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Page 1
CAVE: Connectome Annotation Versioning Engine.
Dorkenwald S, Schneider-Mizell CM, Brittain D, Halageri A, Jordan C, Kemnitz N, Castro MA, Silversmith W, Maitin-Shephard J, Troidl J, Pfister H, Gillet V, Xenes D, Bae JA, Bodor AL, Buchanan J, Bumbarger DJ, Elabbady L, Jia Z, Kapner D, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Reid RC, da Costa NM, Seung HS, Collman F. Dorkenwald S, et al. Among authors: bumbarger dj. bioRxiv [Preprint]. 2023 Jul 28:2023.07.26.550598. doi: 10.1101/2023.07.26.550598. bioRxiv. 2023. PMID: 37546753 Free PMC article. Preprint.
Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity.
Turner NL, Macrina T, Bae JA, Yang R, Wilson AM, Schneider-Mizell C, Lee K, Lu R, Wu J, Bodor AL, Bleckert AA, Brittain D, Froudarakis E, Dorkenwald S, Collman F, Kemnitz N, Ih D, Silversmith WM, Zung J, Zlateski A, Tartavull I, Yu SC, Popovych S, Mu S, Wong W, Jordan CS, Castro M, Buchanan J, Bumbarger DJ, Takeno M, Torres R, Mahalingam G, Elabbady L, Li Y, Cobos E, Zhou P, Suckow S, Becker L, Paninski L, Polleux F, Reimer J, Tolias AS, Reid RC, da Costa NM, Seung HS. Turner NL, et al. Among authors: bumbarger dj. Cell. 2022 Mar 17;185(6):1082-1100.e24. doi: 10.1016/j.cell.2022.01.023. Epub 2022 Feb 24. Cell. 2022. PMID: 35216674 Free PMC article.
Structure and function of axo-axonic inhibition.
Schneider-Mizell CM, Bodor AL, Collman F, Brittain D, Bleckert A, Dorkenwald S, Turner NL, Macrina T, Lee K, Lu R, Wu J, Zhuang J, Nandi A, Hu B, Buchanan J, Takeno MM, Torres R, Mahalingam G, Bumbarger DJ, Li Y, Chartrand T, Kemnitz N, Silversmith WM, Ih D, Zung J, Zlateski A, Tartavull I, Popovych S, Wong W, Castro M, Jordan CS, Froudarakis E, Becker L, Suckow S, Reimer J, Tolias AS, Anastassiou CA, Seung HS, Reid RC, Costa NMD. Schneider-Mizell CM, et al. Among authors: bumbarger dj. Elife. 2021 Dec 1;10:e73783. doi: 10.7554/eLife.73783. Elife. 2021. PMID: 34851292 Free PMC article.
Oligodendrocyte precursor cells ingest axons in the mouse neocortex.
Buchanan J, Elabbady L, Collman F, Jorstad NL, Bakken TE, Ott C, Glatzer J, Bleckert AA, Bodor AL, Brittain D, Bumbarger DJ, Mahalingam G, Seshamani S, Schneider-Mizell C, Takeno MM, Torres R, Yin W, Hodge RD, Castro M, Dorkenwald S, Ih D, Jordan CS, Kemnitz N, Lee K, Lu R, Macrina T, Mu S, Popovych S, Silversmith WM, Tartavull I, Turner NL, Wilson AM, Wong W, Wu J, Zlateski A, Zung J, Lippincott-Schwartz J, Lein ES, Seung HS, Bergles DE, Reid RC, da Costa NM. Buchanan J, et al. Among authors: bumbarger dj. Proc Natl Acad Sci U S A. 2022 Nov 29;119(48):e2202580119. doi: 10.1073/pnas.2202580119. Epub 2022 Nov 23. Proc Natl Acad Sci U S A. 2022. PMID: 36417438 Free PMC article.
Nematode model systems in evolution and development.
Sommer RJ, Bumbarger DJ. Sommer RJ, et al. Among authors: bumbarger dj. Wiley Interdiscip Rev Dev Biol. 2012 May-Jun;1(3):389-400. doi: 10.1002/wdev.33. Epub 2012 Jan 27. Wiley Interdiscip Rev Dev Biol. 2012. PMID: 23801489 Review.
NEURD offers automated proofreading and feature extraction for connectomics.
Celii B, Papadopoulos S, Ding Z, Fahey PG, Wang E, Papadopoulos C, Kunin A, Patel S, Bae JA, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Cobos E, Dorkenwald S, Elabbady L, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Schneider-Mizell CM, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yu SC, Yin W, Xenes D, Kitchell LM, Rivlin PK, Rose VA, Bishop CA, Wester B, Froudarakis E, Walker EY, Sinz FH, Seung HS, Collman F, da Costa NM, Reid RC, Pitkow X, Tolias AS, Reimer J. Celii B, et al. Among authors: bumbarger dj. bioRxiv [Preprint]. 2024 Sep 23:2023.03.14.532674. doi: 10.1101/2023.03.14.532674. bioRxiv. 2024. PMID: 36993282 Free PMC article. Preprint.
Functional connectomics reveals general wiring rule in mouse visual cortex.
Ding Z, Fahey PG, Papadopoulos S, Wang EY, Celii B, Papadopoulos C, Chang A, Kunin AB, Tran D, Fu J, Ding Z, Patel S, Ntanavara L, Froebe R, Ponder K, Muhammad T, Alexander Bae J, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Cobos E, Dorkenwald S, Elabbady L, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Schneider-Mizell CM, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Yatsenko D, Froudarakis E, Sinz F, Josić K, Rosenbaum R, Sebastian Seung H, Collman F, da Costa NM, Clay Reid R, Walker EY, Pitkow X, Reimer J, Tolias AS. Ding Z, et al. Among authors: bumbarger dj. bioRxiv [Preprint]. 2024 Oct 14:2023.03.13.531369. doi: 10.1101/2023.03.13.531369. bioRxiv. 2024. PMID: 36993398 Free PMC article. Preprint.
Binary and analog variation of synapses between cortical pyramidal neurons.
Dorkenwald S, Turner NL, Macrina T, Lee K, Lu R, Wu J, Bodor AL, Bleckert AA, Brittain D, Kemnitz N, Silversmith WM, Ih D, Zung J, Zlateski A, Tartavull I, Yu SC, Popovych S, Wong W, Castro M, Jordan CS, Wilson AM, Froudarakis E, Buchanan J, Takeno MM, Torres R, Mahalingam G, Collman F, Schneider-Mizell CM, Bumbarger DJ, Li Y, Becker L, Suckow S, Reimer J, Tolias AS, Macarico da Costa N, Reid RC, Seung HS. Dorkenwald S, et al. Among authors: bumbarger dj. Elife. 2022 Nov 16;11:e76120. doi: 10.7554/eLife.76120. Elife. 2022. PMID: 36382887 Free PMC article.
Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex.
Schneider-Mizell CM, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Elabbady L, Gamlin C, Kapner D, Kinn S, Mahalingam G, Seshamani S, Suckow S, Takeno M, Torres R, Yin W, Dorkenwald S, Bae JA, Castro MA, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J; MICrONS Consortium; Reimer J, Tolias AS, Seung HS, Reid RC, Collman F, Maçarico da Costa N. Schneider-Mizell CM, et al. Among authors: bumbarger dj. bioRxiv [Preprint]. 2024 Jan 6:2023.01.23.525290. doi: 10.1101/2023.01.23.525290. bioRxiv. 2024. PMID: 36747710 Free PMC article. Preprint.
A scalable and modular automated pipeline for stitching of large electron microscopy datasets.
Mahalingam G, Torres R, Kapner D, Trautman ET, Fliss T, Seshamani S, Perlman E, Young R, Kinn S, Buchanan J, Takeno MM, Yin W, Bumbarger DJ, Gwinn RP, Nyhus J, Lein E, Smith SJ, Reid RC, Khairy KA, Saalfeld S, Collman F, Macarico da Costa N. Mahalingam G, et al. Among authors: bumbarger dj. Elife. 2022 Jul 26;11:e76534. doi: 10.7554/eLife.76534. Elife. 2022. PMID: 35880860 Free PMC article.
26 results