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Showing 1–17 of 17 results
Advanced filters: Author: Vijay Ramani Clear advanced filters

  • Perez, Goronzy et al. present ChIP-DIP, which enables multiplex genomic mapping of hundreds of epitopes from a single sample. The authors apply ChIP-DIP to localize modified histones, transcription factors and other chromatin-interacting proteins at scale, in both cell lines and primary cells.

    • Vijay Ramani
    News & Views
    Nature Genetics
    Volume: 56, P: 2596-2597

  • Here authors present SAMOSA-ChAAT, a method for resolving how chromatin-interacting proteins restructure individual chromatin fibers, in high throughput and at scale. They provide evidence that the imitation switch family remodeling enzymes sense nucleosome density to program internucleosomal spacing on individual molecules.

    • Nour J. Abdulhay
    • Laura J. Hsieh
    • Vijay Ramani
    ResearchOpen Access
    Nature Structural & Molecular Biology
    Volume: 30, P: 1571-1581

  • Despite the availability of chromatin conformation capture experiments, discerning the relationship between the 1D genome and 3D conformation remains a challenge. Here, the authors propose a method that produces low-dimensional latent representations that summarize intra-chromosomal Hi-C contacts.

    • Kevin B. Dsouza
    • Alexandra Maslova
    • Maxwell W. Libbrecht
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-19

  • Two low-input tagmentation-based long-read sequencing methods, single-molecule real-time sequencing by tagmentation (SMRT-Tag), which identifies genetic variation and CpG methylation, and single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which detects chromatin accessibility, are presented. Application of SAMOSA-Tag to prostate cancer patient-derived xenograft samples identifies metastasis-associated epigenomic alterations.

    • Arjun S. Nanda
    • Ke Wu
    • Vijay Ramani
    ResearchOpen Access
    Nature Genetics
    Volume: 56, P: 1300-1309

  • Maintaining a pH gradient across a fuel cell improves device efficiency and flexibility in device chemistry. Here the authors develop an efficient microscale bipolar interface for direct borohydride fuel cells, enabling sustained operations with a pH differential between the anolyte and the catholyte.

    • Zhongyang Wang
    • Javier Parrondo
    • Vijay Ramani
    Research
    Nature Energy
    Volume: 4, P: 281-289

  • Platinum-group-metal-free, non-iron catalysts are highly desirable for the oxygen reduction reaction at proton exchange membrane (PEM) fuel cell cathodes, as they avoid the detrimental Fenton reactions. Now, a cobalt and nitrogen co-doped carbon catalyst with atomically dispersed porphyrin-like CoN4C12 sites is reported with an improved activity and durability in PEM fuel cell conditions.

    • Xiaohong Xie
    • Cheng He
    • Yuyan Shao
    Research
    Nature Catalysis
    Volume: 3, P: 1044-1054

  • Infant gliomas behave differently to their childhood or adult counterparts. Here, the authors perform a large-scale genetic analysis of these tumours, revealing genetic alterations which may offer therapeutic opportunities.

    • Ana S. Guerreiro Stucklin
    • Scott Ryall
    • Cynthia Hawkins
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-13

  • Low-cost catalysts for oxygen reduction, such as Fe–N–C materials, often suffer from poor stability in fuel cells due to the generation of oxidizing radical species. Here the authors locate Ta–TiOx additives in the vicinity of Fe–N–C catalysts and show that they can successfully scavenge radicals, improving durability.

    • Hua Xie
    • Xiaohong Xie
    • Liangbing Hu
    Research
    Nature Energy
    Volume: 7, P: 281-289

  • The spatial organization of the genome plays an important but unclearly defined role in gene regulation. Here, the authors integrate Hi-C, RNA-seq and ATAC-seq data to map cardiogenesis from pluripotent stem cells and describe an RBM20-dependent splicing factory assembling the TTN locus with other RBM20 targets.

    • Alessandro Bertero
    • Paul A. Fields
    • Charles E. Murry
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-19

  • Chung et al. examine the levels of glycoprotein non-metastatic melanoma protein B (GPNMB) in the blood of patients with renal cell carcinoma who acquire resistance to immune checkpoint inhibitor therapy. Findings show that GPNMB levels are elevated and could serve as a prognosticator of and potential treatment target for treatment-resistant cancer.

    • Jin-Sung Chung
    • Vijay Ramani
    • Kiyoshi Ariizumi
    ResearchOpen Access
    Communications Medicine
    Volume: 5, P: 1-16

  • Germline mono-allelic loss of the tumour suppressor NF1 predisposes patients to the development of benign lesions but rarely further progression into cancer development. Here the authors use mouse models to show that an NF1 heterozygous microenvironment accelerates the formation of benign tumours but impairs progression to malignancy.

    • Jean-Philippe Brosseau
    • Chung-Ping Liao
    • Lu Q. Le
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-11

  • Ramani et al. describe a protocol for in situ DNase Hi-C as an alternative to traditional Hi-C methods that use restriction enzymes. The use of DNase I for chromatin digestion circumvents the resolution limit imposed when relying on genomic restriction sites.

    • Vijay Ramani
    • Darren A Cusanovich
    • Zhijun Duan
    Protocols
    Nature Protocols
    Volume: 11, P: 2104-2121

  • This review provides an overview of analysis and experimental design of single-cell omics in the brain, emphasizing epigenomics and spatial omics. The authors discuss how the computational and experimental designs are interlinked, with both being guided by the biological questions.

    • Boyan Bonev
    • Gonçalo Castelo-Branco
    • Tomasz J. Nowakowski
    Reviews
    Nature Neuroscience
    Volume: 27, P: 2292-2309

  • Single-cell combinatorial indexed Hi-C (sciHi-C) is a streamlined protocol for generating thousands of high-quality single-cell chromosome conformation data sets that resemble bulk Hi-C data in aggregate.

    • Vijay Ramani
    • Xinxian Deng
    • Jay Shendure
    Research
    Nature Methods
    Volume: 14, P: 263-266