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2020 – today
- 2023
[j42]Supratim Mukherjee
, Galina Ovchinnikova, Dimitri Stamatis, Cindy Tianqing Li, I-Min A. Chen, Nikos Kyrpides, T. B. K. Reddy:
Standardized naming of microbiome samples in Genomes OnLine Database. Database J. Biol. Databases Curation 2023 (2023)- [j41]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:
Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters. Frontiers Bioinform. 3 (2023) - [j40]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:
The IMG/M data management and analysis system v.7: content updates and new features. Nucleic Acids Res. 51(D1): 723-732 (2023) - [j39]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:
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nucleic Acids Res. 51(D1): 733-743 (2023) - [j38]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:
Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9. Nucleic Acids Res. 51(D1): 957-963 (2023) - [i1]Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Muaaz G. Awan, Georgios A. Pavlopoulos, Ariful Azad, Nikos Kyrpides, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Extreme-scale many-against-many protein similarity search. CoRR abs/2303.01845 (2023) - 2022
- [c5]Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Muaaz G. Awan, Georgios A. Pavlopoulos, Ariful Azad, Nikos Kyrpides, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Extreme-Scale Many-against-Many Protein Similarity Search. SC 2022: 1:1-1:12 - 2021
- [j37]Joan Carles Pons, David Páez-Espino, Gabriel Riera, Natalia Ivanova, Nikos Kyrpides, Mercè Llabrés:
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. Bioinform. 37(13): 1805-1813 (2021) - [j36]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:
Genomes OnLine Database (GOLD) v.8: overview and updates. Nucleic Acids Res. 49(Database-Issue): D723-D733 (2021) - [j35]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:
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 49(Database-Issue): D751-D763 (2021) - [j34]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:
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. Nucleic Acids Res. 49(Database-Issue): D764-D775 (2021) - 2020
- [j33]Krishnaveni Palaniappan, I-Min A. Chen, Ken Chu, Anna Ratner, Rekha Seshadri, Nikos Kyrpides, Natalia N. Ivanova, Nigel J. Mouncey:
IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. Nucleic Acids Res. 48(Database-Issue): D422-D430 (2020)
2010 – 2019
- 2019
- [j32]Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Hema Y. Katta, Alejandro Mojica, I-Min A. Chen, Nikos Kyrpides, T. B. K. Reddy:
Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Res. 47(Database-Issue): D649-D659 (2019) - [j31]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:
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47(Database-Issue): D666-D677 (2019) - [j30]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:
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. Nucleic Acids Res. 47(Database-Issue): D678-D686 (2019) - [j29]Stephen Nayfach, Zhou Jason Shi, Rekha Seshadri, Katherine S. Pollard, Nikos Kyrpides:
New insights from uncultivated genomes of the global human gut microbiome. Nat. 568(7753): 505-510 (2019) - [j28]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:
Establishment of computational biology in Greece and Cyprus: Past, present, and future. PLoS Comput. Biol. 15(12) (2019) - 2017
- [j27]Georgios A. Pavlopoulos, David Páez-Espino, Nikos Kyrpides, Ioannis Iliopoulos:
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. Adv. Bioinformatics 2017: 1278932:1-1278932:8 (2017) - [j26]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:
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. Nucleic Acids Res. 45(Database-Issue): D446-D456 (2017) - [j25]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:
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 45(Database-Issue): D457-D465 (2017) - [j24]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:
IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 45(Database-Issue): D507-D516 (2017) - [j23]Michalis Hadjithomas, I-Min A. Chen, Ken Chu, Jinghua Huang, Anna Ratner, Krishna Palaniappan, Evan Andersen, Victor M. Markowitz, Nikos Kyrpides, Natalia Ivanova:
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes. Nucleic Acids Res. 45(Database-Issue): D560-D565 (2017) - 2016
- [j22]Lynette Hirschman, Karën Fort, Stéphanie Boué, Nikos Kyrpides, Rezarta Islamaj Dogan, Kevin Bretonnel Cohen:
Crowdsourcing and curation: perspectives from biology and natural language processing. Database J. Biol. Databases Curation 2016 (2016) - 2015
- [j21]T. B. K. Reddy, Alex D. Thomas, Dimitri Stamatis, Jon Bertsch, Michelle Isbandi, Jakob Jansson, Jyothi Mallajosyula, Ioanna Pagani, Elizabeth A. Lobos, Nikos Kyrpides:
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res. 43(Database-Issue): 1099-1106 (2015) - 2014
- [j20]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:
IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 42(Database-Issue): 560-567 (2014) - [j19]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:
IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res. 42(Database-Issue): 568-573 (2014) - 2012
- [j18]Andreas Wilke, Travis Harrison, Jared Wilkening, Dawn Field, Elizabeth M. Glass, Nikos Kyrpides, Konstantinos Mavrommatis, Folker Meyer:
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinform. 13: 141 (2012) - [j17]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:
IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 40(Database-Issue): 115-122 (2012) - [j16]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:
IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 40(Database-Issue): 123-129 (2012) - [j15]Ioanna Pagani, Konstantinos Liolios, Jakob Jansson, I-Min A. Chen, Tatyana Smirnova, Bahador Nosrat, Victor M. Markowitz, Nikos Kyrpides:
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 40(Database-Issue): 571-579 (2012) - 2011
- [c4]Folker Meyer, Nikos Kyrpides:
Proposal for Open Discussion - Informatics Challenges for Next Generation Sequencing Metagenomics Experiments. BIOINFORMATICS 2011: 363-366 - 2010
- [j14]Sean D. Hooper, Daniel Dalevi, Amrita Pati, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
Estimating DNA coverage and abundance in metagenomes using a gamma approximation. Bioinform. 26(3): 295-301 (2010) - [j13]Konstantinos Liolios, I-Min A. Chen, Konstantinos Mavrommatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, Nikos Kyrpides:
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 38(Database-Issue): 346-354 (2010) - [j12]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:
The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 38(Database-Issue): 382-390 (2010)
2000 – 2009
- 2009
- [j11]Victor M. Markowitz, Konstantinos Mavrommatis, Natalia Ivanova, I-Min A. Chen, Ken Chu, Nikos Kyrpides:
IMG ER: a system for microbial genome annotation expert review and curation. Bioinform. 25(17): 2271-2278 (2009) - 2008
- [j10]Konstantinos Liolios, Konstantinos Mavrommatis, Nektarios Tavernarakis, Nikos Kyrpides:
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 36(Database-Issue): 475-479 (2008) - [j9]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:
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 36(Database-Issue): 528-533 (2008) - [j8]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:
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 36(Database-Issue): 534-538 (2008) - [c3]Daniel Dalevi, Natalia Ivanova, Konstantinos Mavrommatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos Kyrpides, Victor M. Markowitz:
Annotation of metagenome short reads using proxygenes. ECCB 2008: 7-13 - 2007
- [j7]Charles Bland, Teresa L. Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos Kyrpides, Philip Hugenholtz:
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinform. 8 (2007) - 2006
- [j6]Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos Kyrpides:
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 34(Database-Issue): 332-334 (2006) - [j5]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:
The integrated microbial genomes (IMG) system. Nucleic Acids Res. 34(Database-Issue): 344-348 (2006) - [c2]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:
An experimental metagenome data management and analysis system. ISMB (Supplement of Bioinformatics) 2006: 359-367 - 2005
- [c1]Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Natalia Ivanova, Nikos Kyrpides:
The Integrated Microbial Genomes (IMG) System: A Case Study in Biological Data Management. VLDB 2005: 1067-1078 - 2003
- [j4]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:
The ERGOTM genome analysis and discovery system. Nucleic Acids Res. 31(1): 164-171 (2003) - 2001
- [j3]Axel Bernal, Uy Ear, Nikos Kyrpides:
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 29(1): 126-127 (2001) - 2000
- [j2]Ross A. Overbeek, Niels Larsen, Gordon D. Pusch, Mark D'Souza, Evgeni Selkov Jr., Nikos Kyrpides, Michael Fonstein, Natalia Maltsev, Evgeni Selkov:
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28(1): 123-125 (2000)
1990 – 1999
- 1999
- [j1]Nikos Kyrpides:
Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinform. 15(9): 773-774 (1999)
Coauthor Index
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