Pavel Tomancak - Publications

Affiliations: 
MPI-CBG, Dresden, Sachsen, Germany 
Area:
gene expression regulation, embryogenesis

66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Skouloudaki K, Papadopoulos DK, Tomancak P, Knust E. The apical protein Apnoia interacts with Crumbs to regulate tracheal growth and inflation. Plos Genetics. 15: e1007852. PMID 30645584 DOI: 10.1371/journal.pgen.1007852  1
2019 Papadopoulos DK, Skouloudaki K, Engström Y, Terenius L, Rigler R, Zechner C, Vukojević V, Tomancak P. Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch. Development (Cambridge, England). PMID 30642837 DOI: 10.1242/dev.168179  1
2018 Maharana S, Wang J, Papadopoulos DK, Richter D, Pozniakovsky A, Poser I, Bickle M, Rizk S, Guillén-Boixet J, Franzmann T, Jahnel M, Marrone L, Chang YT, Sterneckert J, Tomancak P, et al. RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science (New York, N.Y.). PMID 29650702 DOI: 10.1126/science.aar7366  1
2018 Wolff C, Tinevez JY, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P, Pavlopoulos A. Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb. Elife. 7. PMID 29595475 DOI: 10.7554/eLife.34410  0.64
2017 Reynolds JJ, Bicknell LS, Carroll P, Higgs MR, Shaheen R, Murray JE, Papadopoulos DK, Leitch A, Murina O, Tarnauskaitė Ž, Wessel SR, Zlatanou A, Vernet A, von Kriegsheim A, Mottram RM, ... ... Tomancak P, et al. Mutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism. Nature Genetics. PMID 28191891 DOI: 10.1038/ng.3790  1
2016 Jambor H, Mejstrik P, Tomancak P. Rapid Ovary Mass-Isolation (ROMi) to Obtain Large Quantities of Drosophila Egg Chambers for Fluorescent In Situ Hybridization. Methods in Molecular Biology (Clifton, N.J.). 1478: 253-262. PMID 27730587 DOI: 10.1007/978-1-4939-6371-3_15  0.76
2016 Icha J, Schmied C, Sidhaye J, Tomancak P, Preibisch S, Norden C. Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development. Journal of Visualized Experiments : Jove. PMID 27167079 DOI: 10.3791/53966  0.64
2016 Lewitus E, Kelava I, Kalinka AT, Tomancak P, Huttner WB. Comment on "Cortical folding scales universally with surface area and thickness, not number of neurons". Science (New York, N.Y.). 351: 825. PMID 26912886 DOI: 10.1126/science.aad2029  1
2016 Sarov M, Barz C, Jambor H, Hein MY, Schmied C, Suchold D, Stender B, Janosch S, Kj VV, Krishnan RT, Krishnamoorthy A, Ferreira IR, Ejsmont RK, Finkl K, Hasse S, ... ... Tomancak P, et al. A genome-wide resource for the analysis of protein localisation in Drosophila. Elife. 5. PMID 26896675 DOI: 10.7554/eLife.12068  1
2016 Börner K, Jain D, Vazquez-Pianzola P, Vengadasalam S, Steffen N, Fyodorov DV, Tomancak P, Konev A, Suter B, Becker PB. A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis. Developmental Biology. PMID 26851213 DOI: 10.1016/j.ydbio.2016.01.039  1
2015 Schmied C, Steinbach P, Pietzsch T, Preibisch S, Tomancak P. An automated workflow for parallel processing of large multiview SPIM recordings. Bioinformatics (Oxford, England). PMID 26628585 DOI: 10.1093/bioinformatics/btv706  0.64
2015 Papadopoulos DK, Krmpot AJ, Nikolić SN, Krautz R, Terenius L, Tomancak P, Rigler R, Gehring WJ, Vukojević V. Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy. Mechanisms of Development. PMID 26428533 DOI: 10.1016/j.mod.2015.09.004  1
2015 Pietzsch T, Saalfeld S, Preibisch S, Tomancak P. BigDataViewer: visualization and processing for large image data sets. Nature Methods. 12: 481-3. PMID 26020499 DOI: 10.1038/nmeth.3392  1
2015 Dunst S, Kazimiers T, von Zadow F, Jambor H, Sagner A, Brankatschk B, Mahmoud A, Spannl S, Tomancak P, Eaton S, Brankatschk M. Endogenously tagged rab proteins: a resource to study membrane trafficking in Drosophila. Developmental Cell. 33: 351-65. PMID 25942626 DOI: 10.1016/j.devcel.2015.03.022  1
2015 Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P. Systematic imaging reveals features and changing localization of mRNAs in Drosophila development. Elife. 4. PMID 25838129 DOI: 10.7554/eLife.05003  1
2015 Reynaud EG, Peychl J, Huisken J, Tomancak P. Guide to light-sheet microscopy for adventurous biologists. Nature Methods. 12: 30-4. PMID 25549268 DOI: 10.1038/nmeth.3222  1
2015 Heyn P, Kalinka AT, Tomancak P, Neugebauer KM. Introns and gene expression: cellular constraints, transcriptional regulation, and evolutionary consequences. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 37: 148-54. PMID 25400101 DOI: 10.1002/bies.201400138  1
2014 Lewitus E, Kelava I, Kalinka AT, Tomancak P, Huttner WB. An adaptive threshold in mammalian neocortical evolution. Plos Biology. 12: e1002000. PMID 25405475 DOI: 10.1371/journal.pbio.1002000  1
2014 Schmied C, Stamataki E, Tomancak P. Open-source solutions for SPIMage processing. Methods in Cell Biology. 123: 505-29. PMID 24974045 DOI: 10.1016/B978-0-12-420138-5.00027-6  1
2014 Preibisch S, Amat F, Stamataki E, Sarov M, Singer RH, Myers E, Tomancak P. Efficient Bayesian-based multiview deconvolution. Nature Methods. 11: 645-8. PMID 24747812 DOI: 10.1038/nmeth.2929  1
2014 Jug F, Pietzsch T, Preibisch S, Tomancak P. Bioimage Informatics in the context of Drosophila research. Methods (San Diego, Calif.). 68: 60-73. PMID 24732429 DOI: 10.1016/j.ymeth.2014.04.004  1
2014 Gualda E, Moreno N, Tomancak P, Martins GG. Going "open" with mesoscopy: a new dimension on multi-view imaging. Protoplasma. 251: 363-72. PMID 24442669 DOI: 10.1007/s00709-013-0599-3  1
2014 Heyn P, Kircher M, Dahl A, Kelso J, Tomancak P, Kalinka AT, Neugebauer KM. The earliest transcribed zygotic genes are short, newly evolved, and different across species. Cell Reports. 6: 285-92. PMID 24440719 DOI: 10.1016/j.celrep.2013.12.030  1
2013 Pitrone PG, Schindelin J, Stuyvenberg L, Preibisch S, Weber M, Eliceiri KW, Huisken J, Tomancak P. OpenSPIM: an open-access light-sheet microscopy platform. Nature Methods. 10: 598-9. PMID 23749304 DOI: 10.1038/nmeth.2507  1
2012 Kayserili MA, Gerrard DT, Tomancak P, Kalinka AT. An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis. Plos Genetics. 8: e1003200. PMID 23300473 DOI: 10.1371/journal.pgen.1003200  1
2012 Pietzsch T, Preibisch S, Tomancák P, Saalfeld S. ImgLib2--generic image processing in Java. Bioinformatics (Oxford, England). 28: 3009-11. PMID 22962343 DOI: 10.1093/bioinformatics/bts543  0.64
2012 Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nature Methods. 9: 697-710. PMID 22743775 DOI: 10.1038/nmeth.2084  1
2012 Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, et al. Fiji: an open-source platform for biological-image analysis. Nature Methods. 9: 676-82. PMID 22743772 DOI: 10.1038/nmeth.2019  1
2012 Cardona A, Tomancak P. Current challenges in open-source bioimage informatics. Nature Methods. 9: 661-5. PMID 22743770 DOI: 10.1038/nmeth.2082  1
2012 Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ. TrakEM2 software for neural circuit reconstruction. Plos One. 7: e38011. PMID 22723842 DOI: 10.1371/journal.pone.0038011  1
2012 Saalfeld S, Fetter R, Cardona A, Tomancak P. Elastic volume reconstruction from series of ultra-thin microscopy sections. Nature Methods. 9: 717-20. PMID 22688414 DOI: 10.1038/nmeth.2072  1
2012 Kalinka AT, Tomancak P. The evolution of early animal embryos: conservation or divergence? Trends in Ecology & Evolution. 27: 385-93. PMID 22520868 DOI: 10.1016/j.tree.2012.03.007  1
2012 Kelava I, Reillo I, Murayama AY, Kalinka AT, Stenzel D, Tomancak P, Matsuzaki F, Lebrand C, Sasaki E, Schwamborn JC, Okano H, Huttner WB, Borrell V. Abundant occurrence of basal radial glia in the subventricular zone of embryonic neocortex of a lissencephalic primate, the common marmoset Callithrix jacchus. Cerebral Cortex (New York, N.Y. : 1991). 22: 469-81. PMID 22114084 DOI: 10.1093/cercor/bhr301  1
2011 Ejsmont RK, Ahlfeld P, Pozniakovsky A, Stewart AF, Tomancak P, Sarov M. Recombination-mediated genetic engineering of large genomic DNA transgenes. Methods in Molecular Biology (Clifton, N.J.). 772: 445-58. PMID 22065454 DOI: 10.1007/978-1-61779-228-1_26  1
2011 Ejsmont RK, Bogdanzaliewa M, Lipinski KA, Tomancak P. Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis. Methods in Molecular Biology (Clifton, N.J.). 772: 423-43. PMID 22065453 DOI: 10.1007/978-1-61779-228-1_25  1
2011 Uddin MS, Lee HK, Preibisch S, Tomancak P. 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. 17: 607-13. PMID 21682937 DOI: 10.1017/S1431927611000262  1
2011 Kalinka AT, Tomancak P. linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics (Oxford, England). 27: 2011-2. PMID 21596792 DOI: 10.1093/bioinformatics/btr311  1
2010 Kalinka AT, Varga KM, Gerrard DT, Preibisch S, Corcoran DL, Jarrells J, Ohler U, Bergman CM, Tomancak P. Gene expression divergence recapitulates the developmental hourglass model. Nature. 468: 811-4. PMID 21150996 DOI: 10.1038/nature09634  1
2010 Cardona A, Saalfeld S, Preibisch S, Schmid B, Cheng A, Pulokas J, Tomancak P, Hartenstein V. An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy. Plos Biology. 8. PMID 20957184 DOI: 10.1371/journal.pbio.1000502  1
2010 Reynaud EG, Tomancak P. Meeting report: first light sheet based fluorescence microscopy workshop. Biotechnology Journal. 5: 798-804. PMID 20652906 DOI: 10.1002/biot.201000177  1
2010 Arunachalam M, Jayasurya K, Tomancak P, Ohler U. An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. Bioinformatics (Oxford, England). 26: 2109-15. PMID 20624780 DOI: 10.1093/bioinformatics/btq358  1
2010 Saalfeld S, Cardona A, Hartenstein V, Toman?ák P. As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Bioinformatics (Oxford, England). 26: i57-63. PMID 20529937 DOI: 10.1093/bioinformatics/btq219  1
2010 Preibisch S, Saalfeld S, Schindelin J, Tomancak P. Software for bead-based registration of selective plane illumination microscopy data. Nature Methods. 7: 418-9. PMID 20508634 DOI: 10.1038/nmeth0610-418  1
2010 Tomancak P, Ohler U. Mapping the complexity of transcription control in higher eukaryotes. Genome Biology. 11: 115. PMID 20441601 DOI: 10.1186/gb-2010-11-4-115  1
2010 Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Hériché JK. Visualization of image data from cells to organisms. Nature Methods. 7: S26-41. PMID 20195255 DOI: 10.1038/nmeth.1431  1
2010 Langer CC, Ejsmont RK, Schönbauer C, Schnorrer F, Tomancak P. In vivo RNAi rescue in Drosophila melanogaster with genomic transgenes from Drosophila pseudoobscura. Plos One. 5: e8928. PMID 20126626 DOI: 10.1371/journal.pone.0008928  1
2009 Cardona A, Saalfeld S, Tomancak P, Hartenstein V. Drosophila brain development: closing the gap between a macroarchitectural and microarchitectural approach. Cold Spring Harbor Symposia On Quantitative Biology. 74: 235-48. PMID 20028843 DOI: 10.1101/sqb.2009.74.037  1
2009 Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biology. 10: R73. PMID 19589141 DOI: 10.1186/gb-2009-10-7-r73  1
2009 Ejsmont RK, Sarov M, Winkler S, Lipinski KA, Tomancak P. A toolkit for high-throughput, cross-species gene engineering in Drosophila. Nature Methods. 6: 435-7. PMID 19465918 DOI: 10.1038/nmeth.1334  1
2009 Saalfeld S, Cardona A, Hartenstein V, Tomancak P. CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics (Oxford, England). 25: 1984-6. PMID 19376822 DOI: 10.1093/bioinformatics/btp266  1
2009 Preibisch S, Saalfeld S, Tomancak P. Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics (Oxford, England). 25: 1463-5. PMID 19346324 DOI: 10.1093/bioinformatics/btp184  1
2009 Preibisch S, Saalfeld S, Rohlfing T, Tomancak P. Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching Progress in Biomedical Optics and Imaging - Proceedings of Spie. 7259. DOI: 10.1117/12.812612  1
2008 Quijano C, Tomancak P, Lopez-Marti J, Suyama M, Bork P, Milan M, Torrents D, Manzanares M. Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution. Genome Biology. 9: R176. PMID 19087263 DOI: 10.1186/gb-2008-9-12-r176  1
2008 Lécuyer E, Tomancak P. Mapping the gene expression universe. Current Opinion in Genetics & Development. 18: 506-12. PMID 18809490 DOI: 10.1016/j.gde.2008.08.003  1
2008 Preibisch S, Rohlfing T, Hasak MP, Tomancak P. Mosaicing of single plane illumination microscopy images using groupwise registration and fast content-based image fusion Progress in Biomedical Optics and Imaging - Proceedings of Spie. 6914. DOI: 10.1117/12.770893  1
2008 Preibisch S, Ejsmont R, Rohlfing T, Tomancak P. Towards digital representation of Drosophila embryogenesis 2008 5th Ieee International Symposium On Biomedical Imaging: From Nano to Macro, Proceedings, Isbi. 324-327. DOI: 10.1109/ISBI.2008.4540998  1
2007 Lécuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, Krause HM. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell. 131: 174-87. PMID 17923096 DOI: 10.1016/j.cell.2007.08.003  1
2007 Magalhães TR, Palmer J, Tomancak P, Pollard KS. Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach. Bmc Neuroscience. 8: 59. PMID 17672901 DOI: 10.1186/1471-2202-8-59  1
2007 Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biology. 8: R145. PMID 17645804 DOI: 10.1186/gb-2007-8-7-r145  1
2005 Aboobaker AA, Tomancak P, Patel N, Rubin GM, Lai EC. Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proceedings of the National Academy of Sciences of the United States of America. 102: 18017-22. PMID 16330759 DOI: 10.1073/pnas.0508823102  1
2003 Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biology. 4: R42. PMID 12844358 DOI: 10.1186/gb-2003-4-7-r42  1
2002 Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GM. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biology. 3: RESEARCH0088. PMID 12537577  1
2002 Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. 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. 99: 757-62. PMID 11805330 DOI: 10.1073/pnas.231608898  1
2000 Tomancak P, Piano F, Riechmann V, Gunsalus KC, Kemphues KJ, Ephrussi A. A Drosophila melanogaster homologue of Caenorhabditis elegans par-1 acts at an early step in embryonic-axis formation. Nature Cell Biology. 2: 458-60. PMID 10878812 DOI: 10.1038/35017101  1
1998 Muckenthaler M, Gunkel N, Frishman D, Cyrklaff A, Tomancak P, Hentze MW. Iron-regulatory protein-1 (IRP-1) is highly conserved in two invertebrate species--characterization of IRP-1 homologues in Drosophila melanogaster and Caenorhabditis elegans. European Journal of Biochemistry / Febs. 254: 230-7. PMID 9660175 DOI: 10.1046/j.1432-1327.1998.2540230.x  1
1998 Tomancak P, Guichet A, Zavorszky P, Ephrussi A. Oocyte polarity depends on regulation of gurken by Vasa. Development (Cambridge, England). 125: 1723-32. PMID 9521910  1
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