Daniel Machado

3.9k total citations · 4 hit papers
36 papers, 2.0k citations indexed

About

Daniel Machado is a scholar working on Molecular Biology, Biomedical Engineering and General Health Professions. According to data from OpenAlex, Daniel Machado has authored 36 papers receiving a total of 2.0k indexed citations (citations by other indexed papers that have themselves been cited), including 26 papers in Molecular Biology, 7 papers in Biomedical Engineering and 4 papers in General Health Professions. Recurrent topics in Daniel Machado's work include Microbial Metabolic Engineering and Bioproduction (22 papers), Gene Regulatory Network Analysis (17 papers) and Bioinformatics and Genomic Networks (8 papers). Daniel Machado is often cited by papers focused on Microbial Metabolic Engineering and Bioproduction (22 papers), Gene Regulatory Network Analysis (17 papers) and Bioinformatics and Genomic Networks (8 papers). Daniel Machado collaborates with scholars based in Portugal, United States and Germany. Daniel Machado's co-authors include Markus J. Herrgård, Kiran Raosaheb Patil, Sergej Andrejev, Isabel Rocha, Eugénio C. Ferreira, Yong‐Kyu Kim, Rafael S. Costa, Peer Bork, Oleksandr M. Maistrenko and Kaustubh R. Patil and has published in prestigious journals such as Nucleic Acids Research, Nature Communications and SHILAP Revista de lepidopterología.

In The Last Decade

Daniel Machado

33 papers receiving 2.0k citations

Hit Papers

align trajectories

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.

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

2018 419 citations Daniel Machado, Sergej Andrejev et al. profile →
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

2021 209 citations Sonja Blasche, Yong‐Kyu Kim et al. profile →
Polarization of microbial communities between competitive and cooperative metabolism

2021 208 citations Daniel Machado, Oleksandr M. Maistrenko et al. Nature Ecology & Evolution profile →
Ecological modelling approaches for predicting emergent properties in microbial communities

2022 135 citations Daniel Machado, Isabel Rocha et al. Nature Ecology & Evolution profile →

Peers — A (Enhanced Table)

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

Name	h						Papers	Cites
Daniel Machado Portugal	19	1.6k	431	253	241	153	36	2.0k
Christoph Kaleta Germany	30	2.1k 1.4×	342 0.8×	178 0.7×	407 1.7×	498 3.3×	90	3.0k
Aleksej Zelezniak Sweden	23	1.8k 1.2×	261 0.6×	141 0.6×	308 1.3×	205 1.3×	40	2.5k
Ophelia S. Venturelli United States	21	1.2k 0.8×	256 0.6×	182 0.7×	403 1.7×	291 1.9×	38	1.9k
Aaron A. Best United States	13	1.2k 0.7×	398 0.9×	77 0.3×	131 0.5×	118 0.8×	32	1.5k
Wai Kit Ong United States	12	1.9k 1.2×	304 0.7×	173 0.7×	353 1.5×	268 1.8×	15	2.5k
Filipe Branco dos Santos Netherlands	23	1.0k 0.7×	225 0.5×	347 1.4×	130 0.5×	162 1.1×	48	1.4k
Eugen Bauer Germany	15	903 0.6×	138 0.3×	115 0.5×	147 0.6×	173 1.1×	18	1.5k
Yingying Li China	23	1.1k 0.7×	488 1.1×	201 0.8×	71 0.3×	156 1.0×	106	2.2k
Curt R. Fischer United States	23	2.1k 1.4×	497 1.2×	177 0.7×	326 1.4×	367 2.4×	41	2.9k
Ravi U. Sheth United States	15	1.1k 0.7×	160 0.4×	113 0.4×	234 1.0×	193 1.3×	18	1.4k

Countries citing papers authored by Daniel Machado

Since Specialization

Citations

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

Fields of papers citing papers by Daniel Machado

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

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

Co-authorship network of co-authors of Daniel Machado

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

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

Machado, Daniel. (2024). A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities. mSystems. 9(2). e0083323–e0083323. 3 indexed citations

Melkonian, Chrats, Inge Kjærbølling, Sonja Blasche, et al.. (2023). Microbial interactions shape cheese flavour formation. Nature Communications. 14(1). 8348–8348. 47 indexed citations

Machado, Daniel, Isabel Rocha, Jeremy M. Chacón, et al.. (2022). Ecological modelling approaches for predicting emergent properties in microbial communities. Nature Ecology & Evolution. 6(7). 855–865. 135 indexed citations breakdown →

Machado, Daniel, Oleksandr M. Maistrenko, Sergej Andrejev, et al.. (2021). Polarization of microbial communities between competitive and cooperative metabolism. Nature Ecology & Evolution. 5(2). 195–203. 208 indexed citations breakdown →

Machado, Daniel, Filipa Palha, Pedro Silva Moreira, et al.. (2020). Stigmatizing Attitudes Toward Patients With Psychiatric Disorders Among Medical Students and Professionals. Frontiers in Psychiatry. 11. 326–326. 56 indexed citations

Kang, Kang, B. Mikael Bergdahl, Daniel Machado, et al.. (2019). Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations. GigaScience. 8(4). 27 indexed citations

Machado, Daniel. (2018). Revista do Instituto de Geociências - USP. SHILAP Revista de lepidopterología. 6 indexed citations

Gonçalves, Emanuel, Marco Sciacovelli, Ana S.H. Costa, et al.. (2017). Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells. Metabolic Engineering. 45. 149–157. 26 indexed citations

Machado, Daniel, et al.. (2016). Current state and challenges for dynamic metabolic modeling. Current Opinion in Microbiology. 33. 97–104. 36 indexed citations

10.

Monk, Jonathan M., Anna Koza, Miguel A. Campodonico, et al.. (2016). Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Systems. 3(3). 238–251.e12. 105 indexed citations

11.

Machado, Daniel, Markus J. Herrgård, & Isabel Rocha. (2016). Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. PLoS Computational Biology. 12(10). e1005140–e1005140. 52 indexed citations

12.

Lima, Ana, et al.. (2016). A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli. IFAC-PapersOnLine. 49(26). 270–276. 2 indexed citations

13.

Machado, Daniel, Markus J. Herrgård, & Isabel Rocha. (2015). Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli. Frontiers in Bioengineering and Biotechnology. 3. 154–154. 27 indexed citations

14.

Machado, Daniel, L. R. Rodrigues, & Isabel Rocha. (2014). A kinetic model for curcumin production in Escherichia coli. Biosystems. 125. 16–21. 9 indexed citations

15.

Machado, Daniel & Markus J. Herrgård. (2014). Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism. PLoS Computational Biology. 10(4). e1003580–e1003580. 283 indexed citations

16.

Machado, Daniel, et al.. (2013). SIGN LANGUAGE: HOW THE NURSING STAFF INTERACTS TO TAKE CARE OF DEAF PATIENTS?. Revista de Pesquisa Cuidado é Fundamental Online. 5(3). 283–292. 8 indexed citations

17.

Morgado, Pedro, et al.. (2013). 994 – Stigmatizing Attitudes Towards Mental Ill Patients Among Medical Students And Professionals. European Psychiatry. 28(S1). 2 indexed citations

18.

Machado, Daniel, Rafael S. Costa, Eugénio C. Ferreira, Isabel Rocha, & Bruce Tidor. (2012). Exploring the gap between dynamic and constraint-based models of metabolism. Metabolic Engineering. 14(2). 112–119. 29 indexed citations

19.

Machado, Daniel, Rafael S. Costa, Miguel Rocha, et al.. (2011). Modeling formalisms in Systems Biology. AMB Express. 1(1). 45–45. 122 indexed citations

20.

Costa, Rafael S., Daniel Machado, Isabel Rocha, & Eugénio C. Ferreira. (2011). Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling. IET Systems Biology. 5(3). 157–163. 14 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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