Journal: Nature Methods

Abbreviation

Nat Methods

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Nature

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ISSN

1548-7105
1548-7091

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Publications 1 - 10 of 130
  • Image-based transcriptomics in thousands of single human cells at single-molecule resolution
    Item type: Journal Article
    Battich, Nico; Stoeger, Thomas; Pelkmans, Lucas (2013)
    Nature Methods
    Fluorescence in situ hybridization (FISH) is widely used to obtain information about transcript copy number and subcellular localization in single cells. However, current approaches do not readily scale to the analysis of whole transcriptomes. Here we show that branched DNA technology combined with automated liquid handling, high-content imaging and quantitative image analysis allows highly reproducible quantification of transcript abundance in thousands of single cells at single-molecule resolution. In addition, it allows extraction of a multivariate feature set quantifying subcellular patterning and spatial properties of transcripts and their cell-to-cell variability. This has multiple implications for the functional interpretation of cell-to-cell variability in gene expression and enables the unbiased identification of functionally relevant in situ signatures of the transcriptome without the need for perturbations. Because this method can be incorporated in a wide variety of high-throughput image-based approaches, we expect it to be broadly applicable.
  • Unsupervised modeling of cell morphology dynamics for time-lapse microscopy
    Item type: Journal Article
    Zhong, Qing; Busetto, Alberto Giovanni; Fededa, Juan P.; et al. (2012)
    Nature Methods
  • A gene-fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins
    Item type: Journal Article
    Kleinlogel, Sonja; Terpitz, Ulrich; Legrum, Barbara; et al. (2011)
    Nature Methods
  • Inferring causal molecular networks: empirical assessment through a community-based effort
    Item type: Journal Article
    Hill, Steven M.; Heiser, Laura M.; Cokelaer, Thomas; et al. (2016)
    Nature Methods
    It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense.
  • Reproducible isolation of distinct, overlapping segments of the phosphoproteome
    Item type: Journal Article
    Bodenmiller, Bernd; Mueller, Lukas N.; Mueller, Markus; et al. (2007)
    Nature Methods
  • Critical Assessment of Metagenome Interpretation: the second round of challenges
    Item type: Journal Article
    Meyer, Fernando; Fritz, Adrian; Deng, Zhi-Luo; et al. (2022)
    Nature Methods
    Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
  • Visual proteomics of the human pathogen Leptospira interrogans
    Item type: Journal Article
    Beck, Martin; Malmström, Johan A.; Lange, Vinzenz; et al. (2009)
    Nature Methods
  • Analysis and validation of proteomic data generated by tandem mass spectrometry
    Item type: Journal Article
    Nesvizhskii, Alexey I.; Vitek, Olga; Aebersold, Ruedi (2007)
    Nature Methods
  • Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system
    Item type: Journal Article
    Collins, Ben C.; Gillet, Ludovic C.; Rosenberger, George; et al. (2013)
    Nature Methods
  • Unlocking capacities of genomics for the COVID-19 response and future pandemics
    Item type: Other Journal Item
    Knyazev, Sergey; Chhugani, Karishma; Sarwal, Varuni; et al. (2022)
    Nature Methods
    During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.
Publications 1 - 10 of 130