Wang, Fang Wang, Qihan Mohanty, Vakul Liang, Shaoheng Dou, Jinzhuang Han, Jincheng Minussi, Darlan Conterno Gao, Ruli Ding, Li Navin, Nicholas
...
Published in
Genome Biology
We present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles, and a statistical routine named lineage speciation analysis (LSA), whichty facilitates discovery of fitness-associated alterations and genes from SCCN lineage trees. ...
Akbari, Vahid Garant, Jean-Michel O’Neill, Kieran Pandoh, Pawan Moore, Richard Marra, Marco A. Hirst, Martin Jones, Steven J. M.
Published in
Genome Biology
The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. However, there is currently no complete software for detecting SNPs, phasing haplotypes, and mapping methylation to these from nanopore sequence data. Here, we present Nano...
Guo, Hongyu Li, Jun
Published in
Genome Biology
On single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact expression levels are unavailable, that is, without using a reference dataset. Based on an observation that the expected over-expression of marker genes is ofte...
Cheifet, Barbara
Published in
Genome Biology
Long, Yanping Liu, Zhijian Jia, Jinbu Mo, Weipeng Fang, Liang Lu, Dongdong Liu, Bo Zhang, Hong Chen, Wei Zhai, Jixian
...
Published in
Genome Biology
The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nu...
Schmeing, Stephan Robinson, Mark D.
Published in
Genome Biology
In high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions at each step of a project. Simulations are a critical part of method comparisons, but for standard Illumina sequencing of genomic DNA, they are often oversimplified, which leads to optimistic results for most tools. Re...
Bernstein, David B. Sulheim, Snorre Almaas, Eivind Segrè, Daniel
Published in
Genome Biology
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources o...
Roller, Maša Stamper, Ericca Villar, Diego Izuogu, Osagie Martin, Fergal Redmond, Aisling M. Ramachanderan, Raghavendra Harewood, Louise Odom, Duncan T. Flicek, Paul
...
Published in
Genome Biology
Background To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals. Results The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-spec...
Wang, Dongfang Hou, Siyu Zhang, Lei Wang, Xiliang Liu, Baolin Zhang, Zemin
Published in
Genome Biology
The integration of single-cell RNA-sequencing datasets from multiple sources is critical for deciphering cell-to-cell heterogeneities and interactions in complex biological systems. We present a novel unsupervised batch effect removal framework, called iMAP, based on both deep autoencoders and generative adversarial networks. Compared with current ...
Przytycki, Pawel F. Pollard, Katherine S.
Published in
Genome Biology
Single-cell and bulk genomics assays have complementary strengths and weaknesses, and alone neither strategy can fully capture regulatory elements across the diversity of cells in complex tissues. We present CellWalker, a method that integrates single-cell open chromatin (scATAC-seq) data with gene expression (RNA-seq) and other data types using a ...