Ki-67 is necessary during DNA replication for fork protection and genome stability
The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years, but investigations on its biological functions have lagged. Recently, Ki-67 has been shown to regula... (Source: Genome Biology)
Source: Genome Biology - April 22, 2024 Category: Genetics & Stem Cells Authors: Konstantinos Stamatiou, Florentin Huguet, Lukas V. Serapinas, Christos Spanos, Juri Rappsilber and Paola Vagnarelli Tags: Research Source Type: research
Minimum information and guidelines for reporting a multiplexed assay of variant effect
Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniq... (Source: Genome Biology)
Source: Genome Biology - April 19, 2024 Category: Genetics & Stem Cells Authors: Melina Claussnitzer, Victoria N. Parikh, Alex H. Wagner, Jeremy A. Arbesfeld, Carol J. Bult, Helen V. Firth, Lara A. Muffley, Alex N. Nguyen Ba, Kevin Riehle, Frederick P. Roth, Daniel Tabet, Benedetta Bolognesi, Andrew M. Glazer and Alan F. Rubin Tags: Correspondence Source Type: research
Measuring, visualizing, and diagnosing reference bias with biastools
Many bioinformatics methods seek to reduce reference bias, but no methods exist to comprehensively measure it. Biastools analyzes and categorizes instances of reference bias. It works in various scenarios: when t... (Source: Genome Biology)
Source: Genome Biology - April 19, 2024 Category: Genetics & Stem Cells Authors: Mao-Jan Lin, Sheila Iyer, Nae-Chyun Chen and Ben Langmead Tags: Software Source Type: research
RBM22 regulates RNA polymerase II 5 ′ pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5
Splicing factors are vital for the regulation of RNA splicing, but some have also been implicated in regulating transcription. The underlying molecular mechanisms of their involvement in transcriptional proces... (Source: Genome Biology)
Source: Genome Biology - April 19, 2024 Category: Genetics & Stem Cells Authors: Xian Du, Wenying Qin, Chunyu Yang, Lin Dai, Mingkui San, Yingdan Xia, Siyu Zhou, Mengyang Wang, Shuang Wu, Shaorui Zhang, Huiting Zhou, Fangshu Li, Fang He, Jingfeng Tang, Jia-Yu Chen, Yu Zhou & hellip; Tags: Research Source Type: research
spVC for the detection and interpretation of spatial gene expression variation
Spatially resolved transcriptomics technologies have opened new avenues for understanding gene expression heterogeneity in spatial contexts. However, existing methods for identifying spatially variable genes o... (Source: Genome Biology)
Source: Genome Biology - April 19, 2024 Category: Genetics & Stem Cells Authors: Shan Yu and Wei Vivian Li Tags: Method Source Type: research
Single Cell Atlas: a single-cell multi-omics human cell encyclopedia
Single-cell sequencing datasets are key in biology and medicine for unraveling insights into heterogeneous cell populations with unprecedented resolution. Here, we construct a single-cell multi-omics map of hu... (Source: Genome Biology)
Source: Genome Biology - April 19, 2024 Category: Genetics & Stem Cells Authors: Lu Pan, Paolo Parini, Roman Tremmel, Joseph Loscalzo, Volker M. Lauschke, Bradley A. Maron, Paola Paci, Ingemar Ernberg, Nguan Soon Tan, Zehuan Liao, Weiyao Yin, Sundararaman Rengarajan and Xuexin Li Tags: Database Source Type: research
Library size confounds biology in spatial transcriptomics data
Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including no... (Source: Genome Biology)
Source: Genome Biology - April 18, 2024 Category: Genetics & Stem Cells Authors: Dharmesh D. Bhuva, Chin Wee Tan, Agus Salim, Claire Marceaux, Marie A. Pickering, Jinjin Chen, Malvika Kharbanda, Xinyi Jin, Ning Liu, Kristen Feher, Givanna Putri, Wayne D. Tilley, Theresa E. Hickey, Marie-Liesse Asselin-Labat, Belinda Phipson and Meliss Tags: Short Report Source Type: research
Characterizing glucokinase variant mechanisms using a multiplexed abundance assay
Amino acid substitutions can perturb protein activity in multiple ways. Understanding their mechanistic basis may pinpoint how residues contribute to protein function. Here, we characterize the mechanisms unde... (Source: Genome Biology)
Source: Genome Biology - April 16, 2024 Category: Genetics & Stem Cells Authors: Sarah Gersing, Thea K. Schulze, Matteo Cagiada, Amelie Stein, Frederick P. Roth, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen Tags: Research Source Type: research
Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods
Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strat... (Source: Genome Biology)
Source: Genome Biology - April 15, 2024 Category: Genetics & Stem Cells Authors: Drew Neavin, Anne Senabouth, Himanshi Arora, Jimmy Tsz Hang Lee, Aida Ripoll-Cladellas, Lude Franke, Shyam Prabhakar, Chun Jimmie Ye, Davis J. McCarthy, Marta Mel é, Martin Hemberg and Joseph E. Powell Tags: Method Source Type: research
Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes
Aneuploidy, an abnormal number of chromosomes within a cell, is a hallmark of cancer. Patterns of aneuploidy differ across cancers, yet are similar in cancers affecting closely related tissues. The selection p... (Source: Genome Biology)
Source: Genome Biology - April 15, 2024 Category: Genetics & Stem Cells Authors: Juman Jubran, Rachel Slutsky, Nir Rozenblum, Lior Rokach, Uri Ben-David and Esti Yeger-Lotem Tags: Research Source Type: research
Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq
We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis functions to account for the dependence of multiple time points in scRNA-seq studies, and uses ... (Source: Genome Biology)
Source: Genome Biology - April 15, 2024 Category: Genetics & Stem Cells Authors: Yue Fan, Lei Li and Shiquan Sun Tags: Method Source Type: research
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identif... (Source: Genome Biology)
Source: Genome Biology - April 15, 2024 Category: Genetics & Stem Cells Authors: Ling-Yi Wu, Yasas Wijesekara, Gon çalo J. Piedade, Nikolaos Pappas, Corina P. D. Brussaard and Bas E. Dutilh Tags: Research Source Type: research
Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies
In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We ... (Source: Genome Biology)
Source: Genome Biology - April 11, 2024 Category: Genetics & Stem Cells Authors: Xiaowen Feng and Heng Li Tags: Research Source Type: research
Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes
Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genom... (Source: Genome Biology)
Source: Genome Biology - April 11, 2024 Category: Genetics & Stem Cells Authors: Thomas Roder, Gr égory Pimentel, Pascal Fuchsmann, Mireille Tena Stern, Ueli von Ah, Guy Vergères, Stephan Peischl, Ola Brynildsrud, Rémy Bruggmann and Cornelia Bär Tags: Software Source Type: research
PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorizat... (Source: Genome Biology)
Source: Genome Biology - April 8, 2024 Category: Genetics & Stem Cells Authors: Claudia Skok Gibbs, Omar Mahmood, Richard Bonneau and Kyunghyun Cho Tags: Method Source Type: research
