Publications – Saka Group

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.

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.

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 research, 2024

doi:10.1093/nar/gkae592.

Molecular robotic agents that survey molecular landscapes for information retrieval.

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

Nature communications, 2024

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

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.

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

Vierdag WAM, Saka SK.

Frontiers in bioinformatics, 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.

Nature 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.

Molecular systems biology, 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.

Nature cell biology, 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.

Nature 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.

British journal of 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.

Nature 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.

Nature chemistry, 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.