Matthew Ruffalo

1.2k total citations
16 papers, 333 citations indexed

About

Matthew Ruffalo is a scholar working on Molecular Biology, Cancer Research and Hematology. According to data from OpenAlex, Matthew Ruffalo has authored 16 papers receiving a total of 333 indexed citations (citations by other indexed papers that have themselves been cited), including 13 papers in Molecular Biology, 6 papers in Cancer Research and 2 papers in Hematology. Recurrent topics in Matthew Ruffalo's work include Single-cell and spatial transcriptomics (5 papers), Bioinformatics and Genomic Networks (5 papers) and Gene Regulatory Network Analysis (4 papers). Matthew Ruffalo is often cited by papers focused on Single-cell and spatial transcriptomics (5 papers), Bioinformatics and Genomic Networks (5 papers) and Gene Regulatory Network Analysis (4 papers). Matthew Ruffalo collaborates with scholars based in United States, Israel and China. Matthew Ruffalo's co-authors include Mehmet Koyutürk, Thomas LaFramboise, Ziv Bar‐Joseph, Roded Sharan, Amir Alavi, Zhilin Huang, Soumya Ray, Qi Song, Jaroslaw P. Maciejewski and Holleh Husseinzadeh and has published in prestigious journals such as Nucleic Acids Research, Nature Communications and Blood.

In The Last Decade

Matthew Ruffalo

14 papers receiving 325 citations

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Matthew Ruffalo United States	8	258	77	76	40	34	16	333
Mohammadamin Edrisi United States	6	228 0.9×	45 0.6×	108 1.4×	16 0.4×	49 1.4×	9	350
Niran Abeygunawardena United Kingdom	5	552 2.1×	65 0.8×	87 1.1×	51 1.3×	28 0.8×	5	657
Francisco Salavert Spain	12	322 1.2×	106 1.4×	72 0.9×	17 0.4×	11 0.3×	14	409
Santhilata Kuppili Venkata United Kingdom	2	304 1.2×	35 0.5×	103 1.4×	37 0.9×	11 0.3×	5	407
Yungang Xu China	14	477 1.8×	42 0.5×	128 1.7×	38 0.9×	48 1.4×	29	638
Tianming Zhou United States	7	308 1.2×	34 0.4×	34 0.4×	26 0.7×	16 0.5×	7	343
Jia Wei China	6	679 2.6×	56 0.7×	176 2.3×	31 0.8×	46 1.4×	12	725
Martin Haubrock Germany	12	371 1.4×	50 0.6×	118 1.6×	22 0.6×	21 0.6×	20	470
Daniel Visentin United Kingdom	2	408 1.6×	91 1.2×	37 0.5×	30 0.8×	42 1.2×	2	489
Catherine Snow United Kingdom	3	411 1.6×	53 0.7×	73 1.0×	36 0.9×	9 0.3×	3	544

Countries citing papers authored by Matthew Ruffalo

Since Specialization

Citations

This map shows the geographic impact of Matthew Ruffalo's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Matthew Ruffalo with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Matthew Ruffalo more than expected).

Fields of papers citing papers by Matthew Ruffalo

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Matthew Ruffalo. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Matthew Ruffalo. The network helps show where Matthew Ruffalo may publish in the future.

Co-authorship network of co-authors of Matthew Ruffalo

This figure shows the co-authorship network connecting the top 25 collaborators of Matthew Ruffalo. A scholar is included among the top collaborators of Matthew Ruffalo based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Matthew Ruffalo. Matthew Ruffalo is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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16 of 16 papers shown

Ruffalo, Matthew, et al.. (2026). SPRM: spatial process and relationship modeling for multiplexed images. Bioinformatics Advances. 6(1). vbag019–vbag019.

Ruffalo, Matthew, et al.. (2025). 3DCellComposer − A versatile pipeline utilizing 2D cell segmentation methods for 3D cell segmentation. Methods. 242. 113–122. 2 indexed citations

Song, Qi, Matthew Ruffalo, & Ziv Bar‐Joseph. (2023). Using single cell atlas data to reconstruct regulatory networks. Nucleic Acids Research. 51(7). e38–e38. 7 indexed citations

Trevino, Alexandro E., et al.. (2023). Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. Bioinformatics. 39(Supplement_1). i140–i148. 6 indexed citations

Yuan, Ye, Carlos Cosme, Taylor Adams, et al.. (2022). CINS: Cell Interaction Network inference from Single cell expression data. PLoS Computational Biology. 18(9). e1010468–e1010468. 6 indexed citations

Ruffalo, Matthew & Ziv Bar‐Joseph. (2019). Protein interaction disruption in cancer. BMC Cancer. 19(1). 370–370. 8 indexed citations

Ruffalo, Matthew, Roby Thomas, Jian Chen, et al.. (2019). Network-guided prediction of aromatase inhibitor response in breast cancer. PLoS Computational Biology. 15(2). e1006730–e1006730. 5 indexed citations

Alavi, Amir, et al.. (2018). A web server for comparative analysis of single-cell RNA-seq data. Nature Communications. 9(1). 4768–4768. 38 indexed citations

Ruffalo, Matthew, et al.. (2018). Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer. Genes Chromosomes and Cancer. 58(1). 34–42. 10 indexed citations

10.

Ruffalo, Matthew, et al.. (2017). Reconstructing cancer drug response networks using multitask learning. BMC Systems Biology. 11(1). 96–96. 5 indexed citations

11.

Ruffalo, Matthew & Ziv Bar‐Joseph. (2016). Genome wide predictions of miRNA regulation by transcription factors. Bioinformatics. 32(17). i746–i754. 8 indexed citations

12.

Ruffalo, Matthew, Holleh Husseinzadeh, Hideki Makishima, et al.. (2015). Whole-exome sequencing enhances prognostic classification of myeloid malignancies. Journal of Biomedical Informatics. 58. 104–113. 9 indexed citations

13.

Ruffalo, Matthew, Mehmet Koyutürk, & Roded Sharan. (2015). Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PLoS Computational Biology. 11(12). e1004595–e1004595. 52 indexed citations

14.

Husseinzadeh, Holleh, E.P. Evans, Kenichi Yoshida, et al.. (2012). Whole Exome Sequencing to Predict Response to Hypomethylating Agents in MDS. Blood. 120(21). 1698–1698.

15.

Ruffalo, Matthew, Mehmet Koyutürk, Soumya Ray, & Thomas LaFramboise. (2012). Accurate estimation of short read mapping quality for next-generation genome sequencing. Bioinformatics. 28(18). i349–i355. 24 indexed citations

16.

Ruffalo, Matthew, Thomas LaFramboise, & Mehmet Koyutürk. (2011). Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics. 27(20). 2790–2796. 153 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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