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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
...embeddings as input. Our gene470 embeddings are computed based on the pre-trained Enformer Avsec et al (2021). We471 tested other choices and they did not work as well as the setting based on Enformer.472 The loss is computed based on the measured genes between the raw input data and473 imputed outputs...
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Method: A model-based constrained deep learning clustering approach for spatially resolved single-cell data
- Xiang Lin,
- Le Gao,
- Nathan Whitener,
- Ashley Ahmed,
- and Zhi Wei
Genome Res. October 2022 32: 1906-1917; Published in Advance October 5, 2022, doi:10.1101/gr.276477.121
...and ground truth labels on a data set with n cells. NMI is defined as where I(U,G) represents the mutual information between U and G and is defined as and H(U) and H(G) are the entropies: AC is defined as the best matching between predicted and true clusters, which is given as where are the true labels...
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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
...when data sets are analyzed in isolation. However, SpiceMix requires a common feature space, which limits its application to data sets with few overlapping genes. We address this limitation using LLOKI embeddings as an alternative input to SpiceMix, providing a unified feature space across data sets...
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Method: Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
- Hang Zhang,
- Yi Zhang,
- Kai Ming Ting,
- Jie Zhang,
- and Qiuran Zhao
Genome Res. February 2025 35: 355-367; Published in Advance February 5, 2025, doi:10.1101/gr.278983.124
...transcriptomics (ST) data set, the spatial information L and the gene expression information E are integrated to produce a graph that contains both cell location and gene expression information. (B) A graph-embedding scheme converts a graph into a vector representation, as shown on the left, which is ready...
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Method: Designing realistic regulatory DNA with autoregressive language models
- Avantika Lal,
- David Garfield,
- Tommaso Biancalani,
- and Gokcen Eraslan
Genome Res. September 2024 34: 1411-1420; Published in Advance September 25, 2024, doi:10.1101/gr.279142.124
...representing any desired function. The model, now conditioned on the prompt tokens, generates a DNA sequence 1 nt at a time (Fig. 1D). In parallel, we train a supervised sequence-to-activity regression model on the same data set (Fig. 1E), and apply it to the generated sequences to select those that best match...
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Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
...the consequences of this design choice by comparing human WTA with a smaller probe pool targeting 1812 human genes with five probes per target. In matched 200 μm AOIs in formalin-fixed paraffin embedded (FFPE) tonsil tissue, counts from the single WTA probe were well correlated to the mean count of the five probes...
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LETTER: Dynamic evolution at pericentromeres
- Anne E. Hall,
- Gregory C. Kettler,
- and Daphne Preuss
Genome Res. March 2006 16: 355-364; Published in Advance February 6, 2006, doi:10.1101/gr.4399206
...that are homologous to Arabidopsis thaliana pericentromeres (peri- CEN s) III and V, and used FISH to demonstrate they have been maintained near centromere satellite arrays in each species. Sequence analysis revealed a set of highly conserved genes, yet we discovered substantial differences in intergenic length...
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Research: Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
- Marco Mariotti,
- Didac Santesmasses,
- Salvador Capella-Gutierrez,
- Andrea Mateo,
- Carme Arnan,
- Rory Johnson,
- Salvatore D'Aniello,
- Sun Hee Yim,
- Vadim N. Gladyshev,
- Florenci Serras,
- Montserrat Corominas,
- Toni Gabaldón,
- and Roderic Guigó
Genome Res. September 2015 25: 1256-1267; Published in Advance July 20, 2015, doi:10.1101/gr.190538.115
...Selenoprofiles to search for SelD/SPS genes in all available fully sequenced eukaryotic and prokaryotic s, 505 and 8263, respectively. We then utilized a combination of approaches to reconstruct their phylogenetic history. Methods and analyses are fully discussed in Supplemental Material S1–S6. SelD as a marker...
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Research: Cnidarian microRNAs frequently regulate targets by cleavage
- Yehu Moran,
- David Fredman,
- Daniela Praher,
- Xin Z. Li,
- Liang Meng Wee,
- Fabian Rentzsch,
- Phillip D. Zamore,
- Ulrich Technau,
- and Hervé Seitz
Genome Res. April 2014 24: 651-663; Published in Advance March 18, 2014, doi:10.1101/gr.162503.113
...cleavage. (A) Distribution of miRNA:mRNA alignment mismatch scores in Nematostella vectensis, Homo sapiens, Drosophila melanogaster, and Arabidopsis thaliana, shown as the difference in abundance between miRNAs and matching shuffledmiRNAs, counting the fraction of sequences in each set having a best match...
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Editorial: Innovations in computational biology: RECOMB 2024 Special Issue
- Jian Ma and
- Bonnie Berger
Genome Res. September 2024 34: vii-viii; doi:10.1101/gr.280036.124
....1101/gr.279142.124 ↵Li L, Dannenfelser R, Cruz C, Yao V. 2024. A best-match approach for gene set analyses in embedding spaces. Genome Res (this issue) 34: 1421–1433. doi:10.1101/gr.279141.124 ↵Park C, Mani S, Beltran-Velez N, Maurer K, Huang T, Li S, Gohil S, Livak KJ, Knowles DA, Wu CJ, et al. 2024...

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