Nikos Kyrpides

According to our database, Nikos Kyrpides authored at least 47 papers between 1999 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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., May, 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., January, 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, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos Kyrpides, Natalia Ivanova

Nucleic Acids Res., January, 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, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos Kyrpides, Simon Roux

Nucleic Acids Res., January, 2023

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, January, 2023

2022

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

Proceedings of the SC22: International Conference for High Performance Computing, 2022

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, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos Kyrpides

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

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, Emiley A. Eloe-Fadrosh, Natalia N. Ivanova, Nikos Kyrpides

Nucleic Acids Res., 2021

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

2020

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

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, Ioannis S. Vizirianakis, Metaxia Vlassi, Vasilis J. Promponas, Christos A. Ouzounis

PLoS Comput. Biol., 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

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, Nikos Kyrpides

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/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, Sean P. Jungbluth, Tanja Woyke, Emiley A. Eloe-Fadrosh, Natalia N. Ivanova, Nikos Kyrpides

Nucleic Acids Res., 2019

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, Georgios A. Pavlopoulos, Matthew B. Sullivan, Barbara J. Campbell, Feng Chen, Katherine D. McMahon, Steven J. Hallam, Vincent J. Denef, Ricardo Cavicchioli, Sean M. Caffrey, Wolfgang R. Streit, John Webster, Kim M. Handley, Ghasem H. Salekdeh, Nicolas Tsesmetzis, João C. Setubal, Phillip B. Pope, Wen-Tso Liu, Adam R. Rivers, Natalia Ivanova, Nikos Kyrpides

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-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

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, Kristin Tennessen, Torben Nielsen, Natalia Ivanova, Nikos Kyrpides

Nucleic Acids Res., 2017

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis.

Georgios A. Pavlopoulos, David Páez-Espino, Nikos Kyrpides, Ioannis Iliopoulos

Adv. Bioinformatics, 2017

2016

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

2015

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

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, Neha Varghese, Konstantinos Mavrommatis, Amrita Pati, Natalia Ivanova, Nikos Kyrpides

Nucleic Acids Res., 2014

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, Neha Varghese, Kristin Tennessen, Konstantinos Mavrommatis, Amrita Pati, Natalia Ivanova, Nikos Kyrpides

Nucleic Acids Res., 2014

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: 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, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides

Nucleic Acids Res., 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, Iain Anderson, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides

Nucleic Acids Res., 2012

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

2011

Proposal for Open Discussion - Informatics Challenges for Next Generation Sequencing Metagenomics Experiments.

Folker Meyer, Nikos Kyrpides

Proceedings of the BIOINFORMATICS 2011, 2011

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

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

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

2009

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

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/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, Philip Hugenholtz, Nikos Kyrpides

Nucleic Acids Res., 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

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

Proceedings of the ECCB'08 Proceedings, 2008

2007

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

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, Natalia Ivanova, Nikos Kyrpides

Nucleic Acids Res., 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

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, Nikos Kyrpides

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

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

Proceedings of the 31st International Conference on Very Large Data Bases, Trondheim, Norway, August 30, 2005

2003

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, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vassieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, Nikos Kyrpides

Nucleic Acids Res., 2003

2001

Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.

Axel Bernal, Uy Ear, Nikos Kyrpides

Nucleic Acids Res., 2001

2000

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

1999

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

Nikos Kyrpides

Bioinform., 1999