Searching journal content for articles similar to Magalhães et al. 28 (7): 1090.

Displaying results 1-10 of 5773

For checked items

view abstracts
download to citation manager

Select this article
Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...genotype imputation from LPS data. Among these, Beagle (Browning et al. 2018) and Gencove's loimpute software (Wasik et al. 2021) have been some of the most popular examples. However, they present limitations in scalability for large cohorts and increased computational costs with large reference panels...
OPEN ACCESS ARTICLE
Select this article
Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
- Degui Zhi,
- Xiaoqian Jiang,
- and Arif Harmanci
Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
...panels for genotype imputation, which is a fundamental step in genetic analysis and a computationally resource intensive process that requires access to large protected reference panels. It is therefore performed using an outsourcing approach via “imputation servers,” for example, the Michigan Imputation...
OPEN ACCESS ARTICLE
Select this article
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
...version: In this window In a new window Figure 1. Overview of Spatial Integration for Imputation and Deconvolution (SIID). Given Xenium and Visium expression matrices AX and AV, respectively, with corresponding gene panels GX and GV (with GX ⊂ GV), and a Xenium to Visium spatial mapping Γ, SIID finds...
OPEN ACCESS ARTICLE
Select this article
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
...suitable for laboratories with different resources. Whereas the workflow complexity of PCL-seq is comparable to noncommercial methods such as PIC (Honda et al. 2021) and Light-seq (Kishi et al. 2022), PCL-seq offers broader applicability. (4) Cost-effectiveness and high sensitivity. PCL-seq is highly cost...
Select this article
Resource: The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
- Simon Bray,
- John Chilton,
- Matthias Bernt,
- Nicola Soranzo,
- Marius van den Beek,
- Bérénice Batut,
- Helena Rasche,
- Martin Čech,
- Peter J.A. Cock,
- Björn Grüning,
- and Anton Nekrutenko
Genome Res. February 2023 33: 261-268; Published in Advance February 24, 2023, doi:10.1101/gr.276963.122
...is a tool and workflow specification that is independent of a particular workflow manager; it aims to increase the portability of scientific workflows by allowing workflows written in CWL to be executed by any CWL-supporting workflow manager. Thus, the tasks of workflow composition and workflow execution...
OPEN ACCESS ARTICLE
Select this article
Method: A complete pedigree-based graph workflow for rare candidate variant analysis
- Charles Markello,
- Charles Huang,
- Alex Rodriguez,
- Andrew Carroll,
- Pi-Chuan Chang,
- Jordan Eizenga,
- Thomas Markello,
- David Haussler,
- and Benedict Paten
Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
.... Although pan graphs have helped to reduce reference mapping bias, further performance improvements are possible. We introduce VG-Pedigree, a pedigree-aware workflow based on the pan-mapping tool of Giraffe and the variant calling tool DeepTrio using a specially trained model for Giraffe-based alignments...
Select this article
Resource: Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders
- Guangsheng Pei,
- Yin-Ying Wang,
- Lukas M. Simon,
- Yulin Dai,
- Zhongming Zhao,
- and Peilin Jia
Genome Res. January 2021 31: 146-158; Published in Advance December 3, 2020, doi:10.1101/gr.265769.120
....ResultsOverview of workflowOur goal is to decode CTCs in spatiotemporal specificity throughout human brain development and then uncover disease-relevant cell types for major brain disorders. To this end, we collected various public data sources and conducted a range of bioinformatics and functional genomic analyses (Fig. 1...
Select this article
Resource: Gene expression networks in the Drosophila Genetic Reference Panel
- Logan J. Everett,
- Wen Huang,
- Shanshan Zhou,
- Mary Anna Carbone,
- Richard F. Lyman,
- Gunjan H. Arya,
- Matthew S. Geisz,
- Junwu Ma,
- Fabio Morgante,
- Genevieve St. Armour,
- Lavanya Turlapati,
- Robert R.H. Anholt,
- and Trudy F.C. Mackay
Genome Res. March 2020 30: 485-496; Published in Advance March 6, 2020, doi:10.1101/gr.257592.119
...and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression...
OPEN ACCESS ARTICLE
Select this article
Resource: Hackathons as a means of accelerating scientific discoveries and knowledge transfer
- Amel Ghouila,
- Geoffrey Henry Siwo,
- Jean-Baka Domelevo Entfellner,
- Sumir Panji,
- Katrina A. Button-Simons,
- Sage Zenon Davis,
- Faisal M. Fadlelmola,
- The DREAM of Malaria Hackathon Participants,
- Michael T. Ferdig,
- and Nicola Mulder
Genome Res. May 2018 28: 759-765; Published in Advance April 12, 2018, doi:10.1101/gr.228460.117
...researchers within the team, with only limited internal oversight and critical analysis of the workflow prior to publication. Here, we show how hackathons can be a means of enhancing collaborative science by enabling peer review before results of analyses are published by cross-validating the design...
OPEN ACCESS ARTICLE
Select this article
Method: netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis
- Rebecca Elyanow,
- Bianca Dumitrascu,
- Barbara E. Engelhardt,
- and Benjamin J. Raphael
Genome Res. February 2020 30: 195-204; Published in Advance January 28, 2020, doi:10.1101/gr.251603.119
...regularization takes advantage of prior knowledge of gene–gene interactions, encouraging pairs of genes with known interactions to be nearby each other in the low-dimensional representation. The resulting matrix factorization imputes gene abundance for both zero and nonzero counts and can be used to cluster...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Magalhães et al. 28 (7): 1090.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: