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.

Nat Methods, 2024

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

Molecular robotic agents that survey molecular landscapes for information retrieval.

Woo S, Saka SK, Xuan F, Yin P.

Nat Commun, 2024

doi:10.1038/s41467-024-46978-2.

Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels.

Hong F, Kishi JY, Delgado RN, Jeong J, Saka SK, Su H, Cepko CL, Yin P.

Nat Methods, 2023

doi:10.1038/s41592-023-02115-3.

Enablers and challenges of spatial omics, a melting pot of technologies.

Alexandrov T, Saez-Rodriguez J, Saka SK.

Mol Syst Biol, 2023

doi:10.15252/msb.202110571.

Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.

Kishi JY, Liu N, West ER, Sheng K, Jordanides JJ, Serrata M, Cepko CL, Saka SK, Yin P.

Nat Methods, 2022

doi:10.1038/s41592-022-01604-1.

Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST.

Schaefer IM, Hemming ML, Lundberg MZ, Serrata MP, Goldaracena I, Liu N, Yin P, Paulo JA, Gygi SP, George S, Morgan JA, Bertagnolli MM, Sicinska ET, Chu C, Zheng S, Mariño-Enríquez A, Hornick JL, Raut CP, Ou WB, Demetri GD, Saka SK, Fletcher JA.

Br J Cancer, 2022

doi:10.1038/s41416-022-01990-5.

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.

Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK.

Nat Methods, 2021

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Super-resolution labelling with Action-PAINT.

Liu N, Dai M, Saka SK, Yin P.

Nat Chem, 2019

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Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues.

Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P.

Nat Biotechnol, 2019

doi:10.1038/s41587-019-0207-y.

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues.

Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P.

Nat Methods, 2019

doi:10.1038/s41592-019-0404-0.

Highly multiplexedin situprotein imaging with signal amplification by Immuno-SABER

Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P.

2018

doi:10.1101/507566.

SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues

Kishi JY, Beliveau BJ, Lapan SW, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P.

2018

doi:10.1101/401810.

Multiplexedin situprotein imaging using DNA-barcoded antibodies with extended hybridization chain reactions

Wang Y, Zeng Y, Saka SK, Xie W, Goldaracena I, Kohman RE, Yin P, Church GM.

2018

doi:10.1101/274456.

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.

Beliveau BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu CT, Yin P.

Proc Natl Acad Sci U S A, 2018

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OligoMiner: A rapid, flexible environment for the design of genome-scale oligonucleotidein situhybridization probes

Beliveau BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu C, Yin P.

2017

doi:10.1101/171504.

Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT.

Schueder F, Lara-Gutiérrez J, Beliveau BJ, Saka SK, Sasaki HM, Woehrstein JB, Strauss MT, Grabmayr H, Yin P, Jungmann R.

Nat Commun, 2017

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Mapping molecules in scanning far-field fluorescence nanoscopy.

Ta H, Keller J, Haltmeier M, Saka SK, Schmied J, Opazo F, Tinnefeld P, Munk A, Hell SW.

Nat Commun, 2015

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A contamination-insensitive probe for imaging specific biomolecules by secondary ion mass spectrometry.

Kabatas S, Vreja IC, Saka SK, Höschen C, Kröhnert K, Opazo F, Rizzoli SO, Diederichsen U.

Chem Commun (Camb), 2015

doi:10.1039/c5cc03895b.

Secondary-ion mass spectrometry of genetically encoded targets.

Vreja IC, Kabatas S, Saka SK, Kröhnert K, Höschen C, Opazo F, Diederichsen U, Rizzoli SO.

Angew Chem Int Ed Engl, 2015

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Multi-protein assemblies underlie the mesoscale organization of the plasma membrane.

Saka SK, Honigmann A, Eggeling C, Hell SW, Lang T, Rizzoli SO.

Nat Commun, 2014

doi:10.1038/ncomms5509.

Correlated optical and isotopic nanoscopy.

Saka SK, Vogts A, Kröhnert K, Hillion F, Rizzoli SO, Wessels JT.

Nat Commun, 2014

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Super-resolution imaging prompts re-thinking of cell biology mechanisms: selected cases using stimulated emission depletion microscopy.

Saka S, Rizzoli SO.

Bioessays, 2012

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