Author details

Full Name

William Stafford Noble

Affiliation

ORCID

Career Start Year

2001

Papers

279

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36594573	Inference of 3D genome architecture by modeling overdispersion of Hi-C data.		2023
36308683	A Pipeline for Peptide Detection Using Multiple Decoys.	Methods in Molecular Biology	2023
37607941	Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum.	Nat Commun	2023
37790381	Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories.		2023
37861703	Evaluating Proteomics Imputation Methods with Improved Criteria.		2023
37280678	Epiphany: predicting Hi-C contact maps from 1D epigenomic signals.		2023
37280210	Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.	Nat Commun	2023
37205597	CTCF-mediated insulation and chromatin environment modulate <i>Car5b</i> escape from X inactivation.	bioRxiv	2023
37146053	Matrix prior for data transfer between single cell data types in latent Dirichlet allocation.		2023
36702456	MS1Connect: a mass spectrometry run similarity measure.		2023
36493778	Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation.		2023
37261867	Bridging the False Discovery Gap.		2023
36945528	Tigerfish designs oligonucleotide-based hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes.		2023
36633229	Efficient Indexing of Peptides for Database Search Using Tide.		2023
37066300	A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup.	bioRxiv	2023
36945371	Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types.	bioRxiv	2023
36993219	MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes.		2023
37428809	Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation.	PLoS Comput Biol	2023
36602949	Ten simple rules for defining a computational biology project.		2023
36598107	The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.	J Proteome Res	2023
37546906	ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.		2023
37421399	LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis.		2023
37419111	Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.	Mol Cell	2023
35119864	Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics.	J Proteome Res	2022
36251758	Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning.	Journal of Computational Biology	2022
35512256	Tandem Mass Spectrometry-Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing.	Am J Clin Pathol	2022
36166314	Improving Peptide-Level Mass Spectrometry Analysis via Double Competition.	Journal of Proteome Research	2022
35696663	Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning.	Journal of Proteome Research	2022
35549345	Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data.	J Proteome Res	2022
36124797	Linking cells across single-cell modalities by synergistic matching of neighborhood structure.		2022
36124786	Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition.		2022
35474001	Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.	Nature	2022
35050714	SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport.	Journal of Computational Biology	2022
34985990	Single-Cell Multiomics Integration by SCOT.	Journal of Computational Biology	2022
35288709	Systematic reconstruction of cellular trajectories across mouse embryogenesis.	Nat Genet	2022
34837041	Navigating the pitfalls of applying machine learning in genomics.	Nat Rev Genet	2022
34479627	Author Correction: Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome.		2021
34236864	Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.	Journal of Proteome Research	2021
34169593	Large-scale tandem mass spectrum clustering using fast nearest neighbor searching.	Rapid Commun Mass Spectrom	2021
33576390	HiCRep.py: fast comparison of Hi-C contact matrices in Python.		2021
33888511	Comprehensive characterization of tissue-specific chromatin accessibility in L2 <i>Caenorhabditis elegans</i> nematodes.	Genome Res	2021
34252924	DIAmeter: matching peptides to data-independent acquisition mass spectrometry data.	Bioinformatics	2021
33760340	Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments.	Environmental Microbiology	2021
34342226	ppx: Programmatic Access to Proteomics Data Repositories.	J Proteome Res	2021
33596079	mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection.	Journal of Proteome Research	2021
32966546	Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputedÂ data.		2021
34579774	Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation.	Genome Biol	2021
34734806	Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells.	Elife	2021
34608323	A wider field of view to predict expression.	Nature Methods	2021
31536770	Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.	Methods	2020