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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: gary a. bioRxiv [Preprint]. 2024 Dec 7:2024.12.04.626766. doi: 10.1101/2024.12.04.626766. bioRxiv. 2024. PMID: 39677693 Free PMC article. Preprint.
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, Moll… See abstract for full author list ➔ Hunker AC, et al. Among authors: gary a. bioRxiv [Preprint]. 2024 Sep 29:2024.09.27.615553. doi: 10.1101/2024.09.27.615553. bioRxiv. 2024. PMID: 39386678 Free PMC article. Preprint.
Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species.
Mich JK, Sunil S, Johansen N, Martinez RA, Leytze M, Gore BB, Mahoney JT, Ben-Simon Y, Bishaw Y, Brouner K, Campos J, Canfield R, Casper T, Dee N, Egdorf T, Gary A, Gibson S, Goldy J, Groce EL, Hirschstein D, Loftus L, Lusk N, Malone J, Martin NX, Monet D, Omstead V, Opitz-Araya X, Oster A, Pom CA, Potekhina L, Reding M, Rimorin C, Ruiz A, Sedeño-Cortés AE, Shapovalova NV, Taormina M, Taskin N, Tieu M, Valera Cuevas NJ, Weed N, Way S, Yao Z, McMillen DA, Kunst M, McGraw M, Thyagarajan B, Waters J, Bakken TE, Yao S, Smith KA, Svoboda K, Podgorski K, Kojima Y, Horwitz GD, Zeng H, Daigle TL, Lein ES, Tasic B, Ting JT, Levi BP. Mich JK, et al. Among authors: gary a. bioRxiv [Preprint]. 2023 Sep 21:2023.09.20.558718. doi: 10.1101/2023.09.20.558718. bioRxiv. 2023. PMID: 37790503 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: gary a. bioRxiv [Preprint]. 2024 Sep 26:2024.06.10.597244. doi: 10.1101/2024.06.10.597244. bioRxiv. 2024. PMID: 38915722 Free PMC article. Preprint.
Connecting single-cell transcriptomes to projectomes in mouse visual cortex.
Sorensen SA, Gouwens NW, Wang Y, Mallory M, Budzillo A, Dalley R, Lee B, Gliko O, Kuo HC, Kuang X, Mann R, Ahmadinia L, Alfiler L, Baftizadeh F, Baker K, Bannick S, Bertagnolli D, Bickley K, Bohn P, Brown D, Bomben J, Brouner K, Chen C, Chen K, Chvilicek M, Collman F, Daigle T, Dawes T, de Frates R, Dee N, DePartee M, Egdorf T, El-Hifnawi L, Enstrom R, Esposito L, Farrell C, Gala R, Glomb A, Gamlin C, Gary A, Goldy J, Gu H, Hadley K, Hawrylycz M, Henry A, Hill D, Hirokawa KE, Huang Z, Johnson K, Juneau Z, Kebede S, Kim L, Lee C, Lesnar P, Li A, Glomb A, Li Y, Liang E, Link K, Maxwell M, McGraw M, McMillen DA, Mukora A, Ng L, Ochoa T, Oldre A, Park D, Pom CA, Popovich Z, Potekhina L, Rajanbabu R, Ransford S, Reding M, Ruiz A, Sandman D, Siverts L, Smith KA, Stoecklin M, Sulc J, Tieu M, Ting J, Trinh J, Vargas S, Vumbaco D, Walker M, Wang M, Wanner A, Waters J, Williams G, Wilson J, Xiong W, Lein E, Berg J, Kalmbach B, Yao S, Gong H, Luo Q, Ng L, Sümbül U, Jarsky T, Yao Z, Tasic B, Zeng H. Sorensen SA, et al. Among authors: gary a. bioRxiv [Preprint]. 2023 Nov 26:2023.11.25.568393. doi: 10.1101/2023.11.25.568393. bioRxiv. 2023. PMID: 38168270 Free PMC article. Preprint.
Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas.
Jin K, Yao Z, van Velthoven CTJ, Kaplan ES, Glattfelder K, Barlow ST, Boyer G, Carey D, Casper T, Chakka AB, Chakrabarty R, Clark M, Departee M, Desierto M, Gary A, Gloe J, Goldy J, Guilford N, Guzman J, Hirschstein D, Lee C, Liang E, Pham T, Reding M, Ronellenfitch K, Ruiz A, Sevigny J, Shapovalova N, Shulga L, Sulc J, Torkelson A, Tung H, Levi B, Sunkin SM, Dee N, Esposito L, Smith K, Tasic B, Zeng H. Jin K, et al. Among authors: gary a. bioRxiv [Preprint]. 2023 Jul 27:2023.07.26.550355. doi: 10.1101/2023.07.26.550355. bioRxiv. 2023. PMID: 38168182 Free PMC article. Preprint.
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, Brouner K, Campos J, Carr AJ, Casper T, Chakrabarty R, Clark M, Compos J, Cool J, Valera Cuevas NJ, Dalley R, Darvas M, Ding SL, Dolbeare T, Mac Donald CL, Egdorf T, Esposito L, Ferrer R, Gala R, Gary A, Gloe J, Guilford N, Guzman J, Ho W, Jarksy T, Johansen N, Kalmbach BE, Keene LM, Khawand S, Kilgore M, Kirkland A, Kunst M, Lee BR, Malone J, Maltzer Z, Martin N, McCue R, McMillen D, Meyerdierks E, Meyers KP, Mollenkopf T, Montine M, Nolan AL, Nyhus J, Olsen PA, Pacleb M, Pham T, Pom CA, Postupna N, Ruiz A, Schantz AM, Sorensen SA, Staats B, Sullivan M, Sunkin SM, Thompson C, Tieu M, Ting J, Torkelson A, Tran T, Wang MQ, Waters J, Wilson AM, Haynor D, Gatto N, Jayadev S, Mufti S, Ng L, Mukherjee S, Crane PK, Latimer CS, Levi BP, Smith K, Close JL, Miller JA, Hodge RD, Larson EB, Grabowski TJ, Hawrylycz M, Keene CD, Lein ES. Gabitto MI, et al. Among authors: gary a. Res Sq [Preprint]. 2023 May 23:rs.3.rs-2921860. doi: 10.21203/rs.3.rs-2921860/v1. Res Sq. 2023. Update in: Nat Neurosci. 2024 Dec;27(12):2366-2383. doi: 10.1038/s41593-024-01774-5 PMID: 37292694 Free PMC article. Updated. Preprint.
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: gary a. 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.
Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex.
Chartrand T, Dalley R, Close J, Goriounova NA, Lee BR, Mann R, Miller JA, Molnar G, Mukora A, Alfiler L, Baker K, Bakken TE, Berg J, Bertagnolli D, Braun T, Brouner K, Casper T, Csajbok EA, Dee N, Egdorf T, Enstrom R, Galakhova AA, Gary A, Gelfand E, Goldy J, Hadley K, Heistek TS, Hill D, Jorstad N, Kim L, Kocsis AK, Kruse L, Kunst M, Leon G, Long B, Mallory M, McGraw M, McMillen D, Melief EJ, Mihut N, Ng L, Nyhus J, Oláh G, Ozsvár A, Omstead V, Peterfi Z, Pom A, Potekhina L, Rajanbabu R, Rozsa M, Ruiz A, Sandle J, Sunkin SM, Szots I, Tieu M, Toth M, Trinh J, Vargas S, Vumbaco D, Williams G, Wilson J, Yao Z, Barzo P, Cobbs C, Ellenbogen RG, Esposito L, Ferreira M, Gouwens NW, Grannan B, Gwinn RP, Hauptman JS, Jarsky T, Keene CD, Ko AL, Koch C, Ojemann JG, Patel A, Ruzevick J, Silbergeld DL, Smith K, Sorensen SA, Tasic B, Ting JT, Waters J, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Kalmbach B, Lein ES. Chartrand T, et al. Among authors: gary a. Science. 2023 Oct 13;382(6667):eadf0805. doi: 10.1126/science.adf0805. Epub 2023 Oct 13. Science. 2023. PMID: 37824667
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex.
Lee BR, Dalley R, Miller JA, Chartrand T, Close J, Mann R, Mukora A, Ng L, Alfiler L, Baker K, Bertagnolli D, Brouner K, Casper T, Csajbok E, Donadio N, Driessens SLW, Egdorf T, Enstrom R, Galakhova AA, Gary A, Gelfand E, Goldy J, Hadley K, Heistek TS, Hill D, Hou WH, Johansen N, Jorstad N, Kim L, Kocsis AK, Kruse L, Kunst M, León G, Long B, Mallory M, Maxwell M, McGraw M, McMillen D, Melief EJ, Molnar G, Mortrud MT, Newman D, Nyhus J, Opitz-Araya X, Ozsvár A, Pham T, Pom A, Potekhina L, Rajanbabu R, Ruiz A, Sunkin SM, Szöts I, Taskin N, Thyagarajan B, Tieu M, Trinh J, Vargas S, Vumbaco D, Waleboer F, Walling-Bell S, Weed N, Williams G, Wilson J, Yao S, Zhou T, Barzó P, Bakken T, Cobbs C, Dee N, Ellenbogen RG, Esposito L, Ferreira M, Gouwens NW, Grannan B, Gwinn RP, Hauptman JS, Hodge R, Jarsky T, Keene CD, Ko AL, Korshoej AR, Levi BP, Meier K, Ojemann JG, Patel A, Ruzevick J, Silbergeld DL, Smith K, Sørensen JC, Waters J, Zeng H, Berg J, Capogna M, Goriounova NA, Kalmbach B, de Kock CPJ, Mansvelder HD, Sorensen SA, Tamas G, Lein ES, Ting JT. Lee BR, et al. Among authors: gary a. Science. 2023 Oct 13;382(6667):eadf6484. doi: 10.1126/science.adf6484. Epub 2023 Oct 13. Science. 2023. PMID: 37824669
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