A benchmark of computational pipelines for single-cell histone modification data
Single-cell histone post translational modification (scHPTM) assays such as scCUT&Tag or scChIP-seq allow single-cell mapping of diverse epigenomic landscapes within complex tissues and are likely to unlock ou... (Source: Genome Biology)
Source: Genome Biology - June 20, 2023 Category: Genetics & Stem Cells Authors: F élix Raimundo, Pacôme Prompsy, Jean-Philippe Vert and Céline Vallot Tags: Research Source Type: research
CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies fr... (Source: Genome Biology)
Source: Genome Biology - June 20, 2023 Category: Genetics & Stem Cells Authors: Bingxin Lu, Kit Curtius, Trevor A. Graham, Ziheng Yang and Chris P. Barnes Tags: Method Source Type: research
The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species
The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is... (Source: Genome Biology)
Source: Genome Biology - June 19, 2023 Category: Genetics & Stem Cells Authors: Timothy P. L. Smith, Derek M. Bickhart, Didier Boichard, Amanda J. Chamberlain, Appolinaire Djikeng, Yu Jiang, Wai Y. Low, Hubert Pausch, Sebastian Demyda-Peyr ás, James Prendergast, Robert D. Schnabel and Benjamin D. Rosen Tags: Correspondence Source Type: research
The effect of background noise and its removal on the analysis of single-cell expression data
In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from ce... (Source: Genome Biology)
Source: Genome Biology - June 19, 2023 Category: Genetics & Stem Cells Authors: Philipp Janssen, Zane Kliesmete, Beate Vieth, Xian Adiconis, Sean Simmons, Jamie Marshall, Cristin McCabe, Holger Heyn, Joshua Z. Levin, Wolfgang Enard and Ines Hellmann Tags: Research Source Type: research
Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis
Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits. (Source: Genome Biology)
Source: Genome Biology - June 19, 2023 Category: Genetics & Stem Cells Authors: Long Li, Zhitao Tian, Jie Chen, Zengdong Tan, Yuting Zhang, Hu Zhao, Xiaowei Wu, Xuan Yao, Weiwei Wen, Wei Chen and Liang Guo Tags: Research Source Type: research
Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting
Despite the recent rise of RNA-seq datasets combining single-cell (sc) resolution with 4-thiouridine (4sU) labelling, analytical methods exploiting their power to dissect transcriptional bursting are lacking. ... (Source: Genome Biology)
Source: Genome Biology - June 16, 2023 Category: Genetics & Stem Cells Authors: David M. Edwards, Philip Davies and Daniel Hebenstreit Tags: Method Source Type: research
Matchtigs: minimum plain text representation of k-mer sets
We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacteri... (Source: Genome Biology)
Source: Genome Biology - June 9, 2023 Category: Genetics & Stem Cells Authors: Sebastian Schmidt, Shahbaz Khan, Jarno N. Alanko, Giulio E. Pibiri and Alexandru I. Tomescu Tags: Method Source Type: research
Author Correction: INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing
(Source: Genome Biology)
Source: Genome Biology - June 9, 2023 Category: Genetics & Stem Cells Authors: Dimitrije Ivan čić, Júlia Mir-Pedrol, Jessica Jaraba-Wallace, Núria Rafel, Avencia Sanchez-Mejias and Marc Güell Tags: Author Correction Source Type: research
Protein length distribution is remarkably uniform across the tree of life
In every living species, the function of a protein depends on its organization of structural domains, and the length of a protein is a direct reflection of this. Because every species evolved under different e... (Source: Genome Biology)
Source: Genome Biology - June 8, 2023 Category: Genetics & Stem Cells Authors: Yannis Nevers, Natasha M. Glover, Christophe Dessimoz and Odile Lecompte Tags: Research Source Type: research
Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Recent deep learning models that predict the Hi-C contact map from DNA sequence achieve promising accuracy but cannot generalize to new cell types and or even capture differences among training cell types. We ... (Source: Genome Biology)
Source: Genome Biology - June 6, 2023 Category: Genetics & Stem Cells Authors: Rui Yang, Arnav Das, Vianne R. Gao, Alireza Karbalayghareh, William S. Noble, Jeffery A. Bilmes and Christina S. Leslie Tags: Method Source Type: research
Pervasive tandem duplications and convergent evolution shape coral genomes
Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central... (Source: Genome Biology)
Source: Genome Biology - June 1, 2023 Category: Genetics & Stem Cells Authors: Benjamin Noel, France Denoeud, Alice Rouan, Carol Buitrago-L ópez, Laura Capasso, Julie Poulain, Emilie Boissin, Mélanie Pousse, Corinne Da Silva, Arnaud Couloux, Eric Armstrong, Quentin Carradec, Corinne Cruaud, Karine Labadie, Julie Lê-Hoang, Sylvie Tags: Research Source Type: research
mutscan —a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data
Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by selective enrichment of sequences with desirable properties followed by quantification by ... (Source: Genome Biology)
Source: Genome Biology - June 1, 2023 Category: Genetics & Stem Cells Authors: Charlotte Soneson, Alexandra M. Bendel, Guillaume Diss and Michael B. Stadler Tags: Software Source Type: research
A survey of mapping algorithms in the long-reads era
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend fra... (Source: Genome Biology)
Source: Genome Biology - June 1, 2023 Category: Genetics & Stem Cells Authors: Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux and Camille Marchet Tags: Review Source Type: research
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries
We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it could serve as t... (Source: Genome Biology)
Source: Genome Biology - May 31, 2023 Category: Genetics & Stem Cells Authors: Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, Ren é Rahn, Martin Vingron and Knut Reinert Tags: Method Source Type: research
Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis
Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants... (Source: Genome Biology)
Source: Genome Biology - May 30, 2023 Category: Genetics & Stem Cells Authors: Christian Kappel, Thomas Friedrich, Vicky Oberkofler, Li Jiang, Tim Crawford, Michael Lenhard and Isabel B äurle Tags: Research Source Type: research
