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Saka Group

Spatial biology from molecules to tissues: high-dimensional investigation of cellular organisation

Publications

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SpatialData: an open and universal data framework for spatial omics.

Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B, Pollaris L, Lehner L, Vöhringer H, Kats I, Saeys Y, Saka SK, Huber W, Gerstung M, Moore J, Theis FJ, Stegle O

Nature methods, 2024

doi:10.1038/s41592-024-02212-x.

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

HuBMAP Consortium (Snyder MP, Lin S, Posgai A, Atkinson M, Regev A, Rood J, Rozenblatt-Rosen O, Gaffney L, Hupalowska A, Satija R, Gehlenborg N, Shendure J, Laskin J, Harbury P, Nystrom NA, Silverstein JC, Bar-Joseph Z, Zhang K, Borner K, Lin Y, Conroy R, Procaccini D, Roy AL, Pillai A, Brown M, Galis ZS, Cai L, Shendure J, Trapnell C, Lin S, Jackson D, Snyder MP, Nolan G, Greenleaf WJ, Lin Y, Plevritis S, Ahadi S, Nevins SA, Lee H, Schuerch CM, Black S, Venkataraaman VG, Esplin E, Horning A, Bahmani A, Zhang K, Sun X, Jain S, Hagood J, Pryhuber G, Kharchenko P, Atkinson M, Bodenmiller B, Brusko T, Clare-Salzler M, Nick H, Otto K, Posgai A, Wasserfall C, Jorgensen M, Brusko M, Maffioletti S, Caprioli RM, Spraggins JM, Gutierrez D, Patterson NH, Neumann EK, Harris R, deCaestecker M, Fogo AB, van de Plas R, Lau K, Cai L, Yuan GC, Zhu Q, Dries R, Yin P, Saka SK, Kishi JY, Wang Y, Goldaracena I, Laskin J, Ye DY, Burnum-Johnson KE, Piehowski PD, Ansong C, Zhu Y, Harbury P, Desai T, Mulye J, Chou P, Nagendran M, Bar-Joseph Z, Teichmann SA, Paten B, Murphy RF, Ma J, Kiselev VY, Kingsford C, Ricarte A, Keays M, Akoju SA, Ruffalo M, Gehlenborg N, Kharchenko P, Vella M, McCallum C, Borner K, Cross LE, Friedman SH, Heiland R, Herr B, Macklin P, Quardokus EM, Record L, Sluka JP, Weber GM, Nystrom NA, Silverstein JC, Blood PD, Ropelewski AJ, Shirey WE, Scibek RM, Mabee P, Lenhardt WC, Robasky K, Michailidis S, Satija R, Marioni J, Regev A, Butler A, Stuart T, Fisher E, Ghazanfar S, Rood J, Gaffney L, Eraslan G, Biancalani T, Vaishnav ED, Conroy R, Procaccini D, Roy A, Pillai A, Brown M, Galis Z, Srinivas P, Pawlyk A, Sechi S, Wilder E, Anderson J)

NATURE, 2019

doi:10.1038/s41586-019-1629-x.

SpatialData: an open and universal data framework for spatial omics.

Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B, Pollaris L, Lehner L, Vöhringer H, Kats I, Saeys Y, Saka SK, Huber W, Gerstung M, Moore J, Theis FJ, Stegle O

Nature methods, 2024

doi:10.1038/s41592-024-02212-x.

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

HuBMAP Consortium (Snyder MP, Lin S, Posgai A, Atkinson M, Regev A, Rood J, Rozenblatt-Rosen O, Gaffney L, Hupalowska A, Satija R, Gehlenborg N, Shendure J, Laskin J, Harbury P, Nystrom NA, Silverstein JC, Bar-Joseph Z, Zhang K, Borner K, Lin Y, Conroy R, Procaccini D, Roy AL, Pillai A, Brown M, Galis ZS, Cai L, Shendure J, Trapnell C, Lin S, Jackson D, Snyder MP, Nolan G, Greenleaf WJ, Lin Y, Plevritis S, Ahadi S, Nevins SA, Lee H, Schuerch CM, Black S, Venkataraaman VG, Esplin E, Horning A, Bahmani A, Zhang K, Sun X, Jain S, Hagood J, Pryhuber G, Kharchenko P, Atkinson M, Bodenmiller B, Brusko T, Clare-Salzler M, Nick H, Otto K, Posgai A, Wasserfall C, Jorgensen M, Brusko M, Maffioletti S, Caprioli RM, Spraggins JM, Gutierrez D, Patterson NH, Neumann EK, Harris R, deCaestecker M, Fogo AB, van de Plas R, Lau K, Cai L, Yuan GC, Zhu Q, Dries R, Yin P, Saka SK, Kishi JY, Wang Y, Goldaracena I, Laskin J, Ye DY, Burnum-Johnson KE, Piehowski PD, Ansong C, Zhu Y, Harbury P, Desai T, Mulye J, Chou P, Nagendran M, Bar-Joseph Z, Teichmann SA, Paten B, Murphy RF, Ma J, Kiselev VY, Kingsford C, Ricarte A, Keays M, Akoju SA, Ruffalo M, Gehlenborg N, Kharchenko P, Vella M, McCallum C, Borner K, Cross LE, Friedman SH, Heiland R, Herr B, Macklin P, Quardokus EM, Record L, Sluka JP, Weber GM, Nystrom NA, Silverstein JC, Blood PD, Ropelewski AJ, Shirey WE, Scibek RM, Mabee P, Lenhardt WC, Robasky K, Michailidis S, Satija R, Marioni J, Regev A, Butler A, Stuart T, Fisher E, Ghazanfar S, Rood J, Gaffney L, Eraslan G, Biancalani T, Vaishnav ED, Conroy R, Procaccini D, Roy A, Pillai A, Brown M, Galis Z, Srinivas P, Pawlyk A, Sechi S, Wilder E, Anderson J)

NATURE, 2019

doi:10.1038/s41586-019-1629-x.

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