GenArk: towards a million UCSC genome browsers
Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI a... (Source: Genome Biology)
Source: Genome Biology - October 2, 2023 Category: Genetics & Stem Cells Authors: Hiram Clawson, Brian T. Lee, Brian J. Raney, Galt P. Barber, Jonathan Casper, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Christopher M. Lee, Luis R. Nassar, Gerardo Perez, Brittney Wick, Daniel Schmelter, Matthew L. Speir, Joe Tags: Short Report Source Type: research
MBE: model-based enrichment estimation and prediction for differential sequencing data
Characterizing differences in sequences between two conditions, such as with and without drug exposure, using high-throughput sequencing data is a prevalent problem involving quantifying changes in sequence ab... (Source: Genome Biology)
Source: Genome Biology - October 2, 2023 Category: Genetics & Stem Cells Authors: Akosua Busia and Jennifer Listgarten Tags: Method Source Type: research
happi: a hierarchical approach to pangenomics inference
Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable... (Source: Genome Biology)
Source: Genome Biology - September 29, 2023 Category: Genetics & Stem Cells Authors: Pauline Trinh, David S. Clausen and Amy D. Willis Tags: Method Source Type: research
Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing
Dominance and other non-additive genetic effects arise from the interaction between alleles, and historically these phenomena play a major role in quantitative genetics. However, most genome-wide association s... (Source: Genome Biology)
Source: Genome Biology - September 29, 2023 Category: Genetics & Stem Cells Authors: Leilei Cui, Bin Yang, Shijun Xiao, Jun Gao, Amelie Baud, Delyth Graham, Martin McBride, Anna Dominiczak, Sebastian Schafer, Regina Lopez Aumatell, Carme Mont, Albert Fernandez Teruel, Norbert H übner, Jonathan Flint, Richard Mott and Lusheng Huang Tags: Research Source Type: research
A loss-of-function mutation in human Oxidation Resistance 1 disrupts the spatial –temporal regulation of histone arginine methylation in neurodevelopment
Oxidation Resistance 1 (OXR1) gene is a highly conserved gene of the TLDc domain-containing family. OXR1 is involved in fundamental biological and cellular processes, including DNA damage response, antioxidant pa... (Source: Genome Biology)
Source: Genome Biology - September 29, 2023 Category: Genetics & Stem Cells Authors: Xiaolin Lin, Wei Wang, Mingyi Yang, Nadirah Damseh, Mirta Mittelstedt Leal de Sousa, Fadi Jacob, Anna L ång, Elise Kristiansen, Marco Pannone, Miroslava Kissova, Runar Almaas, Anna Kuśnierczyk, Richard Siller, Maher Shahrour, Motee Al-Ashhab, Bassam Abu Tags: Research Source Type: research
DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection
Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constr... (Source: Genome Biology)
Source: Genome Biology - September 20, 2023 Category: Genetics & Stem Cells Authors: Fabian Hausmann, Can Ergen, Robin Khatri, Mohamed Marouf, Sonja H änzelmann, Nicola Gagliani, Samuel Huber, Pierre Machart and Stefan Bonn Tags: Research Source Type: research
Dosage compensation of Z sex chromosome genes in avian fibroblast cells
In birds, sex is genetically determined; however, the molecular mechanism is not well-understood. The avian Z sex chromosome (chrZ) lacks whole chromosome inactivation, in contrast to the mammalian chrX. To in... (Source: Genome Biology)
Source: Genome Biology - September 20, 2023 Category: Genetics & Stem Cells Authors: Ruslan Deviatiiarov, Hiroki Nagai, Galym Ismagulov, Anastasia Stupina, Kazuhiro Wada, Shinji Ide, Noriyuki Toji, Heng Zhang, Woranop Sukparangsi, Sittipon Intarapat, Oleg Gusev and Guojun Sheng Tags: Short Report Source Type: research
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods
Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic differences within tissues, whi... (Source: Genome Biology)
Source: Genome Biology - September 18, 2023 Category: Genetics & Stem Cells Authors: Natalie Charitakis, Agus Salim, Adam T. Piers, Kevin I. Watt, Enzo R. Porrello, David A. Elliott and Mirana Ramialison Tags: Short Report Source Type: research
Author Correction: Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem
(Source: Genome Biology)
Source: Genome Biology - September 18, 2023 Category: Genetics & Stem Cells Authors: Xiangqian Zhu, Zhongping Xu, Guanying Wang, Yulong Cong, Lu Yu, Ruoyu Jia, Yuan Qin, Guangyu Zhang, Bo Li, Daojun Yuan, Lili Tu, Xiyan Yang, Keith Lindsey, Xianlong Zhang and Shuangxia Jin Tags: Author Correction Source Type: research
Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment
Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine... (Source: Genome Biology)
Source: Genome Biology - September 18, 2023 Category: Genetics & Stem Cells Authors: Xiaoting Xia, Fengwei Zhang, Shuang Li, Xiaoyu Luo, Lixin Peng, Zheng Dong, Hubert Pausch, Alexander S. Leonard, Danang Crysnanto, Shikang Wang, Bin Tong, Johannes A. Lenstra, Jianlin Han, Fuyong Li, Tieshan Xu, Lihong Gu & hellip; Tags: Research Source Type: research
COLLAGENE enables privacy-aware federated and collaborative genomic data analysis
We present COLLAGENE... (Source: Genome Biology)
Source: Genome Biology - September 11, 2023 Category: Genetics & Stem Cells Authors: Wentao Li, Miran Kim, Kai Zhang, Han Chen, Xiaoqian Jiang and Arif Harmanci Tags: Software Source Type: research
PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fusion going from 48 to 46 chromosomes in hominin evolution
Resolving complex genomic regions rich in segmental duplications (SDs) is challenging due to the high error rate of long-read sequencing. Here, we describe a targeted approach with a novel genome assembler Pha... (Source: Genome Biology)
Source: Genome Biology - September 11, 2023 Category: Genetics & Stem Cells Authors: Barbara Poszewiecka, Krzysztof Gogolewski, Justyna A. Karolak, Pawe ł Stankiewicz and Anna Gambin Tags: Method Source Type: research
Coupling of co-transcriptional splicing and 3 ’ end Pol II pausing during termination in Arabidopsis
In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulat... (Source: Genome Biology)
Source: Genome Biology - September 11, 2023 Category: Genetics & Stem Cells Authors: Sixian Zhou, Fengli Zhao, Danling Zhu, Qiqi Zhang, Ziwei Dai and Zhe Wu Tags: Research Source Type: research
The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect... (Source: Genome Biology)
Source: Genome Biology - September 11, 2023 Category: Genetics & Stem Cells Authors: Kenneth A. Barr, Katherine L. Rhodes and Yoav Gilad Tags: Research Source Type: research
ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data
Clustering is a critical component of single-cell RNA sequencing (scRNA-seq) data analysis and can help reveal cell types and infer cell lineages. Despite considerable successes, there are few methods tailored... (Source: Genome Biology)
Source: Genome Biology - September 11, 2023 Category: Genetics & Stem Cells Authors: Yang Li, Mingcong Wu, Shuangge Ma and Mengyun Wu Tags: Method Source Type: research
