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Pavel Tomancak

Pavel Tomancak's publications on GoogleScholar

Publications

2014
Lauri, Antonella; Brunet, Thibaut; Handberg-Thorsager, Mette; Fischer, Antje H L; Simakov, Oleg; Steinmetz, Patrick R H; Tomer, Raju; Keller, Patrick; Arendt, Detlev
Development of the annelid axochord: insights into notochord evolution.
Science, 345, no. 6202, pp. 1365-1368, (2014)
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Preibisch, Stephan; Amat, Fernando; Stamataki, Evangelia; Sarov, Mihail; Singer, Robert H.; Myers, Eugene; Tomancak, Pavel
Efficient Bayesian-based multiview deconvolution.
Nat. Methods, 11, no. 6, pp. 645-648, (2014)
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Jug, Florian; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel
Bioimage Informatics in the context of Drosophila research.
Methods, 68, no. 1, pp. 60-73, (2014)
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Jambor, Helena; Mueller, Sandra; Bullock, Simon L; Ephrussi, Anne
A stem-loop structure directs oskar mRNA to microtubule minus ends.
RNA, 20, no. 4, pp. 429-439, (2014)
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Heyn, Patricia; Kircher, Martin; Dahl, Andreas; Kelso, Janet; Tomancak, Pavel; Kalinka, Alex T.; Neugebauer, Karla M.
The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species.
Cell Rep., 6, no. 2, pp. 285-292, (2014)
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Benton, Matthew A; Pavlopoulos, Anastasios
Tribolium embryo morphogenesis: May the force be with you.
Bioarchitecture, 4, no. 1, pp. 16-21, (2014)
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Schmied, Christopher; Stamataki, Evangelia; Tomancak, Pavel
Open-source solutions for SPIMage processing.
Methods Cell Biol., 123, pp. 505-529, (2014)
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Gualda, Emilio; Moreno, Nuno; Tomancak, Pavel; Martins, Gabriel G
Going "open" with Mesoscopy: a new dimension on multi-view imaging.
Protoplasma, 251, no. 2, pp. 363-372, (2014)
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2013
Viktorinová, Ivana; Dahmann, Christian
Microtubule Polarity Predicts Direction of Egg Chamber Rotation in Drosophila.
Curr. Biol., 23, no. 15, pp. 1472-1477, (2013)
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Benton, Matthew A; Akam, Michael; Pavlopoulos, Anastasios
Cell and tissue dynamics during Tribolium embryogenesis revealed by versatile fluorescence labeling approaches.
Development, 140, no. 15, pp. 3210-3220, (2013)
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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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Lewitus, Eric; Kalinka, Alex T.
Neocortical development as an evolutionary platform for intragenomic conflict.
Front. Neuroanat., 7, (2013)
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Saalfeld, Stephan
Towards Large Scale Reconstruction of Neuro-Anatomy at Nanometer Resolution
[Doctoral Thesis] Technische Universität Dresden, (2013)
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Kalinka, Alex T.; Kelava, Iva; Lewitus, Eric
Our robust intellect.
Trends Genet., 29, no. 3, pp. 125-127, (2013)
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Nagarajan, Radhakrishnan; Kalinka, Alex T.; Hogan, William R
Evidence of community structure in Biomedical Research Grant Collaborations.
J. Biomed. Inform., 46, no. 1, pp. 40-46, (2013)
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Karimova, Madina; Abi-Ghanem, Josephine; Berger, Nicolas; Surendranath, Vineeth; Pisabarro, Maria Teresa; Buchholz, Frank
Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system.
Nucleic Acids Res., 41, no. 2, (2013)
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Kalinka, Alex T.
The probability of drawing intersections: extending the hypergeometric distribution
arXiv, (2013)
Surendranath, Vineeth; Theis, Mirko; Habermann, Bianca; Buchholz, Frank
Designing efficient and specific endoribonuclease-prepared siRNAs.
Methods Mol. Biol., 942, pp. 193-204, (2013)
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Lewitus, Eric; Kelava, Iva; Kalinka, Alex T.; Tomancak, Pavel; Huttner, Wieland B.
An Adaptive Threshold in Mammalian Neocortical Evolution
arXiv, (2013)
2012
Kayserili, Melek Asli; Gerrard, Dave T.; Tomancak, Pavel; Kalinka, Alex T.
An excess of gene expression divergence on the x chromosome in Drosophila embryos: implications for the faster-x hypothesis.
PLoS Genet., 8, no. 12, (2012)
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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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Eliceiri, Kevin W; Berthold, Michael R; Goldberg, Ilya G; Ibáñez, Luis; Manjunath, B S; Martone, Maryann E; Murphy, Robert F; Peng, Hanchuan; Plant, Anne L; Roysam, Badrinath; Stuurmann, Nico; Swedlow, Jason R; Tomancak, Pavel; Carpenter, Anne E
Biological imaging software tools.
Nat. Methods, 9, no. 7, pp. 697-710, (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?
TREE, 27, no. 7, pp. 385-393, (2012)
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Kelava, Iva; Reillo, Isabel; Murayama, Ayako Y; Kalinka, Alex T.; Stenzel, Denise; Tomancak, Pavel; Matsuzaki, Fumio; Lebrand, CĂ©cile; Sasaki, Erika; Schwamborn, Jens C; Okano, Hideyuki; Huttner, Wieland B.; Borrell, VĂ­ctor
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, no. 2, pp. 469-481, (2012)
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Cardona, Albert; Saalfeld, Stephan; Schindelin, Johannes; Arganda-Carreras, Ignacio; Preibisch, Stephan; Longair, Mark; Tomancak, Pavel; Hartenstein, Volker; Douglas, Rodney J
TrakEM2 Software for Neural Circuit Reconstruction.
PLoS ONE, 7, no. 6, (2012)
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Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel; Saalfeld, Stephan
ImgLib2 – Generic Image Processing in Java
Bioinformatics, 28, no. 22, pp. 3009-3011, (2012)
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2011
Jambor, Helena; Brunel, Christine; Ephrussi, Anne
Dimerization of oskar 3' UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte.
RNA, 17, no. 12, pp. 2049-2057, (2011)
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Uddin, Mohammad Shorif; Lee, Hwee Kuan; Preibisch, Stephan; Tomancak, Pavel
Restoration of Uneven Illumination in Light Sheet Microscopy Images.
Microsc. microanal., 17, no. 4, pp. 607-613, (2011)
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Lipinski, Kamil A; Puchta, Olga; Surandranath, Vineeth; Kudla, Marek; Golik, Pawel
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, no. 10, pp. 2935-2948, (2011)
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Kalinka, Alex T.; Tomancak, Pavel
linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type.
Bioinformatics, 27, no. 14, pp. 2011-2012, (2011)
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Preibisch, Stephan
Reconstruction of Multi-Tile Microscopic Acquisitions
[Doctoral Thesis] Technische Universität Dresden, (2011)
Ejsmont, Radoslaw K; Ahlfeld, Peter; Pozniakovsky, Andrei I.; Stewart, A Francis; Tomancak, Pavel; Sarov, Mihail
Recombination-mediated genetic engineering of large genomic DNA transgenes.
Methods Mol. Biol., 772, pp. 445-458, (2011)
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Ejsmont, Radoslaw K; Bogdanzaliewa, Maria; Lipinski, Kamil A; Tomancak, Pavel
Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis.
Methods Mol. Biol., 772, pp. 423-443, (2011)
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Ejsmont, Radoslaw K
A toolkit for visualization of patterns of gene expression in live Drosophila embryos
[Doctoral Thesis] Technische Universität Dresden, (2011)
2010
Kalinka, Alex T.; Varga, Karolina M.; Gerrard, Dave T.; Preibisch, Stephan; Corcoran, David L.; Jarrels, Julia; Ohler, Uwe; Bergman, Casey M.; Tomancák, Pavel
Gene expression divergence recapitulates the developmental hourglass model
Nature, 468, no. 7325, pp. 811-814, (2010)
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Carrillo Oesterreich, Fernando; Preibisch, Stephan; Neugebauer, Karla M.
Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
Mol. Cell, 40, no. 4, pp. 571-581, (2010)
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Oteiza, Pablo; Köppen, Mathias; Krieg, Michael; Pulgar, Eduardo; Farias, Cecilia; Melo, Cristina; Preibisch, Stephan; Müller, Daniel J. ; Tada, Masazumi; Hartel, Steffen; Heisenberg, Carl-Philipp; Concha, Miguel L
Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ.
Development, 137, no. 20, pp. 3459-3468, (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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Capek, Richard Karel; Weber, Michael; EychmĂĽller, Alexander
Alternative Incorporation Procedure of Quantum Dots in Polymer Microspheres
Chem. Mater., 22, no. 17, pp. 4912-4918, (2010)
Reynaud, Emmanuel G.; Tomancák, Pavel
Meeting report: First light sheet based fluorescence microscopy workshop.
Biotechnol. J., 5, no. 8, pp. 798-804, (2010)
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Arunachalam, Manonmani; Jayasurya, Karthik; Tomancák, Pavel; Ohler, Uwe
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
Bioinformatics, 26, no. 17, pp. 2109-2115, (2010)
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Saalfeld, Stephan; Cardona, Albert; Hartenstein, Volker; Tomancák, Pavel
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets
Bioinformatics, 26, no. 12, pp. 57-63, (2010)
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Cardona, Albert; Saalfeld, Stephan; Arganda, Ignacio; Pereanu, Wayne; Schindelin, Johannes; Hartenstein, Volker
Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts.
J. Neurosci., 30, no. 22, pp. 7538-7553, (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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Tomancák, Pavel; Ohler, Uwe
Mapping the complexity of transcription control in higher eukaryotes
Genome Biol., 11, no. 4, (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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Weber, Michael
Interspecimen registration of long-term, time-lapse selective plane illumination microscopy recordings of Drosophila melanogaster embryogenesis
[Diploma Thesis] Technische Universität Dresden, (2010)
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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Preibisch, Stephan; Tomancák, Pavel; Saalfeld, Stephan
Into ImgLib - Generic Image Processing in Java
[Conference Paper] ImageJ User and Developer Conference, Luxembourg, (2010)
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Jastrzebowska, Karolina
Evolution of gene expression regulation during embryonic development of Drosophila species
[Doctoral Thesis] Technische Universität Dresden, (2010)
2009
Cardona, Albert; Saalfeld, Stephan; Tomancák, Pavel; Hartenstein, Volker
Drosophila Brain Development: Closing the Gap between a Macroarchitectural and Microarchitectural Approach.
Cold Spring Harb. Symp. Quant. Biol., 74, pp. 235-248, (2009)
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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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Rach, Elizabeth; Yuan, Hsiang-Yu; Majoros, William H; Tomancák, Pavel; Ohler, Uwe
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.
Genome Biol., 10, no. 7, (2009)
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Arunachalam, Manonmani
Computational discovery of Cis-regulatory elements in multiple Drosophila species
[Doctoral Thesis] Technische Universität Dresden, (2009)
Preibisch, Stephan; Saalfeld, Stephan; Rohlfing, Torsten; Tomancák, Pavel
Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching
[Conference Paper] SPIE Medical Imaging Conference, Lake Buena Vista, Fla., (2009)
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2008
Lécuyer, Eric; Tomancák, Pavel
Mapping the gene expression universe.
Curr. Opin. Genet. Dev., 18, no. 6, pp. 506-512, (2008)
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Preibisch, Stephan; Ejsmont, Radoslaw K; Rohlfing, Torsten; Tomancák, Pavel
Towards digital representation of Drosophila embryogenesis
[Conference Paper] IEEE International Symposium on Biomedical Imaging : from Nano to Macro ; 5, Paris, (2008)
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Quijano, Carlos; Tomancák, Pavel; Lopez-Marti, Jesus; Suyama, Mikita; Bork, Peer; Milan, Marco; Torrents, David; Manzanares, Miguel
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.
Genome Biol., 9, no. 12, pp. 176-176, (2008)
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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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Preibisch, Stephan; Saalfeld, Stephan; Tomancák, Pavel
Fast stitching of large 3d biological datasets
[Conference Paper] ImageJ User and Developer Conference, Luxembourg, (2008)
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Saalfeld, Stephan; Tomancák, Pavel
Automatic landmark correspondence detection for ImageJ
[Conference Paper] ImageJ User and Developer Conference, Luxembourg, (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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Magalhães, Tiago R; Palmer, Jessica; Tomancák, Pavel; Pollard, Katherine S
Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach.
BMC neuroscience, 8, pp. 59-59, (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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Berman, Benjamin P; Tomancák, Pavel; Nibu, Yutaka; Pfeiffer, Barret D; Celniker, Susan E; Levine, Michael; Rubin, Gerald M; Eisen, Michael B
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, no. 2, pp. 757-762, (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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1998
Muckenthaler, Martina; Gunkel, Niki; Frishman, Dmitrij; Cyrklaff, Anna; Tomancák, Pavel; Hentze, Matthias W.
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, no. 2, pp. 230-237, (1998)
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Tomancák, Pavel; Guichet, Antoine; Zavorszky, Peter; Ephrussi, Anne
Oocyte polarity depends on regulation of gurken by Vasa.
Development, 125, no. 9, pp. 1723-1732, (1998)
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