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Author Title [ Type(Desc)] Year
Journal Article
Guenther EL, Ge P, Trinh H, Sawaya MR, Cascio D, Boyer DR, Gonen T, Z Zhou H, Eisenberg DS.  2018.  Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.. Nature Structural & Molecular Biology.
M de la Cruz J, Hattne J, Shi D, Seidler P, Rodriguez J, Reyes FE, Sawaya MR, Cascio D, Weiss SC, Kim SKyung et al..  2017.  Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.. Nature Methods. 14(4):399-402.
Muenster S, Jain A, Mietke A, Pavlopoulos A, Grill SW, Tomancak P.  2019.  Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects.. Nature.
Finkelstein A, Fontolan L, Economo MN, Li N, Romani S, Svoboda K.  2021.  Attractor dynamics gate cortical information flow during decision-making.. Nature Neuroscience. 24(6):843-50.
David AF, Roudot P, Legant WR, Betzig E, Danuser G, Gerlich DW.  2019.  Augmin accumulation on long-lived microtubules drives amplification and kinetochore-directed growth.. Journal of Cell Biology. 218(7):2150-68.
Bai X, Melesse M, Turpin CGSorensen, Sloan D, Chen C-Y, Wang W-C, Lee P-Y, Simmons JR, Nebenfuehr B, Mitchell D et al..  2020.  Aurora B functions at the apical surface after specialized cytokinesis during morphogenesis in C. elegans.. Development. 147(1):1-16.
Scheffer L.K, Karsh B, Vitaladevun S..  2013.  Automated alignment of imperfect EM images for neural reconstruction.. arXiv. :arXiv:1304.6034[q-bio.QM].
Yang Z, Ye C, Bogovic JA, Carass A, Jedynak BM, Ying SH, Prince JL.  2015.  Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease.. NeuroImage. 127:435-44.
L Stapel C, Lombardot B, Broaddus C, Kainmueller D, Jug F, Myers EW, Vastenhouw NL.  2016.  Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.. Development (Cambridge, England). 143(3):540-6.
Kreshuk A, Koethe U, Pax E, Bock DD, Hamprecht FA.  2014.  Automated detection of synapses in serial section transmission electron microscopy image stacks.. PloS one. 9:e87351.
Yu Y, Peng H.  2011.  Automated high speed stitching of large 3D microscopic images.. 2011 8TH IEEE International Symposium on Biomedical Imaging: From Nano to Macro. :238-41.
Dell AI, Bender JA, Branson K, Couzin ID, de Polavieja GG, Noldus LPJJ, Pérez-Escudero A, Perona P, Straw AD, Wikelski M et al..  2014.  Automated image-based tracking and its application in ecology.. Trends in Ecology and Evolution. 29(7):417-428.
Weissbrod A, Shapiro A, Vasserman G, Edry L, Dayan M, Yitzhaky A, Hertzberg L, Feinerman O, Kimchi T.  2013.  Automated long-term tracking and social behavioural phenotyping of animal colonies within a semi-natural environment.. Nature Communications. 4:2018.
Dankert H, Wang L, Hoopfer ED, Anderson DJ, Perona P.  2009.  Automated monitoring and analysis of social behavior in Drosophila.. Nature Methods. 6(4):297-303.
Ohayon S, Avni O, Taylor AL, Perona P, Egnor SERoian.  2013.  Automated multi-day tracking of marked mice for the analysis of social behaviour.. Journal of Neuroscience Methods. 219(1):10-19.
Li PH, Lindsey LF, Januszewski M, Zheng Z, Bates AShakeel, Taisz I, Tyka M, Nichols M, Li F, Perlman E et al..  2019.  Automated reconstruction of a serial-section EM drosophila brain with flood-filling networks and local realignment.. bioRxiv.
Zhao T, Xie J, Amat F, Clack N, Ahammad P, Peng H, Long F, Myers E.  2011.  Automated reconstruction of neuronal morphology based on local geometrical and global structural models.. Neuroinformatics. 9(2-3):247-61.
Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J.  2023.  Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.. Nature Biotechnology. 41(1):44-49.
Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J.  2022.  Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.. Nature Biotechnology.
Jaensch S, Decker M, Hyman AA, Myers EW.  2010.  Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos.. Bioinformatics. 26(12):i13-20.
Clack NG, O’Connor DH, Huber D, Petreanu L, Hires A, Peron S, Svoboda K, Myers EW.  2012.  Automated tracking of whiskers in videos of head fixed rodents.. PLoS Computational Biology. 8:e1002591.
Bharioke A, Chklovskii DB.  2015.  Automatic adaptation to fast input changes in a time-invariant neural circuit.. PLoS Computational Biology. 11(8):e1004315.
Ravbar P, Branson K, Simpson JH.  2019.  An automatic behavior recognition system classifies animal behaviors using movements and their temporal context.. Journal of Neuroscience Methods. 326:108352.
Duy NThe, Lamecker H, Kainmueller D, Zachow S.  2012.  Automatic detection and classification of teeth in CT data.. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention. 15(Pt 1):609-16.
Buhmann J, Sheridan A, Gerhard S, Krause R, Nguyen T, Heinrich L, Schlegel P, Lee W-CAllen, Wilson R, Saalfeld S et al..  2021.  Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset. Nature Methods. 18(7):771-4.