for liquid culture Methods in Molecular Biology : Molecular Methods for
Evolutionary Studies Volume 772, Part 6, 423-443 (1 citation)
41. Ejsmont R.K., Ahlfeld P., Pozniakovsky A., Stewart F., Tomancak P., Sarov M. (2011) Engineering of
large genomic DNA transgenes for protein tagging in Drosophila by Red/ET recombineering Methods in Molecular Biology : Molecular Methods for Evolutionary Studies Volume 772, Part 6, 445-
458 (1 citation)
PUBLICATIONS DURING POSTDOC PERIOD: 2000 - 2005
42. Tomancak P., Berman B.P., Beaton A., Weiszmann R., Kwan E., Hartenstein V., Celniker S.E., Rubin
G.M. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis.
Genome Biol. 8(7):R145. (190 citations)
43. Aboobaker A.A., Tomancak P., Patel N., Rubin G.M., Lai E.C. (2005) Drosophila microRNAs exhibit
diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci U S A. 2005
Dec 13;102(50):18017-22. (155 citations)
44. Lai E.C., Tomancak P., Williams R.W., Rubin G.M. (2003) Computational
identification of Drosophila microRNA genes. Genome Biol. 4(7):R42 (648
citations) co-first author
Highlighted in:
Julius Brennecke and Stephen M Cohen (2003) Towards a complete description of the
microRNA complement of animal genomes Genome Biology 4:228
45. Tomancak P., Beaton A., Weiszmann R., Kwan E., Shu S., Lewis S. E., Richards S.,
Ashburner M., Hartenstein V., Celniker S. E., Rubin G. M., (2002) Systematic
determination of patterns of gene expression during Drosophila embryogenesis.
Genome Biol. 3(12):R88 (440 citations)
Highlighted in:
Haiqiong Montalta-He and Heinrich Reichert (2003) Impressive expressions: developing a
systematic database of gene-expression patterns in Drosophila embryogenesis Genome
Biology 2003, 4:205
46. Berman B.P., Nibu Y., Pfeiffer B.D., Tomancak P., Celniker S.E., Levine M., Rubin G.M., Eisen M.B.
(2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules
involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A. Jan 22;99(2):757-
62. (541 citations)
Highlighted in:
Faculty of 1000: 2002. F1000.com/1002148 (FFa 14)
PUBLICATIONS DURING PHD TRAINING: 1995 - 1999
CV 2013 Pavel Tomancak
47. Tomancak P., Piano F., Riechmann V., Gunsalus K.C., Kemphues K.J., Ephrussi A. (2000) A Drosophila
melanogaster homologue of Caenorhabditis elegans par-1 acts at an early step in embryonic-axis
formation. Nat Cell Biol. 2(7), 458-60. (142 citations)
Highlighted in: Jason Morris, Ruth Lehmann and Caryn Navarro (2000) PARallels in Axis Formation Science Vol. 288 no. 5472
pp. 1759-1760
48. Tomancak P., Guichet A., Zavorsky P., Ephrussi, A. (1998) Oocyte polarity depends on regulation of
gurken by Vasa. Development 125, 1723-1732. (149 citations)
49. Muckenthaler M., Gunkel N., Frishman D., Cyrklaff A., Tomancak P., Hentze M.W. (1998) Iron-
regulatory protein-1 (IRP-1) is highly conserved in two invertebrate species--characterization of IRP-1
homologues in Drosophila melanogaster and Caenorhabditis elegans. Eur J Biochem. Jun 1;254(2):230-7.
(42 citations)
CV 2013 Pavel Tomancak
ACADEMIC REFERENCES
Dr. Anne Ephrussi
Head of Developmental Biology Unit, EICAT Coordinator and Senior Scientist
EMBL Heidelberg
Meyerhofstraße 1, 69117 Heidelberg, Germany
Tel: +49 6221 387- 8429/8283
E-mail: [email protected]
Dr. Gerald M. Rubin
Vice President and Executive Director of Janelia Farm Research Campus
Janelia Farm Research Campus
19700 Helix Drive
Ashburn, VA 20147
Email: [email protected]
Dr. Eugene Myers
Janelia Farm Research Campus
19700 Helix Drive
Ashburn, VA 20147
Tel: 571.209.4153
Email: [email protected]
Dr. Marino Zerial
Director
Max Planck Institute of Molecular Cell Biology and Genetics, MPI-CBG
Pfotenhauerstrasse 108
01307 Dresden, Germany
Tel: +49-351-210-1100
Email: [email protected]
Dr. Jonathon Howard
Director
Max Planck Institute of Molecular Cell Biology and Genetics, MPI-CBG
Pfotenhauerstrasse 108
01307 Dresden, Germany
Tel: +49-351-210-2500
Email: [email protected]
Dr. Elisabeth Knust
Director
Max Planck Institute of Molecular Cell Biology and Genetics, MPI-CBG
Pfotenhauerstrasse 108
01307 Dresden, Germany
Tel: +49-351-210-2500
Email: [email protected]