Pedro Mendes

23.4k total citations · 6 hit papers
113 papers, 11.4k citations indexed

About

Pedro Mendes is a scholar working on Molecular Biology, Biomedical Engineering and Hematology. According to data from OpenAlex, Pedro Mendes has authored 113 papers receiving a total of 11.4k indexed citations (citations by other indexed papers that have themselves been cited), including 93 papers in Molecular Biology, 8 papers in Biomedical Engineering and 7 papers in Hematology. Recurrent topics in Pedro Mendes's work include Microbial Metabolic Engineering and Bioproduction (57 papers), Gene Regulatory Network Analysis (42 papers) and Bioinformatics and Genomic Networks (32 papers). Pedro Mendes is often cited by papers focused on Microbial Metabolic Engineering and Bioproduction (57 papers), Gene Regulatory Network Analysis (42 papers) and Bioinformatics and Genomic Networks (32 papers). Pedro Mendes collaborates with scholars based in United States, United Kingdom and Germany. Pedro Mendes's co-authors include Lloyd W. Sumner, Douglas B. Kell, Richard A. Dixon, Julio R. Banga, Alberto de la Fuente, Stefan Hoops, Ursula Kummer, Sven Sahle, Jürgen Pahle and Ralph Gauges and has published in prestigious journals such as Nucleic Acids Research, Environmental Science & Technology and Nature Biotechnology.

In The Last Decade

Pedro Mendes

113 papers receiving 11.0k citations

Hit Papers

align trajectories sort by overperformance

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

COPASI—a COmplex PAthway SImulator

2006 1.8k citations Pedro Mendes et al. profile →
Plant metabolomics: large-scale phytochemistry in the functional genomics era

2003 754 citations Lloyd W. Sumner, Pedro Mendes et al. profile →
ChEBI in 2016: Improved services and an expanding collection of metabolites

2015 648 citations Janna Hastings, Gareth Owen et al. Nucleic Acids Research profile →
Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods

2003 615 citations Carmen G. Moles, Pedro Mendes et al. Genome Research profile →
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.

1998 528 citations Pedro Mendes, Douglas B. Kell profile →
Potential of metabolomics as a functional genomics tool

2004 507 citations Pedro Mendes, Lloyd W. Sumner et al. profile →

Author Peers

Peers are selected by citation overlap in the author's most active subfields. citations · hero ref

Author						Papers	Cites
Pedro Mendes	8.5k	1.5k	887	761	759	113	11.4k
Oliver Kohlbacher	8.7k 1.0×	876 0.6×	596 0.7×	752 1.0×	511 0.7×	268	12.1k
Rainer Breitling	10.9k 1.3×	2.5k 1.7×	868 1.0×	1.6k 2.1×	459 0.6×	214	16.4k
Robert Powers	7.1k 0.8×	563 0.4×	686 0.8×	716 0.9×	574 0.8×	263	10.6k
Wei Chen	15.5k 1.8×	1.3k 0.9×	357 0.4×	492 0.6×	1.3k 1.7×	483	18.4k
Shigehiko Kanaya	5.7k 0.7×	1.5k 1.1×	560 0.6×	1.1k 1.4×	557 0.7×	286	8.1k
Yu‐Dong Cai	11.8k 1.4×	702 0.5×	585 0.7×	438 0.6×	2.4k 3.1×	491	15.6k
Johan Trygg	8.8k 1.0×	1.9k 1.3×	2.1k 2.4×	590 0.8×	442 0.6×	178	15.6k
Jiřı́ Damborský	9.5k 1.1×	687 0.5×	1.7k 1.9×	840 1.1×	801 1.1×	328	13.7k
Ying Xu	6.1k 0.7×	1.1k 0.7×	762 0.9×	815 1.1×	224 0.3×	263	8.5k
Hans V. Westerhoff	14.9k 1.7×	1.1k 0.8×	1.5k 1.7×	2.0k 2.6×	560 0.7×	468	20.5k

Countries citing papers authored by Pedro Mendes

Since Specialization

Citations

This map shows the geographic impact of Pedro Mendes'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 Pedro Mendes with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Pedro Mendes more than expected).

Fields of papers citing papers by Pedro Mendes

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Pedro Mendes. 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 Pedro Mendes. The network helps show where Pedro Mendes may publish in the future.

Co-authorship network of co-authors of Pedro Mendes

This figure shows the co-authorship network connecting the top 25 collaborators of Pedro Mendes. A scholar is included among the top collaborators of Pedro Mendes 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 Pedro Mendes. Pedro Mendes is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

Mendes, Pedro, et al.. (2025). Mathematical modeling reveals ferritin as the strongest cellular driver of dietary iron transfer block in enterocytes. PLoS Computational Biology. 21(3). e1012374–e1012374. 1 indexed citations

Archambault, Linda, et al.. (2023). Corrected and Republished from: “Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling”. mSphere. 8(2). e0065622–e0065622. 2 indexed citations

Archambault, Linda, et al.. (2021). Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling. mSphere. 6(6). e0087521–e0087521. 7 indexed citations

Archambault, Linda, et al.. (2021). Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review. Microorganisms. 9(2). 417–417. 18 indexed citations

Mendes, Pedro, et al.. (2021). Optimization of Agent-Based Models Through Coarse-Graining. PubMed. 8(1). 167–178. 2 indexed citations

Parmar, Jignesh H. & Pedro Mendes. (2019). A computational model to understand mouse iron physiology and disease. PLoS Computational Biology. 15(1). e1006680–e1006680. 8 indexed citations

Parmar, Jignesh H., Julia Quintana, David Ramírez, et al.. (2018). An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Molecular Microbiology. 110(3). 357–369. 13 indexed citations

Hastings, Janna, Gareth Owen, Adriano Dekker, et al.. (2015). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research. 44(D1). D1214–D1219. 648 indexed citations breakdown →

Millard, Pierre, Jean‐Charles Portais, & Pedro Mendes. (2015). Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC Systems Biology. 9(1). 64–64. 24 indexed citations

10.

Messiha, Hanan L., Naglis Malys, Kathleen Carroll, et al.. (2014). Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast. Nottingham ePrints (University of Nottingham). 12 indexed citations

11.

Smallbone, Kieran & Pedro Mendes. (2013). Large-Scale Metabolic Models: From Reconstruction to Differential Equations. Industrial Biotechnology. 9(4). 179–184. 46 indexed citations

12.

Heavner, Ben, et al.. (2012). Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Systems Biology. 6(1). 55–55. 103 indexed citations

13.

Mendes, Pedro, et al.. (2009). A general map of iron metabolism and tissue-specific subnetworks. Molecular BioSystems. 5(5). 422–443. 72 indexed citations

14.

Laubenbacher, Reinhard, Abdul Salam Jarrah, Suzy V. Torti, et al.. (2009). A systems biology view of cancer. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer. 1796(2). 129–139. 76 indexed citations

15.

Sauro, Herbert M., David Harel, Adelinde M. Uhrmacher, et al.. (2006). Challenges for modeling and simulation methods in systems biology. Winter Simulation Conference. 1720–1730. 13 indexed citations

16.

Lei, Zhentian, et al.. (2005). A Two-dimensional Electrophoresis Proteomic Reference Map and Systematic Identification of 1367 Proteins from a Cell Suspension Culture of the Model Legume Medicago truncatula. Molecular & Cellular Proteomics. 4(11). 1812–1825. 90 indexed citations

17.

Moles, Carmen G., Pedro Mendes, & Julio R. Banga. (2003). Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods. Genome Research. 13(11). 2467–2474. 615 indexed citations breakdown →

18.

Snoep, Jacky L., Pedro Mendes, & Hans V. Westerhoff. (1999). Teaching metabolic control analysis and kinetic modelling.. The Biochemist. 21(4). 25–28. 2 indexed citations

19.

Mendes, Pedro & Douglas B. Kell. (1997). Making cells work — metabolic engineering for everyone. Trends in biotechnology. 15(1). 6–7. 9 indexed citations

20.

Mendes, Pedro & Douglas B. Kell. (1996). On the analysis of the inverse problem of metabolic pathways using artificial neural networks. Biosystems. 38(1). 15–28. 21 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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