Browse by Research Team

Algorithms for Molecular Biology

"Hook"-calibration of GeneChip-microarrays: chip characteristics and expression measures.
Binder, H. and Krohn, K. and Preibisch, S.
Algorithms for Molecular Biology 3 : 11. 29 August 2008

"Hook"-calibration of GeneChip-microarrays: theory and algorithm.
Binder, H. and Preibisch, S.
Algorithms for Molecular Biology 3 : 12. 29 August 2008

BMC Biology

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F. and Neuschulz, A. and Junker, J.P. and Rajewsky, N. and Preibisch, S.
BMC Biology 20 (1): 277. 13 December 2022

Bioinformatics

FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.
Preusser, F. and Dos Santos, N. and Contzen, J. and Stachelscheid, H. and Costa, E.T. and Mergenthaler, P. and Preibisch, S.
Bioinformatics 37 (18): 3088-3090. 15 September 2021

An automated workflow for parallel processing of large multiview SPIM recordings.
Schmied, C. and Steinbach, P. and Pietzsch, T. and Preibisch, S. and Tomancak, P.
Bioinformatics 32 (7): 1112-1114. 1 April 2016

ImgLib2-generic image processing in Java.
Pietzsch, T. and Preibisch, S. and Tomancak, P. and Saalfeld, S.
Bioinformatics 28 (22): 3009-3011. 15 November 2012

Globally optimal stitching of tiled 3D microscopic image acquisitions.
Preibisch, S. and Saalfeld, S. and Tomancak, P.
Bioinformatics 25 (11): 1463-1465. 1 June 2009

Biomedical Optics Express

Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror.
Vladimirov, N. and Preusser, F. and Wisniewski, J. and Yaniv, Z. and Desai, R.A. and Woehler, A. and Preibisch, S.
Biomedical Optics Express 12 (4): 2186-2203. 1 April 2021

Biophysical Journal

Specific and nonspecific hybridization of oligonucleotide probes on microarrays.
Binder, H. and Preibisch, S.
Biophysical Journal 89 (1): 337-352. July 2005

Current Opinion in Systems Biology

Light-microscopy methods in C. elegans research.
Breimann, L. and Preusser, F. and Preibisch, S.
Current Opinion in Systems Biology 13 : 82-92. February 2019

Development

Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ.
Oteiza, P. and Koeppen, M. and Krieg, M. and Pulgar, E. and Farias, C. and Melo, C. and Preibisch, S. and Mueller, D. and Tada, M. and Hartel, S. and Heisenberg, C.P. and Concha, M.L.
Development 137 (20): 3459-3468. 15 October 2010

Epigenetics & Chromatin

DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis.
La Fortezza, M. and Grigolon, G. and Cosolo, A. and Pindyurin, A. and Breimann, L. and Blum, H. and van Steensel, B. and Classen, A.K.
Epigenetics & Chromatin 11 (1): 27. 5 June 2018

Genes & Development

Oscillations of MyoD and Hes1 proteins regulate the maintenance of activated muscle stem cells.
Lahmann, I. and Bröhl, D. and Zyrianova, T. and Isomura, A. and Czajkowski, M.T. and Kapoor, V. and Griger, J. and Ruffault, P.L. and Mademtzoglou, D. and Zammit, P.S. and Wunderlich, T. and Spuler, S. and Kühn, R. and Preibisch, S. and Wolf, J. and Kageyama, R. and Birchmeier, C.
Genes & Development 33 (9-10): 524-535. 1 May 2019

Journal Of Physics: Condensed Matter

GeneChip microarrays-signal intensities, RNA concentrations and probe sequences.
Binder, H. and Preibisch, S.
Journal Of Physics: Condensed Matter 18 (18): S537-S566. 10 May 2006

Journal of Cell Biology

Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking.
Smith, C.S. and Preibisch, S. and Joseph, A. and Abrahamsson, S. and Rieger, B. and Myers, E. and Singer, R.H. and Grunwald, D.
Journal of Cell Biology 209 (4): 609-619. 25 May 2015

Journal of Cell Science

The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L. and Morao, A.K. and Kim, J. and Jimenez, D.S. and Maryn, N. and Bikkasani, K. and Carrozza, M.J. and Albritton, S.E. and Kramer, M. and Street, L.A. and Cerimi, K. and Schumann, V.F. and Bahry, E. and Preibisch, S. and Woehler, A. and Ercan, S.
Journal of Cell Science 135 (2): jcs258818. January 2022

Journal of Visualized Experiments

Using light sheet fluorescence microscopy to image zebrafish eye development.
Icha, J. and Schmied, C. and Sidhaye, J. and Tomancak, P. and Preibisch, S. and Norden, C.
Journal of Visualized Experiments 2016 (110): e53966. 10 April 2016

Langmuir

Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays.
Binder, H. and Preibisch, S. and Kirsten, T.
Langmuir 21 (20): 9287-9302. 27 September 2005

Methods

Bioimage informatics in the context of drosophila research.
Jug, F. and Pietzsch, T. and Preibisch, S. and Tomancak, P.
Methods 68 (1): 60-73. 15 June 2014

Methods in Molecular Biology

Calibration of microarray gene-expression data.
Binder, H. and Preibisch, S. and Berger, H.
Methods in Molecular Biology 576 : 375-407. 2010

Microscopy and Microanalysis

Restoration of uneven illumination in light sheet microscopy images.
Uddin, M.S. and Lee, H.K. and Preibisch, S. and Tomancak, P.
Microscopy and Microanalysis 17 (4): 607-613. August 2011

Molecular Cell

Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
Carrillo Oesterreich, F. and Preibisch, S. and Neugebauer, K.M.
Molecular Cell 40 (4): 571-581. 24 November 2010

Molecular Systems Biology

Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency.
Friedrich, D. and Friedel, L. and Finzel, A. and Herrmann, A. and Preibisch, S. and Loewer, A.
Molecular Systems Biology 15 (12): e9068. 1 December 2019

Nature

Gene expression divergence recapitulates the developmental hourglass model.
Kalinka, A.T. and Varga, K.M. and Gerrard, D.T. and Preibisch, S. and Corcoran, D.L. and Jarrells, J. and Ohler, U. and Bergman, C.M. and Tomancak, P.
Nature 468 (7325): 811-814. 9 December 2010

Nature Methods

Best practice standards for circular RNA research.
Nielsen, A.F. and Bindereif, A. and Bozzoni, I. and Hanan, M. and Hansen, T.B. and Irimia, M. and Kadener, S. and Kristensen, L.S. and Legnini, I. and Morlando, M. and Jarlstad Olesen, M.T. and Pasterkamp, R.J. and Preibisch, S. and Rajewsky, N. and Suenkel, C. and Kjems, J.
Nature Methods 19 (10): 1208-1220. October 2022

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.
Hörl, D. and Rojas Rusak, F. and Preusser, F. and Tillberg, P. and Randel, N. and Chhetri, R.K. and Cardona, A. and Keller, P.J. and Harz, H. and Leonhardt, H. and Treier, M. and Preibisch, S.
Nature Methods 16 (9): 870-874. September 2019

The author file: Stephan Preibisch.
Marx, V.
Nature Methods 16 (9): 793. September 2019

Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.
Vladimirov, N. and Wang, C. and Höckendorf, B. and Pujala, A. and Tanimoto, M. and Mu, Y. and Yang, C.T. and Wittenbach, J.D. and Freeman, J. and Preibisch, S. and Koyama, M. and Keller, P.J. and Ahrens, M.B.
Nature Methods 15 (12): 1117-1125. December 2018

BigDataViewer: visualization and processing for large image data sets.
Pietzsch, T. and Saalfeld, S. and Preibisch, S. and Tomancak, P.
Nature Methods 12 (6): 481-483. 28 May 2015

Efficient Bayesian-based multiview deconvolution.
Preibisch, S. and Amat, F. and Stamataki, E. and Sarov, M. and Singer, R.H. and Myers, E. and Tomancak, P.
Nature Methods 11 (6): 645-648. June 2014

OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone, P.G. and Schindelin, J. and Stuyvenberg, L. and Preibisch, S. and Weber, M. and Eliceiri, K.W. and Huisken, J. and Tomancak, P.
Nature Methods 10 (7): 598-599. July 2013

Fiji: an open-source platform for biological-image analysis.
Schindelin, J. and Arganda-Carreras, I. and Frise, E. and Kaynig, V. and Longair, M. and Pietzsch, T. and Preibisch, S. and Rueden, C. and Saalfeld, S. and Schmid, B. and Tinevez, J.Y. and White, D.J. and Hartenstein, V. and Eliceiri, K. and Tomancak, P. and Cardona, A.
Nature Methods 9 (7): 676-682. July 2012

Software for bead-based registration of selective plane illumination microscopy data.
Preibisch, S. and Saalfeld, S. and Schindelin, J. and Tomancak, P.
Nature Methods 7 (6): 418-419. June 2010

Nature Reviews Methods Primers

Light sheet fluorescence microscopy.
Stelzer, E.H.K. and Strobl, F. and Chang, B.J. and Preusser, F. and Preibisch, S. and McDole, K. and Fiolka, R.
Nature Reviews Methods Primers 1 (1): 73. 3 November 2021

PLoS Biology

An integrated micro- and macroarchitectural analysis of the drosophila brain by computer-assisted serial section electron microscopy.
Cardona, A. and Saalfeld, S. and Preibisch, S. and Schmid, B. and Cheng, A. and Pulokas, J. and Tomancak, P. and Hartenstein, V.
PLoS Biology 8 (10): e1000502. 5 October 2010

PLoS ONE

TrakEM2 software for neural circuit reconstruction.
Cardona, A. and Saalfeld, S. and Schindelin, J. and Arganda-Carreras, I. and Preibisch, S. and Longair, M. and Tomancak, P. and Hartenstein, V. and Douglas, R.J.
PLoS ONE 7 (6): e38011. 19 June 2012

Physical Review A

Autoionization in time-dependent density-functional theory.
Kapoor, V.
Physical Review A 93 (6): 063408. 8 June 2016

Proceedings of the National Academy of Sciences of the United States of America

Resolving titin's lifecycle and the spatial organization of protein turnover in mouse cardiomyocytes.
Rudolph, F. and Hüttemeister, J. and da Silva Lopes, K. and Jüttner, R. and Yu, L. and Bergmann, N. and Friedrich, D. and Preibisch, S. and Wagner, E. and Lehnart, S.E. and Gregorio, C.C. and Gotthardt, M.
Proceedings of the National Academy of Sciences of the United States of America 116 (50): 25126-25136. 10 December 2019

Science Advances

Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer.
Le Poul, Y. and Xin, Y. and Ling, L. and Mühling, B. and Jaenichen, R. and Hörl, D. and Bunk, D. and Harz, H. and Leonhardt, H. and Wang, Y. and Osipova, E. and Museridze, M. and Dharmadhikari, D. and Murphy, E. and Rohs, R. and Preibisch, S. and Prud'homme, B. and Gompel, N.
Science Advances 6 (49): eabe2955. 2 December 2020

Scientific Reports

MTrack: automated detection, tracking, and analysis of dynamic microtubules.
Kapoor, V. and Hirst, W.G. and Hentschel, C. and Preibisch, S. and Reber, S.
Scientific Reports 9 (1): 3794. 7 March 2019

Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells.
Mönke, G. and Cristiano, E. and Finzel, A. and Friedrich, D. and Herzel, H. and Falcke, M. and Loewer, A.
Scientific Reports 7 : 46571. 18 April 2017

arXiv

An automated workflow for parallel processing of large multiview SPIM recordings.
Schmied, C. and Steinbach, P. and Pietzsch, T. and Preibisch, S. and Tomancak, P.
arXiv : 1507.08575v3. 11 August 2015

bioRxiv

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F. and Neuschulz, A. and Junker, J.P. and Rajewsky, N. and Preibisch, S.
bioRxiv : 2022.04.25.489360v1. 26 April 2022

RS-FISH: Precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Long, X. and Harrington, K.I.S. and Lionnet, T. and Preibisch, S.
bioRxiv : 2021.03.09.434205v2. 18 October 2021

The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L. and Morao, A.K. and Kim, J. and Jimenez, D. and Maryn, N. and Bikkasani, K. and Carrozza, M.J. and Albritton, S.E. and Kramer, M. and Street, L.A. and Cerimi, K. and Schumann, V.F. and Bahry, E. and Preibisch, S. and Woehler, A. and Ercan, S.
bioRxiv : 2021.04.11.438056. 24 September 2021

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C. and Hirsch, P. and Guignard, L. and McDole, K. and Wan, Y. and Lemon, W.C. and Keller, P.J. and Preibisch, S. and Funke, J.
bioRxiv : 2021.07.28.454016. 29 July 2021

Dual-view light-sheet imaging through tilted glass interface using a deformable mirror.
Vladimirov, N. and Preusser, F. and Wisniewski, J. and Yaniv, Z. and Desai, R.A. and Woehler, A. and Preibisch, S.
bioRxiv : 2020.10.20.345306. 21 October 2020

FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.
Preusser, F. and dos Santos, N. and Contzen, J. and Stachelscheid, H. and Costa, E.T. and Mergenthaler, P. and Preibisch, S.
bioRxiv : 2020.09.10.291286. 11 September 2020

Deciphering the regulatory logic of a Drosophila enhancer through systematic sequence mutagenesis and quantitative image analysis.
Le Poul, Y. and Xin, Y. and Ling, L. and Mühling, B. and Jaenichen, R. and Hörl, D. and Bunk, D. and Harz, H. and Leonhardt, H. and Wang, Y. and Osipova, E. and Museridze, M. and Dharmadhikari, D. and Murphy, E. and Rohs, R. and Preibisch, S. and Prud'homme, B. and Gompel, N.
bioRxiv : 2020.06.24.169748. 25 June 2020

Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency.
Friedrich, D. and Friedel, L. and Herrmann, A. and Preibisch, S. and Loewer, A.
bioRxiv : 679449. 21 June 2019

MTrack: automated detection, tracking, and analysis of dynamic microtubules.
Kapoor, V. and Hirst, W.G. and Hentschel, C. and Preibisch, S. and Reber, S.
bioRxiv : 368191. 13 July 2018

BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples.
Hörl, D. and Rojas Rusak, F. and Preusser, F. and Tillberg, P. and Randel, N. and Chhetri, R.K. and Cardona, A. and Keller, P.J. and Harz, H. and Leonhardt, H. and Treier, M. and Preibisch, S.
bioRxiv : 343954. 10 June 2018

Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking.
Wolff, C. and Tinevez, J.Y. and Pietzsch, T. and Stamataki, E. and Harich, B. and Preibisch, S. and Shorte, S. and Keller, P.J. and Tomancak, P. and Pavlopoulos, A.
bioRxiv : 112623. 28 February 2017

eLife

Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.
Wolff, C. and Tinevez, J.Y. and Pietzsch, T. and Stamataki, E. and Harich, B. and Guignard, L. and Preibisch, S. and Shorte, S. and Keller, P.J. and Tomancak, P. and Pavlopoulos, A.
eLife 7 : e34410. 29 March 2018