Single-cell RNA-seq mapping of chicken peripheral blood leukocytes
Single-cell transcriptomics provides means to study cell populations at the level of individual cells. In leukocyte biology this approach could potentially aid the identification of subpopulations and function... (Source: BMC Genomics)
Source: BMC Genomics - January 29, 2024 Category: Genetics & Stem Cells Authors: Matilda Maxwell, Robert S öderlund, Sonja Härtle and Eva Wattrang Tags: Research Source Type: research
CrustyBase v.2.0: new features and enhanced utilities to support open science
Transcriptomes present a rich, multi-dimensional subset of genomics data. They provide broad insights into genetic sequence, and more significantly gene expression, across biological samples. This technology i... (Source: BMC Genomics)
Source: BMC Genomics - January 29, 2024 Category: Genetics & Stem Cells Authors: Cameron J. Hyde and Tomer Ventura Tags: Database Source Type: research
Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity
Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing has utili... (Source: BMC Genomics)
Source: BMC Genomics - January 29, 2024 Category: Genetics & Stem Cells Authors: Saranga Wijeratne, Maria E. Hernandez Gonzalez, Kelli Roach, Katherine E. Miller, Kathleen M. Schieffer, James R. Fitch, Jeffrey Leonard, Peter White, Benjamin J. Kelly, Catherine E. Cottrell, Elaine R. Mardis, Richard K. Wilson and Anthony R. Miller Tags: Research Source Type: research
Insights into the multi-chromosomal mitochondrial genome structure of the xero-halophytic plant Haloxylon Ammodendron (C.A.Mey.) Bunge ex Fenzl
Haloxylon ammodendron holds significance as an ecological plant, showcasing remarkable adaptability to desert conditions, halophytic environments, and sand fixation. With its potential for carbon sequestration, i... (Source: BMC Genomics)
Source: BMC Genomics - January 29, 2024 Category: Genetics & Stem Cells Authors: Lulu Yang, Jia Liu, Wenjun Guo, Zehan Zheng, Yafei Xu, Houjun Xia and Tian Xiao Tags: Research Source Type: research
Genome-wide identification and expression characterization of the GH3 gene family of tea plant (Camellia sinensis)
To comprehensively understand the characteristics of the GH3 gene family in tea plants (Camellia sinensis), we identified 17 CsGH3 genes and analyzed their physicochemical properties, phylogenetic relationships, ... (Source: BMC Genomics)
Source: BMC Genomics - January 27, 2024 Category: Genetics & Stem Cells Authors: Xinge Wang, Chunyu Jia, Lishuang An, Jiangyan Zeng, Aixia Ren, Xin Han, Yiqing Wang and Shuang Wu Tags: Research Source Type: research
Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce
Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt... (Source: BMC Genomics)
Source: BMC Genomics - January 27, 2024 Category: Genetics & Stem Cells Authors: Tin Hang Hung, Ernest T. Y. Wu, Pauls Zelti ņš, Āris Jansons, Aziz Ullah, Nadir Erbilgin, Joerg Bohlmann, Jean Bousquet, Inanc Birol, Sonya M. Clegg and John J. MacKay Tags: Research Source Type: research
A transcriptomic examination of encased rotifer embryos reveals the developmental trajectory leading to long-term dormancy; are they “animal seeds”?
Organisms from many distinct evolutionary lineages acquired the capacity to enter a dormant state in response to environmental conditions incompatible with maintaining normal life activities. Most studied orga... (Source: BMC Genomics)
Source: BMC Genomics - January 27, 2024 Category: Genetics & Stem Cells Authors: Tamar Hashimshony, Liron Levin, Andreas C. Fr öbius, Nitsan Dahan, Vered Chalifa-Caspi, Reini Hamo, Oshri Gabai-Almog, Idit Blais, Yehuda G. Assaraf and Esther Lubzens Tags: Research Source Type: research
LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants
Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated... (Source: BMC Genomics)
Source: BMC Genomics - January 26, 2024 Category: Genetics & Stem Cells Authors: Jinfeng Lu, Camilo Toro, David R. Adams, Cristiane Araujo Martins Moreno, Wan-Ping Lee, Yuk Yee Leung, Mathew B. Harms, Badri Vardarajan and Erin L. Heinzen Tags: Software Source Type: research
Star allele search: a pharmacogenetic annotation database and user-friendly search tool of publicly available 1000 Genomes Project biospecimens
Here we describe a new public pharmacogenetic (PGx) annotation database of a large (n = 3,202) and diverse biospecimen collection of 1000 Genomes Project cell lines and DNAs. The database is searchable with a use... (Source: BMC Genomics)
Source: BMC Genomics - January 26, 2024 Category: Genetics & Stem Cells Authors: N. Gharani, G. Calendo, D. Kusic, J. Madzo and L. Scheinfeldt Tags: Database Source Type: research
ECDEP: identifying essential proteins based on evolutionary community discovery and subcellular localization
In cellular activities, essential proteins play a vital role and are instrumental in comprehending fundamental biological necessities and identifying pathogenic genes. Current deep learning approaches for pred... (Source: BMC Genomics)
Source: BMC Genomics - January 26, 2024 Category: Genetics & Stem Cells Authors: Chen Ye, Qi Wu, Shuxia Chen, Xuemei Zhang, Wenwen Xu, Yunzhi Wu, Youhua Zhang and Yi Yue Tags: Research Source Type: research
Identification of ARF genes in Cucurbita pepo L and analysis of expression patterns, and functional analysis of CpARF22 under drought, salt stress
Auxin transcription factor (ARF) is an important transcription factor that transmits auxin signals and is involved in plant growth and development as well as stress response. However, genome-wide identificatio... (Source: BMC Genomics)
Source: BMC Genomics - January 25, 2024 Category: Genetics & Stem Cells Authors: Ming-jun Zhang, Ying-yu Xue, Shuang Xu, Xuan-ru Jin and Xing-chu Man Tags: Research Source Type: research
Differential gene expression and microRNA profile in corpora allata-corpora cardiaca of Aedes aegypti mosquitoes with weak juvenile hormone signalling
The corpora allata-corpora cardiaca (CA-CC) is an endocrine gland complex that regulates mosquito development and reproduction through the synthesis of juvenile hormone (JH). Epoxidase (Epox) is a key enzyme in t... (Source: BMC Genomics)
Source: BMC Genomics - January 25, 2024 Category: Genetics & Stem Cells Authors: Zhi Qi, Kayvan Etebari, Marcela Nouzova, Fernando G. Noriega and Sassan Asgari Tags: Research Source Type: research
Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae
Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stew... (Source: BMC Genomics)
Source: BMC Genomics - January 25, 2024 Category: Genetics & Stem Cells Authors: Daliang Liu, Zhihan Zhang, Yanlin Hao, Mengge Li, Houlin Yu, Xingruo Zhang, Haoyang Mi, Lin Cheng and Yiyong Zhao Tags: Research Source Type: research
High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly
Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short read... (Source: BMC Genomics)
Source: BMC Genomics - January 24, 2024 Category: Genetics & Stem Cells Authors: Ludwig Mann, Kristin Balasch, Nicola Schmidt and Tony Heitkam Tags: Software Source Type: research
Genome-wide identification of B-box zinc finger (BBX) gene family in Medicago sativa and their roles in abiotic stress responses
B-box (BBX) family is a class of zinc finger transcription factors (TFs) that play essential roles in regulating plant growth, development, as well as abiotic stress. However, no systematic analysis of BBX genes ... (Source: BMC Genomics)
Source: BMC Genomics - January 24, 2024 Category: Genetics & Stem Cells Authors: Shuxia Li, Shuaiqi Guo, Xueqin Gao, Xiaotong Wang, Yaling Liu, Jing Wang, Xiaohong Li, Jinqing Zhang and Bingzhe Fu Tags: Research Source Type: research
