DISSECT: deep semi-supervised consistency regularization for accurate cell type fraction and gene expression estimation
Cell deconvolution is the estimation of cell type fractions and cell type-specific gene expression from mixed data. An unmet challenge in cell deconvolution is the scarcity of realistic training data and the d... (Source: Genome Biology)
Source: Genome Biology - April 30, 2024 Category: Genetics & Stem Cells Authors: Robin Khatri, Pierre Machart and Stefan Bonn Tags: Method Source Type: research
Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins
Metazoans inherited genes from unicellular ancestors that perform essential biological processes such as cell division, metabolism, and protein translation. Multicellularity requires careful control and coordi... (Source: Genome Biology)
Source: Genome Biology - April 29, 2024 Category: Genetics & Stem Cells Authors: Anna S. Trigos, Felicia Bongiovanni, Yangyi Zhang, Maia Zethoven, Richard Tothill, Richard Pearson, Anthony T. Papenfuss and David L. Goode Tags: Research Source Type: research
Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes
Untranslated regions (UTRs) are important mediators of post-transcriptional regulation. The length of UTRs and the composition of regulatory elements within them are known to vary substantially across genes, b... (Source: Genome Biology)
Source: Genome Biology - April 29, 2024 Category: Genetics & Stem Cells Authors: Nechama Wieder, Elston N. D ’Souza, Alexandra C. Martin-Geary, Frederik H. Lassen, Jonathan Talbot-Martin, Maria Fernandes, Sonia P. Chothani, Owen J. L. Rackham, Sebastian Schafer, Julie L. Aspden, Daniel G. MacArthur, Robert W. Davies and Nicola Whiff Tags: Research Source Type: research
hadge: a comprehensive pipeline for donor deconvolution in single-cell studies
Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonuc... (Source: Genome Biology)
Source: Genome Biology - April 26, 2024 Category: Genetics & Stem Cells Authors: Fabiola Curion, Xichen Wu, Lukas Heumos, Mylene Mariana Gonzales Andr é, Lennard Halle, Matiss Ozols, Melissa Grant-Peters, Charlotte Rich-Griffin, Hing-Yuen Yeung, Calliope A. Dendrou, Herbert B. Schiller and Fabian J. Theis Tags: Software Source Type: research
NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads
Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient error correction and assembly too... (Source: Genome Biology)
Source: Genome Biology - April 26, 2024 Category: Genetics & Stem Cells Authors: Jiang Hu, Zhuo Wang, Zongyi Sun, Benxia Hu, Adeola Oluwakemi Ayoola, Fan Liang, Jingjing Li, Jos é R. Sandoval, David N. Cooper, Kai Ye, Jue Ruan, Chuan-Le Xiao, Depeng Wang, Dong-Dong Wu and Sheng Wang Tags: Software Source Type: research
Enhancing prime editor flexibility with coiled-coil heterodimers
Prime editing enables precise base substitutions, insertions, and deletions at targeted sites without the involvement of double-strand DNA breaks or exogenous donor DNA templates. However, the large size of pr... (Source: Genome Biology)
Source: Genome Biology - April 26, 2024 Category: Genetics & Stem Cells Authors: Shuangshuang Mu, Huangyao Chen, Qianru Li, Shixue Gou, Xiaoyi Liu, Junwei Wang, Wei Zheng, Menglong Chen, Qin Jin, Liangxue Lai, Kepin Wang and Hui Shi Tags: Research Source Type: research
Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification
Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. In Centrifuger, the Burrows-Wheeler transformed genome sequences are losslessly c... (Source: Genome Biology)
Source: Genome Biology - April 25, 2024 Category: Genetics & Stem Cells Authors: Li Song and Ben Langmead Tags: Software Source Type: research
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
