Pavel Tomancak's publications on GoogleScholar
| 2013 |
| Pitrone, Peter Gabriel; Schindelin, Johannes; Stuyvenberg, Luke; Preibisch, Stephan W.; Weber, Michael; Eliceiri, Kevin W; Huisken, Jan; Tomancak, Pavel |
| OpenSPIM: an open access light sheet microscopy platform |
| Nat. Methods, see also http://arxiv.org/abs/1302.1987, pp. 1-2, (2013) |
| Download PDFDownload Supplementary Text FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video File |
| 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, http://arxiv.org/abs/1305.0717, pp. 1-1, (2013) |
| Lewitus, Eric; Kalinka, Alex T. |
| Neocortical development as an evolutionary platform for intragenomic conflict. |
| Front Neuroanat, 7, pp. 2-2, (2013) |
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| 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, http://arxiv.org/abs/1304.5412, pp. 1-1, (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 W.; 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) |
| Download PDFDownload Supplementary Image FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video File |
| 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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| Cardona, Albert; Saalfeld, Stephan; Schindelin, Johannes; Arganda-Carreras, Ignacio; Preibisch, Stephan W.; 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 W.; Tomancak, Pavel; Saalfeld, Stephan |
| ImgLib2 – Generic Image Processing in Java |
| Bioinformatics, 28, no. 22, pp. 3009-3011, (2012) |
| Download PDFDownload Supplementary Text FileDownload Supplementary Video File |
| 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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| 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 W.; 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 W. |
| 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 W.; 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 W.; 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 W.; 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 W.; 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 W.; 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) |
| Download PDFDownload Supplementary Text FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video FileDownload Supplementary Video File |
| 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 W.; 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 W.; 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 W.; 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 W.; 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 W.; 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 W.; 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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