Publications

My publications are also listed on Google Scholar. Some of my recent papers are listed on my NCBI bibliography. Bold=Cohen lab member, *=corresponding author

  • L. Aho, M. Winter, M. DeCarlo, A. Frismantiene, Y. Blum, P. A. Gagliardi, O. Pertz, and A. R. Cohen*, The cell signaling structure function, in review and arXiv, 2024.

  • A.R. Cohen and P.M.B. Vitányi, The cluster structure function, IEEE Transactions on Pattern Analysis & Machine Intelligence, PMID: 37018105, 2023.
  • Maška, M., incl. L. Aho and A. R. Cohen , et al. The Cell Tracking Challenge: 10 years of objective benchmarking. Nat Methods 20, 1010–1020 (2023). https://doi.org/10.1038/s41592-023-01879-y
  • P. A. Gagliardi, incl. A. R. Cohen, et al., Automatic detection of spatio-temporal signaling patterns in cell collectives. J Cell Biol, 2023; 222 (10): e202207048. doi: https://doi.org/10.1083/jcb.202207048

  • P. Ender, P. A. Gagliardi, M. Dobrzynski, C. Dessauges, T. Höhener, M.A. Jacques, A. R. Cohen, O. Pertz, Spatio-temporal Control of ERK Pulse Frequency Coordinates Fate Decisions during Mammary Acinar Morphogenesis, Developmental Cell. 2022 Sep 26;57(18):2153-2167.e6. https://doi.org/10.1016/j.devcel.2022.08.008.
  • Mark Winter and Andrew R. Cohen*, LEVERSC: Cross-Platform Scriptable Multichannel 3-D Visualization for Fluorescence Microscopy Images. Frontiers in Bioinformatics, vol. 2, 2022-March-17.https://doi.org/10.3389/fbinf.2022.740078

  • A. Villasante, S. T. Robinson, A. R Cohen, R. Lock, X. E. Guo, G. Vunjak-Novakovic, Human serum enhances biomimicry of engineered tissue models of bone and cancer, Frontiers Bioengineering and Biotechnology, 13 July 2021 | https://doi.org/10.3389/fbioe.2021.658472.
  • P. A. Gagliardi, M. Dobrzyski, M.A. Jacques, C. Dessauges, P. Ender, Y. Blum, R. M. Hughes, A. R Cohen, O. Pertz, Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival, Developmental Cell, Vol 56(12),  https://doi.org/10.1016/j.devcel.2021.05.007, JUNE 21, 2021
  • X. Zhao, Y. Wang, E. Wait, W. Mankowski, Christopher S. Bjornsson, A. R. Cohen, K. L. Zuloaga, S. Temple, 3D image analysis of the Complete Ventricular-Subventricular Zone Stem Cell Niche reveals Significant Vasculature changes and Progenitor Deficits in Males versus Females with Aging, Stem Cell Reports, 2021 Apr 13;16(4):836-850, https://doi.org/10.1016/j.stemcr.2021.03.012.
  • M. R. Winter, M. Morgulis, T. Gildor, A. R. Cohen and S. Ben-Tabou de-Leon, Calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization,  PLOS Computational Biology 17(2): e1008780. https://doi.org/10.1371/journal.pcbi.1008780. Also, bioarxiv, 2021.

  • A.R. Cohen* and P.M.B. Vitányi, Web Similarity in Sets of Search Terms Using Database Queries, SN Computer Science, 1, 161 (2020). https://doi.org/10.1007/s42979-020-00148-5.  Also arXiv 1502.05957 (pdf).
  • PL Graney, S Ben-Shaul, S Landau, A Bajpai, B Singh, J Eager, A. R. Cohen, S Levenberg, KL Spiller, Macrophages of diverse phenotypes drive vascularization of engineered tissues, Science Advances, 6 (18), 2020.

  • E. Wait, M. Winter and A. R. Cohen, Hydra image processor: 5-D GPU image analysis library with MATLAB and Python wrappers,  Bioinformatics, 2019. (link).
  • M. Winter, W. Mankowski, E. Wait, E. C. De La Hoz, A. Aguinaldo and A. R. Cohen, Separating Touching Cells using Pixel Replicated Elliptical Shape Models, IEEE Transactions on Medical Imaging, 38:4, pp 883-893, October 2018. (pdf)
  • K. E. Pourfarhangi1, E. C. De La Hoz, A. R. Cohen and B. Gligorijevic, Contact guidance is cell cycle-dependent, APL Bioengineering 2, 031904, 2018; https://doi.org/10.1063/1.5026419.
  • Seo, J. Ho, Agarwal, Ekta, Bryant, K. G, Caino, M. Cecilia, Kim, E. Tae, Kossenkov, A. V., Tang, Hsin-Yao, Languino, L. R., Gabrilovich, D. I, Cohen, A. R., Speicher, D. W., Altieri, and D. C., Syntaphilin Ubiquitination Regulates Mitochondrial Dynamics And Tumor Cell Movements, Cancer Research, 2018. DOI: 10.1158/0008-5472.CAN-18-0595.
  • Apostolopoulou, M., Kiehl, T. R., Winter, M., De La Hoz, E., Boles, N. C., Bjornsson, C. S., Zuloaga, K. L., Goderie, S. K., Wang, Yue, Cohen, A. R., Temple, S., Non-monotonic Changes in Progenitor Cell Behavior and Gene Expression during Aging of the Adult V-SVZ Neural Stem Cell Nich, Stem Cell Reports, vol. 9, no. 6, pp. 1931-1947, 12/ 2017. doi: 10.1016/j.stemcr.2017.10.005
  • A. M. Valm, S. Cohen, W. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, J. Lippincott-Schwartz, Applying systems-level spectral imaging and analysis to reveal the organelle interactome, Nature, Letter. advance online publication, 05/24/2017. doi:10.1038/nature22369
  • M. Caino, J. Seo, A.  Aguinaldo, E. Wait, K. Bryant, A. Kossenkov, J. Hayden, V. Vaira, A. Morotti, S. Ferrero, S. Bosari, D. Gabrilovich, L. Languino, A. R. Cohen, and D. Altieri. A Neuronal Network of Mitochondrial Dynamics Regulates Metastasis. Nature Communications, 2016. doi:10.1038/ncomms13730.
  • E. Cardenas De La Hoz, M. R. Winter, M. Apostolopoulou, S. Temple, A. R. Cohen*, Measuring Process Dynamics and Nuclear Migration for Clones of Neural Progenitor Cells,  ECCV 2016 Workshops, Volume 9913, Springer Lecture Notes in Computer Science pp 291-305 (pdf).  PMC: pending.
  • M. Winter, W. Mankowski, E. Wait, S. Temple and A. R. Cohen*, LEVER: software tools for segmentation, tracking and lineaging of proliferating cells, Bioinformatics. 2016, (pdf) doi:10.1093/bioinformatics/btw406.
  • R. Joshi, W. Mankowski, M. Winter, J. S. Saini, T. A. Blenkinsop, J. H. Stern, S. Temple* and A. R. Cohen*, Automated measurement of cobblestone morphology for characterizing stem cell-derived retinal pigment epithelial cell cultures, Journal of Ocular Pharmacology and Therapeutics, Special Issue: Cell-based Therapies for Eye Disease. 2016 Jun;32(5):331-9. doi:10.1089/jop.2015.0163. (pdf), pubmed ID 27191513.
    + GitLab source code repository for this paper:
    https://git-bioimage.coe.drexel.edu/opensource/rpe
  • A. Newhart, S. L. Powers, P. K. Shastrula, I. Sierra, L. M. Joo, J. E. Hayden, A. R. Cohen, and Susan M. Janicki, RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition, Molecular Biology of the Cell, 2016 27:7 pp. 1154-1169; doi:10.1091/mbc.E15-02-0099,  pubmed ID 26842893.
  • A. Jolly, CH Luan, B. Dusel, S. Dunne, M. Winding, V. Dixit, C. Robins, J. Saluk, D. Logan, A. Carpenter, M. Sharma, D. Dean, A.R. Cohen* and V.I. Gelfand*, A genome-wide RNAi screen for microtubule 1 bundle formation and lysosome motility regulation in Drosophila S2 cells, Cell Reports. 2016 14(3) pp. 611-620; doi:10.1016/j.celrep.2015.12.051, pubmed ID 26774481.
  • M. Winter, M. Liu, D. Monteleone, J. Melunis, U. Hershberg, S. K. Goderie, S. Temple*, and A. R. Cohen*, Computational Image Analysis Reveals Intrinsic Multigenerational Differences Between Anterior and Posterior Cerebral Cortex Neural Progenitor Cells, Stem Cell Reports, vol. 5, pp. 609-620, 10/13/2015, http://dx.doi.org/10.1016/j.stemcr.2015.08.002, pubmed ID 26344906 .
    + CloneView open data repository for this paper: http://n2t.net/ark:/87918/d91591
    + GitLab source code repository for this paper: https://git-bioimage.coe.drexel.edu/opensource/lever/tree/master
  • A.R.Cohen and P.M.B. Vitanyi, Normalized Compression Distance of Multisets with Applications, IEEE Transactions on Pattern Analysis and Machine Intelligence. 2015 Aug;37(8):1602-14, http://dx.doi.org/10.1109/TPAMI.2014.2375175, (pdf), pubmed ID 26352998.
  • A. R. Cohen, Extracting meaning from biological imaging data, Molecular Biology of the Cell, 2014; 25(22):3470-3, (pdf), pubmed ID 25368423.
  • E. Wait, M. Winter, C. Bjornsson, E. Kokovay, Y. Wang, S. Goderie, S. Temple and A. R. Cohen*, Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences. BMC Bioinformatics, 15:328. doi:10.1186/1471-2105-15-328. October 3, 2014, pubmed:25281197.
  • N. Chenouard, I. Smal, F. de Chaumont, M. Maska, I. F. Sbalzarini, Y. Gong,J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. Godinez, K. Rohr,Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. Magnusson, J. Jaldon, H. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Tinevez, S. Shorte, J. Willemse, K. Celler, G. van Wezel, H. Dan, Y. Tsai, C. Ortiz de Solarzano, J.C. Olivo-Marin, E. Meijering, Objective Comparison of Particle Tracking Methods. Nature Methods. 2014 Mar;11(3):281-9. doi: 10.1038/nmeth.2808. Epub 2014 Jan 19 (PMC)
  • Winter, M., C. Fang, G. Banker, B. Roysam, and A. R. Cohen*, Axonal Transport Analysis Using Multitemporal Association Tracking. International Journal of Computational Biology and Drug Design 2012;5(1):35-48. (PMC)
  • Winter, M., E. Wait, B. Roysam, S. Goderie, E. Kokovay, S. Temple*, and A.R. Cohen*, Vertebrate Neural Stem Cell Segmentation, Tracking and Lineaging with Validation and Editing. Nature Protocols, 2011. 6(12): p. 1942-52. (PMC)
  • Clark, B., M. Winter, A.R. Cohen*, and B. Link*, Generation of Rab-based transgenic lines for in vivo studies of endosome biology in zebrafish. Developmental Dynamics, 2011. 240(11): p. 2452-65. (PMC)
  • A.R. Cohen, F. Gomes, B. Roysam, and M. Cayouette, Computational prediction of neural progenitor cell fates. Nature Methods, 2010. 7(3): p. 213 – 218. [Selected for a News and Views in Nature Methods, March 2010. Evaluated for Faculty of 1000: Biology, Feb 17, 2010 by William Harris, University of Cambridge, UK. Ranked as a “must read”. Images from this work were featured as cover art on a Nature Journal special supplement on live cell imaging (cover art and interview)  (8/26/2010)]
  • A.R. Cohen, C. Bjornsson, S. Temple, G. Banker and B. Roysam, Automatic Summarization of Changes in Biological Image Sequences using Algorithmic Information Theory. Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2009. 31(8): pp. 1386-1403.
  • W. He, T. A. Hamilton, A. R. Cohen, T. J. Holmes, J. N. Turner, and B. Roysam, Automated Three-Dimensional Tracing of HRP Stained Neurons From A Stack Of Brightfield Optical Slices, Microscopy and Microanalysis, vol. 9, 296-310, 2003.
  • A. R. Cohen, B. Roysam, and J. N. Turner, Automated Tracing and Volume Measurements of Neurons from 3-D Confocal Fluorescence Microscopy Data, Journal of Microscopy, Vol. 173, Pt. 2, February 1994.
  • B. Roysam, A. R. Cohen, P. H. Getto, and P. R. Boyce, A Numerical Approach to the Computation of Light Propagation through Turbid Media: Application to the Evaluation of Lighted Exit Signs, IEEE Transactions on Industry Applications, Vol. 29, No. 3, pp. 661-669, May /June 1993 (invited paper). Frontiers in Bioengineering and Biotechnology

Select Peer Reviewed Publications *=corresponding author, bold=Cohen lab member

Other publications

  • Wait, E., M. Winter, S. Song, D. Monteleone, C. Bjornsson, S. Goderie, S. Temple and A. R. Cohen* (2015). Collaborative Visualization in the Browser for Segmentation, Tracking, and Lineaging with 5-D Biological Microscopy Images. BioImage Informatics Conference, Gaithersburg, MD, 2015.
  • R. Joshi, S. R. Swaminathan, M. Winter, J. S. Saini, T. A. Blenkinsop, J. Stern, S. Temple and A. R. Cohen*, Measuring visual structure in phase and fluorescence microscopy using image compression. BioImage Informatics Conference, Gaithersburg, MD, 2015.
  • W. C. Mankowski, G. Konica, M. R. Winter, F. Chen, C. Maus, R. Merkle, U. Klingmuller, T. Hofer, A. Kan, S. Heinzel, S. Oostindie, P. Hodgkin, and A. R. Cohen*,Multi-Modal Segmentation for Quantifying Fluorescent Cell Cycle Indicators Throughout Clonal Development . BioImage Informatics Conference, Gaithersburg, MD, 2015.
  • W. C. Mankowski, M. R. Winter, E. Wait, M. Lodder, T. Schumacher, S. H. Naik and A. R. Cohen*, Segmentation of occluded hematopoietic stem cells from tracking. Conf Proc IEEE Eng Med Biol Soc 2014: 5510-5513 (pdf) (PMC).
  • Koerner, M., E. Wait, M. Winter, C. Bjornsson, E. Kokovay, Y. Wang, S. K. Goderie, S. Temple and A. R. Cohen*, Multisensory interface for 5D stem cell image volumes. Conf Proc IEEE Eng Med Biol Soc 2014: 1178-1181 (pdf) (PMC).
  • E. Wait, M. Winter, C. Bjornsson, E. Kokovay, Y. Wang, S. Goderie, S. Temple and A. R. Cohen*, Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences. 4th Symposium on Biological Data Visualization, 11-12 July, Boston, MA., 2014 (pdf).
  • Winter, M., C. Fang, G. Banker, B. Roysam, and A. R. Cohen*, Axonal Transport Analysis Using Multitemporal Association Tracking, in Microscopic Image Analysis with Applications in Biology. 2011: Chicago IL.
  • A. R. Cohen, C. Bjornsson, Y. Chen, G. Banker, E. Ladi, E. Robey, S. Temple, and B. Roysam, Automatic Summarization of Changes in Image Sequences using Algorithmic Information Theory, IEEE International Symposium on Biomedical Imaging, May 2008: Paris, France (invited paper).
  • B. Roysam, A. R. Cohen, P. H. Getto, and P. R. Boyce, Computational Visualization of Lighted Exit Signs Through Complex Smoke Media, 26th IEEE Conference on Industry Applications, October 1991 (Prize Paper Award).