Subfield · Biophysics
Most cited papers in Biophysics
What are the most cited papers in Biophysics?
The most cited paper in Biophysics is "U-Net: Convolutional Networks for Biomedical Image Segmentation" (Olaf Ronneberger, Philipp F. Fischer, Thomas Brox, 2015), with 92,751 citations. Next come "Fiji: an open-source platform for biological-image analysis" (73,171) and "NIH Image to ImageJ: 25 years of image analysis" (67,169).
Showing 50 of 100 papers. Every paper with more than 2,845 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | U-Net: Convolutional Networks for Biomedical Image Segmentation Olaf Ronneberger, Philipp F. Fischer, Thomas Brox · Lecture notes in computer science | 2015 | 92,751 |
| 2 | Fiji: an open-source platform for biological-image analysis Johannes Schindelin, Ignacio Arganda‐Carreras, Erwin Frise et al. · Nature Methods | 28 Jun 2012 | 73,171 |
| 3 | NIH Image to ImageJ: 25 years of image analysis Caroline A Schneider, Wayne S. Rasband, Kevin W. Eliceiri · Nature Methods | 28 Jun 2012 | 67,169 |
| 4 | Tissue sulfhydryl groups George L. Ellman · Archives of Biochemistry and Biophysics | May 1959 | 26,451 |
| 5 | phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data Paul J. McMurdie, Susan Holmes · PLoS ONE | 22 Apr 2013 | 23,323 |
| 6 | Comprehensive Integration of Single-Cell Data Tim Stuart, Andrew W. Butler, Paul Hoffman et al. · Cell | Jun 2019 | 17,471 |
| 7 | Visualizing and Understanding Convolutional Networks Matthew D. Zeiler, Rob Fergus · Lecture notes in computer science | 2014 | 15,691 |
| 8 | A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP) Takeshi Yanai, David P. Tew, Nicholas Charles Handy · Chemical Physics Letters | Jul 2004 | 15,226 |
| 9 | The Unreasonable Effectiveness of Deep Features as a Perceptual Metric Richard Zhang, Phillip Isola, Alexei A. Efros et al. | Jun 2018 | 13,833 |
| 10 | Fast, sensitive and accurate integration of single-cell data with Harmony Ilya Korsunsky, Nghia Millard, Jean Fan et al. · Nature Methods | 18 Nov 2019 | 11,339 |
| 11 | UCSF ChimeraX : Structure visualization for researchers, educators, and developers Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al. · Protein Science | 3 Sep 2020 | 10,674 |
| 12 | nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation Fabian Isensee, Paul F. Jaeger, Simon A. A. Kohl et al. · Nature Methods | 7 Dec 2020 | 9,588 |
| 13 | Two-Photon Laser Scanning Fluorescence Microscopy Winfried T. Denk, James H. Strickler, Watt W. Webb · Science | 6 Apr 1990 | 9,531 |
| 14 | User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability Paul A. Yushkevich, Joseph Piven, Heather C. Hazlett et al. · NeuroImage | 21 Mar 2006 | 9,244 |
| 15 | QuPath: Open source software for digital pathology image analysis Peter Bankhead, Maurice Bernard Loughrey, José A. Fernández et al. · Scientific Reports | 28 Nov 2017 | 9,140 |
| 16 | Imaging Intracellular Fluorescent Proteins at Nanometer Resolution Eric Betzig, George H. Patterson, Rachid Sougrat et al. · Science | 10 Aug 2006 | 9,061 |
| 17 | Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool Edward Y. Chen, Christopher M. Tan, Yan Kou et al. · BMC Bioinformatics | 15 Apr 2013 | 8,650 |
| 18 | Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) Michael J. Rust, Mark Bates, Xiaowei Zhuang · Nature Methods | 9 Aug 2006 | 8,412 |
| 19 | Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets Evan Z. Macosko, Anindita Basu, Rahul Satija et al. · Cell | May 2015 | 8,040 |
| 20 | Unified segmentation John Ashburner, Karl John Friston · NeuroImage | 2 Apr 2005 | 7,633 |
| 21 | SCENIC: single-cell regulatory network inference and clustering Sara Aibar, Carmen Bravo González‐Blas, Thomas Moerman et al. · Nature Methods | 9 Oct 2017 | 7,321 |
| 22 | Apparent hydroxyl radical production by peroxynitrite: implications for endothelial injury from nitric oxide and superoxide. Joseph S. Beckman, ThomasJ Beckman, Jake Y. Chen et al. · Proceedings of the National Academy of Sciences | Feb 1990 | 7,073 |
| 23 | The sva package for removing batch effects and other unwanted variation in high-throughput experiments Jeffrey T. Leek, William Evan Johnson, Hilary S. Parker et al. · Bioinformatics | 17 Jan 2012 | 6,930 |
| 24 | Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS) Katrin D. Kneipp, Yang Wang, Harald Kneipp et al. · Physical Review Letters | 3 Mar 1997 | 6,807 |
| 25 | EasySpin, a comprehensive software package for spectral simulation and analysis in EPR Stefan W. Stoll, Arthur Schweiger · Journal of Magnetic Resonance | 27 Sep 2005 | 6,580 |
| 26 | ImageJ2: ImageJ for the next generation of scientific image data Curtis Rueden, Johannes Schindelin, Mark Hiner et al. · BMC Bioinformatics | 29 Nov 2017 | 6,379 |
| 27 | THE GREEN FLUORESCENT PROTEIN Roger Y. Tsien · Annual Review of Biochemistry | Jun 1998 | 6,213 |
| 28 | Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy Stefan W. Hell, Jan Wichmann · Optics Letters | Jun 1994 | 6,210 |
| 29 | Computer Visualization of Three-Dimensional Image Data Using IMOD James R. Kremer, David N. Mastronarde, J. Richard McIntosh · Journal of Structural Biology | 1996 | 6,195 |
| 30 | Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain Brian Avants, Charles L. Epstein, Murray Grossman et al. · Medical Image Analysis | 26 Jun 2007 | 6,189 |
| 31 | Genome-wide atlas of gene expression in the adult mouse brain Ed S. Lein et al. · Nature | 6 Dec 2006 | 6,052 |
| 32 | UCSF ChimeraX: Meeting modern challenges in visualization and analysis Thomas D. Goddard, Conrad C. Huang, Elaine C. Meng et al. · Protein Science | 14 Jul 2017 | 6,046 |
| 33 | Dimensionality reduction for visualizing single-cell data using UMAP Étienne Becht, Leland McInnes, John Healy et al. · Nature Biotechnology | 3 Dec 2018 | 5,903 |
| 34 | Emergence of simple-cell receptive field properties by learning a sparse code for natural images Bruno A. Olshausen, David J. Field · Nature | Jun 1996 | 5,901 |
| 35 | Predictive coding in the visual cortex: a functional interpretation of some extra-classical receptive-field effects Rajesh P. N. Rao, Dana H. Ballard · Nature Neuroscience | 1999 | 5,887 |
| 36 | A guided tour into subcellular colocalization analysis in light microscopy Susanne Bolte, Fabrice P. Cordelières · Journal of Microscopy | Dec 2006 | 5,686 |
| 37 | Assessment of the Perdew–Burke–Ernzerhof exchange-correlation functional Matthias Ernzerhof, Gustavo E. Scuseria · The Journal of Chemical Physics | 15 Mar 1999 | 5,577 |
| 38 | CellProfiler: image analysis software for identifying and quantifying cell phenotypes Anne E. Carpenter, Thouis R. Jones, Michael R. Lamprecht et al. · Genome biology | 31 Oct 2006 | 5,571 |
| 39 | Cytoscape 2.8: new features for data integration and network visualization Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski et al. · Bioinformatics | 12 Dec 2010 | 5,078 |
| 40 | Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate Christopher R. Genovese, Nicole A. Lazar, Thomas E. Nichols · NeuroImage | Apr 2002 | 5,056 |
| 41 | Determining cell type abundance and expression from bulk tissues with digital cytometry Aaron M. Newman, Chloé Beate Steen, Chih Long Liu et al. · Nature Biotechnology | 6 May 2019 | 5,050 |
| 42 | Guidelines for limiting exposure to time-varying electric, magnetic, and electromagnetic fields (up to 300 GHz) Anders Ahlbom · Health Physics | 1998 | 4,948 |
| 43 | Rapid colorimetric assay for cell growth and survival François Denizot, Rita Lang · Journal of Immunological Methods | May 1986 | 4,918 |
| 44 | Raman microspectroscopy of soot and related carbonaceous materials: Spectral analysis and structural information A. Sadezky, Harald Muckenhuber, Hinrich Grothe et al. · Carbon | 24 Mar 2005 | 4,884 |
| 45 | xCell: digitally portraying the tissue cellular heterogeneity landscape Dvir Aran, Zicheng Hu, Atul Janardhan Butte · Genome biology | 15 Nov 2017 | 4,825 |
| 46 | Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein Nathan C. Shaner, Robert E. Campbell, Paul A. Steinbach et al. · Nature Biotechnology | 21 Nov 2004 | 4,783 |
| 47 | On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation Sebastian Bach, Alexander Binder, Grégoire Montavon et al. · PLoS ONE | 10 Jul 2015 | 4,700 |
| 48 | Cellpose: a generalist algorithm for cellular segmentation Carsen Stringer, Tim Wang, Michalis Michaelos et al. · Nature Methods | 14 Dec 2020 | 4,662 |
| 49 | Determination of Glucose in Blood Using Glucose Oxidase with an Alternative Oxygen Acceptor P. Trinder · Annals of Clinical Biochemistry International Journal of Laboratory Medicine | 1969 | 4,629 |
| 50 | Redox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple Freya Q. Schafer, Garry R. Buettner · Free Radical Biology and Medicine | Jun 2001 | 4,588 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.