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Method: Partial alignment of multislice spatially resolved transcriptomics data
- Xinhao Liu,
- Ron Zeira,
- and Benjamin J. Raphael
Genome Res. July 2023 33: 1124-1132; Published in Advance August 8, 2023, doi:10.1101/gr.277670.123
...Xinhao Liu1, Ron Zeira2 and Benjamin J. Raphael1 1Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA; 2Verily Life Sciences, Tel Aviv 6789141, Israel Corresponding author: braphael@princeton.eduAbstractSpatially resolved transcriptomics (SRT) technologies measure...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...repertoire can be fully resolved. The B cells were collected following a measles, mumps, and rubella (MMR) vaccination, resulting in a population of cells that were activated in response to this specific immune challenge. Single-cell, full-length transcriptome sequencing of these B cells results in whole...
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Method: Unified integration of spatial transcriptomics across platforms with LLOKI
- Ellie Haber,
- Ajinkya Deshpande,
- Jian Ma,
- and Spencer Krieger
Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
..., Pittsburgh, Pennsylvania 15213, USA Corresponding authors: jianma@cs.cmu.edu, skrieger@andrew.cmu.eduAbstractSpatial transcriptomics (ST) has transformed our understanding of tissue architecture and cellular interactions, but integrating ST data across platforms remains challenging due to differences in gene...
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Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...offers new insights for analyzing ageing effect with spatial transcriptomics.31 Keywords: Spatial Transcriptomics, Foundation Model, Data Denoising, Data32 Imputation, Survival Analysis, Ageing33 Introduction34 Spatially-resolved transcriptomic (SRT) technologies have enabled the investigation of35...
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Method: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
- Hongyu Zheng,
- Hirak Sarkar,
- and Benjamin J. Raphael
Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
.... Order determined by a coin flip. Corresponding author: braphael@princeton.eduAbstractSpatially resolved transcriptomics (SRT) technologies measure gene expression across thousands of spatial locations within a tissue slice. Multiple SRT technologies are currently available and others are in active...
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Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
- Lin Li,
- Xianbin Su,
- and Ze-Guang Han
Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
...transcriptomics (ST) data. DeCEP constructs functional networks tailored to spatial contexts, focusing on regions of interest (ROIs) and their corresponding neighborhoods. DeCEP then identifies spatially dependent hub genes and assigns DeCEP scores.For ST data, DeCEP requires a spot-by-gene expression matrix...
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Method: Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain
- Bowei Kang,
- Yalan Yang,
- Kaining Hu,
- Xiangbin Ruan,
- Yi-Lin Liu,
- Pinky Lee,
- Jasper Lee,
- Jingshu Wang,
- and Xiaochang Zhang
Genome Res. October 2023 33: 1774-1787; Published in Advance October 31, 2023, doi:10.1101/gr.277864.123
...(Zhu et al. 2022), suggesting that scRNA-seq is suitable for identifying cell type–specific PAs. However, it remains challenging to call differential PAs reliably owing to technical biases associated with scRNA-seq library preparation. Moreover, oligo(dT) capture-based spatial transcriptomics has been...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...to extract spatially resolved expression profiles. Although DSP can simultaneously analyze more than 180 proteins and 18,000 genes, its reliance on probes specific to the human or mouse transcriptome limits its use for other species. Alternative techniques, such as ZipSeq (Hu et al. 2020), PIC (Honda et al...
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Method: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
- An Wang,
- Stephanie Hicks,
- Donald Geman,
- and Laurent Younes
Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
...existing label-free methods in both computational efficiency and accuracy in resolving refined spatial organization or rare cell types in spatial transcriptomics and scRNA-seq data.geneCover excels at identifying a minimally redundant marker panel that captures various sources of meaningful transcriptional...
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Method: Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq
- Yike Xie,
- Abbas Habibalahi,
- Ayad G. Anwer,
- Kanu Wahi,
- Jacqueline Bailey,
- Francis Lin,
- Catherine Gatt,
- Emma M.V. Johansson,
- Tatyana Chtanova,
- Jeff Holst,
- Ewa Goldys,
- and Fabio Zanini
Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
...Seq that combines hyperspectral autofluorescence imaging with transcriptomics on the same cell. SpectralSeq is applied to Michigan Cancer Foundation-7 (MCF-7) breast cancer cells and identifies a subpopulation of cells exhibiting bright autofluorescence rings at the plasma membrane in optical channel 13 (λex = 431...
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