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Author Title [ Type(Desc)] Year
Journal Article
R Johnson J, Chao T-Y, Lavis LD, Raines RT.  2007.  Cytotoxic ribonucleases: the dichotomy of Coulombic forces.. Biochemistry. 46(36):10308-16.
Patton W, Rhoades JL, Zouinkhi M, Ackerman DG, Malin-Mayor C, Adjavon D, Heinrich L, Bennett D, Zubov Y, Team CMProject et al..  2024.  DaCapo: a modular deep learning framework for scalable 3D image segmentation. arXiv.
Tjian R.  2007.  Daniel E. Koshland, Jr. 1920-2007.. Cell. 130:579-80.
Zeldin OB, Brewster AS, Hattne J, Uervirojnangkoorn M, Lyubimov AY, Zhou Q, Zhao M, Weis WI, Sauter NK, Brunger AT.  2015.  Data Exploration Toolkit for serial diffraction experiments.. Acta Crystallographica Section D: Biological Crystallography. 71(Pt 2):352-6.
Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D et al..  2016.  Data publication with the structural biology data grid supports live analysis.. Nature Communications. 7:10882.
Ackerman D, Avetissian E, Bleck CKE, Bogovic JA, Innerberger M, Korff W, Li W-P, Lu Z, Petruncio A, Preibisch S et al..  2024.  Data Release: High-Resolution Imaging and Segmentation of P7 Mouse Tissue Microarchitecture Using FIB-SEM and Machine Learning. bioRxiv.
Zhou J, Peng H, Suen CY.  2008.  Data-driven decomposition for multi-class classification.. Pattern Recognition. 41:67-76.
Hocine S, Singer RH.  2011.  A date with telomerase: pick you up at S phase.. Molecular Cell. 44(5):685-6.
Zocchi D, Nguyen M, Marquez-Legorreta E, Siwanowicz I, Singh C, Prober DA, Hillman EMC, Ahrens MB.  2025.  Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits.. Curr Biol. 35(1):163-176.e4.
Zocchi D, Nguyen M, Marquez-Legorreta E, Siwanowicz I, Singh C, Prober DA, Hillman EMC, Ahrens MB.  2024.  Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits.. Curr Biol.
Boyken SE, Benhaim MA, Busch F, Jia M, Back MJ, Choi H, Klima JC, Chen Z, Walkey C, Mileant A et al..  2019.  De novo design of tunable, pH-driven conformational changes.. Science. 364(6441):658-64.
Chen Y, Yserentant K, Hong K, Kuang Y, Bhowmick A, Charles-Orszag A, Lord SJ, Lu L, Hou K, Mann SI et al..  2025.  De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy. bioRxiv.
Willy NM, Ferguson JP, Akatay A, Huber S, Djakbarova U, Silahli S, Cakez C, Hasan F, Chang HC, Travesset A et al..  2021.  De novo endocytic clathrin coats develop curvature at early stages of their formation.. Development Cell. 56(22):3146-3159.e5.
Chen Z, Shiozaki M, Haas KM, Zhao S, Guo C, Polacco BJ, Yu Z, Krogan NJ, Kaake RM, Vale RD et al..  2023.  De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography. Cell. 186(23):5041-5053.e19.
Huang R, Xu Y, Wan W, Shou X, Qian J, You Z, Liu B, Chang C, Zhou T, Lippincott-Schwartz J et al..  2015.  Deacetylation of nuclear LC3 drives autophagy initiation under starvation.. Molecular cell. 57(3):456-66.
Avidor-Reiss T, Maer AM, Koundakjian E, Polyanovsky A, Keil T, Subramaniam S, Zuker CS.  2004.  Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis.. Cell. 117(4):527-39.
Henriques R, Leterrier C, Weigel A.  2023.  Decoding life's inner workings: advances in quantitative bioimaging.. Open Biology. 13(11):230329.
Allier C, Schneider MC, Innerberger M, Heinrich L, Bogovic JA, Saalfeld S.  2024.  Decomposing heterogeneous dynamical systems with graph neural networks. arXiv.
Shields BC, Kahuno E, Kim C, Apostolides PF, Brown J, Lindo S, Mensh BD, Dudman JT, Lavis LD, Tadross MR.  2017.  Deconstructing behavioral neuropharmacology with cellular specificity.. Science (New York, N.Y.). 356(6333)
Atasoy D, J Betley N, Su HH, Sternson SM.  2012.  Deconstruction of a neural circuit for hunger.. Nature. 488(7410):172-7.
Ellis EE, Adkins CT, Galovska NM, Lavis LD, R Johnson J.  2013.  Decoupled roles for the atypical, bifurcated binding pocket of the ybfF hydrolase.. Chembiochem : A European Journal of Chemical Biology. 14(9):1134-44.
Leonardo A, Konishi M.  1999.  Decrystallization of adult birdsong by perturbation of auditory feedback.. Nature. 399(6735):466-70.
Humberg T-H, Bruegger P, Afonso B, Zlatic M, Truman JW, Gershow M, Samuel A, Sprecher SG.  2018.  Dedicated photoreceptor pathways in Drosophila larvae mediate navigation by processing either spatial or temporal cues.. Nature Communications. 9(1):1260.
Branson K.  2018.  A deep (learning) dive into a cell.. Nature Methods. 15(4):253-4.
Speiser A, Müller L-R, Matti U, Obara CJ, Legant WR, Kreshuk A, Macke JH, Ries J, Turaga SC.  2021.  Deep learning enables fast and dense single-molecule localization with high accuracy. Nature Methods. 18(9)