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Pavel Tomancak

Patterns of gene expression in animal development

The overall goal of our research is to understand how the information contained in animal genomes transforms into coordinated cellular behaviors that collectively represent development. It can be argued that the most direct manifestation of the genomic program is the tissue specific regulation of gene expression. Therefore, by describing the gene expression patterns in the context of cellular anatomy of the developing system, we take the necessary, first step towards understanding the information transfer from genome sequences to developmental processes. We combine wet-lab and informatics approaches working closely with experimentalists as well as the growing group of computational biologists in Dresden.

We focus on Drosophila embryogenesis as primary model system and insist on limiting our approaches to the ones that can be applied to many and potentially all genes in the genome. Initially we used high-throughput methods such as RNA in situ hybridization to visualize patterns of gene expression during embryonic development (APOGEE and FlyFish in collaboration with Eric Lecuyer and Henry Krause). More recently we developed the FlyFos system that allows systematic generation of faithful, fluorescently labeled, live  transgenic gene expression reporters. We develop novel imaging approaches based on Selective Plane Illumination Microscopy (SPIM) that will allow us to monitor the entire developing system, distinguishing all cells and associating gene activity reporters to them. We have developed a unique Open Access platform for building a simple light-sheet microscope called OpenSPIM. The SPIM mediated recording will provide the most qualitatively complete representation of patterns of gene expression and will lay down the observational foundation for systems biology analysis of development. These advanced imaging approaches necessitate new developments in quantitative 3D image analysis and to that end we pursue several projects that combine computer vision and biology (Fiji and CATMAID).

The observed complexity of gene expression regulation in embryogenesis arises, to large extent, from evolution of cis-regulatory sequences. The mechanisms of action of natural selection on non-coding sequences remain relatively poorly understood. We use the morphologically highly similar embryonic development of sequenced Drosophilid species to study the sequence determinants underlying divergence of gene expression patterns. We use high-throughput methods such as micro-arrays and deep sequencing, to uncover divergent gene expression profiles. In the course of this work we found unique, quantitative supporting evidence for a fundamental law of nature, the hourglass model of morphological evolution. We use the hourglass hypothesis as motivation to evaluate, using the tools we developed in D. melanogaster, the divergence of embryonic patterns in different species before, during and after the insect phylotypic stage. We hope that by linking the divergence in sequence, to the divergence in gene expression regulation and the embryo phenotype we will provide new insights into the evolutionary mechanisms shaping the gene regulatory networks in early embryogenesis. 

Hot News

Whenever journal policies allow it we will post pre-prints of our papers on arXiv or bioRxiv . Current active pre-print is

Christopher Schmied, Peter Steinbach, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak An automated workflow for parallel processing of large multiview SPIM recordings arxiv.org/abs/1507.08575

For all arXiv pre-prints click here (arXiv) and here (bioRxiv)

Feedback welcome!

Link to a database of gene expression and RNA localisation patterns in Drosophila oogenesis and embryogenesis
Haeckel embryos constructed from Drosophila embryo images. Click to download the high-resolution image.
FlyFos Transgenome
Resource of tagged genomic transgenes
OpenSPIM
Open Access Selective Plane Illumination Microscopy
Fiji Is Just ImageJ
Open Source platform for research in biological image analysis

Selected Publications

2015
Pietzsch, Tobias; Saalfeld, Stephan; Preibisch, Stephan; Tomancak, Pavel
BigDataViewer: visualization and processing for large image data sets.
Nat Methods, 12, no. 6, pp. 481-483, (2015)
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Jambor, Helena; Surendranath, Vineeth; Kalinka, Alex T.; Mejstrik, Pavel; Saalfeld, Stephan; Tomancak, Pavel
Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.
Elife, 4, (2015)
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2014
Preibisch, Stephan; Amat, Fernando; Stamataki, Evangelia; Sarov, Mihail; Singer, Robert H.; Myers, Gene; Tomancak, Pavel
Efficient Bayesian-based multiview deconvolution.
Nat Methods, 11, no. 6, pp. 645-648, (2014)
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2013
Pitrone, Peter Gabriel; Schindelin, Johannes; Stuyvenberg, Luke; Preibisch, Stephan; Weber, Michael; Eliceiri, Kevin W; Huisken, Jan; Tomancak, Pavel
OpenSPIM: an open access light sheet microscopy platform
Nat Methods, 10, no. 7, pp. 598-599, (2013)
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2012
Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Dan; Hartenstein, Volker; Eliceiri, Kevin W; Tomancak, Pavel; Cardona, Albert
Fiji: an open-source platform for biological-image analysis.
Nat Methods, 9, no. 7, pp. 676-682, (2012)
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Cardona, Albert; Tomancak, Pavel
Current challenges in open-source bioimage informatics.
Nat Methods, 9, no. 7, pp. 661-665, (2012)
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Saalfeld, Stephan; Fetter, Richard; Cardona, Albert; Tomancak, Pavel
Elastic volume reconstruction from series of ultra-thin microscopy sections.
Nat Methods, 9, no. 7, pp. 717-720, (2012)
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Kalinka, Alex T.; Tomancak, Pavel
The evolution of early animal embryos: conservation or divergence?
Trends Ecol Evol, 27, no. 7, pp. 385-393, (2012)
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2010
Kalinka, Alex T.; Varga, Karolina M; Gerrard, Dave T.; Preibisch, Stephan; Corcoran, David L.; Jarrells, Julia; Ohler, Uwe; Bergman, Casey M.; Tomancak, Pavel
Gene expression divergence recapitulates the developmental hourglass model.
Nature, 468, no. 7325, pp. 811-814, (2010)
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Cardona, Albert; Saalfeld, Stephan; Preibisch, Stephan; Schmid, Benjamin; Cheng, Anchi; Pulokas, Jim; Tomancák, Pavel; Hartenstein, Volker
An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.
PLoS Biol, 8, no. 10, (2010)
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Preibisch, Stephan; Saalfeld, Stephan; Schindelin, Johannes; Tomancák, Pavel
Software for bead-based registration of selective plane illumination microscopy data
Nat Methods, 7, no. 6, pp. 418-419, (2010)
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Walter, Thomas; Shattuck, David W; Baldock, Richard; Bastin, Mark E; Carpenter, Anne E; Duce, Suzanna; Ellenberg, Jan; Fraser, Adam; Hamilton, Nicholas; Pieper, Steve; Ragan, Mark A; Schneider, Jurgen E; Tomancák, Pavel; Hériché, Jean-Karim
Visualization of image data from cells to organisms
Nat Methods, 7, no. 3s, pp. 26-41, (2010)
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Langer, Christoph C. H.; Ejsmont, Radoslaw K; Schönbauer, Cornelia; Schnorrer, Frank; Tomancák, Pavel
In Vivo RNAi Rescue in Drosophila melanogaster with Genomic Transgenes from Drosophila pseudoobscura
PLoS ONE, 5, no. 1, (2010)
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2009
Saalfeld, Stephan; Cardona, Albert; Hartenstein, Volker; Tomancák, Pavel
CATMAID: collaborative annotation toolkit for massive amounts of image data.
Bioinformatics, 25, no. 15, pp. 1984-1986, (2009)
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Preibisch, Stephan; Saalfeld, Stephan; Tomancák, Pavel
Globally optimal stitching of tiled 3D microscopic image acquisitions.
Bioinformatics, 25, no. 11, pp. 1463-1465, (2009)
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Ejsmont, Radoslaw K; Sarov, Mihail; Winkler, Sylke; Lipinski, Kamil A; Tomancák, Pavel
A toolkit for high-throughput, cross-species gene engineering in Drosophila.
Nat Methods, 6, no. 6, pp. 435-437, (2009)
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2008
Preibisch, Stephan; Rohlfing, Torsten; Hasak, Michael P.; Tomancák, Pavel
Mosaicing of Single Plane Illumination Microscopy Images Using Groupwise Registration and Fast Content-Based Image Fusion
[Conference Paper] Medical Imaging Symposium, San Diego, Calif., (2008)
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2007
Lécuyer, Eric; Yoshida, Hiroyuki; Parthasarathy, Neela; Alm, Christina; Babak, Tomas; Cerovina, Tanja; Hughes, Timothy R; Tomancák, Pavel; Krause, Henry M
Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.
Cell, 131, no. 1, pp. 174-187, (2007)
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Berman, Benjamin P; Tomancák, Pavel; Beaton, Amy; Weiszmann, Richard; Kwan, Elaine; Hartenstein, Volker; Celniker, Susan E; Rubin, Gerald M
Global analysis of patterns of gene expression during Drosophila embryogenesis.
Genome Biol, 8, no. 7, pp. 145-145, (2007)
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2005
Aboobaker, A. Aziz; Tomancák, Pavel; Patel, Nipam; Rubin, Gerald M; Lai, Eric C.
Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development.
Proc Natl Acad Sci U.S.A., 102, no. 50, pp. 18017-18022, (2005)
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2003
Lai, Eric C.; Tomancák, Pavel; Williams, Robert W; Rubin, Gerald M
Computational identification of Drosophila microRNA genes.
Genome Biol, 4, no. 7, pp. 42-42, (2003)
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2002
Tomancák, Pavel; Beaton, Amy; Weiszmann, Richard; Kwan, Elaine; Shu, ShengQiang; Lewis, Suzanna E; Richards, Stephen; Ashburner, Michael; Hartenstein, Volker; Celniker, Susan E; Rubin, Gerald M
Systematic determination of patterns of gene expression during Drosophila embryogenesis.
Genome Biol, 3, no. 12, pp. 88-88, (2002)
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2000
Tomancák, Pavel; Piano, Fabio; Riechmann, Veit; Gunsalus, Kristin C.; Kemphues, Kenneth J.; Ephrussi, Anne
A Drosophila melanogaster homologue of Caenorhabditis elegans par-1 acts at an early step in embryonic-axis formation.
Nat Cell Biol, 2, no. 7, pp. 458-460, (2000)
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