Searching journal content for articles similar to Mountain et al. 12 (11): 1766.

Displaying results 1-10 of 6009

For checked items

view abstracts
download to citation manager

Select this article
Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...SNPs for which v1 has an alternate allele. We stratify the error types because they appear with different frequencies. rtoa and ator differ owing to reference bias: If a read comes from a haplotype with a true alternate allele, it may systematically align with the reference allele incorrectly...
Select this article
Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...structure into continuous representations that can be seamlessly integrated into genetic analysis pipelines. Using both simulated data sets and empirical data from the UK Biobank (N ≈ 420,000), we demonstrate that SPCs outperform PCs in adjusting for fine-scale population structure. In simulations, SPCs...
OPEN ACCESS ARTICLE
Select this article
Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...-truth sequences. It compares favorably to the existing methods. MethodsOverviewOur method, pan-based haplotype inference (PHI), takes as input a pan graph reference and short-read sequencing data from a target haploid . We assume that the given pan graph has been constructed using high-quality, haplotype...
Select this article
Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...more general single-cell genotypes and mutation models remains a research question.Applying ScisTree2 in studies of cancer biology and stem cell biologyInference of the cell lineage tree is very relevant to single-cell cancer genomics. For example, finding clonal populations is a common problem...
OPEN ACCESS ARTICLE
Select this article
Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...to annotate samples based on cell-type composition. By comparing aggregation strategies, we find that regressing confounders within studies and prioritizing larger studies optimizes network reconstruction. We apply these findings to infer three consensus networks (universal, cancer, noncancer) and 27 context...
OPEN ACCESS ARTICLE
Select this article
Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...previously inferred from amplicon sequencing in combination with segregation studies or from STR-typing strategies, a genomic map is lacking (Doxiadis et al. 2000, 2013; de Groot et al. 2017, 2022). Hence, the enigma persists for the biological mechanism that makes the DRB region prone to expansion...
OPEN ACCESS ARTICLE
Select this article
Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...-modal setting in which, for example, one data modality is “undercharacterized”; that is, we are missing measurements of that modality in one or more conditions or time points of interest. Although several existing methods have been developed for this type of cross-modal inference, they were developed for bulk...
OPEN ACCESS ARTICLE
Select this article
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
...and to establish a database of alleles of V and J genes inferred from AIRR-seq data and their population frequencies with free public access through VDJ.online database.Adaptive immune repertoire diversity plays a crucial role in shaping the immune response and forming immunological memory. Most immune repertoire...
OPEN ACCESS ARTICLE
Select this article
Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...functional predictions of ERC have been empirically validated, its predictive power has hitherto been limited by its inability to tackle the large numbers of species in contemporary comparative genomics data sets. This study introduces ERC2.0, an enhanced methodology for studying ERC across phylogenies...
Select this article
Method: Bayesian inference of sample-specific coexpression networks
- Enakshi Saha,
- Viola Fanfani,
- Panagiotis Mandros,
- Marouen Ben Guebila,
- Jonas Fischer,
- Katherine H. Shutta,
- Dawn L. DeMeo,
- Camila M. Lopes-Ramos,
- and John Quackenbush
Genome Res. September 2024 34: 1397-1410; Published in Advance August 12, 2024, doi:10.1101/gr.279117.124
...to an external reference population and, hence, are susceptible to varying inference depending on the reference used.We developed Bayesian optimized networks obtained by assimilating omic data (BONOBO), an empirical Bayesian model that derives individual sample-specific coexpression networks (Fig. 1...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Mountain et al. 12 (11): 1766.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: