Most cited papers in Microbial Metabolic Engineering and Bioproduction
What are the most cited papers in Microbial Metabolic Engineering and Bioproduction?
The most cited paper in Microbial Metabolic Engineering and Bioproduction is "Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks" (Paul T. Shannon, Andrew Markiel, Owen W. Ozier et al., 2003), with 55,788 citations. Next come "Gene Ontology: tool for the unification of biology" (45,425) and "KEGG: Kyoto Encyclopedia of Genes and Genomes" (40,289).
Showing 50 of 98 papers. Every paper with more than 2,175 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Paul T. Shannon, Andrew Markiel, Owen W. Ozier et al. · Genome Research | Nov 2003 | 55,788 |
| 2 | Gene Ontology: tool for the unification of biology Michael Ashburner, Catherine A. Ball, Judith A. Blake et al. · Nature Genetics | May 2000 | 45,425 |
| 3 | KEGG: Kyoto Encyclopedia of Genes and Genomes Minoru I. Kanehisa · Nucleic Acids Research | 2000 | 40,289 |
| 4 | KEGG: Kyoto Encyclopedia of Genes and Genomes Hiroyuki Ogata, Susumu Goto, Kazushige Sato et al. · Nucleic Acids Research | 1999 | 32,529 |
| 5 | Coot : model-building tools for molecular graphics Paul Emsley, Kevin D. Cowtan · Acta Crystallographica Section D Biological Crystallography | 26 Nov 2004 | 31,846 |
| 6 | PHENIX : a comprehensive Python-based system for macromolecular structure solution Paul D. Adams, Pavel V. Afonine, G. Bunkóczi et al. · Acta Crystallographica Section D Biological Crystallography | 21 Jan 2010 | 24,924 |
| 7 | STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Damian Szklarczyk, Annika L. Gable, David B. Lyon et al. · Nucleic Acids Research | 16 Nov 2018 | 19,535 |
| 8 | Metascape provides a biologist-oriented resource for the analysis of systems-level datasets Yingyao Zhou, Bin Zhou, Lars Pache et al. · Nature Communications | 3 Apr 2019 | 16,072 |
| 9 | The Molecular Signatures Database Hallmark Gene Set Collection Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir et al. · Cell Systems | Dec 2015 | 15,167 |
| 10 | SWISS-MODEL: homology modelling of protein structures and complexes Andrew Mark Waterhouse, Martino Bertoni, Stefan Bienert et al. · Nucleic Acids Research | 7 May 2018 | 14,049 |
| 11 | clusterProfiler 4.0: A universal enrichment tool for interpreting omics data Tianzhi Wu, Erqiang Hu, Shuangbin Xu et al. · The Innovation | Jul 2021 | 13,194 |
| 12 | The RAST Server: Rapid Annotations using Subsystems Technology Ramy Karam Aziz et al. · BMC Genomics | 8 Feb 2008 | 12,071 |
| 13 | The Phyre2 web portal for protein modeling, prediction and analysis Lawrence A. Kelley, Stefans Mezulis, Christopher M. Yates et al. · Nature Protocols | 7 May 2015 | 10,412 |
| 14 | KEGG: new perspectives on genomes, pathways, diseases and drugs Minoru I. Kanehisa, Miho Furumichi, Mao Tanabe et al. · Nucleic Acids Research | 26 Oct 2016 | 9,650 |
| 15 | A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. R Sikorski, Phillip Hieter · Genetics | May 1989 | 8,848 |
| 16 | Network biology: understanding the cell's functional organization Albert-Ĺaszló Barabási, Zoltán N. Oltvai · Nature Reviews Genetics | 21 Jan 2004 | 8,151 |
| 17 | KEGG as a reference resource for gene and protein annotation Minoru I. Kanehisa, Yoko Sato, Masayuki Kawashima et al. · Nucleic Acids Research | 17 Oct 2015 | 8,051 |
| 18 | Deciphering key features in protein structures with the new ENDscript server Xavier Robert, Patrice Gouet · Nucleic Acids Research | 21 Apr 2014 | 7,532 |
| 19 | PICRUSt2 for prediction of metagenome functions Gavin M. Douglas, Vincent J. Maffei, Jesse Zaneveld et al. · Nature Biotechnology | Jun 2020 | 7,006 |
| 20 | KEGG for taxonomy-based analysis of pathways and genomes Minoru I. Kanehisa, Miho Furumichi, Yoko Sato et al. · Nucleic Acids Research | 13 Oct 2022 | 6,767 |
| 21 | I-TASSER: a unified platform for automated protein structure and function prediction Ambrish Roy, Alper Küçükural, Yang Zhang · Nature Protocols | 25 Mar 2010 | 6,400 |
| 22 | Features of promising technologies for pretreatment of lignocellulosic biomass Nathan S. Mosier · Bioresource Technology | 30 Sep 2004 | 6,242 |
| 23 | A novel genetic system to detect protein–protein interactions Stanley Fields, Ok-Kyu Song · Nature | Jul 1989 | 6,181 |
| 24 | Hydrolysis of lignocellulosic materials for ethanol production: a review Ye Sun, Jay Jiayang Cheng · Bioresource Technology | May 2002 | 6,062 |
| 25 | The Reactome pathway Knowledgebase Antonio Fabregat et al. · Nucleic Acids Research | 9 Dec 2015 | 6,015 |
| 26 | The Path Forward for Biofuels and Biomaterials Arthur J. Ragauskas, Charlotte K. Williams, Brian H. Davison et al. · Science | 26 Jan 2006 | 5,734 |
| 27 | SWISS-MODEL: an automated protein homology-modeling server Torsten F. Schwede · Nucleic Acids Research | 24 Jun 2003 | 5,709 |
| 28 | KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases Chen Xie, Xizeng Mao, Jiaju Huang et al. · Nucleic Acids Research | 27 Jun 2011 | 5,545 |
| 29 | Lethality and centrality in protein networks Hawoong Jeong, S. P. Mason, Albert-Ĺaszló Barabási et al. · Nature | May 2001 | 5,436 |
| 30 | The KEGG resource for deciphering the genome Minoru Kanehisa · Nucleic Acids Research | 17 Dec 2003 | 5,322 |
| 31 | The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function David Warde-Farley, Sylva L. Donaldson, Ovi Comes et al. · Nucleic Acids Research | 21 Jun 2010 | 5,203 |
| 32 | The National Center for Biotechnology Information D. A. Benson, Mark S. Boguski, David J. Lipman et al. · Genomics | Feb 1990 | 5,163 |
| 33 | eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale Carlos P. Cantalapiedra, Ana Hernández-Plaza, Ivica Letunić et al. · Molecular Biology and Evolution | 30 Sep 2021 | 5,074 |
| 34 | SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information Marco Biasini, Stefan Bienert, Andrew Mark Waterhouse et al. · Nucleic Acids Research | 29 Apr 2014 | 4,784 |
| 35 | High-throughput functional annotation and data mining with the Blast2GO suite Stefan Götz, Juan Miguel Garcia-Gomez, Javier Terol et al. · Nucleic Acids Research | 15 Apr 2008 | 4,734 |
| 36 | The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Ross Overbeek, Robert Olson, Gordon D. Pusch et al. · Nucleic Acids Research | 29 Nov 2013 | 4,729 |
| 37 | Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production Michael E. Himmel, Shi-You Ding, David K. Johnson et al. · Science | 8 Feb 2007 | 4,628 |
| 38 | Technology development for the production of biobased products from biorefinery carbohydrates—the US Department of Energy’s “Top 10” revisited Joseph J. Bozell, Gene R. Petersen · Green Chemistry | 2010 | 4,564 |
| 39 | Functional profiling of the Saccharomyces cerevisiae genome Guri N. Giaever et al. · Nature | 25 Jul 2002 | 4,557 |
| 40 | Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale Joseph L. DeRisi, Vishwanath R. Iyer, Patrick O. Brown · Science | 24 Oct 1997 | 4,526 |
| 41 | Hierarchical Organization of Modularity in Metabolic Networks E. Ravasz, A. L. Somera, D. A. Mongru et al. · Science | 29 Aug 2002 | 4,320 |
| 42 | Systems Biology: A Brief Overview Hiroaki Kitano · Science | Mar 2002 | 4,305 |
| 43 | What is flux balance analysis? Jeffrey D. Orth, Ines Thiele, Bernhard Ørn Palsson · Nature Biotechnology | Mar 2010 | 4,197 |
| 44 | Functional cartography of complex metabolic networks Roger Guimerà, Luı́s A. Nunes Amaral · Nature | Feb 2005 | 4,113 |
| 45 | The large-scale organization of metabolic networks H. Jeong, B. Tombor, R. Albert et al. · Nature | Oct 2000 | 4,056 |
| 46 | Pretreatment technologies for an efficient bioethanol production process based on enzymatic hydrolysis: A review Pablo Alvira, Elia Tomás‐Pejó, Mercedes Ballesteros et al. · Bioresource Technology | 30 Dec 2009 | 3,907 |
| 47 | Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances Qiang Hu, Milton R. Sommerfeld, Eric E. Jarvis et al. · The Plant Journal | May 2008 | 3,771 |
| 48 | Methods for Pretreatment of Lignocellulosic Biomass for Efficient Hydrolysis and Biofuel Production Parveen Kumar, Diane M. Barrett, Michael J. Delwiche et al. · Industrial & Engineering Chemistry Research | 20 Mar 2009 | 3,763 |
| 49 | Assessment of protein models with three-dimensional profiles Roland Lüthy, James U. Bowie, David S Eisenberg · Nature | Mar 1992 | 3,562 |
| 50 | WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs Yuxing Liao, Jing Wang, Eric J. Jaehnig et al. · Nucleic Acids Research | 2 May 2019 | 3,539 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.