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Page 1
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics.
Martin N, Olsen P, Quon J, Campos J, Cuevas NV, Nagra J, VanNess M, Maltzer Z, Gelfand EC, Oyama A, Gary A, Wang Y, Alaya A, Ruiz A, Reynoldson C, Bielstein C, Pom CA, Huang C, Slaughterbeck C, Liang E, Alexander J, Ariza J, Malone J, Melchor J, Colbert K, Brouner K, Shulga L, Reding M, Latimer P, Sanchez R, Barta S, Egdorf T, Madigan Z, Pagan CM, Close JL, Long B, Kunst M, Lein ES, Zeng H, McMillen D, Waters J. Martin N, et al. Among authors: lein es. bioRxiv [Preprint]. 2024 Dec 7:2024.12.04.626766. doi: 10.1101/2024.12.04.626766. bioRxiv. 2024. PMID: 39677693 Free PMC article. Preprint.
The commitment of the human cell atlas to humanity.
Amit I, Ardlie K, Arzuaga F, Awandare G, Bader G, Bernier A, Carninci P, Donnelly S, Eils R, Forrest ARR, Greely HT, Guigo R, Hacohen N, Haniffa M, Kirby ES, Knoppers BM, Kriegstein A, Lein ES, Linnarsson S, Majumder PP, Merad M, Meyer K, Mhlanga MM, Nolan G, Ntusi NAB, Pe'er D, Prabhakar S, Raven-Adams M, Regev A, Rozenblatt-Rosen O, Saha S, Saltzman A, Shalek AK, Shin JW, Stunnenberg H, Teichmann SA, Tickle T, Villani AC, Wells C, Wold B, Yang H, Zhuang X. Amit I, et al. Among authors: lein es. Nat Commun. 2024 Nov 20;15(1):10019. doi: 10.1038/s41467-024-54306-x. Nat Commun. 2024. PMID: 39567491 Free PMC article. Review.
Distinctive physiology of molecularly identified medium spiny neurons in the macaque putamen.
Ting JT, Johansen NJ, Kalmbach BE, Taskin N, Lee B, Clark JK, Kendrick R, Ng L, Radaelli C, Weed N, Enstrom R, Ransford S, Redford I, Walling-Bell S, Dalley R, Tieu M, Goldy J, Jorstad N, Smith K, Bakken T, Lein ES, Owen SF. Ting JT, et al. Among authors: lein es. Cell Rep. 2024 Nov 26;43(11):114963. doi: 10.1016/j.celrep.2024.114963. Epub 2024 Nov 7. Cell Rep. 2024. PMID: 39514389 Free article.
Integrated multimodal cell atlas of Alzheimer's disease.
Gabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, Ding Y, Mahoney JT, Dee N, Goldy J, Melief EJ, Agrawal A, Kana O, Zhen X, Barlow ST, Brouner K, Campos J, Campos J, Carr AJ, Casper T, Chakrabarty R, Clark M, Cool J, Dalley R, Darvas M, Ding SL, Dolbeare T, Egdorf T, Esposito L, Ferrer R, Fleckenstein LE, Gala R, Gary A, Gelfand E, Gloe J, Guilford N, Guzman J, Hirschstein D, Ho W, Hupp M, Jarsky T, Johansen N, Kalmbach BE, Keene LM, Khawand S, Kilgore MD, Kirkland A, Kunst M, Lee BR, Leytze M, Mac Donald CL, Malone J, Maltzer Z, Martin N, McCue R, McMillen D, Mena G, Meyerdierks E, Meyers KP, Mollenkopf T, Montine M, Nolan AL, Nyhus JK, Olsen PA, Pacleb M, Pagan CM, Peña N, Pham T, Pom CA, Postupna N, Rimorin C, Ruiz A, Saldi GA, Schantz AM, Shapovalova NV, Sorensen SA, Staats B, Sullivan M, Sunkin SM, Thompson C, Tieu M, Ting JT, Torkelson A, Tran T, Valera Cuevas NJ, Walling-Bell S, Wang MQ, Waters J, Wilson AM, Xiao M, Haynor D, Gatto NM, Jayadev S, Mufti S, Ng L, Mukherjee S, Crane PK, Latimer CS, Levi BP, Smith KA, Close JL, Miller JA, Hodge RD, Larson EB, Grabowski TJ, Hawrylycz M, Keene CD, Lein ES. Gabitto MI, et al. Among authors: lein es. Nat Neurosci. 2024 Dec;27(12):2366-2383. doi: 10.1038/s41593-024-01774-5. Epub 2024 Oct 14. Nat Neurosci. 2024. PMID: 39402379 Free PMC article.
SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease.
Hawrylycz M, Kaplan ES, Travaglini KJ, Gabitto MI, Miller JA, Ng L, Close JL, Hodge RD, Long B, Mollenkopf T, Mufti S, Gatto NM, Larson EB, Crane PK, Grabowski TJ, Keene CD, Lein ES. Hawrylycz M, et al. Among authors: lein es. Nat Aging. 2024 Oct;4(10):1331-1334. doi: 10.1038/s43587-024-00719-8. Nat Aging. 2024. PMID: 39402332
Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits.
Hunker AC, Wirthlin ME, Gill G, Johansen NJ, Hooper M, Omstead V, Taskin N, Weed N, Vargas S, Bendrick JL, Gore B, Ben-Simon Y, Bishaw Y, Opitz-Araya X, Martinez RA, Way S, Thyagarajan B, Lerma MN, Laird W, Sven O, Sanchez REA, Alexander JR, Amaya A, Amster A, Ayala A, Baker PM, Barcelli T, Barta S, Bertagnolli D, Bielstein C, Bishwakarma P, Bowlus J, Boyer G, Brouner K, Casian B, Casper T, Chakka AB, Chakrabarty R, Clark M, Colbert K, Daniel S, Dawe T, Departee M, DiValentin P, Donadio NP, Dotson NI, Dwivedi D, Egdorf T, Fliss T, Gary A, Goldy J, Grasso C, Groce EL, Gudsnuk K, Han W, Haradon Z, Hastings S, Helback O, Ho WV, Huang C, Johnson T, Jones DL, Juneau Z, Kenney J, Leibly M, Li S, Liang E, Loeffler H, Lusk NA, Madigan Z, Malloy J, Malone J, McCue R, Melchor J, Mich JK, Moosman S, Morin E, Naidoo R, Newman D, Ngo K, Nguyen K, Oster AL, Ouellette B, Oyama AA, Pena N, Pham T, Phillips E, Pom C, Potekhina L, Ransford S, Reding M, Rette DF, Reynoldson C, Rimorin C, Rios Sigler A, Rocha DB, Ronellenfitch K, Ruiz A, Sawyer L, Sevigny J, Shapovalova NV, Shepard N, Shulga L, Soliman S, Staats B, Taormina MJ, Tieu M, Wang Y, Wilkes J, Wood T, Zhou T, Williford A, Dee N, Mollenkopf … See abstract for full author list ➔ Hunker AC, et al. Among authors: lein es. bioRxiv [Preprint]. 2024 Sep 29:2024.09.27.615553. doi: 10.1101/2024.09.27.615553. bioRxiv. 2024. PMID: 39386678 Free PMC article. Preprint.
Areal specializations in the morpho-electric and transcriptomic properties of primate layer 5 extratelencephalic projection neurons.
Dembrow NC, Sawchuk S, Dalley R, Opitz-Araya X, Hudson M, Radaelli C, Alfiler L, Walling-Bell S, Bertagnolli D, Goldy J, Johansen N, Miller JA, Nasirova K, Owen SF, Parga-Becerra A, Taskin N, Tieu M, Vumbaco D, Weed N, Wilson J, Lee BR, Smith KA, Sorensen SA, Spain WJ, Lein ES, Perlmutter SI, Ting JT, Kalmbach BE. Dembrow NC, et al. Among authors: lein es. Cell Rep. 2024 Sep 24;43(9):114718. doi: 10.1016/j.celrep.2024.114718. Epub 2024 Sep 14. Cell Rep. 2024. PMID: 39277859 Free PMC article.
Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex.
Johansen NJ, Kempynck N, Zemke NR, Somasundaram S, De Winter S, Hooper M, Dwivedi D, Lohia R, Wehbe F, Li B, Abaffyová D, Armand EJ, De Man J, Eksi EC, Hecker N, Hulselmans G, Konstantakos V, Mauduit D, Mich JK, Partel G, Daigle TL, Levi BP, Zhang K, Tanaka Y, Gillis J, Ting JT, Ben-Simon Y, Miller J, Ecker JR, Ren B, Aerts S, Lein ES, Tasic B, Bakken TE. Johansen NJ, et al. Among authors: lein es. bioRxiv [Preprint]. 2024 Sep 20:2024.08.21.609075. doi: 10.1101/2024.08.21.609075. bioRxiv. 2024. PMID: 39229027 Free PMC article. Preprint.
Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque.
Kussick E, Johansen N, Taskin N, Wynalda B, Martinez R, Groce EL, Reding M, Liang E, Shulga L, Huang C, Casper T, Clark M, Ho W, Gao Y, van Velthoven CTJ, Sobieski C, Ferrer R, Berg MR, Curtis BC, English C, Day JC, Fortuna M, Donadio N, Newman D, Yao S, Chakka AB, Goldy J, Torkelson A, Guzman JB, Chakrabarty R, Nguy B, Guilford N, Pham TH, Wright V, Ronellenfitch K, Gudsnuk K, Thyagarajan B, Smith KA, Dee N, Zeng H, Yao Z, Tasic B, Levi BP, Hodge R, Bakken TE, Lein ES, Ting JT, Daigle TL. Kussick E, et al. Among authors: lein es. bioRxiv [Preprint]. 2024 Jul 31:2024.07.30.605864. doi: 10.1101/2024.07.30.605864. bioRxiv. 2024. PMID: 39131318 Free PMC article. Preprint.
A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types.
Ben-Simon Y, Hooper M, Narayan S, Daigle T, Dwivedi D, Way SW, Oster A, Stafford DA, Mich JK, Taormina MJ, Martinez RA, Opitz-Araya X, Roth JR, Allen S, Ayala A, Bakken TE, Barcelli T, Barta S, Bendrick J, Bertagnolli D, Bowlus J, Boyer G, Brouner K, Casian B, Casper T, Chakka AB, Chakrabarty R, Chance RK, Chavan S, Departee M, Donadio N, Dotson N, Egdorf T, Gabitto M, Garcia J, Gary A, Gasperini M, Goldy J, Gore BB, Graybuck L, Greisman N, Haeseleer F, Halterman C, Helback O, Hockemeyer D, Huang C, Huff S, Hunker A, Johansen N, Juneau Z, Kalmbach B, Khem S, Kussick E, Kutsal R, Larsen R, Lee C, Lee AY, Leibly M, Lenz GH, Liang E, Lusk N, Malone J, Mollenkopf T, Morin E, Newman D, Ng L, Ngo K, Omstead V, Oyama A, Pham T, Pom CA, Potekhina L, Ransford S, Rette D, Rimorin C, Rocha D, Ruiz A, Sanchez REA, Sedeno-Cortes A, Sevigny JP, Shapovalova N, Shulga L, Sigler AR, Siverts LA, Somasundaram S, Stewart K, Szelenyi E, Tieu M, Trader C, van Velthoven CTJ, Walker M, Weed N, Wirthlin M, Wood T, Wynalda B, Yao Z, Zhou T, Ariza J, Dee N, Reding M, Ronellenfitch K, Mufti S, Sunkin SM, Smith KA, Esposito L, Waters J, Thyagarajan B, Yao S, Lein ES, Zeng H, Levi BP, Ngai J, Ting J, Ta… See abstract for full author list ➔ Ben-Simon Y, et al. Among authors: lein es. bioRxiv [Preprint]. 2024 Sep 26:2024.06.10.597244. doi: 10.1101/2024.06.10.597244. bioRxiv. 2024. PMID: 38915722 Free PMC article. Preprint.
115 results