I-Min A. Chen

Publication Activity (10 Years)

Years Active: 1989-2023
Publications (10 Years): 14

Top Topics

Genomic Sequences

Comparative Analysis

Essential Genes

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Publications

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) (2023)
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) (2023)
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) (2023)
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)
Simon Roux, A. 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) (2021)
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) (2021)
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) (2021)
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) (2020)
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) (2019)
A. 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) (2019)
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) (2019)
A. 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) (2017)
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) (2017)
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) (2017)
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) (2014)
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) (2014)
I-Min A. Chen, Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Ken Chu
Maintaining a microbial genome & metagenome data analysis system in an academic setting. SSDBM (2014)
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) (2012)
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) (2012)
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) (2012)
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) (2010)
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) (2010)
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) (2009)
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) (2008)
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) (2008)
Victor M. Markowitz, I-Min A. Chen, Anthony Kosky
Gene Expression Data Management: A Case Study. EDBT (2002)
I-Min A. Chen, Anthony Kosky, Victor M. Markowitz, Ernest Szeto, Thodoros Topaloglou
Advanced Query Mechanisms for Biological Databases. ISMB (1998)
I-Min A. Chen, Doron Rotem
Integrating Information from Multiple Independently Developed Data Sources. CIKM (1998)
Anthony Kosky, I-Min A. Chen, Victor M. Markowitz, Ernest Szeto
Exploring Heterogeneous Biological Databases: Tools and Applications. EDBT (1998)
I-Min A. Chen, Anthony Kosky, Victor M. Markowitz, Ernest Szeto
Developing and Accessing Scientific Databases with the OPM Data Management Tools. ICDE (1997)
I-Min A. Chen, Anthony Kosky, Victor M. Markowitz, Ernest Szeto
Developing and Accessing Scientific Databases with the Object-Protocol (OPM) Data Management Tools SSDBM (1997)
I-Min A. Chen, Anthony Kosky, Victor M. Markowitz, Ernest Szeto
Constructing and Maintaining Scientific Database Views in the Framework of the Object-Protocol Model. SSDBM (1997)
I-Min A. Chen
Query Answering Using Discovered Rules. ICDE (1996)
I-Min A. Chen, Victor M. Markowitz, Stanley Letovsky, Peter Li, Kenneth H. Fasman
Version Management for Scientific Databases. EDBT (1996)
I-Min A. Chen, Victor M. Markowitz
An Overview of the Object-Protocol Model (OPM) and OPM Data Management Tools. Inf. Syst. 20 (5) (1995)
I-Min A. Chen, Victor M. Markowitz
Modeling Scientific Experiments with an Object Data Model. ICDE (1995)
I-Min A. Chen, Richard Hull, Dennis McLeod
An Execution Model for Limited Ambiguity Rules and Its Application to Derived Data Update. ACM Trans. Database Syst. 20 (4) (1995)
I-Min A. Chen, Richard Hull, Dennis McLeod
Local Ambiguity and Derived Data Update. RIDE-ADS (1994)
Victor M. Markowitz, I-Min A. Chen
Data Management Tools for Genomic Applications: A Progress Report. DEXA (1993)
I-Min A. Chen, Dennis McLeod
A Unified Approach to Data and Meta-data Modifications for Data/Knowledge Bases. Theoretical Studies in Computer Science (1992)
I-Min A. Chen, Rei-Chi Lee
An Approach to Deriving Object Hierarchies from Database Schema and Contents. ISMIS (1991)
I-Min A. Chen, Dennis McLeod
Derived Data Update in Semantic Databases. VLDB (1989)