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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
...@milaboratories.comAbstractAllelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research...
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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...RNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, USA. ♱Corresponding authors: izg5139@psu.edu, nadav.ahituv@ucsf.edu Abstract Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene...
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Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
- Li Song,
- Gali Bai,
- X. Shirley Liu,
- Bo Li,
- and Heng Li
Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
...genes, the killer immunoglobulin-like receptor (KIR) gene family residing on 19q13.4 is also highly polymorphic and can modulate the activity of natural killer (NK) cells and T cells (Vilches and Parham 2002). There are 17 KIRs in humans, including eight inhibitory KIRs (KIR2DL1, KIR2DL2, KIR2DL3, KIR2...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...the sequence correlations among these s, potentially introducing ambiguity and biases in metagenomic profiling. Here, we present PanTax, a pan graph-based taxonomic profiler that overcomes the shortcomings of sequence-based approaches, because pan graphs possess the capability to depict the full range...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...IP-seq protocol, named spa-ChIP-seq, which enables scalable processing of eight to 96 ChIP-seq samples from cross-linked cells to a sequencing-ready library in approximately 3 days with an estimated cost of $70 per sample. Benchmarking spa-ChIP-seq against manual ChIP-seq performed in parallel demonstrates...
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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
..., such as the T cell receptor binding (GO:0042608), which was logical considering the need for adaptability in immune processes.In addition, upon detailed examination of the detected gene fusions, we also observed that: (1) Certain genes could partner with multiple other genes, resulting in different fusions (Fig...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...mechanisms 25 linking aging and PD pathology remain unclear. Leveraging advancements in single-cell 26 genomics, this study utilizes single-nucleus multiome sequencing to capture transcriptomic and 27 epigenetic profiles from 40,125 cells across the lifespan of the mouse substantia nigra. Our 28 analysis...
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Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
- Wei-Hao Lee,
- Lechuan Li,
- Ruth Dannenfelser,
- and Vicky Yao
Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
...; 4Rice Synthetic Biology Institute, Rice University, Houston, Texas 77005, USA ↵5 These authors contributed equally to this work. Corresponding author: vy@rice.eduAbstractAs sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...reveals a complex series of structural events induced by HPV integration (Ramirez et al. 2021).Hybridization-based enrichment has also been used to characterize specific transcripts in single-cell applications. Singh et al. targeted T cell and B cell antigen receptor (TCR and BCR) genes in unfragmented 10...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...enhancer activity in the Hep G2, HuH-7, HCCLM3, MHCC97-H, HT-29, and HCT 116 cell lines but not in the 293T cell line (Fig. 7B). In this study, the HuH-7 and Hep G2 cell lines were used for further verification and functional studies because they are common cell lines used for luciferase assays...

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