Enabling high-plex spectral imaging via DNA-barcoded signal tuning and panel optimization

Reinhardt R, Straka T, Vierdag W, Jevdokimenko K, Hecht F, Pianfetti E, Hudelmaier T, Lai H, Fouquet W, Fahrbach F, Roberti MJ, Kreshuk A, Saka SK.

2026

doi:10.64898/2026.03.18.709053.

ProPER: Programmable, multiplexed detection of molecular proximities and RNA life-cycle stages in situ

Trojanowski J, Zilke J, Pak V, Geissen E, Chalupska R, Reinhardt R, AlMehallawi S, Kishi JY, Heck J, Haase K, Saka SK.

2026

doi:10.64898/2026.04.24.718482.

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.

Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions.

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

Nucleic Acids Res, 2024

doi:10.1093/nar/gkae592.

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.

A perspective on FAIR quality control in multiplexed imaging data processing.

Vierdag WAM, Saka SK.

Front Bioinform, 2024

doi:10.3389/fbinf.2024.1336257.

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.

Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP).

Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, HuBMAP Consortium, Börner K, Snyder MP.

Nat Cell Biol, 2023

doi:10.1038/s41556-023-01194-w.

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

doi:10.1038/s41592-021-01316-y.

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

HuBMAP Consortium.

Nature, 2019

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

Super-resolution labelling with Action-PAINT.

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

Nat Chem, 2019

doi:10.1038/s41557-019-0325-7.

Highly multiplexed in situ protein 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.

Multiplexed in situ protein 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

doi:10.1073/pnas.1714530115.

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

doi:10.1038/s41467-017-02028-8.

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

doi:10.1038/ncomms8977.

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

doi:10.1002/anie.201411692.

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

doi:10.1038/ncomms4664.

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

Saka S, Rizzoli SO.

Bioessays, 2012

doi:10.1002/bies.201100080.