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Items: 1 to 50 of 74

1.

The apical protein Apnoia interacts with Crumbs to regulate tracheal growth and inflation.

Skouloudaki K, Papadopoulos DK, Tomancak P, Knust E.

PLoS Genet. 2019 Jan 15;15(1):e1007852. doi: 10.1371/journal.pgen.1007852. eCollection 2019 Jan.

2.

Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch.

Papadopoulos DK, Skouloudaki K, Engström Y, Terenius L, Rigler R, Zechner C, Vukojević V, Tomancak P.

Development. 2019 Jan 25;146(12). pii: dev168179. doi: 10.1242/dev.168179.

3.

Imaging Flies by Fluorescence Microscopy: Principles, Technologies, and Applications.

Dunst S, Tomancak P.

Genetics. 2019 Jan;211(1):15-34. doi: 10.1534/genetics.118.300227.

4.

Content-aware image restoration: pushing the limits of fluorescence microscopy.

Weigert M, Schmidt U, Boothe T, Müller A, Dibrov A, Jain A, Wilhelm B, Schmidt D, Broaddus C, Culley S, Rocha-Martins M, Segovia-Miranda F, Norden C, Henriques R, Zerial M, Solimena M, Rink J, Tomancak P, Royer L, Jug F, Myers EW.

Nat Methods. 2018 Dec;15(12):1090-1097. doi: 10.1038/s41592-018-0216-7. Epub 2018 Nov 26.

PMID:
30478326
5.

Multiscale imaging of plant development by light-sheet fluorescence microscopy.

Ovečka M, von Wangenheim D, Tomančák P, Šamajová O, Komis G, Šamaj J.

Nat Plants. 2018 Sep;4(9):639-650. doi: 10.1038/s41477-018-0238-2. Epub 2018 Sep 5. Review.

PMID:
30185982
6.

RNA buffers the phase separation behavior of prion-like RNA binding proteins.

Maharana S, Wang J, Papadopoulos DK, Richter D, Pozniakovsky A, Poser I, Bickle M, Rizk S, Guillén-Boixet J, Franzmann TM, Jahnel M, Marrone L, Chang YT, Sterneckert J, Tomancak P, Hyman AA, Alberti S.

Science. 2018 May 25;360(6391):918-921. doi: 10.1126/science.aar7366. Epub 2018 Apr 12.

7.

Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.

Wolff C, Tinevez JY, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P, Pavlopoulos A.

Elife. 2018 Mar 29;7. pii: e34410. doi: 10.7554/eLife.34410.

8.

The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation.

Handberg-Thorsager M, Gutierrez-Mazariegos J, Arold ST, Kumar Nadendla E, Bertucci PY, Germain P, Tomançak P, Pierzchalski K, Jones JW, Albalat R, Kane MA, Bourguet W, Laudet V, Arendt D, Schubert M.

Sci Adv. 2018 Feb 21;4(2):eaao1261. doi: 10.1126/sciadv.aao1261. eCollection 2018 Feb.

9.

Ectopic expression of S28A-mutated Histone H3 modulates longevity, stress resistance and cardiac function in Drosophila.

Joos JP, Saadatmand AR, Schnabel C, Viktorinová I, Brand T, Kramer M, Nattel S, Dobrev D, Tomancak P, Backs J, Kleinbongard P, Heusch G, Lorenz K, Koch E, Weber S, El-Armouche A.

Sci Rep. 2018 Feb 13;8(1):2940. doi: 10.1038/s41598-018-21372-3.

10.

Small molecule screen in embryonic zebrafish using modular variations to target segmentation.

Richter S, Schulze U, Tomançak P, Oates AC.

Nat Commun. 2017 Dec 1;8(1):1901. doi: 10.1038/s41467-017-01469-5.

11.

Epithelial rotation is preceded by planar symmetry breaking of actomyosin and protects epithelial tissue from cell deformations.

Viktorinová I, Henry I, Tomancak P.

PLoS Genet. 2017 Nov 27;13(11):e1007107. doi: 10.1371/journal.pgen.1007107. eCollection 2017 Nov.

12.

An objective comparison of cell-tracking algorithms.

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C.

Nat Methods. 2017 Dec;14(12):1141-1152. doi: 10.1038/nmeth.4473. Epub 2017 Oct 30.

13.

Assessing phototoxicity in live fluorescence imaging.

Laissue PP, Alghamdi RA, Tomancak P, Reynaud EG, Shroff H.

Nat Methods. 2017 Jun 29;14(7):657-661. doi: 10.1038/nmeth.4344.

PMID:
28661494
14.

Mutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism.

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, Logan CV, Bye H, Li Y, Brean A, Maddirevula S, Challis RC, Skouloudaki K, Almoisheer A, Alsaif HS, Amar A, Prescott NJ, Bober MB, Duker A, Faqeih E, Seidahmed MZ, Al Tala S, Alswaid A, Ahmed S, Al-Aama JY, Altmüller J, Al Balwi M, Brady AF, Chessa L, Cox H, Fischetto R, Heller R, Henderson BD, Hobson E, Nürnberg P, Percin EF, Peron A, Spaccini L, Quigley AJ, Thakur S, Wise CA, Yoon G, Alnemer M, Tomancak P, Yigit G, Taylor AM, Reijns MA, Simpson MA, Cortez D, Alkuraya FS, Mathew CG, Jackson AP, Stewart GS.

Nat Genet. 2017 Apr;49(4):537-549. doi: 10.1038/ng.3790. Epub 2017 Feb 13.

15.
16.

Sample Preparation and Mounting of Drosophila Embryos for Multiview Light Sheet Microscopy.

Schmied C, Tomancak P.

Methods Mol Biol. 2016;1478:189-202. Review.

PMID:
27730582
17.

Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development.

Girstmair J, Zakrzewski A, Lapraz F, Handberg-Thorsager M, Tomancak P, Pitrone PG, Simpson F, Telford MJ.

BMC Dev Biol. 2016 Jun 30;16(1):22. doi: 10.1186/s12861-016-0122-0.

18.

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development.

Icha J, Schmied C, Sidhaye J, Tomancak P, Preibisch S, Norden C.

J Vis Exp. 2016 Apr 10;(110):e53966. doi: 10.3791/53966.

19.

Comment on "Cortical folding scales universally with surface area and thickness, not number of neurons".

Lewitus E, Kelava I, Kalinka AT, Tomancak P, Huttner WB.

Science. 2016 Feb 19;351(6275):825. doi: 10.1126/science.aad2029.

20.

A genome-wide resource for the analysis of protein localisation in Drosophila.

Sarov M, Barz C, Jambor H, Hein MY, Schmied C, Suchold D, Stender B, Janosch S, K J VV, Krishnan RT, Krishnamoorthy A, Ferreira IR, Ejsmont RK, Finkl K, Hasse S, Kämpfer P, Plewka N, Vinis E, Schloissnig S, Knust E, Hartenstein V, Mann M, Ramaswami M, VijayRaghavan K, Tomancak P, Schnorrer F.

Elife. 2016 Feb 20;5:e12068. doi: 10.7554/eLife.12068.

21.

A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis.

Börner K, Jain D, Vazquez-Pianzola P, Vengadasalam S, Steffen N, Fyodorov DV, Tomancak P, Konev A, Suter B, Becker PB.

Dev Biol. 2016 Mar 15;411(2):217-230. doi: 10.1016/j.ydbio.2016.01.039. Epub 2016 Feb 2.

22.

An automated workflow for parallel processing of large multiview SPIM recordings.

Schmied C, Steinbach P, Pietzsch T, Preibisch S, Tomancak P.

Bioinformatics. 2016 Apr 1;32(7):1112-4. doi: 10.1093/bioinformatics/btv706. Epub 2015 Dec 1.

23.

Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy.

Papadopoulos DK, Krmpot AJ, Nikolić SN, Krautz R, Terenius L, Tomancak P, Rigler R, Gehring WJ, Vukojević V.

Mech Dev. 2015 Nov;138 Pt 2:218-225. doi: 10.1016/j.mod.2015.09.004. Epub 2015 Sep 30.

24.

BigDataViewer: visualization and processing for large image data sets.

Pietzsch T, Saalfeld S, Preibisch S, Tomancak P.

Nat Methods. 2015 Jun;12(6):481-3. doi: 10.1038/nmeth.3392. No abstract available.

PMID:
26020499
25.

Endogenously tagged rab proteins: a resource to study membrane trafficking in Drosophila.

Dunst S, Kazimiers T, von Zadow F, Jambor H, Sagner A, Brankatschk B, Mahmoud A, Spannl S, Tomancak P, Eaton S, Brankatschk M.

Dev Cell. 2015 May 4;33(3):351-65. doi: 10.1016/j.devcel.2015.03.022.

26.

Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.

Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P.

Elife. 2015 Apr 2;4. doi: 10.7554/eLife.05003.

27.

Guide to light-sheet microscopy for adventurous biologists.

Reynaud EG, Peychl J, Huisken J, Tomancak P.

Nat Methods. 2015 Jan;12(1):30-4. doi: 10.1038/nmeth.3222. No abstract available.

PMID:
25549268
28.

An adaptive threshold in mammalian neocortical evolution.

Lewitus E, Kelava I, Kalinka AT, Tomancak P, Huttner WB.

PLoS Biol. 2014 Nov 18;12(11):e1002000. doi: 10.1371/journal.pbio.1002000. eCollection 2014 Nov.

29.

Introns and gene expression: cellular constraints, transcriptional regulation, and evolutionary consequences.

Heyn P, Kalinka AT, Tomancak P, Neugebauer KM.

Bioessays. 2015 Feb;37(2):148-54. doi: 10.1002/bies.201400138. Epub 2014 Nov 14.

30.

Open-source solutions for SPIMage processing.

Schmied C, Stamataki E, Tomancak P.

Methods Cell Biol. 2014;123:505-29. doi: 10.1016/B978-0-12-420138-5.00027-6.

PMID:
24974045
31.

Efficient Bayesian-based multiview deconvolution.

Preibisch S, Amat F, Stamataki E, Sarov M, Singer RH, Myers E, Tomancak P.

Nat Methods. 2014 Jun;11(6):645-8. doi: 10.1038/nmeth.2929. Epub 2014 Apr 20.

32.

Bioimage Informatics in the context of Drosophila research.

Jug F, Pietzsch T, Preibisch S, Tomancak P.

Methods. 2014 Jun 15;68(1):60-73. doi: 10.1016/j.ymeth.2014.04.004. Epub 2014 Apr 13. Review.

33.

Going "open" with mesoscopy: a new dimension on multi-view imaging.

Gualda E, Moreno N, Tomancak P, Martins GG.

Protoplasma. 2014 Mar;251(2):363-72. doi: 10.1007/s00709-013-0599-3. Epub 2014 Jan 18.

PMID:
24442669
34.

The earliest transcribed zygotic genes are short, newly evolved, and different across species.

Heyn P, Kircher M, Dahl A, Kelso J, Tomancak P, Kalinka AT, Neugebauer KM.

Cell Rep. 2014 Jan 30;6(2):285-92. doi: 10.1016/j.celrep.2013.12.030. Epub 2014 Jan 16.

35.

OpenSPIM: an open-access light-sheet microscopy platform.

Pitrone PG, Schindelin J, Stuyvenberg L, Preibisch S, Weber M, Eliceiri KW, Huisken J, Tomancak P.

Nat Methods. 2013 Jul;10(7):598-9. doi: 10.1038/nmeth.2507. Epub 2013 Jun 9. No abstract available.

PMID:
23749304
36.

An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis.

Kayserili MA, Gerrard DT, Tomancak P, Kalinka AT.

PLoS Genet. 2012;8(12):e1003200. doi: 10.1371/journal.pgen.1003200. Epub 2012 Dec 27.

37.

ImgLib2--generic image processing in Java.

Pietzsch T, Preibisch S, Tomancák P, Saalfeld S.

Bioinformatics. 2012 Nov 15;28(22):3009-11. doi: 10.1093/bioinformatics/bts543. Epub 2012 Sep 8. Erratum in: Bioinformatics. 2013 Jan 15;29(2):298.

38.

Biological imaging software tools.

Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow JR, Tomancak P, Carpenter AE.

Nat Methods. 2012 Jun 28;9(7):697-710. doi: 10.1038/nmeth.2084. Erratum in: Nat Methods. 2012 Oct;9(10):1031. Stuurmann, Nico [corrected to Stuurman, Nico].

39.

Fiji: an open-source platform for biological-image analysis.

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, Cardona A.

Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019.

40.

Current challenges in open-source bioimage informatics.

Cardona A, Tomancak P.

Nat Methods. 2012 Jun 28;9(7):661-5. doi: 10.1038/nmeth.2082.

PMID:
22743770
41.

TrakEM2 software for neural circuit reconstruction.

Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ.

PLoS One. 2012;7(6):e38011. doi: 10.1371/journal.pone.0038011. Epub 2012 Jun 19.

42.

Elastic volume reconstruction from series of ultra-thin microscopy sections.

Saalfeld S, Fetter R, Cardona A, Tomancak P.

Nat Methods. 2012 Jun 10;9(7):717-20. doi: 10.1038/nmeth.2072.

PMID:
22688414
43.

The evolution of early animal embryos: conservation or divergence?

Kalinka AT, Tomancak P.

Trends Ecol Evol. 2012 Jul;27(7):385-93. doi: 10.1016/j.tree.2012.03.007. Epub 2012 Apr 18.

PMID:
22520868
44.

Abundant occurrence of basal radial glia in the subventricular zone of embryonic neocortex of a lissencephalic primate, the common marmoset Callithrix jacchus.

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.

Cereb Cortex. 2012 Feb;22(2):469-81. doi: 10.1093/cercor/bhr301. Epub 2011 Nov 23.

45.

Recombination-mediated genetic engineering of large genomic DNA transgenes.

Ejsmont RK, Ahlfeld P, Pozniakovsky A, Stewart AF, Tomancak P, Sarov M.

Methods Mol Biol. 2011;772:445-58. doi: 10.1007/978-1-61779-228-1_26.

PMID:
22065454
46.

Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis.

Ejsmont RK, Bogdanzaliewa M, Lipinski KA, Tomancak P.

Methods Mol Biol. 2011;772:423-43. doi: 10.1007/978-1-61779-228-1_25.

PMID:
22065453
47.

Restoration of uneven illumination in light sheet microscopy images.

Uddin MS, Lee HK, Preibisch S, Tomancak P.

Microsc Microanal. 2011 Aug;17(4):607-13. doi: 10.1017/S1431927611000262. Epub 2011 Jun 20.

PMID:
21682937
48.

linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type.

Kalinka AT, Tomancak P.

Bioinformatics. 2011 Jul 15;27(14):2011-2. doi: 10.1093/bioinformatics/btr311. Epub 2011 May 19.

49.

Gene expression divergence recapitulates the developmental hourglass model.

Kalinka AT, Varga KM, Gerrard DT, Preibisch S, Corcoran DL, Jarrells J, Ohler U, Bergman CM, Tomancak P.

Nature. 2010 Dec 9;468(7325):811-4. doi: 10.1038/nature09634.

PMID:
21150996
50.

An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.

Cardona A, Saalfeld S, Preibisch S, Schmid B, Cheng A, Pulokas J, Tomancak P, Hartenstein V.

PLoS Biol. 2010 Oct 5;8(10). pii: e1000502. doi: 10.1371/journal.pbio.1000502.

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