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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...that deletion cassette replacement introduced short donor 25 DNA tracts of variable length, resulting in a finely recombined mapping population. Using only 26 the known location of the gene deletions, which marks where donor DNA is introduced, we 27 identify a 6.5 kb-region shaping yeast growth. We further...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...), NPC lines, and developmental timepoints, to generate a list of putative enhancer regions to investigate using the phNPC model. Whereas other enhancer mapping tools such as massively parallel reporter assays (MPRAs) have been used to identify putative enhancer regions in primary human cortical cells...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole- resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...fine-mapped vascular disease loci and highlighted evidence suggesting mechanisms by which noncoding SNPs at two loci affect risk for pulse pressure/large artery stroke and abdominal aortic aneurysm through respective effects on transcriptional regulation of POU4F1 and LDAH. Together, we highlight...
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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
...RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels Brigitta Szabo, Therese C. Mandl, Bernhard Woldrich, Gregor Diensthuber, David Martin, Michael F. Jantsch and Konstantin Licht Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...to generate a comprehensive map of small-scale inversions within large synteny blocks in a Nomascus siki (NSI), providing a detailed and fine-structure picture of small-scale, previously hidden, inversions comprising genes potentially important for gibbon intraspecific divergence and speciation...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...A chromosome-scale epigenetic map of the Hydra reveals conserved regulators of cell state Jack F. Cazet1, Stefan Siebert1,2, Hannah Morris Little1, Philip Bertemes3, Abby S. Primack1, Peter Ladurner3, Matthias Achrainer3, Mark T. Fredriksen4, R. Travis Moreland4, Sumeeta Singh4, Suiyuan Zhang4...
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Method: Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction
- Shuai Zeng,
- Duolin Wang,
- Lei Jiang,
- and Dong Xu
Genome Res. September 2024 34: 1445-1454; Published in Advance July 26, 2024, doi:10.1101/gr.279132.124
...in protein translocation in cells. The development of large protein language models (PLMs) and prompt-based learning provide a new opportunity for SP prediction, especially for the categories with limited annotated data. We present a parameter-efficient fine-tuning (PEFT) framework for SP prediction, PEFT...
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Resource: Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
- Ekaterina Khrameeva,
- Ilia Kurochkin,
- Dingding Han,
- Patricia Guijarro,
- Sabina Kanton,
- Malgorzata Santel,
- Zhengzong Qian,
- Shen Rong,
- Pavel Mazin,
- Marat Sabirov,
- Matvei Bulat,
- Olga Efimova,
- Anna Tkachev,
- Song Guo,
- Chet C. Sherwood,
- J. Gray Camp,
- Svante Pääbo,
- Barbara Treutlein,
- and Philipp Khaitovich
Genome Res. May 2020 30: 776-789; Published in Advance May 18, 2020, doi:10.1101/gr.256958.119
...and chimpanzee cerebral organoids, indicating that cell-type composition can be accurately matched between closely related primate species and expression differences within each type identified (Mora-Bermúdez et al. 2016; Kanton et al. 2019; Pollen et al. 2019).Here, we report transcriptome maps of the human...
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Research: Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
- Daniela S. Aliaga Goltsman,
- Christine L. Sun,
- Diana M. Proctor,
- Daniel B. DiGiulio,
- Anna Robaczewska,
- Brian C. Thomas,
- Gary M. Shaw,
- David K. Stevenson,
- Susan P. Holmes,
- Jillian F. Banfield,
- and David A. Relman
Genome Res. October 2018 28: 1467-1480; Published in Advance September 19, 2018, doi:10.1101/gr.236000.118
....View larger version: In this window In a new window Figure 1. Community structure of the pregnancy microbiome over time in 10 subjects. (A) Relative abundance of vaginal bins (y-axis). Abundance was estimated from the number of reads that mapped to each bin and normalized by the length of the bin. The top 10...

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