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Pavel Tomancak

Research Profile

Activities & Behaviors

Physiology

Gene Expression Regulation, Developmental

Procedures

Phenomena

Evolution, Molecular

Genes & Molecular Sequences

Concepts & Ideas

Devices

Oligonucleotide Array Sequence Analysis

Co-author Network

Publications

TOP 3
Kevin W Eliceiri; 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; Nico Stuurman; Michael R Berthold; Anne E Carpenter
Biological imaging software tools.
Johannes Schindelin; Benjamin Schmid; Jean-Yves Tinevez; Pavel Tomancak; Daniel James White; Ignacio Arganda-Carreras; Kevin Eliceiri; Erwin Frise; Volker Hartenstein; Verena Kaynig; Mark Longair; Tobias Pietzsch; Stephan Preibisch; Curtis Rueden; Stephan Saalfeld; Albert Cardona
Fiji: an open-source platform for biological-image analysis.
Albert Cardona; Pavel Tomancak
Current challenges in open-source bioimage informatics.

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All Publications

2012: Kevin W Eliceiri; 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; Nico Stuurman; Michael R Berthold; Anne E Carpenter
Biological imaging software tools.
Nature methods 2012;9(7):697-710.
2012: Johannes Schindelin; Benjamin Schmid; Jean-Yves Tinevez; Pavel Tomancak; Daniel James White; Ignacio Arganda-Carreras; Kevin Eliceiri; Erwin Frise; Volker Hartenstein; Verena Kaynig; Mark Longair; Tobias Pietzsch; Stephan Preibisch; Curtis Rueden; Stephan Saalfeld; Albert Cardona
Fiji: an open-source platform for biological-image analysis.
Nature methods 2012;9(7):676-82.
2012: Albert Cardona; Pavel Tomancak
Current challenges in open-source bioimage informatics.
Nature methods 2012;9(7):661-5.
2012: Stephan Saalfeld; Albert Cardona; Richard Fetter; Pavel Tomancak
Elastic volume reconstruction from series of ultra-thin microscopy sections.
Nature methods 2012;9(7):717-20.
2012: Alex T Kalinka; Pavel Tomancak
The evolution of early animal embryos: conservation or divergence?
Trends in ecology & evolution 2012;27(7):385-93.
2012: Melek A Kayserili; Pavel Tomancak; Dave T Gerrard; Alex T Kalinka
An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis.
PLoS genetics 2012;8(12):e1003200.
2012: Albert Cardona; Ignacio Arganda-Carreras; Volker Hartenstein; Mark Longair; Stephan Preibisch; Stephan Saalfeld; Johannes Schindelin; Pavel Tomancak; Rodney J Douglas
TrakEM2 software for neural circuit reconstruction.
PloS one 2012;7(6):e38011.
2011: Mohammad Shorif Uddin; Hwee Kuan Lee; Stephan Preibisch; Pavel Tomancak
Restoration of uneven illumination in light sheet microscopy images.
Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada 2011;17(4):607-13.
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 (Oxford, England) 2011;27(14):2011-2.
2011: Radoslaw Kamil Ejsmont; Andrei Pozniakovsky; A Francis Stewart; Pavel Tomancak; Peter Ahlfeld; Mihail Sarov
Recombination-mediated genetic engineering of large genomic DNA transgenes.
Methods in molecular biology (Clifton, N.J.) 2011;772():445-58.
2011: Radoslaw Kamil Ejsmont; Kamil Andrzej Lipinski; Maria Bogdanzaliewa; Pavel Tomancak
Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis.
Methods in molecular biology (Clifton, N.J.) 2011;772():423-43.
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 2010;468(7325):811-4.
2010: Manonmani Arunachalam; Karthik Jayasurya; Pavel Tomancak; Uwe Ohler
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
Bioinformatics (Oxford, England) 2010;26(17):2109-15.
2010: Emmanuel G Reynaud; Pavel Tomancak
Meeting report: first light sheet based fluorescence microscopy workshop.
Biotechnology journal 2010;5(8):798-804.
2010: Stephan Preibisch; Stephan Saalfeld; Johannes Schindelin; Pavel Tomancak
Software for bead-based registration of selective plane illumination microscopy data.
Nature methods 2010;7(6):418-9.
2010: Thomas Walter; David W Shattuck; Richard Baldock; Mark E Bastin; Anne E Carpenter; Suzanne Duce; Jan Ellenberg; Adam Fraser; Nicholas Hamilton; Steve Pieper; Mark A Ragan; Jurgen E Schneider; Pavel Tomancak; Jean-Karim Hériché
Visualization of image data from cells to organisms.
Nature methods 2010;7(3 Suppl):S26-41.
2010: Albert Cardona; Stephan Saalfeld; Stephan Preibisch; Benjamin Schmid; Anchi Cheng; Jim Pulokas; Pavel Tomancak; Volker Hartenstein
An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.
PLoS biology 2010;8(10):.
2010: Pavel Tomancak; Uwe Ohler
Mapping the complexity of transcription control in higher eukaryotes.
Genome biology 2010;11(4):115.
2010: Christoph C H Langer; Radoslaw K Ejsmont; Cornelia Schönbauer; Frank Schnorrer; Pavel Tomancak
In vivo RNAi rescue in Drosophila melanogaster with genomic transgenes from Drosophila pseudoobscura.
PloS one 2010;5(1):e8928.
2009: Radoslaw K Ejsmont; Mihail Sarov; Sylke Winkler; Kamil Andrzej Lipinski; Pavel Tomancak
A toolkit for high-throughput, cross-species gene engineering in Drosophila.
Nature methods 2009;6(6):435-7.
2009: Stephan Preibisch; Stephan Saalfeld; Pavel Tomancak
Globally optimal stitching of tiled 3D microscopic image acquisitions.
Bioinformatics (Oxford, England) 2009;25(11):1463-5.
2009: Elizabeth A Rach; Hsiang-Yu Yuan; William H Majoros; Pavel Tomancak; Uwe Ohler
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.
Genome biology 2009;10(7):R73.
2008: Eric Lécuyer; Pavel Tomancak
Mapping the gene expression universe.
Current opinion in genetics & development 2008;18(6):506-12.
2008: Carlos Quijano; Pavel Tomancak; Jesus Lopez-Marti; Mikita Suyama; Peer Bork; Marco Milan; David Torrents; Miguel Manzanares
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.
Genome biology 2008;9(12):R176.
2007: Eric Lécuyer; Hideki Yoshida; Neela Parthasarathy; Christina Alm; Tomas Babak; Tanja Cerovina; Timothy R Hughes; Pavel Tomancak; Henry M Krause
Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.
Cell 2007;131(1):174-87.
2007: Tiago R Magalhães; Jessica Palmer; Pavel Tomancak; Katherine S Pollard
Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach.
BMC neuroscience 2007;8():59.
2007: Pavel Tomancak; 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 biology 2007;8(7):R145.
2005: A Aziz Aboobaker; Pavel Tomancak; Nipam Patel; Gerald M Rubin; Eric C Lai
Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(50):18017-22.
2003: Eric C Lai; Pavel Tomancak; Robert W Williams; Gerald M Rubin
Computational identification of Drosophila microRNA genes.
Genome biology 2003;4(7):R42.
2002: Benjamin P Berman; Yutaka Nibu; Barret D Pfeiffer; Pavel Tomancak; 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.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(2):757-62.
2002: Pavel Tomancak; 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 biology 2002;3(12):RESEARCH0088.