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Matthew Ruffalo · SciRah

Researcher profile · Semantic Scholar

Matthew Ruffalo

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Matthew Ruffalo — researcher profile on SciRah

h-index: 9
Works: 20
Citations: 763

Most-cited papers

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
M. Snyder, Shin Lin, A. Posgai, M. Atkinson +120 more
2019Nature561 citations Open access
Semantic Scholar
A web server for comparative analysis of single-cell RNA-seq data
A. Alavi, Matthew Ruffalo, Aiyappa Parvangada, Zhilin Huang +1 more
2018Nature Communications60 citations Open access
Semantic Scholar
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage
K. Börner, P. Blood, Jonathan C. Silverstein, Matthew Ruffalo +165 more
2025Nature Methods50 citations Open access
Semantic Scholar
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis
Monica T. Dayao, Alexandro E. Trevino, Honesty J. Kim, Matthew Ruffalo +5 more
2023Bioinform.16 citations Open access
Semantic Scholar
Using single cell atlas data to reconstruct regulatory networks
Qi Song, Matthew Ruffalo, Z. Bar-joseph
2023Nucleic Acids Research15 citations Open access
Semantic Scholar
CINS: Cell Interaction Network inference from Single cell expression data
Ye Yuan, C. Cosme, T. Adams, J. Schupp +6 more
2021bioRxiv11 citations Open access
Semantic Scholar
Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer
Mondira Ray, Matthew Ruffalo, Z. Bar-joseph
2018Genes, Chromosomes and Cancer11 citations Open access
Semantic Scholar
Protein interaction disruption in cancer
Matthew Ruffalo, Z. Bar-joseph
2019BMC Cancer9 citations Open access
Semantic Scholar
Genome wide predictions of miRNA regulation by transcription factors
Matthew Ruffalo, Z. Bar-joseph
2016Bioinform.9 citations Open access
Semantic Scholar
Network-guided prediction of aromatase inhibitor response in breast cancer
Matthew Ruffalo, R. Thomas, Jian Chen, Adrian V. Lee +2 more
2019PLoS Comput. Biol.6 citations Open access
Semantic Scholar
HuBMAP Data Portal: A Resource for Multimodal Spatial and Single-Cell Data of Healthy Human Tissues
Morgan L. Turner, Thomas C. Smits, Tiffany Liaw, Brendan Honick +45 more
2025arXiv.org5 citations
Semantic Scholar
Reconstructing cancer drug response networks using multitask learning
Matthew Ruffalo, P. Stojanov, Krishna Pillutla, R. Varma +1 more
2017BMC Systems Biology4 citations Open access
Semantic Scholar
A unified analysis of atlas single-cell data
Hao Chen, Nam D. Nguyen, Matthew Ruffalo, Z. Bar-joseph
2023bioRxiv3 citations Open access
Semantic Scholar
SPRM: spatial process and relationship modeling for multiplexed images
Ted Zhang, Haoran Chen, Young-Je Lee, Matthew Ruffalo +1 more
2026Bioinformatics Advances2 citations
Semantic Scholar
3DCellComposer – A versatile pipeline utilizing 2D cell segmentation methods for 3D cell segmentation
Haoran Chen, Ted Zhang, Matthew Ruffalo, Robert F. Murphy
2025Methods2 citations Open access
Semantic Scholar
Flexible and robust cell-type annotation for highly multiplexed tissue images
Huangqingbo Sun, Shiqiu Yu, Anna Martinez Casals, Anna Bäckström +5 more
2025Cell Systems2 citations Open access
Semantic Scholar
Flexible and robust cell type annotation for highly multiplexed tissue images
Huangqingbo Sun, Shiqiu Yu, Anna Martinez Casals, Anna Bäckström +5 more
2024bioRxiv2 citations Open access
Semantic Scholar
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage
K. Börner, P. Blood, Jonathan C. Silverstein, Matthew Ruffalo +16 more
2024bioRxiv0 citations Open access
Semantic Scholar
Supplementary Material: Spatial feature extraction for enhancing cancer survival analysis in spatial proteomics imaging data
Monica T. Dayao, Alexandro E. Trevino, Honesty J. Kim, Matthew Ruffalo +5 more
20230 citations
Semantic Scholar
HBM-CITEseq: a uniform CITE-seq processing pipeline for the HuBMAP Consortium
Xinyue Lu, Matthew Ruffalo
2022bioRxiv0 citations Open access
Semantic Scholar

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