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3 weeks ago | 
dx.doi.org | Jack Freestone |Lukas Käll |William Noble |Uri Keich
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Jan 15, 2025 | 
nature.com | Rui Yang |Renhe Luo |Martin Rivas |Martín A. Rivas |Darko Barisic |Alireza Karbalayghareh | +11 more
Correction to: Nature Communications https://doi.org/10.1038/s41467-024-53628-0, published online 01 November 2024In this article the affiliation ‘Department of Biochemistry & Molecular Biology; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA’ for Martin A. Rivas was missing. The original article has been corrected.
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Nov 7, 2024 | 
nature.com | William Noble
AbstractTraining machine learning models for tasks such as de novo sequencing or spectral clustering requires large collections of confidently identified spectra. Here we describe a dataset of 2.8 million high-confidence peptide-spectrum matches derived from nine different species. The dataset is based on a previously described benchmark but has been re-processed to ensure consistent data quality and enforce separation of training and test peptides.
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Nov 1, 2024 | 
nature.com | Rui Yang |Renhe Luo |Martin Rivas |Martín A. Rivas |Darko Barisic |Alireza Karbalayghareh | +11 more
AbstractIdentifying cell-type-specific 3D chromatin interactions between regulatory elements can help decipher gene regulation and interpret disease-associated non-coding variants. However, achieving this resolution with current 3D genomics technologies is often infeasible given limited input cell numbers. We therefore present ChromaFold, a deep learning model that predicts 3D contact maps, including regulatory interactions, from single-cell ATAC sequencing (scATAC-seq) data alone.
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Oct 20, 2024 | 
biorxiv.org | Jack Freestone |Michael Riffle |Michael J MacCoss |William Noble
AbstractA pressing statistical challenge in the field of mass spectrometry proteomics is how to assess whether a given software tool provides accurate error control. Each software tool for searching such data uses its own internally implemented methodology for reporting and controlling the error. Many of these software tools are closed source, with incompletely documented methodology, and the strategies for validating the error are inconsistent across tools.
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Jun 4, 2024 | 
biorxiv.org | Jack Freestone |Michael J MacCoss |William Noble |Michael Riffle
AbstractA pressing statistical challenge in the field of mass spectrometry proteomics is how to assess whether a given software tool provides accurate error control. Each software tool for searching such data uses its own internally implemented methodology for reporting and controlling the error. Many of these software tools are closed source, with incompletely documented methodology, and the strategies for validating the error are inconsistent across tools.
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May 1, 2024 | 
nature.com | William Noble
Many of Jennifer Listgarten’s arguments are compelling: in particular, that the protein folding problem is an outlier relative to other grand challenges in science, both in terms of the precise way the problem can be stated and performance measured and in terms of the amount of available, high quality data1.
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Apr 14, 2024 | 
biorxiv.org | Alan Min |Jacob Schreiber |Anshul Kundaje |William Noble
AbstractOver the past 15 years, a variety of next-generation sequencing assays have been developed for measuring the 3D conformation of DNA in the nucleus. Each of these assays gives, for a particular cell or tissue type, a distinct picture of 3D chromatin architecture.
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Feb 14, 2024 | 
nature.com | Chengxiang Qiu |Beth Martin |Riza M. Daza |Megan Taylor |Olivia Fulton |Xinxian Deng | +6 more
AbstractThe house mouse (Mus musculus) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans1,2. Mouse gestation lasts only 3 weeks, during which the genome orchestrates the astonishing transformation of a single-cell zygote into a free-living pup composed of more than 500 million cells.
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Feb 3, 2024 | 
nature.com | Karen H Miga |William Noble
AbstractFluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate > 100 distinct targets in the same sample, pushing the boundaries of FISH-based assays.
