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Genome Biology
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14.03
Papers
5983
Papers 6083
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#1Keith Mitchell (UCLA: University of California, Los Angeles)H-Index: 2
#2Jaqueline J. Brito (SC: University of Southern California)
Last. Russell Jared Littman (UCLA: University of California, Los Angeles)H-Index: 2
view all 26 authors...
BACKGROUND: Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequencing technologies in clinical tools. Computational error correction promises to eliminate sequencing errors, but the relative accuracy of error correction algorithms remains unknow...
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#1Alexander Dilthey (HHU: University of Düsseldorf)H-Index: 20
#2Sebastian A. Meyer (HHU: University of Düsseldorf)H-Index: 1
Last. Achim J. Kaasch (HHU: University of Düsseldorf)H-Index: 13
view all 3 authors...
Hybrid genome assembly has emerged as an important technique in bacterial genomics, but cost and labor requirements limit large-scale application. We present Ultraplexing, a method to improve per-sample sequencing cost and hands-on time of Nanopore sequencing for hybrid assembly by at least 50% compared to molecular barcoding while maintaining high assembly quality. Ultraplexing requires the availability of Illumina data and uses inter-sample genetic variability to assign reads to isolates, whic...
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#1Itai YanaiH-Index: 34
#2Martin J. Lercher (HHU: University of Düsseldorf)H-Index: 40
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#1Juri Kazakevych (Babraham Institute)H-Index: 1
#2Jérémy Denizot (French Institute of Health and Medical Research)H-Index: 10
Last. Marina Célestine (Babraham Institute)
view all 16 authors...
BACKGROUND: How intestinal epithelial cells interact with the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is a conserved chromatin remodeling factor with a poorly understood tissue function. As this factor is highly expressed in the stem and proliferative zones of the intestinal epithelium, we explore its role in this tissue. RESULTS: Specific deletion of Smarcad1 in the mouse intestinal epithelium leads to colitis resistance and substantial...
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#1Tom O Mokveld (TU Delft: Delft University of Technology)H-Index: 1
#2Jasper Linthorst (TU Delft: Delft University of Technology)
Last. Marcel J. T. Reinders (TU Delft: Delft University of Technology)H-Index: 47
view all 5 authors...
The practical use of graph-based reference genomes depends on the ability to align reads to them. Performing substring queries to paths through these graphs lies at the core of this task. The combination of increasing pattern length and encoded variations inevitably leads to a combinatorial explosion of the search space. Instead of heuristic filtering or pruning steps to reduce the complexity, we propose CHOP, a method that constrains the search space by exploiting haplotype information, boundin...
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#1Michael Peeri (TAU: Tel Aviv University)H-Index: 4
#2Tamir Tuller (TAU: Tel Aviv University)H-Index: 34
BACKGROUND: mRNA can form local secondary structure within the protein-coding sequence, and the strength of this structure is thought to influence gene expression regulation. Previous studies suggest that secondary structure strength may be maintained under selection, but the details of this phenomenon are not well understood. RESULTS: We perform a comprehensive study of the selection on local mRNA folding strengths considering variation between species across the tree of life. We show for the f...
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#1Sunil Bodapati (Stanford University)H-Index: 6
#2Timothy Daley (Stanford University)H-Index: 9
Last. Lei S. Qi (Stanford University)H-Index: 30
view all 5 authors...
Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both ...
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#1Peipei Li (Van Andel Institute)H-Index: 3
#2Elizabeth Ensink (Van Andel Institute)
Last. Viviane Labrie (MSU: Michigan State University)H-Index: 16
view all 8 authors...
BACKGROUND: Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in isolated prefrontal cortex neurons from control and PD brain hemispheres. DNA methylation is fine-mapped at enhancers and promoters, genome-wide, by targeted bisulfite sequencing ...
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#1Peng Wang (Chinese Academy of Tropical Agricultural Sciences)H-Index: 12
#2Yingfeng Luo (CAS: Chinese Academy of Sciences)H-Index: 10
Last. Huangkai Zhang (Beijing Institute of Genomics)
view all 29 authors...
BACKGROUND: Mango is one of the world's most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. RESULTS: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the oc...
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#1Xin Liu (UTSW: University of Texas Southwestern Medical Center)H-Index: 24
#2Yong Chen (Rowan University)H-Index: 14
Last. Jian Xu (UTSW: University of Texas Southwestern Medical Center)H-Index: 34
view all 10 authors...
The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CAPTURE method for multiplexed analysis of locus-specific chromatin interactions. The redesigned system allows for quantitative analysis of the spatial configuration of a few to hundreds of enhancers or...
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Genome
Human genetics
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