2017

Vladimir Ulman, Martin Maška, Klas E. G. Magnusson, Olaf Ronneberger, Carsten Haubold, Nathalie Harder, Pavel Matula, Pavel Matula, David Svoboda, Miroslav Radojevic, Ihor Smal, Karl Rohr, Joakim Jaldén, Helen M. Blau, Oleh Dzyubachyk, Boudewijn Lelieveldt, Pengdong Xiao, Yuexiang Li, Siu-Yeung Cho, Alexandre C Dufour, Jean-Christophe Olivo-Marin, Constantino C Reyes-Aldasoro, Jose A Solis-Lemus, Robert Bensch, Thomas Brox, Johannes Stegmaier, Ralf Mikut, Steffen Wolf, Fred A Hamprecht, Tiago Esteves, Pedro Quelhas, Ömer Demirel, Lars Malmström, Florian Jug, Pavel Tomancak, Erik Meijering, Arrate Muñoz-Barrutia, Michal Kozubek, Carlos Ortiz-de-Solorzano
An objective comparison of cell-tracking algorithms.
Nat Methods, 1-1 (2017)
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P Philippe Laissue, Rana A Alghamdi, Pavel Tomancak, Emmanuel G. Reynaud, Hari Shroff
Assessing phototoxicity in live fluorescence imaging.
Nat Methods, 14(7) 657-661 (2017)
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John J Reynolds, Louise S Bicknell, Paula Carroll, Martin R Higgs, Ranad Shaheen, Jennie E Murray, Dimitrios Papadopoulos, Andrea Leitch, Olga Murina, Žygimantė Tarnauskaitė, Sarah R Wessel, Anastasia Zlatanou, Audrey Vernet, Alex von Kriegsheim, Rachel M A Mottram, Clare V Logan, Hannah Bye, Yun Li, Alexander Brean, Sateesh Maddirevula, Rachel C Challis, Kassiani Skouloudaki, Agaadir Almoisheer, Hessa S Alsaif, Ariella Amar, Natalie J Prescott, Michael B Bober, Angela Duker, Eissa Faqeih, Mohammed Zain Seidahmed, Saeed Al Tala, Abdulrahman Alswaid, Saleem Ahmed, Jumana Yousuf Al-Aama, Janine Altmüller, Mohammed Al Balwi, Angela F Brady, Luciana Chessa, Helen Cox, Rita Fischetto, Raoul Heller, Bertram D Henderson, Emma Hobson, Peter Nürnberg, E Ferda Percin, Angela Peron, Luigina Spaccini, Alan J Quigley, Seema Thakur, Carol A Wise, Grace Yoon, Maha Alnemer, Pavel Tomancak, Gökhan Yigit, A Malcolm R Taylor, Martin A M Reijns, Michael A Simpson, David Cortez, Fowzan Sami Alkuraya, Christopher G Mathew, Andrew P Jackson, Grant S Stewart
Mutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism.
Nat Genet, 49(4) 537-549 (2017)

2016

Pavel Tomancak
Universal Rules of Regulation
Cell, 165(5) 1035-1036 (2016)
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Jaroslav Icha, Christopher Schmied, Jaydeep Sidhaye, Pavel Tomancák, Stephan Preibisch, Caren Norden
Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development
J Vis Exp, (110) Art. No. e53966 (2016)
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Christopher Schmied, Peter Steinbach, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak
An automated workflow for parallel processing of large multiview SPIM recordings.
Bioinformatics, 32(7) 1112-1114 (2016)
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Kenneth Börner, Dhawal Jain, Paula Vazquez-Pianzola, Sandra Vengadasalam, Natascha Steffen, Dmitry V Fyodorov, Pavel Tomancak, Alexander Konev, Beat Suter, Peter B Becker
A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis.
Dev Biol, 411(2) 217-230 (2016)
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Mihail Sarov, Christiane Barz, Helena Jambor, Marco Y Hein, Christopher Schmied, Dana Suchold, Bettina Stender, Stephan Janosch, Vinay Vikas Kj, R T Krishnan, Aishwarya Krishnamoorthy, Irene R S Ferreira, Radoslaw K Ejsmont, Katja Finkl, Susanne Hasse, Philipp Kämpfer, Nicole Plewka, Elisabeth Vinis, Siegfried Schloissnig, Elisabeth Knust, Volker Hartenstein, Matthias Mann, Mani Ramaswami, K VijayRaghavan, Pavel Tomancak, Frank Schnorrer
A genome-wide resource for the analysis of protein localisation in Drosophila.
Elife, 5 Art. No. e12068 (2016)
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Eric Lewitus, Iva Kelava, Alex T. Kalinka, Pavel Tomancak, Wieland B. Huttner
Comment on "Cortical folding scales universally with surface area and thickness, not number of neurons".
Science, 351(6275) 825-825 (2016)
---
Christopher Schmied
A live imaging paradigm for studying Drosophila development and evolution
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2016)
---
Christopher Schmied, Pavel Tomancak
Sample Preparation and Mounting of Drosophila Embryos for Multiview Light Sheet Microscopy.
Methods Mol Biol, 1478 189-202 (2016)
---
Helena Jambor, Pavel Mejstrik, Pavel Tomancak
Rapid Ovary Mass-Isolation (ROMi) to Obtain Large Quantities of Drosophila Egg Chambers for Fluorescent In Situ Hybridization.
Methods Mol Biol, 1478 253-262 (2016)
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Johannes Girstmair, Anne Zakrzewski, François Lapraz, Mette Handberg-Thorsager, Pavel Tomancak, Peter Gabriel Pitrone, Fraser Simpson, Maximilian J Telford
Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development.
BMC Dev Biol, 16(1) Art. No. 22 (2016)
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Hendrik Sollich, Ulrich von Zadow, Tobias Pietzsch, Pavel Tomancak, Raimund Dachselt
Exploring Time-dependent Scientific Data Using Spatially Aware Mobiles and Large Displays
In: Proceedings of the 2016 ACM on Interactive Surfaces and Spaces (2016), New York, ACM (2016), 349-354

2015

Dimitrios Papadopoulos, Aleksandar J Krmpot, Stanko N Nikolić, Robert Krautz, Lars Terenius, Pavel Tomancak, Rudolf Rigler, Walter J Gehring, Vladana Vukojević
Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy.
Mech Dev, 138(2) 218-225 (2015)
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Wiebke Jahr, Benjamin Schmid, Christopher Schmied, Florian Fahrbach, Jan Huisken
Hyperspectral light sheet microscopy.
Nat Commun, 6 Art. No. 7990 (2015)
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Tobias Pietzsch, Stephan Saalfeld, Stephan Preibisch, Pavel Tomancak
BigDataViewer: visualization and processing for large image data sets.
Nat Methods, 12(6) 481-483 (2015)
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Sebastian Dunst, Tom Kazimiers, Felix von Zadow, Helena Jambor, Andreas Sagner, Beate Brankatschk, Ali Mahmoud, Stephanie Spannl, Pavel Tomancak, Suzanne Eaton, Marko Brankatschk
Endogenously Tagged Rab Proteins: A Resource to Study Membrane Trafficking in Drosophila.
Dev Cell, 33(3) 351-365 (2015)
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Matt Kanke, Helena Jambor, John Reich, Brittany Marches, Ronald Gstir, Young Hee Ryu, Anne Ephrussi, Paul M Macdonald
oskar RNA plays multiple noncoding roles to support oogenesis and maintain integrity of the germline/soma distinction.
RNA, 21(6) 1096-1109 (2015)
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Florian Jug, Tobias Pietzsch, Dagmar Kainmueller, Gene Myers
Tracking by Assignment Facilitates Data Curation
In: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2014 (2015) IMIC Interactive Medical Image Computing Workshop, Amsterdam, Netherlands, Academic Press (2015), 1-12
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Peter Gabriel Pitrone, Johannes Schindelin, Kevin W Eliceiri, Pavel Tomancak, Pavel Tomancak
OpenSPIM: A do-it-yourself open access light sheet fluorescence microscope
Microscopy and Analysis, 29(16) 7-11 (2015)
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Patricia Heyn, Alex T. Kalinka, Pavel Tomancak, Karla M. Neugebauer
Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences.
Bioessays, 37(2) 148-154 (2015)
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Helena Jambor, Vineeth Surendranath, Alex T. Kalinka, Pavel Mejstrik, Stephan Saalfeld, Pavel Tomancak
Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.
Elife, 4 Art. No. e05003 (2015)
---
Emmanuel G. Reynaud, Jan Peychl, Jan Huisken, Pavel Tomancak
Guide to light-sheet microscopy for adventurous biologists.
Nat Methods, 12(1) 30-34 (2015)

2014

Florian Jug, Tobias Pietzsch, Dagmar Kainmueller, Jan Funke, Matthias Kaiser, Erik van Nimwegen, Carsten Rother, Gene Myers
Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine
In: Bayesian and grAphical models for biomedical imaging first international workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers (2014) Lecture Notes in Computer Science ; 8677, New York, Springer (2014), 25-36
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Eric Lewitus, Iva Kelava, Alex T. Kalinka, Pavel Tomancak, Wieland B. Huttner
An Adaptive Threshold in Mammalian Neocortical Evolution.
PLoS Biol, 12(11) Art. No. e1002000 (2014)
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Antonella Lauri, Thibaut Brunet, Mette Handberg-Thorsager, Antje H L Fischer, Oleg Simakov, Patrick R H Steinmetz, Raju Tomer, Patrick Keller, Detlev Arendt
Development of the annelid axochord: insights into notochord evolution.
Science, 345(6202) 1365-1368 (2014)
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Stephan Preibisch, Fernando Amat, Evangelia Stamataki, Mihail Sarov, Robert H. Singer, Gene Myers, Pavel Tomancak
Efficient Bayesian-based multiview deconvolution.
Nat Methods, 11(6) 645-648 (2014)
---
Florian Jug, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak
Bioimage Informatics in the context of Drosophila research.
Methods, 68(1) 60-73 (2014)
---
Helena Jambor, Sandra Mueller, Simon L Bullock, Anne Ephrussi
A stem-loop structure directs oskar mRNA to microtubule minus ends.
RNA, 20(4) 429-439 (2014)
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Patricia Heyn, Martin Kircher, Andreas Dahl, Janet Kelso, Pavel Tomancak, Alex T. Kalinka, Karla M. Neugebauer
The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species.
Cell Rep, 6(2) 285-292 (2014)
---
Matthew A Benton, Anastasios Pavlopoulos
Tribolium embryo morphogenesis: May the force be with you.
Bioarchitecture, 4(1) 16-21 (2014)
---
Christopher Schmied, Evangelia Stamataki, Pavel Tomancak
Open-source solutions for SPIMage processing.
Methods Cell Biol, 123 505-529 (2014)
---
Ines Wagner, Michael Volkmer, Malvika Sharan, Jose M Villaveces, Felix Oswald, Vineeth Surendranath, Bianca Habermann
morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring.
BMC Bioinformatics, 15 Art. No. 263 (2014)
---
Emilio Gualda, Nuno Moreno, Pavel Tomancak, Gabriel G Martins
Going "open" with Mesoscopy: a new dimension on multi-view imaging.
Protoplasma, 251(2) 363-372 (2014)
---
Alexis Webb, Daniele Soroldoni, Annelie Oswald, Johannes Schindelin, Andrew C. Oates
Generation of dispersed presomitic mesoderm cell cultures for imaging of the zebrafish segmentation clock in single cells.
J Vis Exp, (89) Art. No. e50307 (2014)

2013

Ivana Viktorinová, Christian Dahmann
Microtubule Polarity Predicts Direction of Egg Chamber Rotation in Drosophila.
Curr Biol, 23(15) 1472-1477 (2013)
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Matthew A Benton, Michael Akam, Anastasios Pavlopoulos
Cell and tissue dynamics during Tribolium embryogenesis revealed by versatile fluorescence labeling approaches.
Development, 140(15) 3210-3220 (2013)
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Peter Gabriel Pitrone, Johannes Schindelin, Luke Stuyvenberg, Stephan Preibisch, Michael Weber, Kevin W Eliceiri, Jan Huisken, Pavel Tomancak
OpenSPIM: an open access light sheet microscopy platform
Nat Methods, 10(7) 598-599 (2013)
---
Eric Lewitus, Alex T. Kalinka
Neocortical development as an evolutionary platform for intragenomic conflict.
Front Neuroanat, 7 Art. No. 2 (2013)
---
Stephan Saalfeld
Towards Large Scale Reconstruction of Neuro-Anatomy at Nanometer Resolution
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2013)
---
Alex T. Kalinka, Iva Kelava, Eric Lewitus
Our robust intellect.
Trends Genet, 29(3) 125-127 (2013)
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Radhakrishnan Nagarajan, Alex T. Kalinka, William R Hogan
Evidence of community structure in Biomedical Research Grant Collaborations.
J Biomed Inform, 46(1) 40-46 (2013)
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Madina Karimova, Josephine Abi-Ghanem, Nicolas Berger, Vineeth Surendranath, Maria Teresa Pisabarro, Frank Buchholz
Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system.
Nucleic Acids Res, 41(2) Art. No. e37 (2013)
---
Alex T. Kalinka
The probability of drawing intersections: extending the hypergeometric distribution
arXiv, Art. No. arXiv:1305.0717 (2013)
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Vineeth Surendranath, Mirko Theis, Bianca Habermann, Frank Buchholz
Designing efficient and specific endoribonuclease-prepared siRNAs.
Methods Mol Biol, 942 193-204 (2013)
---
Eric Lewitus, Iva Kelava, Alex T. Kalinka, Pavel Tomancak, Wieland B. Huttner
An Adaptive Threshold in Mammalian Neocortical Evolution
arXiv, Art. No. doi: 10.1101/001289 (2013)

2012

Melek Asli Kayserili, Dave T. Gerrard, Pavel Tomancak, Alex T. Kalinka
An excess of gene expression divergence on the x chromosome in Drosophila embryos: implications for the faster-x hypothesis.
PLoS Genet, 8(12) Art. No. e1003200 (2012)
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Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Dan White, Volker Hartenstein, Kevin W Eliceiri, Pavel Tomancak, Albert Cardona
Fiji: an open-source platform for biological-image analysis.
Nat Methods, 9(7) 676-682 (2012)
---
Albert Cardona, Pavel Tomancak
Current challenges in open-source bioimage informatics.
Nat Methods, 9(7) 661-665 (2012)
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Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurmann, Jason R Swedlow, Pavel Tomancak, Anne E Carpenter
Biological imaging software tools.
Nat Methods, 9(7) 697-710 (2012)
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Stephan Saalfeld, Richard Fetter, Albert Cardona, Pavel Tomancak
Elastic volume reconstruction from series of ultra-thin microscopy sections.
Nat Methods, 9(7) 717-720 (2012)
---
Alex T. Kalinka, Pavel Tomancak
The evolution of early animal embryos: conservation or divergence?
Trends Ecol Evol, 27(7) 385-393 (2012)
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Iva Kelava, Isabel Reillo, Ayako Y Murayama, Alex T. Kalinka, Denise Stenzel, Pavel Tomancak, Fumio Matsuzaki, Cécile Lebrand, Erika Sasaki, Jens C Schwamborn, Hideyuki Okano, Wieland B. Huttner, Víctor Borrell
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 (2012)
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Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein, Rodney J Douglas
TrakEM2 Software for Neural Circuit Reconstruction.
PLoS ONE, 7(6) Art. No. e38011 (2012)
---
Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak, Stephan Saalfeld
ImgLib2 – Generic Image Processing in Java
Bioinformatics, 28(22) 3009-3011 (2012)

2011

Helena Jambor, Christine Brunel, Anne Ephrussi
Dimerization of oskar 3' UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte.
RNA, 17(12) 2049-2057 (2011)
---
Mohammad Shorif Uddin, Hwee Kuan Lee, Stephan Preibisch, Pavel Tomancak
Restoration of Uneven Illumination in Light Sheet Microscopy Images.
Microsc microanal, 17(4) 607-613 (2011)
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Kamil A Lipinski, Olga Puchta, Vineeth Surandranath, Marek Kudla, Pawel Golik
Revisiting the Yeast PPR Proteins - Application of an Iterative Hidden Markov Model Algorithm Reveals New Members of the Rapidly Evolving Family.
Mol Biol Evol, 28(10) 2935-2948 (2011)
---
Alex T. Kalinka, Pavel Tomancak
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 (2011)
---
Stephan Preibisch
Reconstruction of Multi-Tile Microscopic Acquisitions
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2011)
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Radoslaw K Ejsmont, Peter Ahlfeld, Andrei I. Pozniakovsky, A Francis Stewart, Pavel Tomancak, Mihail Sarov
Recombination-mediated genetic engineering of large genomic DNA transgenes.
Methods Mol Biol, 772 445-458 (2011)
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Radoslaw K Ejsmont, Maria Bogdanzaliewa, Kamil A Lipinski, Pavel Tomancak
Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis.
Methods Mol Biol, 772 423-443 (2011)
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Radoslaw K Ejsmont
A toolkit for visualization of patterns of gene expression in live Drosophila embryos
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2011)

2010

Alex T. Kalinka, Karolina M Varga, Dave T. Gerrard, Stephan Preibisch, David L. Corcoran, Julia Jarrells, Uwe Ohler, Casey M. Bergman, Pavel Tomancak
Gene expression divergence recapitulates the developmental hourglass model.
Nature, 468(7325) 811-814 (2010)
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Fernando Carrillo Oesterreich, Stephan Preibisch, Karla M. Neugebauer
Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
Mol Cell, 40(4) 571-581 (2010)
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Pablo Oteiza, Mathias Köppen, Michael Krieg, Eduardo Pulgar, Cecilia Farias, Cristina Melo, Stephan Preibisch, Daniel J. Müller, Masazumi Tada, Steffen Hartel, Carl-Philipp Heisenberg, Miguel L Concha
Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ.
Development, 137(20) 3459-3468 (2010)
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Albert Cardona, Stephan Saalfeld, Stephan Preibisch, Benjamin Schmid, Anchi Cheng, Jim Pulokas, Pavel Tomancák, Volker Hartenstein
An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.
PLoS Biol, 8(10) Art. No. e1000502 (2010)
---
Richard Karel Capek, Michael Weber, Alexander Eychmüller
Alternative Incorporation Procedure of Quantum Dots in Polymer Microspheres
Chem Mater, 22(17) 4912-4918 (2010)
---
Emmanuel G. Reynaud, Pavel Tomancák
Meeting report: First light sheet based fluorescence microscopy workshop.
Biotechnol J, 5(8) 798-804 (2010)
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Manonmani Arunachalam, Karthik Jayasurya, Pavel Tomancák, Uwe Ohler
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
Bioinformatics, 26(17) 2109-2115 (2010)
---
Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomancák
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets
Bioinformatics, 26(12) 57-63 (2010)
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Albert Cardona, Stephan Saalfeld, Ignacio Arganda, Wayne Pereanu, Johannes Schindelin, Volker Hartenstein
Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts.
J Neurosci, 30(22) 7538-7553 (2010)
---
Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin, Pavel Tomancák
Software for bead-based registration of selective plane illumination microscopy data
Nat Methods, 7(6) 418-419 (2010)
---
Pavel Tomancák, Uwe Ohler
Mapping the complexity of transcription control in higher eukaryotes
Genome Biol, 11(4) Art. No. 115 (2010)
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Thomas Walter, David W Shattuck, Richard Baldock, Mark E Bastin, Anne E Carpenter, Suzanna Duce, Jan Ellenberg, Adam Fraser, Nicholas Hamilton, Steve Pieper, Mark A Ragan, Jurgen E Schneider, Pavel Tomancák, Jean-Karim Hériché
Visualization of image data from cells to organisms
Nat Methods, 7(3s) 26-41 (2010)
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Michael Weber
Interspecimen registration of long-term, time-lapse selective plane illumination microscopy recordings of Drosophila melanogaster embryogenesis
Diploma Thesis,Technische Universität Dresden, Dresden, Germany (2010)
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Christoph C. H. Langer, Radoslaw K Ejsmont, Cornelia Schönbauer, Frank Schnorrer, Pavel Tomancák
In Vivo RNAi Rescue in Drosophila melanogaster with Genomic Transgenes from Drosophila pseudoobscura
PLoS ONE, 5(1) Art. No. e8928 (2010)
---
Stephan Preibisch, Pavel Tomancák, Stephan Saalfeld
Into ImgLib - Generic Image Processing in Java
In: Proceedings of ImageJ User and Developer Conference (2010), Amsterdam, Netherlands, Academic Press (2010), 1-1
---
Karolina Jastrzebowska
Evolution of gene expression regulation during embryonic development of Drosophila species
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2010)

2009

Albert Cardona, Stephan Saalfeld, Pavel Tomancák, Volker Hartenstein
Drosophila Brain Development: Closing the Gap between a Macroarchitectural and Microarchitectural Approach.
Cold Spring Harb Symp Quant Biol, 74 235-248 (2009)
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Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomancák
CATMAID: collaborative annotation toolkit for massive amounts of image data.
Bioinformatics, 25(15) 1984-1986 (2009)
---
Stephan Preibisch, Stephan Saalfeld, Pavel Tomancák
Globally optimal stitching of tiled 3D microscopic image acquisitions.
Bioinformatics, 25(11) 1463-1465 (2009)
---
Radoslaw K Ejsmont, Mihail Sarov, Sylke Winkler, Kamil A Lipinski, Pavel Tomancák
A toolkit for high-throughput, cross-species gene engineering in Drosophila.
Nat Methods, 6(6) 435-437 (2009)
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Elizabeth Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancák, Uwe Ohler
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.
Genome Biol, 10(7) Art. No. R73 (2009)
---
Manonmani Arunachalam
Computational discovery of Cis-regulatory elements in multiple Drosophila species
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2009)
---
Stephan Preibisch, Stephan Saalfeld, Torsten Rohlfing, Pavel Tomancák
Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching
In: Medical imaging 2009 : image processing : 8 - 10 Februar 2009 (2009) Ch. 7259(Eds.) Josien P. W. Pluim Proceedings of SPIE ; 7259, Bellingham, USA, SPIE (2009), 1-10

2008

Eric Lécuyer, Pavel Tomancák
Mapping the gene expression universe.
Curr Opin Genet Dev, 18(6) 506-512 (2008)
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Stephan Preibisch, Radoslaw K Ejsmont, Torsten Rohlfing, Pavel Tomancák
Towards digital representation of Drosophila embryogenesis
In: 2008 IEEE International Symposium on Biomedical Imaging : from Nano to Macro : [ISBI '08]; Paris, France, 14-17 May 2008 (2008), Piscataway, USA, IEEE Service Center (2008), 324-327
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Carlos Quijano, Pavel Tomancák, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents, Miguel Manzanares
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.
Genome Biol, 9(12) 176-176 (2008)
---
Stephan Preibisch, Torsten Rohlfing, Michael P. Hasak, Pavel Tomancák
Mosaicing of Single Plane Illumination Microscopy Images Using Groupwise Registration and Fast Content-Based Image Fusion
In: Medical imaging 2008 - image processing : 17-19 February 2008, San Diego, California, USA (2008)(Eds.) Joseph M. Reinhardt Proceedings of SPIE ; 6914, Bellingham, USA, SPIE (2008), 1-8
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Stephan Preibisch, Stephan Saalfeld, Pavel Tomancák
Fast stitching of large 3d biological datasets
In: Proceedings of the ImageJ User and Developer Conference 2008 : [6th & 7th November 2008, Luxembourg] (2008), Luxembourg, Centre de recherche public Henri Tudor (2008), 134-139
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Stephan Saalfeld, Pavel Tomancák
Automatic landmark correspondence detection for ImageJ
In: Proceedings of the ImageJ User and Developer Conference 2008 : [6th & 7th November 2008, Luxembourg] (2008), Luxembourg, Centre de recherche public Henri Tudor (2008), 128-133

2007

Eric Lécuyer, Hiroyuki Yoshida, Neela Parthasarathy, Christina Alm, Tomas Babak, Tanja Cerovina, Timothy R Hughes, Pavel Tomancák, Henry M Krause
Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.
Cell, 131(1) 174-187 (2007)
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Tiago R Magalhães, Jessica Palmer, Pavel Tomancák, Katherine S Pollard
Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach.
BMC neuroscience, 8 59-59 (2007)
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Benjamin P Berman, Pavel Tomancák, Amy Beaton, Richard Weiszmann, Elaine Kwan, Volker Hartenstein, Susan E Celniker, Gerald M Rubin
Global analysis of patterns of gene expression during Drosophila embryogenesis.
Genome Biol, 8(7) 145-145 (2007)

2005

A. Aziz Aboobaker, Pavel Tomancák, Nipam Patel, Gerald M Rubin, Eric C. Lai
Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development.
Proc Natl Acad Sci U.S.A., 102(50) 18017-18022 (2005)

2003

Eric C. Lai, Pavel Tomancák, Robert W Williams, Gerald M Rubin
Computational identification of Drosophila microRNA genes.
Genome Biol, 4(7) 42-42 (2003)

2002

Pavel Tomancák, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker, Gerald M Rubin
Systematic determination of patterns of gene expression during Drosophila embryogenesis.
Genome Biol, 3(12) 88-88 (2002)
---
Benjamin P Berman, Pavel Tomancák, Yutaka Nibu, Barret D Pfeiffer, Susan E Celniker, Michael Levine, Gerald M Rubin, Michael B Eisen
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., 99(2) 757-762 (2002)

2000

Pavel Tomancák, Fabio Piano, Veit Riechmann, Kristin C. Gunsalus, Kenneth J. Kemphues, Anne Ephrussi
A Drosophila melanogaster homologue of Caenorhabditis elegans par-1 acts at an early step in embryonic-axis formation.
Nat Cell Biol, 2(7) 458-460 (2000)

1998

Martina Muckenthaler, Niki Gunkel, Dmitrij Frishman, Anna Cyrklaff, Pavel Tomancák, Matthias W. Hentze
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, 254(2) 230-237 (1998)
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Pavel Tomancák, Antoine Guichet, Peter Zavorszky, Anne Ephrussi
Oocyte polarity depends on regulation of gurken by Vasa.
Development, 125(9) 1723-1732 (1998)