CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
In this study, we introduce CREaTor, an attention-based deep neural network designed to model cis-regulatory patterns for genom... (Source: Genome Biology)
Source: Genome Biology - November 23, 2023 Category: Genetics & Stem Cells Authors: Yongge Li, Fusong Ju, Zhiyuan Chen, Yiming Qu, Huanhuan Xia, Liang He, Lijun Wu, Jianwei Zhu, Bin Shao and Pan Deng Tags: Method Source Type: research
Cytomulate: accurate and efficient simulation of CyTOF data
Recently, many analysis tools have been devised to offer insights into data generated via cytometry by time-of-flight (CyTOF). However, objective evaluations of these methods remain absent as most evaluations ... (Source: Genome Biology)
Source: Genome Biology - November 16, 2023 Category: Genetics & Stem Cells Authors: Yuqiu Yang, Kaiwen Wang, Zeyu Lu, Tao Wang and Xinlei Wang Tags: Method Source Type: research
N-of-one differential gene expression without control samples using a deep generative model
Differential analysis of bulk RNA-seq data often suffers from lack of good controls. Here, we present a generative model that replaces controls, trained solely on healthy tissues. The unsupervised model learns... (Source: Genome Biology)
Source: Genome Biology - November 16, 2023 Category: Genetics & Stem Cells Authors: I ñigo Prada-Luengo, Viktoria Schuster, Yuhu Liang, Thilde Terkelsen, Valentina Sora and Anders Krogh Tags: Method Source Type: research
Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
Using mouse genetic studies and systematic assessments of brain neuroanatomical phenotypes, we set out to identify which of the 30 genes causes brain defects at the autism-associated 16p11.2 locus. (Source: Genome Biology)
Source: Genome Biology - November 15, 2023 Category: Genetics & Stem Cells Authors: Perrine F. Kretz, Christel Wagner, Anna Mikhaleva, Charlotte Montillot, Sylvain Hugel, Ilaria Morella, Meghna Kannan, Marie-Christine Fischer, Maxence Milhau, Ipek Yalcin, Riccardo Brambilla, Mohammed Selloum, Yann Herault, Alexandre Reymond, Stephan C. C Tags: Research Source Type: research
Fake IDs? Widespread misannotation of DNA transposons as a general transcription factor
This study reveals how the general transcriptio... (Source: Genome Biology)
Source: Genome Biology - November 13, 2023 Category: Genetics & Stem Cells Authors: Nozhat T. Hassan and David L. Adelson Tags: Short Report Source Type: research
A genome catalog of the early-life human skin microbiome
Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack represent... (Source: Genome Biology)
Source: Genome Biology - November 10, 2023 Category: Genetics & Stem Cells Authors: Zeyang Shen, Lukian Robert, Milan Stolpman, You Che, Katrina J. Allen, Richard Saffery, Audrey Walsh, Angela Young, Jana Eckert, Clay Deming, Qiong Chen, Sean Conlan, Karen Laky, Jenny Min Li, Lindsay Chatman, Sara Saheb Kashaf & hellip; Tags: Research Source Type: research
Statistical learning quantifies transposable element-mediated cis-regulation
Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from ... (Source: Genome Biology)
Source: Genome Biology - November 10, 2023 Category: Genetics & Stem Cells Authors: Cyril Pulver, Delphine Grun, Julien Duc, Shaoline Sheppard, Evarist Planet, Alexandre Coudray, Rapha ël de Fondeville, Julien Pontis and Didier Trono Tags: Research Source Type: research
Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis
Feature selection is an essential task in single-cell RNA-seq (scRNA-seq) data analysis and can be critical for gene dimension reduction and downstream analyses, such as gene marker identification and cell typ... (Source: Genome Biology)
Source: Genome Biology - November 10, 2023 Category: Genetics & Stem Cells Authors: Hao Huang, Chunlei Liu, Manoj M. Wagle and Pengyi Yang Tags: Research Source Type: research
Author Correction: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
(Source: Genome Biology)
Source: Genome Biology - November 7, 2023 Category: Genetics & Stem Cells Authors: Jennifer R. S. Meadows, Jefrey M. Kidd, Guo-Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laure Tags: Author Correction Source Type: research
Phytochromes transmit photoperiod information via the evening complex in Brachypodium
Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD1 (PPD1) and EARLY FLOWERING3 (ELF3) have been... (Source: Genome Biology)
Source: Genome Biology - November 7, 2023 Category: Genetics & Stem Cells Authors: Mingjun Gao, Yunlong Lu, Feng Geng, Cornelia Klose, Anne-Marie Staudt, He Huang, Duy Nguyen, Hui Lan, Han Lu, Todd C. Mockler, Dmitri A. Nusinow, Andreas Hiltbrunner, Eberhard Sch äfer, Philip A. Wigge and Katja E. Jaeger Tags: Research Source Type: research
The chromatin landscape of the euryarchaeon Haloferax volcanii
Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations fir... (Source: Genome Biology)
Source: Genome Biology - November 6, 2023 Category: Genetics & Stem Cells Authors: Georgi K. Marinov, S. Tansu Bagdatli, Tong Wu, Chuan He, Anshul Kundaje and William J. Greenleaf Tags: Research Source Type: research
Quantification of evolved DNA-editing enzymes at scale with DEQSeq
We introduce DEQSeq, a nanopore sequencing approach that rationalizes the selection of favorable genome editing enzymes from directed molecular evolution experiments. With the ability to capture full-length se... (Source: Genome Biology)
Source: Genome Biology - November 6, 2023 Category: Genetics & Stem Cells Authors: Lukas Theo Schmitt, Aksana Schneider, Jonas Posorski, Felix Lansing, Milica Jelicic, Manavi Jain, Shady Sayed, Frank Buchholz and Duran S ürün Tags: Method Source Type: research
In-organoid single-cell CRISPR screening reveals determinants of hepatocyte differentiation and maturation
Harnessing hepatocytes for basic research and regenerative medicine demands a complete understanding of the genetic determinants underlying hepatocyte differentiation and maturation. Single-cell CRISPR screens... (Source: Genome Biology)
Source: Genome Biology - October 31, 2023 Category: Genetics & Stem Cells Authors: Junbo Liang, Jinsong Wei, Jun Cao, Jun Qian, Ran Gao, Xiaoyu Li, Dingding Wang, Yani Gu, Lei Dong, Jia Yu, Bing Zhao and Xiaoyue Wang Tags: Research Source Type: research
MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing
In this study, we develop a simple and efficient method — multiple genetic abnormality sequencing (MGA-Seq) — to simultaneously detect... (Source: Genome Biology)
Source: Genome Biology - October 30, 2023 Category: Genetics & Stem Cells Authors: Da Lin, Yanyan Zou, Xinyu Li, Jinyue Wang, Qin Xiao, Xiaochen Gao, Fei Lin, Ningyuan Zhang, Ming Jiao, Yu Guo, Zhaowei Teng, Shiyi Li, Yongchang Wei, Fuling Zhou, Rong Yin, Siheng Zhang & hellip; Tags: Method Source Type: research
Landscape of enhancer disruption and functional screen in melanoma cells
The high mutation rate throughout the entire melanoma genome presents a major challenge in stratifying true driver events from the background mutations. Numerous recurrent non-coding alterations, such as those... (Source: Genome Biology)
Source: Genome Biology - October 30, 2023 Category: Genetics & Stem Cells Authors: Zhao Wang, Menghan Luo, Qian Liang, Ke Zhao, Yuelin Hu, Wei Wang, Xiangling Feng, Bolang Hu, Jianjin Teng, Tianyi You, Ran Li, Zhengkai Bao, Wenhao Pan, Tielong Yang, Chao Zhang, Ting Li & hellip; Tags: Research Source Type: research
