Research Groups

* joined first author # joined corresponding author

2021

Krishan Gupta, Manan Lalit, Aditya Biswas, Chad D Sanada, Cassandra Greene, Kyle Hukari, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Naveen Ramalingam, Gaurav Ahuja, Abhik Ghosh, Debarka Sengupta
Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data.
Genome Res, 31(4) 689-697 (2021)
DOI

2020

José M Martín-Durán, Bruno C Vellutini, Ferdinand Marlétaz, Viviana Cetrangolo, Nevena Cvetesic, Daniel Thiel, Simon Henriet, Xavier Grau-Bové, Allan M Carrillo-Baltodano, Wenjia Gu, Alexandra Kerbl, Yamile Marquez, Nicolas Bekkouche, Daniel Chourrout, Jose Luis Gómez-Skarmeta, Manuel Irimia, Boris Lenhard, Katrine Worsaae, Andreas Hejnol
Conservative route to genome compaction in a miniature annelid.
Nat Ecol Evol, 5(2) 231-242 (2020)
DOI
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Alexandra B Schroeder, Ellen T A Dobson, Curtis Rueden, Pavel Tomancak, Florian Jug, Kevin W Eliceiri
The ImageJ ecosystem: Open-source software for image visualization, processing, and analysis.
Protein Sci, 30(1) 234-249 (2020)
DOI
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Akanksha Jain, Vladimir Ulman, Arghyadip Mukherjee, Mangal Prakash, Marina B Cuenca, Lokesh G Pimpale, Stefan Münster, Robert Haase, Kristen A Panfilio, Florian Jug, Stephan W. Grill, Pavel Tomancak#, Anastasios Pavlopoulos#
Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation.
Nat Commun, 11(1) Art. No. 5604 (2020)
Open Access   DOI
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Giulia Serafini, Giorgia Giordani, Luca Grillini, Davide Andrenacci, Giuseppe Gargiulo, Valeria Cavaliere
The Impact of Drosophila Awd/NME1/2 Levels on Notch and Wg Signaling Pathways.
Int J Mol Sci, 21(19) Art. No. 7257 (2020)
Open Access   DOI
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Mangal Prakash, Tim-Oliver Buchholz, Manan Lalit, Pavel Tomancak, Florian Jug, Alexander Krull
Leveraging Self-supervised Denoising for Image Segmentation.
In: IEEE ISBI 2020 : International Conference on Biomedical Imaging : April 2-7, 2020, Iowa City, Iowa, USA : symposium proceeding (2020) IEEE International Symposium on Biomedical Imaging, Piscataway, N.J., IEEE (2020), 428-432
DOI
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Mangal Prakash✳︎, Manan Lalit✳︎, Pavel Tomancak, Alexander Krull, Florian Jug
Fully Unsupervised Probabilistic Noise2Void.
In: IEEE ISBI 2020 : International Conference on Biomedical Imaging : April 2-7, 2020, Iowa City, Iowa, USA : symposium proceeding (2020) IEEE International Symposium on Biomedical Imaging, Piscataway, N.J., IEEE (2020), 154-158
DOI
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Ritika Giri, Dimitrios Papadopoulos, Diana M Posadas, Hemanth K Potluri, Pavel Tomancak, Madhav Mani#, Richard W Carthew#
Ordered patterning of the sensory system is susceptible to stochastic features of gene expression.
Elife, 9 Art. No. e53638 (2020)
Open Access   DOI
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Sona Valuchova, Pavlina Mikulkova, Jana Pecinkova, Jana Klimova, Michal Krumnikl, Petr Bainar, Stefan Heckmann, Pavel Tomancak, Karel Riha
Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy.
Elife, 9 Art. No. e52546 (2020)
Open Access   DOI
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Hiroki R Ueda, Ali Ertürk, Kwanghun Chung, Viviana Gradinaru, Alain Chédotal, Pavel Tomancak, Philipp Keller
Tissue clearing and its applications in neuroscience.
Nat. Rev. Neurosci., 21(2) 61-79 (2020)
DOI
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Robert Haase✳︎, Loic Royer✳︎, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug, Eugene W Myers
CLIJ: GPU-accelerated image processing for everyone.
Nat Methods, 17(1) 5-6 (2020)
DOI

2019

Pavel Vopalensky, Maria Antonietta Tosches, Kaia Achim, Mette Handberg-Thorsager, Detlev Arendt
From spiral cleavage to bilateral symmetry: the developmental cell lineage of the annelid brain.
BMC Biol, 17(1) Art. No. 81 (2019)
Open Access   DOI
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Pavel Tomancak
Evolutionary history of tissue bending.
Science, 366(6463) 300-301 (2019)
DOI
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Jan Kožusznik, Petr Bainar, Jana Klímová, Michal Krumnikl, Pavel Moravec, Václav Svatoň, Pavel Tomančák
SPIM workflow manager for HPC.
Bioinformatics, 35(19) 3875-3876 (2019)
Open Access   DOI
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Martin Maska, Tereza Necasova, David Wiesner, Dmitry V. Sorokin, Igor Peterlik, Vladimir Ulman, David Svoboda
Toward Robust Fully 3D Filopodium Segmentation and Tracking in Time-Lapse Fluorescence Microscopy.
In: 2019 IEEE International Conference on Image Processing : proceedings : September 22-25, 2019, Taipei International Convention Center (TICC), Taipei, Taiwan (2019), Piscataway, N.J., IEEE (2019), 819-823
DOI
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S Ehrig, B Schamberger, C M Bidan, A West, C Jacobi, K Lam, P Kollmannsberger, A Petersen, Pavel Tomancak, K Kommareddy, F D Fischer, P Fratzl, John W C Dunlop
Surface tension determines tissue shape and growth kinetics.
Sci Adv, 5(9) Art. No. 9394 (2019)
Open Access   DOI
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Kassiani Skouloudaki#, Ioannis Christodoulou, Dilan Khalili, Vasilios Tsarouhas, Christos Samakovlis, Pavel Tomancak, Elisabeth Knust#, Dimitrios Papadopoulos#
Yorkie controls tube length and apical barrier integrity during airway development.
J Cell Biol, 218(8) 2762-2781 (2019)
DOI
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Václav Svatoň, Jan Martinovic, Jan Krenek, Thomas Esch, Pavel Tomancak
HPC-as-a-Service via HEAppE Platform.
In: Complex, Intelligent, and Software Intensive Systems : Proceedings of the 13th International Conference on Complex, Intelligent, and Software Intensive Systems (CISIS-2019) (2019)(Eds.) Leonard Barolli (Advances in Intelligent Systems and Computing ; 993), New York, Springer (2019), 280-293
DOI
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Mattias Hogvall, Bruno C Vellutini, José M Martín-Durán, Andreas Hejnol, Graham E Budd, Ralf Janssen
Embryonic expression of priapulid Wnt genes.
Dev Genes Evol, 229(4) 125-135 (2019)
DOI
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Pavel Tomancak
Cell communication in the blink of an eye.
Nature, 571(7766) 484-485 (2019)
DOI
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Dimitrios Papadopoulos#, Pavel Tomancak#
Gene Regulation: Analog to Digital Conversion of Transcription Factor Gradients.
Curr Biol, 29(11) 422-424 (2019)
DOI
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Ivana Viktorinová, Robert Haase, Tobias Pietzsch, Ian Henry, Pavel Tomancak
Analysis of Actomyosin Dynamics at Local Cellular and Tissue Scales Using Time-lapse Movies of Cultured Drosophila Egg Chambers.
J Vis Exp, 148 Art. No. e58587 (2019)
DOI
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Stefan Münster, Akanksha Jain, Alexander Mietke, Anastasios Pavlopoulos, Stephan W. Grill#, Pavel Tomancak#
Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects.
Nature, 568(7752) 395-399 (2019)
DOI
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Dimitrios Papadopoulos#, Kassiani Skouloudaki, Ylva Engström, Lars Terenius, Rudolf Rigler, Christoph Zechner, Vladana Vukojević, Pavel Tomancak#
Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch.
Development, 146(12) Art. No. dev168179 (2019)
DOI
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Kassiani Skouloudaki✳︎#, Dimitrios Papadopoulos✳︎, Pavel Tomancak, Elisabeth Knust#
The apical protein Apnoia interacts with Crumbs to regulate tracheal growth and inflation.
PLoS Genet, 15(1) Art. No. e1007852 (2019)
Open Access   DOI
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Ulrik Günther, Tobias Pietzsch, Aryaman Gupta, Kyle Harrington, Pavel Tomancak, Stefan Gumhold, Ivo F. Sbalzarini
scenery: Flexible Virtual Reality Visualization on the Java VM.
In: 2019 IEEE Visualization Conference (VIS) (2019), Piscataway, N.J., IEEE (2019), 166-170
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Johannes Girstmair, Maximilian J Telford
Reinvestigating the early embryogenesis in the flatworm Maritigrella crozieri highlights the unique spiral cleavage program found in polyclad flatworms.
Evodevo, 10 Art. No. 12 (2019)
Open Access   DOI
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Sebastian Dunst#, Pavel Tomancak#
Imaging Flies by Fluorescence Microscopy: Principles, Technologies, and Applications.
Genetics, 211(1) 15-34 (2019)
DOI
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Anna Castells-Nobau, Ilse Eidhof, Michaela Fenckova, Dova B Brenman-Suttner, Jolanda M Scheffer-de Gooyert, Sheren Christine, Rosa L Schellevis, Kiran van der Laan, Christine Quentin, Lisa van Ninhuijs, Falko Hofmann, Radoslaw K Ejsmont, Simon E Fisher, Jamie M Kramer, Stephan J Sigrist, Anne F Simon, Annette Schenck
Conserved regulation of neurodevelopmental processes and behavior by FoxP in Drosophila.
PLoS ONE, 14(2) Art. No. e211652 (2019)
Open Access   DOI
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Mette Handberg-Thorsager, V Ulman, Pavel Tomançak, Detlev Arendt, M Schubert
A Behavioral Assay to Study Effects of Retinoid Pharmacology on Nervous System Development in a Marine Annelid.
Methods Mol Biol, 2019 193-207 (2019)
DOI

2018

Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Sian Culley, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W Myers
Content-aware image restoration: pushing the limits of fluorescence microscopy.
Nat Methods, 15(12) 1090-1097 (2018)
DOI
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Miroslav Ovečka, Daniel von Wangenheim, Pavel Tomančák, Olga Šamajová, George Komis, Jozef Šamaj
Multiscale imaging of plant development by light-sheet fluorescence microscopy.
Nat Plants, 4(9) 639-650 (2018)
DOI
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Igor Peterlik, David Svoboda, Vladimir Ulman, Dmitry V. Sorokin, Martin Maska
Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia
In: Simulation and synthesis in medical imaging ; third international workshop, SASHIMI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 16, 2018 : proceedings (2018)(Eds.) Ali Gooya (Lecture notes in computer science ;11037), Cham, Springer International Publishing (2018), 71-79
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Shovamayee Maharana, Jie Wang, Dimitrios Papadopoulos, Doris Richter, Andrei I. Pozniakovsky, Ina Poser, Marc Bickle, Sandra Rizk, Jordina Guillén-Boixet, Titus Franzmann, Marcus Jahnel, Lara Marrone, Young-Tae Chang, Jared Sterneckert, Pavel Tomancak, Anthony Hyman#, Simon Alberti#
RNA buffers the phase separation behavior of prion-like RNA binding proteins.
Science, 360(6391) 918-921 (2018)
DOI
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Carsten Wolff#, Jean-Yves Tinevez, Tobias Pietzsch, Evangelia Stamataki, Benjamin Harich, Léo Guignard, Stephan Preibisch, Spencer Shorte, Patrick Keller, Pavel Tomancak#, Anastasios Pavlopoulos#
Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.
Elife, 7 Art. No. e34410 (2018)
Open Access   DOI
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J P Joos, A R Saadatmand, C Schnabel, Ivana Viktorinová, Thomas Brand, M Kramer, S Nattel, D Dobrev, Pavel Tomancak, J Backs, P Kleinbongard, G Heusch, K Lorenz, E Koch, S Weber, A El-Armouche
Ectopic expression of S28A-mutated Histone H3 modulates longevity, stress resistance and cardiac function in Drosophila.
Sci Rep, 8(1) Art. No. 2940 (2018)
Open Access   DOI
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Mette Handberg-Thorsager, Juliana Gutierrez-Mazariegos, Stefan T Arold, Eswar Kumar Nadendla, Paola Y Bertucci, Pierre Germain, Pavel Tomançak, Keely Pierzchalski, Jace W Jones, Ricard Albalat, Maureen A Kane, William Bourguet, Vincent Laudet, Detlev Arendt, Michael Schubert
The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation.
Sci Adv, 4(2) Art. No. eaao1261 (2018)
Open Access   DOI

2017

B Duygu Özpolat, Mette Handberg-Thorsager, Michel Vervoort, Guillaume Balavoine
Cell lineage and cell cycling analyses of the 4d micromere using live imaging in the marine annelid Platynereis dumerilii.
Elife, 6 Art. No. e30463 (2017)
Open Access   DOI
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Sandra Richter, Ulrike Schulze, Pavel Tomançak, Andrew C. Oates
Small molecule screen in embryonic zebrafish using modular variations to target segmentation.
Nat Commun, 8(1) Art. No. 1901 (2017)
Open Access   DOI
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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, 14(12) 1141-1152 (2017)
PDF    DOI
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Ivana Viktorinová, Ian Henry, Pavel Tomancak
Epithelial rotation is preceded by planar symmetry breaking of actomyosin and protects epithelial tissue from cell deformations.
PLoS Genet, 13(11) Art. No. 1007107 (2017)
Open Access   DOI
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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)
DOI

2016

Pavel Tomancak
Universal Rules of Regulation
Cell, 165(5) 1035-1036 (2016)
PDF    DOI
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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)
Open Access   PDF    DOI
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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)
Open Access   PDF    DOI
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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)
Open Access   PDF    DOI
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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)
PDF    DOI
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Christopher Schmied
A live imaging paradigm for studying Drosophila development and evolution
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2016)
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Christopher Schmied, Pavel Tomancak
Sample Preparation and Mounting of Drosophila Embryos for Multiview Light Sheet Microscopy.
Methods Mol Biol, 1478 189-202 (2016)
PDF    DOI
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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)
PDF    DOI
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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)
Open Access   PDF    DOI
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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
DOI

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)
PDF    DOI
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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)
Open Access   DOI
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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)
PDF    DOI
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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)
DOI
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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)
DOI
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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
Microsc Anal, 29(16) 7-11 (2015)
PDF   
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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)
DOI
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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)
Open Access   DOI
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Emmanuel G. Reynaud, Jan Peychl, Jan Huisken, Pavel Tomancak
Guide to light-sheet microscopy for adventurous biologists.
Nat Methods, 12(1) 30-34 (2015)
DOI

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)
Open Access   PDF    DOI
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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)
PDF    DOI
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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)
PDF    DOI
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Florian Jug✳︎, Tobias Pietzsch✳︎, Stephan Preibisch, Pavel Tomancak
Bioimage Informatics in the context of Drosophila research.
Methods, 68(1) 60-73 (2014)
PDF    DOI
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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)
DOI
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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)
Open Access   DOI
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Matthew A Benton, Anastasios Pavlopoulos
Tribolium embryo morphogenesis: May the force be with you.
Bioarchitecture, 4(1) 16-21 (2014)
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Christopher Schmied, Evangelia Stamataki, Pavel Tomancak
Open-source solutions for SPIMage processing.
Methods Cell Biol, 123 505-529 (2014)
PDF    DOI
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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)
Open Access   DOI
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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)
PDF    DOI
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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)
DOI

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)
DOI
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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)
DOI
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Eric Lewitus, Alex T. Kalinka
Neocortical development as an evolutionary platform for intragenomic conflict.
Front Neuroanat, 7 Art. No. 2 (2013)
Open Access   DOI
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Stephan Saalfeld
Towards Large Scale Reconstruction of Neuro-Anatomy at Nanometer Resolution
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2013)
PDF   
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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)
PDF    DOI
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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)
Open Access   PDF    DOI
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Alex T. Kalinka
The probability of drawing intersections: extending the hypergeometric distribution
arXiv, Art. No. arXiv:1305.0717 (2013)
Open Access  
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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)
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Eric Lewitus✳︎, Iva Kelava✳︎, Alex T. Kalinka, Pavel Tomancak, Wieland B. Huttner
An Adaptive Threshold in Mammalian Neocortical Evolution
bioRxiv, Art. No. doi: 10.1101/001289 (2013)
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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)
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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)
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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)
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Tobias Pietzsch✳︎, Stephan Preibisch✳︎, Pavel Tomancak, Stephan Saalfeld
ImgLib2 – Generic Image Processing in Java
Bioinformatics, 28(22) 3009-3011 (2012)
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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)
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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)
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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)
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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)
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Richard Karel Capek, Michael Weber, Alexander Eychmüller
Alternative Incorporation Procedure of Quantum Dots in Polymer Microspheres
Chem Mater, 22(17) 4912-4918 (2010)
DOI
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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)
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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)
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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)
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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)
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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
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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)
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Stephan Preibisch, Stephan Saalfeld, Pavel Tomancák
Globally optimal stitching of tiled 3D microscopic image acquisitions.
Bioinformatics, 25(11) 1463-1465 (2009)
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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)
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Manonmani Arunachalam
Computational discovery of Cis-regulatory elements in multiple Drosophila species
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2009)
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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
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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)
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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
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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 Art. No. 59 (2007)
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Pavel Tomancák, Benjamin P Berman, 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)
Open Access   PDF    DOI

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)
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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)
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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)
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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)
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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)
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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)
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