Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. - Nikos Kyrpides (Bioinform., 1999)

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. - Ross A. Overbeek; Niels Larsen; Gordon D. Pusch; Mark D'Souza; Evgeni Selkov Jr.; Nikos Kyrpides; Michael Fonstein; Natalia Maltsev; Evgeni Selkov (Nucleic Acids Res., 2000)

Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. - Axel Bernal; Uy Ear; Nikos Kyrpides (Nucleic Acids Res., 2001)

The ERGOTM genome analysis and discovery system. - Ross A. Overbeek; Niels Larsen; Theresa Walunas; Mark D'Souza; Gordon D. Pusch; Evgeni Selkov Jr.; Konstantinos Liolios; Viktor Joukov; Denis Kaznadzey; Iain Anderson; Anamitra Bhattacharyya; Henry Burd; et al. (Nucleic Acids Res., 2003)

The Integrated Microbial Genomes (IMG) System: A Case Study in Biological Data Management. - Victor M. Markowitz; Frank Korzeniewski; Krishna Palaniappan; Ernest Szeto; Natalia Ivanova; Nikos Kyrpides (VLDB, 2005)

An experimental metagenome data management and analysis system. - Victor M. Markowitz; Natalia Ivanova; Krishna Palaniappan; Ernest Szeto; Frank Korzeniewski; Athanasios Lykidis; Iain Anderson; Konstantinos Mavrommatis; Victor Kunin; Héctor García Martín; Inna Dubchak; Philip Hugenholtz; et al. (ISMB (Supplement of Bioinformatics), 2006)

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. - Konstantinos Liolios; Nektarios Tavernarakis; Philip Hugenholtz; Nikos Kyrpides (Nucleic Acids Res., 2006)

The integrated microbial genomes (IMG) system. - Victor M. Markowitz; Frank Korzeniewski; Krishna Palaniappan; Ernest Szeto; Greg Werner; Anu Padki; Xueling Zhao; Inna Dubchak; Philip Hugenholtz; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; et al. (Nucleic Acids Res., 2006)

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. - Charles Bland; Teresa L. Ramsey; Fareedah Sabree; Micheal Lowe; Kyndall Brown; Nikos Kyrpides; Philip Hugenholtz (BMC Bioinform., 2007)

Annotation of metagenome short reads using proxygenes. - Daniel Dalevi; Natalia Ivanova; Konstantinos Mavrommatis; Sean D. Hooper; Ernest Szeto; Philip Hugenholtz; Nikos Kyrpides; Victor M. Markowitz (ECCB, 2008)

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. - Konstantinos Liolios; Konstantinos Mavrommatis; Nektarios Tavernarakis; Nikos Kyrpides (Nucleic Acids Res., 2008)

IMG/M: a data management and analysis system for metagenomes. - Victor M. Markowitz; Natalia Ivanova; Ernest Szeto; Krishna Palaniappan; Ken Chu; Daniel Dalevi; I-Min A. Chen; Yuri Grechkin; Inna Dubchak; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; et al. (Nucleic Acids Res., 2008)

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. - Victor M. Markowitz; Ernest Szeto; Krishna Palaniappan; Yuri Grechkin; Ken Chu; I-Min A. Chen; Inna Dubchak; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; Natalia Ivanova; Nikos Kyrpides (Nucleic Acids Res., 2008)

IMG ER: a system for microbial genome annotation expert review and curation. - Victor M. Markowitz; Konstantinos Mavrommatis; Natalia Ivanova; I-Min A. Chen; Ken Chu; Nikos Kyrpides (Bioinform., 2009)

Estimating DNA coverage and abundance in metagenomes using a gamma approximation. - Sean D. Hooper; Daniel Dalevi; Amrita Pati; Konstantinos Mavrommatis; Natalia Ivanova; Nikos Kyrpides (Bioinform., 2010)

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. - Konstantinos Liolios; I-Min A. Chen; Konstantinos Mavrommatis; Nektarios Tavernarakis; Philip Hugenholtz; Victor M. Markowitz; Nikos Kyrpides (Nucleic Acids Res., 2010)

The integrated microbial genomes system: an expanding comparative analysis resource. - Victor M. Markowitz; I-Min A. Chen; Krishna Palaniappan; Ken Chu; Ernest Szeto; Yuri Grechkin; Anna Ratner; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; Natalia Ivanova; Nikos Kyrpides (Nucleic Acids Res., 2010)

Proposal for Open Discussion - Informatics Challenges for Next Generation Sequencing Metagenomics Experiments. - Folker Meyer; Nikos Kyrpides (BIOINFORMATICS, 2011)

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. - Andreas Wilke; Travis Harrison; Jared Wilkening; Dawn Field; Elizabeth M. Glass; Nikos Kyrpides; Konstantinos Mavrommatis; Folker Meyer (BMC Bioinform., 2012)

IMG/M: the integrated metagenome data management and comparative analysis system. - Victor M. Markowitz; I-Min A. Chen; Ken Chu; Ernest Szeto; Krishna Palaniappan; Yuri Grechkin; Anna Ratner; Biju Jacob; Amrita Pati; Marcel Huntemann; Konstantinos Liolios; Ioanna Pagani; et al. (Nucleic Acids Res., 2012)

IMG: the integrated microbial genomes database and comparative analysis system. - Victor M. Markowitz; I-Min A. Chen; Krishna Palaniappan; Ken Chu; Ernest Szeto; Yuri Grechkin; Anna Ratner; Biju Jacob; Jinghua Huang; Peter Williams; Marcel Huntemann; Iain Anderson; et al. (Nucleic Acids Res., 2012)

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. - Ioanna Pagani; Konstantinos Liolios; Jakob Jansson; I-Min A. Chen; Tatyana Smirnova; Bahador Nosrat; Victor M. Markowitz; Nikos Kyrpides (Nucleic Acids Res., 2012)

IMG/M 4 version of the integrated metagenome comparative analysis system. - Victor M. Markowitz; I-Min A. Chen; Ken Chu; Ernest Szeto; Krishna Palaniappan; Manoj Pillay; Anna Ratner; Jinghua Huang; Ioanna Pagani; Susannah Tringe; Marcel Huntemann; Konstantinos Billis; et al. (Nucleic Acids Res., 2014)

IMG 4 version of the integrated microbial genomes comparative analysis system. - Victor M. Markowitz; I-Min A. Chen; Krishna Palaniappan; Ken Chu; Ernest Szeto; Manoj Pillay; Anna Ratner; Jinghua Huang; Tanja Woyke; Marcel Huntemann; Iain Anderson; Konstantinos Billis; et al. (Nucleic Acids Res., 2014)

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. - T. B. K. Reddy; Alex D. Thomas; Dimitri Stamatis; Jon Bertsch; Michelle Isbandi; Jakob Jansson; Jyothi Mallajosyula; Ioanna Pagani; Elizabeth A. Lobos; Nikos Kyrpides (Nucleic Acids Res., 2015)

Crowdsourcing and curation: perspectives from biology and natural language processing. - Lynette Hirschman; Karën Fort; Stéphanie Boué; Nikos Kyrpides; Rezarta Islamaj Dogan; Kevin Bretonnel Cohen (Database J. Biol. Databases Curation, 2016)

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. - Georgios A. Pavlopoulos; David Páez-Espino; Nikos Kyrpides; Ioannis Iliopoulos (Adv. Bioinformatics, 2017)

IMG/M: integrated genome and metagenome comparative data analysis system. - I-Min A. Chen; Victor M. Markowitz; Ken Chu; Krishna Palaniappan; Ernest Szeto; Manoj Pillay; Anna Ratner; Jinghua Huang; Evan Andersen; Marcel Huntemann; Neha Varghese; Michalis Hadjithomas; et al. (Nucleic Acids Res., 2017)

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes. - Michalis Hadjithomas; I-Min A. Chen; Ken Chu; Jinghua Huang; Anna Ratner; Krishna Palaniappan; Evan Andersen; Victor M. Markowitz; Nikos Kyrpides; Natalia Ivanova (Nucleic Acids Res., 2017)

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. - Supratim Mukherjee; Dimitri Stamatis; Jon Bertsch; Galina Ovchinnikova; Olena Verezemska; Michelle Isbandi; Alex D. Thomas; Rida Ali; Kaushal Sharma; Nikos Kyrpides; T. B. K. Reddy (Nucleic Acids Res., 2017)

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. - David Páez-Espino; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; Ernest Szeto; Manoj Pillay; Jinghua Huang; Victor M. Markowitz; Torben Nielsen; Marcel Huntemann; T. B. K. Reddy; et al. (Nucleic Acids Res., 2017)

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. - I-Min A. Chen; Ken Chu; Krishna Palaniappan; Manoj Pillay; Anna Ratner; Jinghua Huang; Marcel Huntemann; Neha Varghese; James R. White; Rekha Seshadri; Tatyana Smirnova; Edward Kirton; et al. (Nucleic Acids Res., 2019)

Genomes OnLine database (GOLD) v.7: updates and new features. - Supratim Mukherjee; Dimitri Stamatis; Jon Bertsch; Galina Ovchinnikova; Hema Y. Katta; Alejandro Mojica; I-Min A. Chen; Nikos Kyrpides; T. B. K. Reddy (Nucleic Acids Res., 2019)

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. - David Páez-Espino; Simon Roux; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; Marcel Huntemann; T. B. K. Reddy; Joan Carles Pons; Mercè Llabrés; Emiley A. Eloe-Fadrosh; Natalia N. Ivanova; et al. (Nucleic Acids Res., 2019)

New insights from uncultivated genomes of the global human gut microbiome. - Stephen Nayfach; Zhou Jason Shi; Rekha Seshadri; Katherine S. Pollard; Nikos Kyrpides (Nat., 2019)

Establishment of computational biology in Greece and Cyprus: Past, present, and future. - Anastasia Chasapi; Michalis Aivaliotis; Lefteris Angelis; Anastasios Chanalaris; Ioannis Iliopoulos; Ilias Kappas; Christos Karapiperis; Nikos Kyrpides; Evangelos Pafilis; Eleftherios Panteris; Pantelis Topalis; George Tsiamis; et al. (PLoS Comput. Biol., 2019)

IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. - Krishnaveni Palaniappan; I-Min A. Chen; Ken Chu; Anna Ratner; Rekha Seshadri; Nikos Kyrpides; Natalia N. Ivanova; Nigel J. Mouncey (Nucleic Acids Res., 2020)

VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. - Joan Carles Pons; David Páez-Espino; Gabriel Riera; Natalia Ivanova; Nikos Kyrpides; Mercè Llabrés (Bioinform., 2021)

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. - I-Min A. Chen; Ken Chu; Krishnaveni Palaniappan; Anna Ratner; Jinghua Huang; Marcel Huntemann; Patrick Hajek; Stephan Ritter; Neha Varghese; Rekha Seshadri; Simon Roux; Tanja Woyke; et al. (Nucleic Acids Res., 2021)

Genomes OnLine Database (GOLD) v.8: overview and updates. - Supratim Mukherjee; Dimitri Stamatis; Jon Bertsch; Galina Ovchinnikova; Jagadish Chandrabose Sundaramurthi; Janey Lee; Mahathi Kandimalla; I-Min A. Chen; Nikos Kyrpides; T. B. K. Reddy (Nucleic Acids Res., 2021)

IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. - Simon Roux; David Páez-Espino; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; T. B. K. Reddy; Stephen Nayfach; Frederik Schulz; Lee Call; Russell Y. Neches; Tanja Woyke; et al. (Nucleic Acids Res., 2021)

Extreme-Scale Many-against-Many Protein Similarity Search. - Oguz Selvitopi; Saliya Ekanayake; Giulia Guidi; Muaaz G. Awan; Georgios A. Pavlopoulos; Ariful Azad; Nikos Kyrpides; Leonid Oliker; Katherine A. Yelick; Aydin Buluç (SC, 2022)

Standardized naming of microbiome samples in Genomes OnLine Database. - Supratim Mukherjee; Galina Ovchinnikova; Dimitri Stamatis; Cindy Tianqing Li; I-Min A. Chen; Nikos Kyrpides; T. B. K. Reddy (Database J. Biol. Databases Curation, 2023)

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. - Antonio Pedro Camargo; Stephen Nayfach; I-Min A. Chen; Krishnaveni Palaniappan; Anna Ratner; Ken Chu; Stephan Ritter; T. B. K. Reddy; Supratim Mukherjee; Frederik Schulz; Lee Call; Russell Y. Neches; et al. (Nucleic Acids Res., 2023)

The IMG/M data management and analysis system v.7: content updates and new features. - I-Min A. Chen; Ken Chu; Krishnaveni Palaniappan; Anna Ratner; Jinghua Huang; Marcel Huntemann; Patrick Hajek; Stephan Ritter; Cody Webb; Dongying Wu; Neha Varghese; T. B. K. Reddy; et al. (Nucleic Acids Res., 2023)

Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9. - Supratim Mukherjee; Dimitri Stamatis; Cindy Tianqing Li; Galina Ovchinnikova; Jon Bertsch; Jagadish Chandrabose Sundaramurthi; Mahathi Kandimalla; Paul A. Nicolopoulos; Alessandro Favognano; I-Min A. Chen; Nikos Kyrpides; T. B. K. Reddy (Nucleic Acids Res., 2023)

Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters. - Fotis A. Baltoumas; Evangelos Karatzas; David Páez-Espino; Nefeli K. Venetsianou; Eleni Aplakidou; Anastasis Oulas; Robert D. Finn; Sergey Ovchinnikov; Evangelos Pafilis; Nikos Kyrpides; Georgios A. Pavlopoulos (Frontiers Bioinform., 2023)